semester i syllabus for m. sc. biochemistry choice based ... · 1992 edition: second edition 4....

48
1 -------------------------------------------------------------------------------------------------------------------------------------- RTM Nagpur University, M.Sc. Biochemistry syllabus, Effective from 2020-21 Including Foundation course & Subject centric course at Semester III and Semester IV. SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based Credit System (Semester Pattern) Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur Effective from 2020-2021 Program Outcomes for M.Sc. Biochemistry (CBCS) Program The M.Sc. Biochemistry program offered by Rashtrasant Tukadoji Maharaj Nagpur University is a Two Years full time program aiming at students becoming career oriented and capable of nurturing their scientific temperaments. Students will get exposure to the depth of core understanding of various dimensions of Biochemistry during these two years the study. The training provided will give students the breadth and depth of scientific knowledge in the important fields of biochemistry. The M.Sc. in Biochemistry at RTM Nagpur University allows specialization in the areas of Biochemistry, Molecular biology, Research Methodologies, Immunology, Toxicology, Nutritional Biochemistry, Clinical Research or Enzymology, and it is intended for students desiring research-oriented careers in the chemical, biochemical or biotech industry, academic institution or research institutes or entry into Ph.D. programs. The students of M. Sc. Biochemistry (CBCS) Program will upon completion of the course have: A strong understanding of fundamentals of biochemical process at an advanced level Better understanding of major thrust areas of the discipline Knowhow on current developments in the biochemical research Capacity to identify, analyze and design safe experimental process, to provide efficient solutions by fair interpretation of data Gain perfect insight into biochemical research ethics for production of quality research and publication. An ability to engage themselves in lifelong learning to foster their growth as a successful researcher and establish themselves as an entrepreneur in the field of biochemistry. Critical understanding of Scientific fundamentals and their application for professional success through focused tests and should demonstrate signs of improvement. Communicate their thoughts unmistakably to individuals from all foundations in composed and spoken arrangement. Collaborate with different fields for advancement of inventive answer for ecological, modern and different issues. Serve society for its progression through productive research and moral practices. Be employment prepared to work in any segment. M.Sc. Biochemistry (CBCS) Program M.Sc. Biochemistry is 4 semester course led by the Department of Biochemistry according to the curriculum given by Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur. Every semester under study consists of four Theory papers, two Practicals (dependent on four Theory papers) and a Seminar. Fourth semester has a semester long Research Project Work, along with Course work of four Theory papers and one practical.

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Page 1: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

1

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER I

SYLLABUS for M Sc BIOCHEMISTRY

Choice Based Credit System (Semester Pattern)

Rashtrasant Tukadoji Maharaj Nagpur University Nagpur

Effective from 2020-2021

Program Outcomes for MSc Biochemistry (CBCS) Program

The MSc Biochemistry program offered by Rashtrasant Tukadoji Maharaj Nagpur

University is a Two Years full time program aiming at students becoming career oriented

and capable of nurturing their scientific temperaments Students will get exposure to the

depth of core understanding of various dimensions of Biochemistry during these two years

the study The training provided will give students the breadth and depth of scientific

knowledge in the important fields of biochemistry The MSc in Biochemistry at RTM

Nagpur University allows specialization in the areas of Biochemistry Molecular biology

Research Methodologies Immunology Toxicology Nutritional Biochemistry Clinical

Research or Enzymology and it is intended for students desiring research-oriented careers in

the chemical biochemical or biotech industry academic institution or research institutes or

entry into PhD programs

The students of M Sc Biochemistry (CBCS) Program will upon completion of the

course have

A strong understanding of fundamentals of biochemical process at an advanced level

Better understanding of major thrust areas of the discipline

Knowhow on current developments in the biochemical research

Capacity to identify analyze and design safe experimental process to provide

efficient solutions by fair interpretation of data

Gain perfect insight into biochemical research ethics for production of quality

research and publication

An ability to engage themselves in lifelong learning to foster their growth as a

successful researcher and establish themselves as an entrepreneur in the field of

biochemistry

Critical understanding of Scientific fundamentals and their application for professional

success through focused tests and should demonstrate signs of improvement

Communicate their thoughts unmistakably to individuals from all foundations in composed

and spoken arrangement

Collaborate with different fields for advancement of inventive answer for ecological modern

and different issues

Serve society for its progression through productive research and moral practices

Be employment prepared to work in any segment

MSc Biochemistry (CBCS) Program

MSc Biochemistry is 4 semester course led by the Department of Biochemistry according

to the curriculum given by Rashtrasant Tukadoji Maharaj Nagpur University Nagpur Every

semester under study consists of four Theory papers two Practicals (dependent on four

Theory papers) and a Seminar Fourth semester has a semester long Research Project Work

along with Course work of four Theory papers and one practical

2

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Scheme of teaching and examination under semester pattern Choice Based Credit System (CBCS) for MSc Program in Biochemistry

M Sc Biochemistry Semester I Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

1T1 Protein Biochemistry

4 - 4 4 3 80 20 100 40

1T2 Advanced Enzymology

4 - 4 4 3 80 20 100 40

1T3 Biochemical Research Techniques

4 - 4 4 3 80 20 100 40

1T4 Plant Biochemistry 4 - 4 4 3 80 20 100 40 1P1 Protein

Biochemistry and Enzymology

- 8 8 4 8 80 20 100 40

1P2 Biochemical Research Techniques and Plant Biochemistry

- 8 8 4 8 80 20 100 40

1S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

3

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

M Sc Biochemistry Semester II Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

2T1 Immunology 4 - 4 4 3 80 20 100 40 2T2 Clinical

Biochemistry 4 - 4 4 3 80 20 100 40

2T3 Cell Biochemistry 4 - 4 4 3 80 20 100 40 2T4 Molecular Biology 4 - 4 4 3 80 20 100 40 2P1 Clinical

Biochemistry and Immunology

- 8 8 4 8 80 20 100 40

2P2 Cell and Molecular Biology

- 8 8 4 8 80 20 100 40

2S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

4

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

M Sc Biochemistry Semester III Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

3T1 Advanced Molecular Biology

4 - 4 4 3 80 20 100 40

3T2 Biotechnology 4 - 4 4 3 80 20 100 40 3T3 A) Toxicology

(Biochemical amp

Environmental

Toxicology

OR

B) Nutrition (Nutritional Biochemistry)

4 - 4 4 3 80 20 100 40

3T4 Foundation I (Biomolecules and Basic metabolism) OR (Subject centric Core 1) Bioresearch Techniques I

4 - 4 4 3 80 20 100 40

3P1 Biotechnology and Molecular Biology

- 8 8 4 8 80 20 100 40

3P2 A) Toxicology

(Biochemical amp

Environmental

Toxicology)

OR

B) Nutrition (Nutritional Biochemistry)

- 8 8 4 8 80 20 100 40

3S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

5

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

M Sc Biochemistry Semester IV

Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

4T1 Advanced Clinical Biochemistry

4 - 4 4 3 80 20 100 40

4T2 Advanced Immunology

4 - 4 4 3 80 20 100 40

4T3 A) Toxicology

(Clinical

Research)

OR

B) Nutrition (Applied Nutritional Biochemistry)

4 - 4 4 3 80 20 100 40

4T4 Foundation 2 (Basic Enzymology) or (Subject centric Core 2) Bioresearch Techniques II

4 - 4 4 3 80 20 100 40

4P1 Advanced

Clinical

Biochemistry amp

Immunology

And

A) Toxicology

(Clinical

Research)

OR

B) Nutrition

(Applied

Nutritional

Biochemistry)

- 8 8 4 8 80 20 100 40

4PROJ Project - 8 8 4 8 80 20 100 40 4S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

6

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 1 (Code 1T1) Protein Biochemistry Learning outcome Students will be able to

1 Basics Protein structure chemical bonding or molecular geometry based on accepted

models

2 Apply quantitative reasoning skills of protein folding and energy physical or

chemical changes that occur

3 Use accepted models to describe the interactions of amino acids and equilibrium

concepts with respect to protein conformations and interactions

4 In the major areas of Mass spectrometry students will be able to

a Describe and understand the capabilities and limitations of instrumental methods

b Explain the instrument components and principles of operation

5 Upon being introduced to the steps of the analytical process students will be able to

correctly select an analytical method and instrument meeting their use objectives

Also students would be able to demonstrate competence in data acquisition by Mass

Spectrometric analysis and interpreting laboratory data

6 With Basics of Protein synthesis machinery students will be able to conceptualize the

process of translation and its regulatory aspects so as to apply the concept for

understanding protein structural dynamics with respect to protein functions

7 Protein sorting and compartmentalization during and after translation will give

fundamental understanding about organelle specific protein functions This will

develop competence amongst the students for application of physical parameters in

protein functional dynamics depending upon organelle specific environment

8 Overall understanding of protein structure function relationship through this paper

will equip the students to propose designs of novel proteins constructed through

utilization of aspects of protein engineering Specific examples of the same would

help them understand and apply the concept of protein engineering to the fullest

7

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T1 Protein Biochemistry

Unit I Proteins and Mass Spectrometry

Overview of protein structure protein folding Ramchandran plot domains and modules

binding sites within proteins protein sequencing

Basics of Mass Spectrometry Ionization mechanisms- protonation deprotonation

cationization transfer of charged molecules to gas phase electron ejection electron capture

Mass analyzers-TOF Ion trap Quadrupole Ionization methods-Electron Impact (EI)

Chemical Ionization (CI) Fast Atom Bombardment (FAB) Field Description (FD) Electron

Spray Ionization (ESI) Matrix Assisted Laser Desorption Ionization (MALDI) Protein

Identification using MS

Unit II Protein biosynthesis

Eukaryotic translation machinery structure and assembly of the ribosome initiation

elongation and termination of translation

Unit III Protein sorting and degradation Intracellular protein sorting movement of proteins between cellular compartments gated

transmembrane and vesicular transport Protein transport and translocation to nucleus mitochondria

chloroplast peroxisomes endoplasmic reticular system Protein degradation

Unit IV Protein Engineering

Design and construction of novel proteins and enzymes Conformation of proteins in general and

enzymes in particular Effect of amino acids on structure of proteins Energy status of a protein

molecule Structure function relations of enzymes Physical methods such as x-ray crystallography

for determination of protein structure Site directed mutagenesis for specific protein function Basic

concepts for design of a new proteinenzyme molecule Specific examples of enzyme engineering -

Dihydrofolate reductase and Subtilisin

Suggested References

1 Modern Protein Chemistry Practical Aspects Published September 12 2001 by CRC Press -

272 Pages Edited By Gary C Howard

2 Biochemistry 5th edition Berg JM Tymoczko JL Stryer L New York W H Freeman 2002

3 Proteins Structures and Molecular Properties Thomas E Creighton Publisher W H Freeman

1992 Edition Second Edition

4 Protein Engineering Protocols (Methods in Molecular Biology) Kristian Muumlller (Editor)

Publisher Humana Press Softcover reprint of hardcover 1st ed 2007 edition (November 10

2010)

5 Protein Degradation Series 4 Volume Set (v 1) R John Mayer (Editor) Publisher Wiley-

VCH 1 edition (March 4 2008)

6 Structural Aspects of Protein Synthesis Anders LiljashttpwwwamazoncomStructural-

Aspects-Protein-Synthesis-

Andersdp981238863Xref=sr_1_1s=booksampie=UTF8ampqid=1323503546ampsr=1-1 -

(Author) Publisher World Scientific Pub Co Inc 1 edition (November 2004)

7 Protein Targeting Transport and Translocation Ross Dalbey (Editor) Publisher Academic

Press 1 edition (May 13 2002)

8 Principles of Physical Biochemistry- KenslE van Holde W Curtis Johnson P Shing Ho

Pearson Prentice Hall 2nd Edition

9 Crystallography made crystal clear 1993 G Rhodes Academic Press

10 Principles and Techniques of Biochemistry and Molecular Biology 6th Edition Wilson Keith

and Walker John (2005) Cambridge University Press New York

11 A textbook of biophysics R N Roy New Central Publication 1st edition

8

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 2 (Code 1T2) Advanced Enzymology Learning outcome Students will be able to

1 Describe structure capacities and the component of activity of

chemicals and interaction with enzymes Learning energy of protein

catalyzed responses and compound restraints and administrative

procedure Enzyme action Enzyme Units Specific action

2 Have a detail and more intricate knowledge of allosteric and other

aspects of enzyme catalysis regulation

3 Have a total comprehension of rate of responses and request of

responses and restraints and their kinetics To gain information on

protein catalysis and isoenzymes and on multienzyme and multienzyme

complexes with specific examples

4 Develop intellectual capacity to relate bioenergetics principles and the

entropy to the law of thermodynamics and Free energy and its

connection to chemical equilibria in consolation to enzyme catalysis

5 Theory related to respiratory mechanisms catalysed by enzymatic

principles of redox biochemistry will help the students to gauge wide

applicability of enzymatic reactions in biological systems Detail

description of Coupled reactions and their role in metabolism and

Chemiosmotic hypothesis of ATP synthesis to understand the

mechanism of energy harnessing mechanism operating in biological

system

9

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 2 Advanced Enzymology

Unit I Kinetics and Regulation of enzyme activity

Review of unisubstrate enzyme kinetics multisubstrate enzyme kinetics Co-operativity

phenomenon Hill and Scatchard plots protein-ligand binding and its measurement detailed

mechanism of catalysis of serine protease carbonic anhydrase and PEP kinase

Metalloenzymes

Unit II Allosteric enzymes and multienzyme systems

Allosteric enzymes sigmoidal kinetics and its physiological significance symmetric and

sequential modes of action and their significance immobilized enzymes and their industrial

applications study of multienzyme complexes with respect to occurrence isolation and their

properties and polygenic nature eg pyruvate dehydrogenase and fatty acid synthase

Unit III Enzyme regulation

General mechanisms of enzyme regulation Feed back inhibition and feed forward

stimulation repression and induction of enzymes reversible and irreversible covalent

modifications of enzymes flexibility and conformational mobility of enzymes convergent

and divergent evolution of enzymes

Unit IV Bioenergetics and oxidative phosphorylation

Energy transformation laws of thermodynamics Gibbs energy free energy change redox

potentials phosphate potential ion electrochemical potential proton electrochemical

potential membrane potential Chemi-osmotic theory mitochondrial respiratory chain order

and organization of carrier proton gradients Characterization of Iron- Sulphur proteins and

Cytochromes Q cycle Respiratory controls and oxidative phosphorylation ATP synthase

complex

Suggested References

1 Enzymes Biochemistry Biotechnology and Clinical Chemistry-Trevor Palmer

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

10

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 3 (Code 1T3) Biochemical Research Techniques Learning outcome Students will be able to

1 The theoretical aspects of designing the Experiments and also study the Quality

control mechanism in Biochemistry

2 Understand the Sampling techniques and interpret the data based on the measures

of the central tendency

3 Learn the discrepancies and deviations of the variable based of measures of

dispersion

4 Study the relationship between variables based on correlation and regression

analysis

5 Deduce the probable outcomes of an experiment based on observations

following laws of probability and also assess the significance of the

interpretation through tests of significance such as t-test

6 To understand the importance and applications of computational methods and

statistical softwares in Biology

11

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 3 Biochemical Research Techniques

Unit I Research Methodology

1 Introduction to research methodology History and definition of research role of

theory hypothesis sampling variables randomness selection of problem purpose of

research and research reporting

2 Experimental research Early experimentation experimental groups control groups

variables method of controlling variables designing and validation of experiments

3 Methods and tools in research Research tools and its reliability and validity

quantitative and qualitative studies observation inquiry forms Q methodology data

collection limitations and sources of error

4 Types of data Analysis Descriptive data analysis Inferential data analysis Computer

data analysis

Unit II Biostatistics

Principles and practice of statistical methods in biological research samples and populations Basic

statistics-average statistics of dispersion coefficient of variation confidence limits Probability

distribution normal binomial and Poisson distribution Mean variants standard deviations and

standard error correlation and regression test of statistical significance and analysis of variance and

covariance

Unit III Data Retrieval Scientific Writing and Presentation

1 Information Search amp Data Retrieval Tools for Web Search Data Retrieval Tools

Data Mining of Biological Databases

2 Report Writing Significance of report writing different steps in report writing types

of report layout of research paper

3 Mechanics and precautions of writing research reports for scientific journals popular

magazines seminarssymposia conferencesworkshops poster session

4 Presentationndash Oral amp Written Presentations in classrooms scientific meets amp public

audience Defence of research thesis

Unit IV Computers

Introduction of computer networks- Topologies and designs Basics of computer operating systems-

windows and Linux Introduction to Markup language-Hyper Text Markup Language (HTML) and

Extensive Markup Language (XML) Spreadsheets and Presentation software

Systems Biology-An introduction

Introduction to Metagenomics

Suggested References

1 Fundamentals of Biostatistics Bernard A Rosner Thomson-BrooksCole 2006

2 Research methodology in social behavioural and life sciences Designs models and

methods Herman J Ader and Gideon Mellenbergh (Ed) SAGE Publications

6 Principles of Genome analysis and genomics Primrose SB Twyman RM Blackwell

Science (2002)

7 Biostatistics-A foundation for Health Science Daniel WW John Wiley (1983)

8 Statistical Methods Medhi J Willey Eastern Limited (1992)

12

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 4 (Code 1T4) Plant Biochemistry Learning outcome Students will be able to

1 Detailed knowledge of plant cellular architecture and the mechanism

of photosynthetic systems for photophosphorylation will enable the

students to get a dissected approach for understanding autotrophic food

synthesis mechanism driven by photon energy operative in plants

2 Hormonal pathways driving plant growth mechanisms form the

foundation for in vitro plant propagation setup and understanding of

Plant tissue culture aspects Students would gain an thorough insight of

growth regulatory mechanism of plants through which they will be able

to devise the hormonal concoction required for organogenesis and related

plant tissue culture applications

3 Students will be able to learn metabolic attributes and driving

principles of plant growth through basic carbohydrate lipid and protein

metabolism Also the students will be developing a comprehension of

importance of nitrogen and sulphur metabolism in plants and associated

plant physiological alterations

4 With in depth knowledge about plant physiochemical aspects the

students will get equipped to develop an understanding about effects

caused by biotic and abiotic stress factors on plant metabolism and

growth They can thus impinge upon the ways to tackle such stress

physiological aspects to promote and resolve plant stresses

5 Practical exposure to biochemical analysis of plant physiological

aspects would improve the students application approach towards plant

biochemistry as tool to protect plant diversity

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 2: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

2

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Scheme of teaching and examination under semester pattern Choice Based Credit System (CBCS) for MSc Program in Biochemistry

M Sc Biochemistry Semester I Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

1T1 Protein Biochemistry

4 - 4 4 3 80 20 100 40

1T2 Advanced Enzymology

4 - 4 4 3 80 20 100 40

1T3 Biochemical Research Techniques

4 - 4 4 3 80 20 100 40

1T4 Plant Biochemistry 4 - 4 4 3 80 20 100 40 1P1 Protein

Biochemistry and Enzymology

- 8 8 4 8 80 20 100 40

1P2 Biochemical Research Techniques and Plant Biochemistry

- 8 8 4 8 80 20 100 40

1S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

3

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

M Sc Biochemistry Semester II Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

2T1 Immunology 4 - 4 4 3 80 20 100 40 2T2 Clinical

Biochemistry 4 - 4 4 3 80 20 100 40

2T3 Cell Biochemistry 4 - 4 4 3 80 20 100 40 2T4 Molecular Biology 4 - 4 4 3 80 20 100 40 2P1 Clinical

Biochemistry and Immunology

- 8 8 4 8 80 20 100 40

2P2 Cell and Molecular Biology

- 8 8 4 8 80 20 100 40

2S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

4

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

M Sc Biochemistry Semester III Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

3T1 Advanced Molecular Biology

4 - 4 4 3 80 20 100 40

3T2 Biotechnology 4 - 4 4 3 80 20 100 40 3T3 A) Toxicology

(Biochemical amp

Environmental

Toxicology

OR

B) Nutrition (Nutritional Biochemistry)

4 - 4 4 3 80 20 100 40

3T4 Foundation I (Biomolecules and Basic metabolism) OR (Subject centric Core 1) Bioresearch Techniques I

4 - 4 4 3 80 20 100 40

3P1 Biotechnology and Molecular Biology

- 8 8 4 8 80 20 100 40

3P2 A) Toxicology

(Biochemical amp

Environmental

Toxicology)

OR

B) Nutrition (Nutritional Biochemistry)

- 8 8 4 8 80 20 100 40

3S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

5

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

M Sc Biochemistry Semester IV

Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

4T1 Advanced Clinical Biochemistry

4 - 4 4 3 80 20 100 40

4T2 Advanced Immunology

4 - 4 4 3 80 20 100 40

4T3 A) Toxicology

(Clinical

Research)

OR

B) Nutrition (Applied Nutritional Biochemistry)

4 - 4 4 3 80 20 100 40

4T4 Foundation 2 (Basic Enzymology) or (Subject centric Core 2) Bioresearch Techniques II

4 - 4 4 3 80 20 100 40

4P1 Advanced

Clinical

Biochemistry amp

Immunology

And

A) Toxicology

(Clinical

Research)

OR

B) Nutrition

(Applied

Nutritional

Biochemistry)

- 8 8 4 8 80 20 100 40

4PROJ Project - 8 8 4 8 80 20 100 40 4S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

6

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 1 (Code 1T1) Protein Biochemistry Learning outcome Students will be able to

1 Basics Protein structure chemical bonding or molecular geometry based on accepted

models

2 Apply quantitative reasoning skills of protein folding and energy physical or

chemical changes that occur

3 Use accepted models to describe the interactions of amino acids and equilibrium

concepts with respect to protein conformations and interactions

4 In the major areas of Mass spectrometry students will be able to

a Describe and understand the capabilities and limitations of instrumental methods

b Explain the instrument components and principles of operation

5 Upon being introduced to the steps of the analytical process students will be able to

correctly select an analytical method and instrument meeting their use objectives

Also students would be able to demonstrate competence in data acquisition by Mass

Spectrometric analysis and interpreting laboratory data

6 With Basics of Protein synthesis machinery students will be able to conceptualize the

process of translation and its regulatory aspects so as to apply the concept for

understanding protein structural dynamics with respect to protein functions

7 Protein sorting and compartmentalization during and after translation will give

fundamental understanding about organelle specific protein functions This will

develop competence amongst the students for application of physical parameters in

protein functional dynamics depending upon organelle specific environment

8 Overall understanding of protein structure function relationship through this paper

will equip the students to propose designs of novel proteins constructed through

utilization of aspects of protein engineering Specific examples of the same would

help them understand and apply the concept of protein engineering to the fullest

7

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T1 Protein Biochemistry

Unit I Proteins and Mass Spectrometry

Overview of protein structure protein folding Ramchandran plot domains and modules

binding sites within proteins protein sequencing

Basics of Mass Spectrometry Ionization mechanisms- protonation deprotonation

cationization transfer of charged molecules to gas phase electron ejection electron capture

Mass analyzers-TOF Ion trap Quadrupole Ionization methods-Electron Impact (EI)

Chemical Ionization (CI) Fast Atom Bombardment (FAB) Field Description (FD) Electron

Spray Ionization (ESI) Matrix Assisted Laser Desorption Ionization (MALDI) Protein

Identification using MS

Unit II Protein biosynthesis

Eukaryotic translation machinery structure and assembly of the ribosome initiation

elongation and termination of translation

Unit III Protein sorting and degradation Intracellular protein sorting movement of proteins between cellular compartments gated

transmembrane and vesicular transport Protein transport and translocation to nucleus mitochondria

chloroplast peroxisomes endoplasmic reticular system Protein degradation

Unit IV Protein Engineering

Design and construction of novel proteins and enzymes Conformation of proteins in general and

enzymes in particular Effect of amino acids on structure of proteins Energy status of a protein

molecule Structure function relations of enzymes Physical methods such as x-ray crystallography

for determination of protein structure Site directed mutagenesis for specific protein function Basic

concepts for design of a new proteinenzyme molecule Specific examples of enzyme engineering -

Dihydrofolate reductase and Subtilisin

Suggested References

1 Modern Protein Chemistry Practical Aspects Published September 12 2001 by CRC Press -

272 Pages Edited By Gary C Howard

2 Biochemistry 5th edition Berg JM Tymoczko JL Stryer L New York W H Freeman 2002

3 Proteins Structures and Molecular Properties Thomas E Creighton Publisher W H Freeman

1992 Edition Second Edition

4 Protein Engineering Protocols (Methods in Molecular Biology) Kristian Muumlller (Editor)

Publisher Humana Press Softcover reprint of hardcover 1st ed 2007 edition (November 10

2010)

5 Protein Degradation Series 4 Volume Set (v 1) R John Mayer (Editor) Publisher Wiley-

VCH 1 edition (March 4 2008)

6 Structural Aspects of Protein Synthesis Anders LiljashttpwwwamazoncomStructural-

Aspects-Protein-Synthesis-

Andersdp981238863Xref=sr_1_1s=booksampie=UTF8ampqid=1323503546ampsr=1-1 -

(Author) Publisher World Scientific Pub Co Inc 1 edition (November 2004)

7 Protein Targeting Transport and Translocation Ross Dalbey (Editor) Publisher Academic

Press 1 edition (May 13 2002)

8 Principles of Physical Biochemistry- KenslE van Holde W Curtis Johnson P Shing Ho

Pearson Prentice Hall 2nd Edition

9 Crystallography made crystal clear 1993 G Rhodes Academic Press

10 Principles and Techniques of Biochemistry and Molecular Biology 6th Edition Wilson Keith

and Walker John (2005) Cambridge University Press New York

11 A textbook of biophysics R N Roy New Central Publication 1st edition

8

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 2 (Code 1T2) Advanced Enzymology Learning outcome Students will be able to

1 Describe structure capacities and the component of activity of

chemicals and interaction with enzymes Learning energy of protein

catalyzed responses and compound restraints and administrative

procedure Enzyme action Enzyme Units Specific action

2 Have a detail and more intricate knowledge of allosteric and other

aspects of enzyme catalysis regulation

3 Have a total comprehension of rate of responses and request of

responses and restraints and their kinetics To gain information on

protein catalysis and isoenzymes and on multienzyme and multienzyme

complexes with specific examples

4 Develop intellectual capacity to relate bioenergetics principles and the

entropy to the law of thermodynamics and Free energy and its

connection to chemical equilibria in consolation to enzyme catalysis

5 Theory related to respiratory mechanisms catalysed by enzymatic

principles of redox biochemistry will help the students to gauge wide

applicability of enzymatic reactions in biological systems Detail

description of Coupled reactions and their role in metabolism and

Chemiosmotic hypothesis of ATP synthesis to understand the

mechanism of energy harnessing mechanism operating in biological

system

9

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 2 Advanced Enzymology

Unit I Kinetics and Regulation of enzyme activity

Review of unisubstrate enzyme kinetics multisubstrate enzyme kinetics Co-operativity

phenomenon Hill and Scatchard plots protein-ligand binding and its measurement detailed

mechanism of catalysis of serine protease carbonic anhydrase and PEP kinase

Metalloenzymes

Unit II Allosteric enzymes and multienzyme systems

Allosteric enzymes sigmoidal kinetics and its physiological significance symmetric and

sequential modes of action and their significance immobilized enzymes and their industrial

applications study of multienzyme complexes with respect to occurrence isolation and their

properties and polygenic nature eg pyruvate dehydrogenase and fatty acid synthase

Unit III Enzyme regulation

General mechanisms of enzyme regulation Feed back inhibition and feed forward

stimulation repression and induction of enzymes reversible and irreversible covalent

modifications of enzymes flexibility and conformational mobility of enzymes convergent

and divergent evolution of enzymes

Unit IV Bioenergetics and oxidative phosphorylation

Energy transformation laws of thermodynamics Gibbs energy free energy change redox

potentials phosphate potential ion electrochemical potential proton electrochemical

potential membrane potential Chemi-osmotic theory mitochondrial respiratory chain order

and organization of carrier proton gradients Characterization of Iron- Sulphur proteins and

Cytochromes Q cycle Respiratory controls and oxidative phosphorylation ATP synthase

complex

Suggested References

1 Enzymes Biochemistry Biotechnology and Clinical Chemistry-Trevor Palmer

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

10

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 3 (Code 1T3) Biochemical Research Techniques Learning outcome Students will be able to

1 The theoretical aspects of designing the Experiments and also study the Quality

control mechanism in Biochemistry

2 Understand the Sampling techniques and interpret the data based on the measures

of the central tendency

3 Learn the discrepancies and deviations of the variable based of measures of

dispersion

4 Study the relationship between variables based on correlation and regression

analysis

5 Deduce the probable outcomes of an experiment based on observations

following laws of probability and also assess the significance of the

interpretation through tests of significance such as t-test

6 To understand the importance and applications of computational methods and

statistical softwares in Biology

11

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 3 Biochemical Research Techniques

Unit I Research Methodology

1 Introduction to research methodology History and definition of research role of

theory hypothesis sampling variables randomness selection of problem purpose of

research and research reporting

2 Experimental research Early experimentation experimental groups control groups

variables method of controlling variables designing and validation of experiments

3 Methods and tools in research Research tools and its reliability and validity

quantitative and qualitative studies observation inquiry forms Q methodology data

collection limitations and sources of error

4 Types of data Analysis Descriptive data analysis Inferential data analysis Computer

data analysis

Unit II Biostatistics

Principles and practice of statistical methods in biological research samples and populations Basic

statistics-average statistics of dispersion coefficient of variation confidence limits Probability

distribution normal binomial and Poisson distribution Mean variants standard deviations and

standard error correlation and regression test of statistical significance and analysis of variance and

covariance

Unit III Data Retrieval Scientific Writing and Presentation

1 Information Search amp Data Retrieval Tools for Web Search Data Retrieval Tools

Data Mining of Biological Databases

2 Report Writing Significance of report writing different steps in report writing types

of report layout of research paper

3 Mechanics and precautions of writing research reports for scientific journals popular

magazines seminarssymposia conferencesworkshops poster session

4 Presentationndash Oral amp Written Presentations in classrooms scientific meets amp public

audience Defence of research thesis

Unit IV Computers

Introduction of computer networks- Topologies and designs Basics of computer operating systems-

windows and Linux Introduction to Markup language-Hyper Text Markup Language (HTML) and

Extensive Markup Language (XML) Spreadsheets and Presentation software

Systems Biology-An introduction

Introduction to Metagenomics

Suggested References

1 Fundamentals of Biostatistics Bernard A Rosner Thomson-BrooksCole 2006

2 Research methodology in social behavioural and life sciences Designs models and

methods Herman J Ader and Gideon Mellenbergh (Ed) SAGE Publications

6 Principles of Genome analysis and genomics Primrose SB Twyman RM Blackwell

Science (2002)

7 Biostatistics-A foundation for Health Science Daniel WW John Wiley (1983)

8 Statistical Methods Medhi J Willey Eastern Limited (1992)

12

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 4 (Code 1T4) Plant Biochemistry Learning outcome Students will be able to

1 Detailed knowledge of plant cellular architecture and the mechanism

of photosynthetic systems for photophosphorylation will enable the

students to get a dissected approach for understanding autotrophic food

synthesis mechanism driven by photon energy operative in plants

2 Hormonal pathways driving plant growth mechanisms form the

foundation for in vitro plant propagation setup and understanding of

Plant tissue culture aspects Students would gain an thorough insight of

growth regulatory mechanism of plants through which they will be able

to devise the hormonal concoction required for organogenesis and related

plant tissue culture applications

3 Students will be able to learn metabolic attributes and driving

principles of plant growth through basic carbohydrate lipid and protein

metabolism Also the students will be developing a comprehension of

importance of nitrogen and sulphur metabolism in plants and associated

plant physiological alterations

4 With in depth knowledge about plant physiochemical aspects the

students will get equipped to develop an understanding about effects

caused by biotic and abiotic stress factors on plant metabolism and

growth They can thus impinge upon the ways to tackle such stress

physiological aspects to promote and resolve plant stresses

5 Practical exposure to biochemical analysis of plant physiological

aspects would improve the students application approach towards plant

biochemistry as tool to protect plant diversity

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 3: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

3

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

M Sc Biochemistry Semester II Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

2T1 Immunology 4 - 4 4 3 80 20 100 40 2T2 Clinical

Biochemistry 4 - 4 4 3 80 20 100 40

2T3 Cell Biochemistry 4 - 4 4 3 80 20 100 40 2T4 Molecular Biology 4 - 4 4 3 80 20 100 40 2P1 Clinical

Biochemistry and Immunology

- 8 8 4 8 80 20 100 40

2P2 Cell and Molecular Biology

- 8 8 4 8 80 20 100 40

2S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

4

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

M Sc Biochemistry Semester III Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

3T1 Advanced Molecular Biology

4 - 4 4 3 80 20 100 40

3T2 Biotechnology 4 - 4 4 3 80 20 100 40 3T3 A) Toxicology

(Biochemical amp

Environmental

Toxicology

OR

B) Nutrition (Nutritional Biochemistry)

4 - 4 4 3 80 20 100 40

3T4 Foundation I (Biomolecules and Basic metabolism) OR (Subject centric Core 1) Bioresearch Techniques I

4 - 4 4 3 80 20 100 40

3P1 Biotechnology and Molecular Biology

- 8 8 4 8 80 20 100 40

3P2 A) Toxicology

(Biochemical amp

Environmental

Toxicology)

OR

B) Nutrition (Nutritional Biochemistry)

- 8 8 4 8 80 20 100 40

3S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

5

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

M Sc Biochemistry Semester IV

Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

4T1 Advanced Clinical Biochemistry

4 - 4 4 3 80 20 100 40

4T2 Advanced Immunology

4 - 4 4 3 80 20 100 40

4T3 A) Toxicology

(Clinical

Research)

OR

B) Nutrition (Applied Nutritional Biochemistry)

4 - 4 4 3 80 20 100 40

4T4 Foundation 2 (Basic Enzymology) or (Subject centric Core 2) Bioresearch Techniques II

4 - 4 4 3 80 20 100 40

4P1 Advanced

Clinical

Biochemistry amp

Immunology

And

A) Toxicology

(Clinical

Research)

OR

B) Nutrition

(Applied

Nutritional

Biochemistry)

- 8 8 4 8 80 20 100 40

4PROJ Project - 8 8 4 8 80 20 100 40 4S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

6

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 1 (Code 1T1) Protein Biochemistry Learning outcome Students will be able to

1 Basics Protein structure chemical bonding or molecular geometry based on accepted

models

2 Apply quantitative reasoning skills of protein folding and energy physical or

chemical changes that occur

3 Use accepted models to describe the interactions of amino acids and equilibrium

concepts with respect to protein conformations and interactions

4 In the major areas of Mass spectrometry students will be able to

a Describe and understand the capabilities and limitations of instrumental methods

b Explain the instrument components and principles of operation

5 Upon being introduced to the steps of the analytical process students will be able to

correctly select an analytical method and instrument meeting their use objectives

Also students would be able to demonstrate competence in data acquisition by Mass

Spectrometric analysis and interpreting laboratory data

6 With Basics of Protein synthesis machinery students will be able to conceptualize the

process of translation and its regulatory aspects so as to apply the concept for

understanding protein structural dynamics with respect to protein functions

7 Protein sorting and compartmentalization during and after translation will give

fundamental understanding about organelle specific protein functions This will

develop competence amongst the students for application of physical parameters in

protein functional dynamics depending upon organelle specific environment

8 Overall understanding of protein structure function relationship through this paper

will equip the students to propose designs of novel proteins constructed through

utilization of aspects of protein engineering Specific examples of the same would

help them understand and apply the concept of protein engineering to the fullest

7

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T1 Protein Biochemistry

Unit I Proteins and Mass Spectrometry

Overview of protein structure protein folding Ramchandran plot domains and modules

binding sites within proteins protein sequencing

Basics of Mass Spectrometry Ionization mechanisms- protonation deprotonation

cationization transfer of charged molecules to gas phase electron ejection electron capture

Mass analyzers-TOF Ion trap Quadrupole Ionization methods-Electron Impact (EI)

Chemical Ionization (CI) Fast Atom Bombardment (FAB) Field Description (FD) Electron

Spray Ionization (ESI) Matrix Assisted Laser Desorption Ionization (MALDI) Protein

Identification using MS

Unit II Protein biosynthesis

Eukaryotic translation machinery structure and assembly of the ribosome initiation

elongation and termination of translation

Unit III Protein sorting and degradation Intracellular protein sorting movement of proteins between cellular compartments gated

transmembrane and vesicular transport Protein transport and translocation to nucleus mitochondria

chloroplast peroxisomes endoplasmic reticular system Protein degradation

Unit IV Protein Engineering

Design and construction of novel proteins and enzymes Conformation of proteins in general and

enzymes in particular Effect of amino acids on structure of proteins Energy status of a protein

molecule Structure function relations of enzymes Physical methods such as x-ray crystallography

for determination of protein structure Site directed mutagenesis for specific protein function Basic

concepts for design of a new proteinenzyme molecule Specific examples of enzyme engineering -

Dihydrofolate reductase and Subtilisin

Suggested References

1 Modern Protein Chemistry Practical Aspects Published September 12 2001 by CRC Press -

272 Pages Edited By Gary C Howard

2 Biochemistry 5th edition Berg JM Tymoczko JL Stryer L New York W H Freeman 2002

3 Proteins Structures and Molecular Properties Thomas E Creighton Publisher W H Freeman

1992 Edition Second Edition

4 Protein Engineering Protocols (Methods in Molecular Biology) Kristian Muumlller (Editor)

Publisher Humana Press Softcover reprint of hardcover 1st ed 2007 edition (November 10

2010)

5 Protein Degradation Series 4 Volume Set (v 1) R John Mayer (Editor) Publisher Wiley-

VCH 1 edition (March 4 2008)

6 Structural Aspects of Protein Synthesis Anders LiljashttpwwwamazoncomStructural-

Aspects-Protein-Synthesis-

Andersdp981238863Xref=sr_1_1s=booksampie=UTF8ampqid=1323503546ampsr=1-1 -

(Author) Publisher World Scientific Pub Co Inc 1 edition (November 2004)

7 Protein Targeting Transport and Translocation Ross Dalbey (Editor) Publisher Academic

Press 1 edition (May 13 2002)

8 Principles of Physical Biochemistry- KenslE van Holde W Curtis Johnson P Shing Ho

Pearson Prentice Hall 2nd Edition

9 Crystallography made crystal clear 1993 G Rhodes Academic Press

10 Principles and Techniques of Biochemistry and Molecular Biology 6th Edition Wilson Keith

and Walker John (2005) Cambridge University Press New York

11 A textbook of biophysics R N Roy New Central Publication 1st edition

8

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 2 (Code 1T2) Advanced Enzymology Learning outcome Students will be able to

1 Describe structure capacities and the component of activity of

chemicals and interaction with enzymes Learning energy of protein

catalyzed responses and compound restraints and administrative

procedure Enzyme action Enzyme Units Specific action

2 Have a detail and more intricate knowledge of allosteric and other

aspects of enzyme catalysis regulation

3 Have a total comprehension of rate of responses and request of

responses and restraints and their kinetics To gain information on

protein catalysis and isoenzymes and on multienzyme and multienzyme

complexes with specific examples

4 Develop intellectual capacity to relate bioenergetics principles and the

entropy to the law of thermodynamics and Free energy and its

connection to chemical equilibria in consolation to enzyme catalysis

5 Theory related to respiratory mechanisms catalysed by enzymatic

principles of redox biochemistry will help the students to gauge wide

applicability of enzymatic reactions in biological systems Detail

description of Coupled reactions and their role in metabolism and

Chemiosmotic hypothesis of ATP synthesis to understand the

mechanism of energy harnessing mechanism operating in biological

system

9

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 2 Advanced Enzymology

Unit I Kinetics and Regulation of enzyme activity

Review of unisubstrate enzyme kinetics multisubstrate enzyme kinetics Co-operativity

phenomenon Hill and Scatchard plots protein-ligand binding and its measurement detailed

mechanism of catalysis of serine protease carbonic anhydrase and PEP kinase

Metalloenzymes

Unit II Allosteric enzymes and multienzyme systems

Allosteric enzymes sigmoidal kinetics and its physiological significance symmetric and

sequential modes of action and their significance immobilized enzymes and their industrial

applications study of multienzyme complexes with respect to occurrence isolation and their

properties and polygenic nature eg pyruvate dehydrogenase and fatty acid synthase

Unit III Enzyme regulation

General mechanisms of enzyme regulation Feed back inhibition and feed forward

stimulation repression and induction of enzymes reversible and irreversible covalent

modifications of enzymes flexibility and conformational mobility of enzymes convergent

and divergent evolution of enzymes

Unit IV Bioenergetics and oxidative phosphorylation

Energy transformation laws of thermodynamics Gibbs energy free energy change redox

potentials phosphate potential ion electrochemical potential proton electrochemical

potential membrane potential Chemi-osmotic theory mitochondrial respiratory chain order

and organization of carrier proton gradients Characterization of Iron- Sulphur proteins and

Cytochromes Q cycle Respiratory controls and oxidative phosphorylation ATP synthase

complex

Suggested References

1 Enzymes Biochemistry Biotechnology and Clinical Chemistry-Trevor Palmer

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

10

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 3 (Code 1T3) Biochemical Research Techniques Learning outcome Students will be able to

1 The theoretical aspects of designing the Experiments and also study the Quality

control mechanism in Biochemistry

2 Understand the Sampling techniques and interpret the data based on the measures

of the central tendency

3 Learn the discrepancies and deviations of the variable based of measures of

dispersion

4 Study the relationship between variables based on correlation and regression

analysis

5 Deduce the probable outcomes of an experiment based on observations

following laws of probability and also assess the significance of the

interpretation through tests of significance such as t-test

6 To understand the importance and applications of computational methods and

statistical softwares in Biology

11

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 3 Biochemical Research Techniques

Unit I Research Methodology

1 Introduction to research methodology History and definition of research role of

theory hypothesis sampling variables randomness selection of problem purpose of

research and research reporting

2 Experimental research Early experimentation experimental groups control groups

variables method of controlling variables designing and validation of experiments

3 Methods and tools in research Research tools and its reliability and validity

quantitative and qualitative studies observation inquiry forms Q methodology data

collection limitations and sources of error

4 Types of data Analysis Descriptive data analysis Inferential data analysis Computer

data analysis

Unit II Biostatistics

Principles and practice of statistical methods in biological research samples and populations Basic

statistics-average statistics of dispersion coefficient of variation confidence limits Probability

distribution normal binomial and Poisson distribution Mean variants standard deviations and

standard error correlation and regression test of statistical significance and analysis of variance and

covariance

Unit III Data Retrieval Scientific Writing and Presentation

1 Information Search amp Data Retrieval Tools for Web Search Data Retrieval Tools

Data Mining of Biological Databases

2 Report Writing Significance of report writing different steps in report writing types

of report layout of research paper

3 Mechanics and precautions of writing research reports for scientific journals popular

magazines seminarssymposia conferencesworkshops poster session

4 Presentationndash Oral amp Written Presentations in classrooms scientific meets amp public

audience Defence of research thesis

Unit IV Computers

Introduction of computer networks- Topologies and designs Basics of computer operating systems-

windows and Linux Introduction to Markup language-Hyper Text Markup Language (HTML) and

Extensive Markup Language (XML) Spreadsheets and Presentation software

Systems Biology-An introduction

Introduction to Metagenomics

Suggested References

1 Fundamentals of Biostatistics Bernard A Rosner Thomson-BrooksCole 2006

2 Research methodology in social behavioural and life sciences Designs models and

methods Herman J Ader and Gideon Mellenbergh (Ed) SAGE Publications

6 Principles of Genome analysis and genomics Primrose SB Twyman RM Blackwell

Science (2002)

7 Biostatistics-A foundation for Health Science Daniel WW John Wiley (1983)

8 Statistical Methods Medhi J Willey Eastern Limited (1992)

12

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 4 (Code 1T4) Plant Biochemistry Learning outcome Students will be able to

1 Detailed knowledge of plant cellular architecture and the mechanism

of photosynthetic systems for photophosphorylation will enable the

students to get a dissected approach for understanding autotrophic food

synthesis mechanism driven by photon energy operative in plants

2 Hormonal pathways driving plant growth mechanisms form the

foundation for in vitro plant propagation setup and understanding of

Plant tissue culture aspects Students would gain an thorough insight of

growth regulatory mechanism of plants through which they will be able

to devise the hormonal concoction required for organogenesis and related

plant tissue culture applications

3 Students will be able to learn metabolic attributes and driving

principles of plant growth through basic carbohydrate lipid and protein

metabolism Also the students will be developing a comprehension of

importance of nitrogen and sulphur metabolism in plants and associated

plant physiological alterations

4 With in depth knowledge about plant physiochemical aspects the

students will get equipped to develop an understanding about effects

caused by biotic and abiotic stress factors on plant metabolism and

growth They can thus impinge upon the ways to tackle such stress

physiological aspects to promote and resolve plant stresses

5 Practical exposure to biochemical analysis of plant physiological

aspects would improve the students application approach towards plant

biochemistry as tool to protect plant diversity

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 4: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

4

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

M Sc Biochemistry Semester III Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

3T1 Advanced Molecular Biology

4 - 4 4 3 80 20 100 40

3T2 Biotechnology 4 - 4 4 3 80 20 100 40 3T3 A) Toxicology

(Biochemical amp

Environmental

Toxicology

OR

B) Nutrition (Nutritional Biochemistry)

4 - 4 4 3 80 20 100 40

3T4 Foundation I (Biomolecules and Basic metabolism) OR (Subject centric Core 1) Bioresearch Techniques I

4 - 4 4 3 80 20 100 40

3P1 Biotechnology and Molecular Biology

- 8 8 4 8 80 20 100 40

3P2 A) Toxicology

(Biochemical amp

Environmental

Toxicology)

OR

B) Nutrition (Nutritional Biochemistry)

- 8 8 4 8 80 20 100 40

3S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

5

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

M Sc Biochemistry Semester IV

Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

4T1 Advanced Clinical Biochemistry

4 - 4 4 3 80 20 100 40

4T2 Advanced Immunology

4 - 4 4 3 80 20 100 40

4T3 A) Toxicology

(Clinical

Research)

OR

B) Nutrition (Applied Nutritional Biochemistry)

4 - 4 4 3 80 20 100 40

4T4 Foundation 2 (Basic Enzymology) or (Subject centric Core 2) Bioresearch Techniques II

4 - 4 4 3 80 20 100 40

4P1 Advanced

Clinical

Biochemistry amp

Immunology

And

A) Toxicology

(Clinical

Research)

OR

B) Nutrition

(Applied

Nutritional

Biochemistry)

- 8 8 4 8 80 20 100 40

4PROJ Project - 8 8 4 8 80 20 100 40 4S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

6

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 1 (Code 1T1) Protein Biochemistry Learning outcome Students will be able to

1 Basics Protein structure chemical bonding or molecular geometry based on accepted

models

2 Apply quantitative reasoning skills of protein folding and energy physical or

chemical changes that occur

3 Use accepted models to describe the interactions of amino acids and equilibrium

concepts with respect to protein conformations and interactions

4 In the major areas of Mass spectrometry students will be able to

a Describe and understand the capabilities and limitations of instrumental methods

b Explain the instrument components and principles of operation

5 Upon being introduced to the steps of the analytical process students will be able to

correctly select an analytical method and instrument meeting their use objectives

Also students would be able to demonstrate competence in data acquisition by Mass

Spectrometric analysis and interpreting laboratory data

6 With Basics of Protein synthesis machinery students will be able to conceptualize the

process of translation and its regulatory aspects so as to apply the concept for

understanding protein structural dynamics with respect to protein functions

7 Protein sorting and compartmentalization during and after translation will give

fundamental understanding about organelle specific protein functions This will

develop competence amongst the students for application of physical parameters in

protein functional dynamics depending upon organelle specific environment

8 Overall understanding of protein structure function relationship through this paper

will equip the students to propose designs of novel proteins constructed through

utilization of aspects of protein engineering Specific examples of the same would

help them understand and apply the concept of protein engineering to the fullest

7

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T1 Protein Biochemistry

Unit I Proteins and Mass Spectrometry

Overview of protein structure protein folding Ramchandran plot domains and modules

binding sites within proteins protein sequencing

Basics of Mass Spectrometry Ionization mechanisms- protonation deprotonation

cationization transfer of charged molecules to gas phase electron ejection electron capture

Mass analyzers-TOF Ion trap Quadrupole Ionization methods-Electron Impact (EI)

Chemical Ionization (CI) Fast Atom Bombardment (FAB) Field Description (FD) Electron

Spray Ionization (ESI) Matrix Assisted Laser Desorption Ionization (MALDI) Protein

Identification using MS

Unit II Protein biosynthesis

Eukaryotic translation machinery structure and assembly of the ribosome initiation

elongation and termination of translation

Unit III Protein sorting and degradation Intracellular protein sorting movement of proteins between cellular compartments gated

transmembrane and vesicular transport Protein transport and translocation to nucleus mitochondria

chloroplast peroxisomes endoplasmic reticular system Protein degradation

Unit IV Protein Engineering

Design and construction of novel proteins and enzymes Conformation of proteins in general and

enzymes in particular Effect of amino acids on structure of proteins Energy status of a protein

molecule Structure function relations of enzymes Physical methods such as x-ray crystallography

for determination of protein structure Site directed mutagenesis for specific protein function Basic

concepts for design of a new proteinenzyme molecule Specific examples of enzyme engineering -

Dihydrofolate reductase and Subtilisin

Suggested References

1 Modern Protein Chemistry Practical Aspects Published September 12 2001 by CRC Press -

272 Pages Edited By Gary C Howard

2 Biochemistry 5th edition Berg JM Tymoczko JL Stryer L New York W H Freeman 2002

3 Proteins Structures and Molecular Properties Thomas E Creighton Publisher W H Freeman

1992 Edition Second Edition

4 Protein Engineering Protocols (Methods in Molecular Biology) Kristian Muumlller (Editor)

Publisher Humana Press Softcover reprint of hardcover 1st ed 2007 edition (November 10

2010)

5 Protein Degradation Series 4 Volume Set (v 1) R John Mayer (Editor) Publisher Wiley-

VCH 1 edition (March 4 2008)

6 Structural Aspects of Protein Synthesis Anders LiljashttpwwwamazoncomStructural-

Aspects-Protein-Synthesis-

Andersdp981238863Xref=sr_1_1s=booksampie=UTF8ampqid=1323503546ampsr=1-1 -

(Author) Publisher World Scientific Pub Co Inc 1 edition (November 2004)

7 Protein Targeting Transport and Translocation Ross Dalbey (Editor) Publisher Academic

Press 1 edition (May 13 2002)

8 Principles of Physical Biochemistry- KenslE van Holde W Curtis Johnson P Shing Ho

Pearson Prentice Hall 2nd Edition

9 Crystallography made crystal clear 1993 G Rhodes Academic Press

10 Principles and Techniques of Biochemistry and Molecular Biology 6th Edition Wilson Keith

and Walker John (2005) Cambridge University Press New York

11 A textbook of biophysics R N Roy New Central Publication 1st edition

8

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 2 (Code 1T2) Advanced Enzymology Learning outcome Students will be able to

1 Describe structure capacities and the component of activity of

chemicals and interaction with enzymes Learning energy of protein

catalyzed responses and compound restraints and administrative

procedure Enzyme action Enzyme Units Specific action

2 Have a detail and more intricate knowledge of allosteric and other

aspects of enzyme catalysis regulation

3 Have a total comprehension of rate of responses and request of

responses and restraints and their kinetics To gain information on

protein catalysis and isoenzymes and on multienzyme and multienzyme

complexes with specific examples

4 Develop intellectual capacity to relate bioenergetics principles and the

entropy to the law of thermodynamics and Free energy and its

connection to chemical equilibria in consolation to enzyme catalysis

5 Theory related to respiratory mechanisms catalysed by enzymatic

principles of redox biochemistry will help the students to gauge wide

applicability of enzymatic reactions in biological systems Detail

description of Coupled reactions and their role in metabolism and

Chemiosmotic hypothesis of ATP synthesis to understand the

mechanism of energy harnessing mechanism operating in biological

system

9

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 2 Advanced Enzymology

Unit I Kinetics and Regulation of enzyme activity

Review of unisubstrate enzyme kinetics multisubstrate enzyme kinetics Co-operativity

phenomenon Hill and Scatchard plots protein-ligand binding and its measurement detailed

mechanism of catalysis of serine protease carbonic anhydrase and PEP kinase

Metalloenzymes

Unit II Allosteric enzymes and multienzyme systems

Allosteric enzymes sigmoidal kinetics and its physiological significance symmetric and

sequential modes of action and their significance immobilized enzymes and their industrial

applications study of multienzyme complexes with respect to occurrence isolation and their

properties and polygenic nature eg pyruvate dehydrogenase and fatty acid synthase

Unit III Enzyme regulation

General mechanisms of enzyme regulation Feed back inhibition and feed forward

stimulation repression and induction of enzymes reversible and irreversible covalent

modifications of enzymes flexibility and conformational mobility of enzymes convergent

and divergent evolution of enzymes

Unit IV Bioenergetics and oxidative phosphorylation

Energy transformation laws of thermodynamics Gibbs energy free energy change redox

potentials phosphate potential ion electrochemical potential proton electrochemical

potential membrane potential Chemi-osmotic theory mitochondrial respiratory chain order

and organization of carrier proton gradients Characterization of Iron- Sulphur proteins and

Cytochromes Q cycle Respiratory controls and oxidative phosphorylation ATP synthase

complex

Suggested References

1 Enzymes Biochemistry Biotechnology and Clinical Chemistry-Trevor Palmer

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

10

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 3 (Code 1T3) Biochemical Research Techniques Learning outcome Students will be able to

1 The theoretical aspects of designing the Experiments and also study the Quality

control mechanism in Biochemistry

2 Understand the Sampling techniques and interpret the data based on the measures

of the central tendency

3 Learn the discrepancies and deviations of the variable based of measures of

dispersion

4 Study the relationship between variables based on correlation and regression

analysis

5 Deduce the probable outcomes of an experiment based on observations

following laws of probability and also assess the significance of the

interpretation through tests of significance such as t-test

6 To understand the importance and applications of computational methods and

statistical softwares in Biology

11

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 3 Biochemical Research Techniques

Unit I Research Methodology

1 Introduction to research methodology History and definition of research role of

theory hypothesis sampling variables randomness selection of problem purpose of

research and research reporting

2 Experimental research Early experimentation experimental groups control groups

variables method of controlling variables designing and validation of experiments

3 Methods and tools in research Research tools and its reliability and validity

quantitative and qualitative studies observation inquiry forms Q methodology data

collection limitations and sources of error

4 Types of data Analysis Descriptive data analysis Inferential data analysis Computer

data analysis

Unit II Biostatistics

Principles and practice of statistical methods in biological research samples and populations Basic

statistics-average statistics of dispersion coefficient of variation confidence limits Probability

distribution normal binomial and Poisson distribution Mean variants standard deviations and

standard error correlation and regression test of statistical significance and analysis of variance and

covariance

Unit III Data Retrieval Scientific Writing and Presentation

1 Information Search amp Data Retrieval Tools for Web Search Data Retrieval Tools

Data Mining of Biological Databases

2 Report Writing Significance of report writing different steps in report writing types

of report layout of research paper

3 Mechanics and precautions of writing research reports for scientific journals popular

magazines seminarssymposia conferencesworkshops poster session

4 Presentationndash Oral amp Written Presentations in classrooms scientific meets amp public

audience Defence of research thesis

Unit IV Computers

Introduction of computer networks- Topologies and designs Basics of computer operating systems-

windows and Linux Introduction to Markup language-Hyper Text Markup Language (HTML) and

Extensive Markup Language (XML) Spreadsheets and Presentation software

Systems Biology-An introduction

Introduction to Metagenomics

Suggested References

1 Fundamentals of Biostatistics Bernard A Rosner Thomson-BrooksCole 2006

2 Research methodology in social behavioural and life sciences Designs models and

methods Herman J Ader and Gideon Mellenbergh (Ed) SAGE Publications

6 Principles of Genome analysis and genomics Primrose SB Twyman RM Blackwell

Science (2002)

7 Biostatistics-A foundation for Health Science Daniel WW John Wiley (1983)

8 Statistical Methods Medhi J Willey Eastern Limited (1992)

12

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 4 (Code 1T4) Plant Biochemistry Learning outcome Students will be able to

1 Detailed knowledge of plant cellular architecture and the mechanism

of photosynthetic systems for photophosphorylation will enable the

students to get a dissected approach for understanding autotrophic food

synthesis mechanism driven by photon energy operative in plants

2 Hormonal pathways driving plant growth mechanisms form the

foundation for in vitro plant propagation setup and understanding of

Plant tissue culture aspects Students would gain an thorough insight of

growth regulatory mechanism of plants through which they will be able

to devise the hormonal concoction required for organogenesis and related

plant tissue culture applications

3 Students will be able to learn metabolic attributes and driving

principles of plant growth through basic carbohydrate lipid and protein

metabolism Also the students will be developing a comprehension of

importance of nitrogen and sulphur metabolism in plants and associated

plant physiological alterations

4 With in depth knowledge about plant physiochemical aspects the

students will get equipped to develop an understanding about effects

caused by biotic and abiotic stress factors on plant metabolism and

growth They can thus impinge upon the ways to tackle such stress

physiological aspects to promote and resolve plant stresses

5 Practical exposure to biochemical analysis of plant physiological

aspects would improve the students application approach towards plant

biochemistry as tool to protect plant diversity

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 5: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

5

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

M Sc Biochemistry Semester IV

Code

Th

eory

P

ract

ical

Teaching scheme (Hours Week)

Cre

dit

s

Examination Scheme

Th

Pra

ct

To

tal

Du

rati

on

in h

rs

Max Marks

To

tal M

ark

s

Minimum Passing Marks

Ext

ern

al

Mar

ks

Inte

rnal

A

ss

Th

Pra

ct

4T1 Advanced Clinical Biochemistry

4 - 4 4 3 80 20 100 40

4T2 Advanced Immunology

4 - 4 4 3 80 20 100 40

4T3 A) Toxicology

(Clinical

Research)

OR

B) Nutrition (Applied Nutritional Biochemistry)

4 - 4 4 3 80 20 100 40

4T4 Foundation 2 (Basic Enzymology) or (Subject centric Core 2) Bioresearch Techniques II

4 - 4 4 3 80 20 100 40

4P1 Advanced

Clinical

Biochemistry amp

Immunology

And

A) Toxicology

(Clinical

Research)

OR

B) Nutrition

(Applied

Nutritional

Biochemistry)

- 8 8 4 8 80 20 100 40

4PROJ Project - 8 8 4 8 80 20 100 40 4S1 Seminar 2 - 2 1 25 25 10 TOTAL 18 16 34 25 520 105 625 170 80

6

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 1 (Code 1T1) Protein Biochemistry Learning outcome Students will be able to

1 Basics Protein structure chemical bonding or molecular geometry based on accepted

models

2 Apply quantitative reasoning skills of protein folding and energy physical or

chemical changes that occur

3 Use accepted models to describe the interactions of amino acids and equilibrium

concepts with respect to protein conformations and interactions

4 In the major areas of Mass spectrometry students will be able to

a Describe and understand the capabilities and limitations of instrumental methods

b Explain the instrument components and principles of operation

5 Upon being introduced to the steps of the analytical process students will be able to

correctly select an analytical method and instrument meeting their use objectives

Also students would be able to demonstrate competence in data acquisition by Mass

Spectrometric analysis and interpreting laboratory data

6 With Basics of Protein synthesis machinery students will be able to conceptualize the

process of translation and its regulatory aspects so as to apply the concept for

understanding protein structural dynamics with respect to protein functions

7 Protein sorting and compartmentalization during and after translation will give

fundamental understanding about organelle specific protein functions This will

develop competence amongst the students for application of physical parameters in

protein functional dynamics depending upon organelle specific environment

8 Overall understanding of protein structure function relationship through this paper

will equip the students to propose designs of novel proteins constructed through

utilization of aspects of protein engineering Specific examples of the same would

help them understand and apply the concept of protein engineering to the fullest

7

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T1 Protein Biochemistry

Unit I Proteins and Mass Spectrometry

Overview of protein structure protein folding Ramchandran plot domains and modules

binding sites within proteins protein sequencing

Basics of Mass Spectrometry Ionization mechanisms- protonation deprotonation

cationization transfer of charged molecules to gas phase electron ejection electron capture

Mass analyzers-TOF Ion trap Quadrupole Ionization methods-Electron Impact (EI)

Chemical Ionization (CI) Fast Atom Bombardment (FAB) Field Description (FD) Electron

Spray Ionization (ESI) Matrix Assisted Laser Desorption Ionization (MALDI) Protein

Identification using MS

Unit II Protein biosynthesis

Eukaryotic translation machinery structure and assembly of the ribosome initiation

elongation and termination of translation

Unit III Protein sorting and degradation Intracellular protein sorting movement of proteins between cellular compartments gated

transmembrane and vesicular transport Protein transport and translocation to nucleus mitochondria

chloroplast peroxisomes endoplasmic reticular system Protein degradation

Unit IV Protein Engineering

Design and construction of novel proteins and enzymes Conformation of proteins in general and

enzymes in particular Effect of amino acids on structure of proteins Energy status of a protein

molecule Structure function relations of enzymes Physical methods such as x-ray crystallography

for determination of protein structure Site directed mutagenesis for specific protein function Basic

concepts for design of a new proteinenzyme molecule Specific examples of enzyme engineering -

Dihydrofolate reductase and Subtilisin

Suggested References

1 Modern Protein Chemistry Practical Aspects Published September 12 2001 by CRC Press -

272 Pages Edited By Gary C Howard

2 Biochemistry 5th edition Berg JM Tymoczko JL Stryer L New York W H Freeman 2002

3 Proteins Structures and Molecular Properties Thomas E Creighton Publisher W H Freeman

1992 Edition Second Edition

4 Protein Engineering Protocols (Methods in Molecular Biology) Kristian Muumlller (Editor)

Publisher Humana Press Softcover reprint of hardcover 1st ed 2007 edition (November 10

2010)

5 Protein Degradation Series 4 Volume Set (v 1) R John Mayer (Editor) Publisher Wiley-

VCH 1 edition (March 4 2008)

6 Structural Aspects of Protein Synthesis Anders LiljashttpwwwamazoncomStructural-

Aspects-Protein-Synthesis-

Andersdp981238863Xref=sr_1_1s=booksampie=UTF8ampqid=1323503546ampsr=1-1 -

(Author) Publisher World Scientific Pub Co Inc 1 edition (November 2004)

7 Protein Targeting Transport and Translocation Ross Dalbey (Editor) Publisher Academic

Press 1 edition (May 13 2002)

8 Principles of Physical Biochemistry- KenslE van Holde W Curtis Johnson P Shing Ho

Pearson Prentice Hall 2nd Edition

9 Crystallography made crystal clear 1993 G Rhodes Academic Press

10 Principles and Techniques of Biochemistry and Molecular Biology 6th Edition Wilson Keith

and Walker John (2005) Cambridge University Press New York

11 A textbook of biophysics R N Roy New Central Publication 1st edition

8

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 2 (Code 1T2) Advanced Enzymology Learning outcome Students will be able to

1 Describe structure capacities and the component of activity of

chemicals and interaction with enzymes Learning energy of protein

catalyzed responses and compound restraints and administrative

procedure Enzyme action Enzyme Units Specific action

2 Have a detail and more intricate knowledge of allosteric and other

aspects of enzyme catalysis regulation

3 Have a total comprehension of rate of responses and request of

responses and restraints and their kinetics To gain information on

protein catalysis and isoenzymes and on multienzyme and multienzyme

complexes with specific examples

4 Develop intellectual capacity to relate bioenergetics principles and the

entropy to the law of thermodynamics and Free energy and its

connection to chemical equilibria in consolation to enzyme catalysis

5 Theory related to respiratory mechanisms catalysed by enzymatic

principles of redox biochemistry will help the students to gauge wide

applicability of enzymatic reactions in biological systems Detail

description of Coupled reactions and their role in metabolism and

Chemiosmotic hypothesis of ATP synthesis to understand the

mechanism of energy harnessing mechanism operating in biological

system

9

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 2 Advanced Enzymology

Unit I Kinetics and Regulation of enzyme activity

Review of unisubstrate enzyme kinetics multisubstrate enzyme kinetics Co-operativity

phenomenon Hill and Scatchard plots protein-ligand binding and its measurement detailed

mechanism of catalysis of serine protease carbonic anhydrase and PEP kinase

Metalloenzymes

Unit II Allosteric enzymes and multienzyme systems

Allosteric enzymes sigmoidal kinetics and its physiological significance symmetric and

sequential modes of action and their significance immobilized enzymes and their industrial

applications study of multienzyme complexes with respect to occurrence isolation and their

properties and polygenic nature eg pyruvate dehydrogenase and fatty acid synthase

Unit III Enzyme regulation

General mechanisms of enzyme regulation Feed back inhibition and feed forward

stimulation repression and induction of enzymes reversible and irreversible covalent

modifications of enzymes flexibility and conformational mobility of enzymes convergent

and divergent evolution of enzymes

Unit IV Bioenergetics and oxidative phosphorylation

Energy transformation laws of thermodynamics Gibbs energy free energy change redox

potentials phosphate potential ion electrochemical potential proton electrochemical

potential membrane potential Chemi-osmotic theory mitochondrial respiratory chain order

and organization of carrier proton gradients Characterization of Iron- Sulphur proteins and

Cytochromes Q cycle Respiratory controls and oxidative phosphorylation ATP synthase

complex

Suggested References

1 Enzymes Biochemistry Biotechnology and Clinical Chemistry-Trevor Palmer

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

10

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 3 (Code 1T3) Biochemical Research Techniques Learning outcome Students will be able to

1 The theoretical aspects of designing the Experiments and also study the Quality

control mechanism in Biochemistry

2 Understand the Sampling techniques and interpret the data based on the measures

of the central tendency

3 Learn the discrepancies and deviations of the variable based of measures of

dispersion

4 Study the relationship between variables based on correlation and regression

analysis

5 Deduce the probable outcomes of an experiment based on observations

following laws of probability and also assess the significance of the

interpretation through tests of significance such as t-test

6 To understand the importance and applications of computational methods and

statistical softwares in Biology

11

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 3 Biochemical Research Techniques

Unit I Research Methodology

1 Introduction to research methodology History and definition of research role of

theory hypothesis sampling variables randomness selection of problem purpose of

research and research reporting

2 Experimental research Early experimentation experimental groups control groups

variables method of controlling variables designing and validation of experiments

3 Methods and tools in research Research tools and its reliability and validity

quantitative and qualitative studies observation inquiry forms Q methodology data

collection limitations and sources of error

4 Types of data Analysis Descriptive data analysis Inferential data analysis Computer

data analysis

Unit II Biostatistics

Principles and practice of statistical methods in biological research samples and populations Basic

statistics-average statistics of dispersion coefficient of variation confidence limits Probability

distribution normal binomial and Poisson distribution Mean variants standard deviations and

standard error correlation and regression test of statistical significance and analysis of variance and

covariance

Unit III Data Retrieval Scientific Writing and Presentation

1 Information Search amp Data Retrieval Tools for Web Search Data Retrieval Tools

Data Mining of Biological Databases

2 Report Writing Significance of report writing different steps in report writing types

of report layout of research paper

3 Mechanics and precautions of writing research reports for scientific journals popular

magazines seminarssymposia conferencesworkshops poster session

4 Presentationndash Oral amp Written Presentations in classrooms scientific meets amp public

audience Defence of research thesis

Unit IV Computers

Introduction of computer networks- Topologies and designs Basics of computer operating systems-

windows and Linux Introduction to Markup language-Hyper Text Markup Language (HTML) and

Extensive Markup Language (XML) Spreadsheets and Presentation software

Systems Biology-An introduction

Introduction to Metagenomics

Suggested References

1 Fundamentals of Biostatistics Bernard A Rosner Thomson-BrooksCole 2006

2 Research methodology in social behavioural and life sciences Designs models and

methods Herman J Ader and Gideon Mellenbergh (Ed) SAGE Publications

6 Principles of Genome analysis and genomics Primrose SB Twyman RM Blackwell

Science (2002)

7 Biostatistics-A foundation for Health Science Daniel WW John Wiley (1983)

8 Statistical Methods Medhi J Willey Eastern Limited (1992)

12

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 4 (Code 1T4) Plant Biochemistry Learning outcome Students will be able to

1 Detailed knowledge of plant cellular architecture and the mechanism

of photosynthetic systems for photophosphorylation will enable the

students to get a dissected approach for understanding autotrophic food

synthesis mechanism driven by photon energy operative in plants

2 Hormonal pathways driving plant growth mechanisms form the

foundation for in vitro plant propagation setup and understanding of

Plant tissue culture aspects Students would gain an thorough insight of

growth regulatory mechanism of plants through which they will be able

to devise the hormonal concoction required for organogenesis and related

plant tissue culture applications

3 Students will be able to learn metabolic attributes and driving

principles of plant growth through basic carbohydrate lipid and protein

metabolism Also the students will be developing a comprehension of

importance of nitrogen and sulphur metabolism in plants and associated

plant physiological alterations

4 With in depth knowledge about plant physiochemical aspects the

students will get equipped to develop an understanding about effects

caused by biotic and abiotic stress factors on plant metabolism and

growth They can thus impinge upon the ways to tackle such stress

physiological aspects to promote and resolve plant stresses

5 Practical exposure to biochemical analysis of plant physiological

aspects would improve the students application approach towards plant

biochemistry as tool to protect plant diversity

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 6: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

6

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 1 (Code 1T1) Protein Biochemistry Learning outcome Students will be able to

1 Basics Protein structure chemical bonding or molecular geometry based on accepted

models

2 Apply quantitative reasoning skills of protein folding and energy physical or

chemical changes that occur

3 Use accepted models to describe the interactions of amino acids and equilibrium

concepts with respect to protein conformations and interactions

4 In the major areas of Mass spectrometry students will be able to

a Describe and understand the capabilities and limitations of instrumental methods

b Explain the instrument components and principles of operation

5 Upon being introduced to the steps of the analytical process students will be able to

correctly select an analytical method and instrument meeting their use objectives

Also students would be able to demonstrate competence in data acquisition by Mass

Spectrometric analysis and interpreting laboratory data

6 With Basics of Protein synthesis machinery students will be able to conceptualize the

process of translation and its regulatory aspects so as to apply the concept for

understanding protein structural dynamics with respect to protein functions

7 Protein sorting and compartmentalization during and after translation will give

fundamental understanding about organelle specific protein functions This will

develop competence amongst the students for application of physical parameters in

protein functional dynamics depending upon organelle specific environment

8 Overall understanding of protein structure function relationship through this paper

will equip the students to propose designs of novel proteins constructed through

utilization of aspects of protein engineering Specific examples of the same would

help them understand and apply the concept of protein engineering to the fullest

7

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T1 Protein Biochemistry

Unit I Proteins and Mass Spectrometry

Overview of protein structure protein folding Ramchandran plot domains and modules

binding sites within proteins protein sequencing

Basics of Mass Spectrometry Ionization mechanisms- protonation deprotonation

cationization transfer of charged molecules to gas phase electron ejection electron capture

Mass analyzers-TOF Ion trap Quadrupole Ionization methods-Electron Impact (EI)

Chemical Ionization (CI) Fast Atom Bombardment (FAB) Field Description (FD) Electron

Spray Ionization (ESI) Matrix Assisted Laser Desorption Ionization (MALDI) Protein

Identification using MS

Unit II Protein biosynthesis

Eukaryotic translation machinery structure and assembly of the ribosome initiation

elongation and termination of translation

Unit III Protein sorting and degradation Intracellular protein sorting movement of proteins between cellular compartments gated

transmembrane and vesicular transport Protein transport and translocation to nucleus mitochondria

chloroplast peroxisomes endoplasmic reticular system Protein degradation

Unit IV Protein Engineering

Design and construction of novel proteins and enzymes Conformation of proteins in general and

enzymes in particular Effect of amino acids on structure of proteins Energy status of a protein

molecule Structure function relations of enzymes Physical methods such as x-ray crystallography

for determination of protein structure Site directed mutagenesis for specific protein function Basic

concepts for design of a new proteinenzyme molecule Specific examples of enzyme engineering -

Dihydrofolate reductase and Subtilisin

Suggested References

1 Modern Protein Chemistry Practical Aspects Published September 12 2001 by CRC Press -

272 Pages Edited By Gary C Howard

2 Biochemistry 5th edition Berg JM Tymoczko JL Stryer L New York W H Freeman 2002

3 Proteins Structures and Molecular Properties Thomas E Creighton Publisher W H Freeman

1992 Edition Second Edition

4 Protein Engineering Protocols (Methods in Molecular Biology) Kristian Muumlller (Editor)

Publisher Humana Press Softcover reprint of hardcover 1st ed 2007 edition (November 10

2010)

5 Protein Degradation Series 4 Volume Set (v 1) R John Mayer (Editor) Publisher Wiley-

VCH 1 edition (March 4 2008)

6 Structural Aspects of Protein Synthesis Anders LiljashttpwwwamazoncomStructural-

Aspects-Protein-Synthesis-

Andersdp981238863Xref=sr_1_1s=booksampie=UTF8ampqid=1323503546ampsr=1-1 -

(Author) Publisher World Scientific Pub Co Inc 1 edition (November 2004)

7 Protein Targeting Transport and Translocation Ross Dalbey (Editor) Publisher Academic

Press 1 edition (May 13 2002)

8 Principles of Physical Biochemistry- KenslE van Holde W Curtis Johnson P Shing Ho

Pearson Prentice Hall 2nd Edition

9 Crystallography made crystal clear 1993 G Rhodes Academic Press

10 Principles and Techniques of Biochemistry and Molecular Biology 6th Edition Wilson Keith

and Walker John (2005) Cambridge University Press New York

11 A textbook of biophysics R N Roy New Central Publication 1st edition

8

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 2 (Code 1T2) Advanced Enzymology Learning outcome Students will be able to

1 Describe structure capacities and the component of activity of

chemicals and interaction with enzymes Learning energy of protein

catalyzed responses and compound restraints and administrative

procedure Enzyme action Enzyme Units Specific action

2 Have a detail and more intricate knowledge of allosteric and other

aspects of enzyme catalysis regulation

3 Have a total comprehension of rate of responses and request of

responses and restraints and their kinetics To gain information on

protein catalysis and isoenzymes and on multienzyme and multienzyme

complexes with specific examples

4 Develop intellectual capacity to relate bioenergetics principles and the

entropy to the law of thermodynamics and Free energy and its

connection to chemical equilibria in consolation to enzyme catalysis

5 Theory related to respiratory mechanisms catalysed by enzymatic

principles of redox biochemistry will help the students to gauge wide

applicability of enzymatic reactions in biological systems Detail

description of Coupled reactions and their role in metabolism and

Chemiosmotic hypothesis of ATP synthesis to understand the

mechanism of energy harnessing mechanism operating in biological

system

9

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 2 Advanced Enzymology

Unit I Kinetics and Regulation of enzyme activity

Review of unisubstrate enzyme kinetics multisubstrate enzyme kinetics Co-operativity

phenomenon Hill and Scatchard plots protein-ligand binding and its measurement detailed

mechanism of catalysis of serine protease carbonic anhydrase and PEP kinase

Metalloenzymes

Unit II Allosteric enzymes and multienzyme systems

Allosteric enzymes sigmoidal kinetics and its physiological significance symmetric and

sequential modes of action and their significance immobilized enzymes and their industrial

applications study of multienzyme complexes with respect to occurrence isolation and their

properties and polygenic nature eg pyruvate dehydrogenase and fatty acid synthase

Unit III Enzyme regulation

General mechanisms of enzyme regulation Feed back inhibition and feed forward

stimulation repression and induction of enzymes reversible and irreversible covalent

modifications of enzymes flexibility and conformational mobility of enzymes convergent

and divergent evolution of enzymes

Unit IV Bioenergetics and oxidative phosphorylation

Energy transformation laws of thermodynamics Gibbs energy free energy change redox

potentials phosphate potential ion electrochemical potential proton electrochemical

potential membrane potential Chemi-osmotic theory mitochondrial respiratory chain order

and organization of carrier proton gradients Characterization of Iron- Sulphur proteins and

Cytochromes Q cycle Respiratory controls and oxidative phosphorylation ATP synthase

complex

Suggested References

1 Enzymes Biochemistry Biotechnology and Clinical Chemistry-Trevor Palmer

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

10

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 3 (Code 1T3) Biochemical Research Techniques Learning outcome Students will be able to

1 The theoretical aspects of designing the Experiments and also study the Quality

control mechanism in Biochemistry

2 Understand the Sampling techniques and interpret the data based on the measures

of the central tendency

3 Learn the discrepancies and deviations of the variable based of measures of

dispersion

4 Study the relationship between variables based on correlation and regression

analysis

5 Deduce the probable outcomes of an experiment based on observations

following laws of probability and also assess the significance of the

interpretation through tests of significance such as t-test

6 To understand the importance and applications of computational methods and

statistical softwares in Biology

11

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 3 Biochemical Research Techniques

Unit I Research Methodology

1 Introduction to research methodology History and definition of research role of

theory hypothesis sampling variables randomness selection of problem purpose of

research and research reporting

2 Experimental research Early experimentation experimental groups control groups

variables method of controlling variables designing and validation of experiments

3 Methods and tools in research Research tools and its reliability and validity

quantitative and qualitative studies observation inquiry forms Q methodology data

collection limitations and sources of error

4 Types of data Analysis Descriptive data analysis Inferential data analysis Computer

data analysis

Unit II Biostatistics

Principles and practice of statistical methods in biological research samples and populations Basic

statistics-average statistics of dispersion coefficient of variation confidence limits Probability

distribution normal binomial and Poisson distribution Mean variants standard deviations and

standard error correlation and regression test of statistical significance and analysis of variance and

covariance

Unit III Data Retrieval Scientific Writing and Presentation

1 Information Search amp Data Retrieval Tools for Web Search Data Retrieval Tools

Data Mining of Biological Databases

2 Report Writing Significance of report writing different steps in report writing types

of report layout of research paper

3 Mechanics and precautions of writing research reports for scientific journals popular

magazines seminarssymposia conferencesworkshops poster session

4 Presentationndash Oral amp Written Presentations in classrooms scientific meets amp public

audience Defence of research thesis

Unit IV Computers

Introduction of computer networks- Topologies and designs Basics of computer operating systems-

windows and Linux Introduction to Markup language-Hyper Text Markup Language (HTML) and

Extensive Markup Language (XML) Spreadsheets and Presentation software

Systems Biology-An introduction

Introduction to Metagenomics

Suggested References

1 Fundamentals of Biostatistics Bernard A Rosner Thomson-BrooksCole 2006

2 Research methodology in social behavioural and life sciences Designs models and

methods Herman J Ader and Gideon Mellenbergh (Ed) SAGE Publications

6 Principles of Genome analysis and genomics Primrose SB Twyman RM Blackwell

Science (2002)

7 Biostatistics-A foundation for Health Science Daniel WW John Wiley (1983)

8 Statistical Methods Medhi J Willey Eastern Limited (1992)

12

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 4 (Code 1T4) Plant Biochemistry Learning outcome Students will be able to

1 Detailed knowledge of plant cellular architecture and the mechanism

of photosynthetic systems for photophosphorylation will enable the

students to get a dissected approach for understanding autotrophic food

synthesis mechanism driven by photon energy operative in plants

2 Hormonal pathways driving plant growth mechanisms form the

foundation for in vitro plant propagation setup and understanding of

Plant tissue culture aspects Students would gain an thorough insight of

growth regulatory mechanism of plants through which they will be able

to devise the hormonal concoction required for organogenesis and related

plant tissue culture applications

3 Students will be able to learn metabolic attributes and driving

principles of plant growth through basic carbohydrate lipid and protein

metabolism Also the students will be developing a comprehension of

importance of nitrogen and sulphur metabolism in plants and associated

plant physiological alterations

4 With in depth knowledge about plant physiochemical aspects the

students will get equipped to develop an understanding about effects

caused by biotic and abiotic stress factors on plant metabolism and

growth They can thus impinge upon the ways to tackle such stress

physiological aspects to promote and resolve plant stresses

5 Practical exposure to biochemical analysis of plant physiological

aspects would improve the students application approach towards plant

biochemistry as tool to protect plant diversity

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 7: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

7

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T1 Protein Biochemistry

Unit I Proteins and Mass Spectrometry

Overview of protein structure protein folding Ramchandran plot domains and modules

binding sites within proteins protein sequencing

Basics of Mass Spectrometry Ionization mechanisms- protonation deprotonation

cationization transfer of charged molecules to gas phase electron ejection electron capture

Mass analyzers-TOF Ion trap Quadrupole Ionization methods-Electron Impact (EI)

Chemical Ionization (CI) Fast Atom Bombardment (FAB) Field Description (FD) Electron

Spray Ionization (ESI) Matrix Assisted Laser Desorption Ionization (MALDI) Protein

Identification using MS

Unit II Protein biosynthesis

Eukaryotic translation machinery structure and assembly of the ribosome initiation

elongation and termination of translation

Unit III Protein sorting and degradation Intracellular protein sorting movement of proteins between cellular compartments gated

transmembrane and vesicular transport Protein transport and translocation to nucleus mitochondria

chloroplast peroxisomes endoplasmic reticular system Protein degradation

Unit IV Protein Engineering

Design and construction of novel proteins and enzymes Conformation of proteins in general and

enzymes in particular Effect of amino acids on structure of proteins Energy status of a protein

molecule Structure function relations of enzymes Physical methods such as x-ray crystallography

for determination of protein structure Site directed mutagenesis for specific protein function Basic

concepts for design of a new proteinenzyme molecule Specific examples of enzyme engineering -

Dihydrofolate reductase and Subtilisin

Suggested References

1 Modern Protein Chemistry Practical Aspects Published September 12 2001 by CRC Press -

272 Pages Edited By Gary C Howard

2 Biochemistry 5th edition Berg JM Tymoczko JL Stryer L New York W H Freeman 2002

3 Proteins Structures and Molecular Properties Thomas E Creighton Publisher W H Freeman

1992 Edition Second Edition

4 Protein Engineering Protocols (Methods in Molecular Biology) Kristian Muumlller (Editor)

Publisher Humana Press Softcover reprint of hardcover 1st ed 2007 edition (November 10

2010)

5 Protein Degradation Series 4 Volume Set (v 1) R John Mayer (Editor) Publisher Wiley-

VCH 1 edition (March 4 2008)

6 Structural Aspects of Protein Synthesis Anders LiljashttpwwwamazoncomStructural-

Aspects-Protein-Synthesis-

Andersdp981238863Xref=sr_1_1s=booksampie=UTF8ampqid=1323503546ampsr=1-1 -

(Author) Publisher World Scientific Pub Co Inc 1 edition (November 2004)

7 Protein Targeting Transport and Translocation Ross Dalbey (Editor) Publisher Academic

Press 1 edition (May 13 2002)

8 Principles of Physical Biochemistry- KenslE van Holde W Curtis Johnson P Shing Ho

Pearson Prentice Hall 2nd Edition

9 Crystallography made crystal clear 1993 G Rhodes Academic Press

10 Principles and Techniques of Biochemistry and Molecular Biology 6th Edition Wilson Keith

and Walker John (2005) Cambridge University Press New York

11 A textbook of biophysics R N Roy New Central Publication 1st edition

8

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 2 (Code 1T2) Advanced Enzymology Learning outcome Students will be able to

1 Describe structure capacities and the component of activity of

chemicals and interaction with enzymes Learning energy of protein

catalyzed responses and compound restraints and administrative

procedure Enzyme action Enzyme Units Specific action

2 Have a detail and more intricate knowledge of allosteric and other

aspects of enzyme catalysis regulation

3 Have a total comprehension of rate of responses and request of

responses and restraints and their kinetics To gain information on

protein catalysis and isoenzymes and on multienzyme and multienzyme

complexes with specific examples

4 Develop intellectual capacity to relate bioenergetics principles and the

entropy to the law of thermodynamics and Free energy and its

connection to chemical equilibria in consolation to enzyme catalysis

5 Theory related to respiratory mechanisms catalysed by enzymatic

principles of redox biochemistry will help the students to gauge wide

applicability of enzymatic reactions in biological systems Detail

description of Coupled reactions and their role in metabolism and

Chemiosmotic hypothesis of ATP synthesis to understand the

mechanism of energy harnessing mechanism operating in biological

system

9

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 2 Advanced Enzymology

Unit I Kinetics and Regulation of enzyme activity

Review of unisubstrate enzyme kinetics multisubstrate enzyme kinetics Co-operativity

phenomenon Hill and Scatchard plots protein-ligand binding and its measurement detailed

mechanism of catalysis of serine protease carbonic anhydrase and PEP kinase

Metalloenzymes

Unit II Allosteric enzymes and multienzyme systems

Allosteric enzymes sigmoidal kinetics and its physiological significance symmetric and

sequential modes of action and their significance immobilized enzymes and their industrial

applications study of multienzyme complexes with respect to occurrence isolation and their

properties and polygenic nature eg pyruvate dehydrogenase and fatty acid synthase

Unit III Enzyme regulation

General mechanisms of enzyme regulation Feed back inhibition and feed forward

stimulation repression and induction of enzymes reversible and irreversible covalent

modifications of enzymes flexibility and conformational mobility of enzymes convergent

and divergent evolution of enzymes

Unit IV Bioenergetics and oxidative phosphorylation

Energy transformation laws of thermodynamics Gibbs energy free energy change redox

potentials phosphate potential ion electrochemical potential proton electrochemical

potential membrane potential Chemi-osmotic theory mitochondrial respiratory chain order

and organization of carrier proton gradients Characterization of Iron- Sulphur proteins and

Cytochromes Q cycle Respiratory controls and oxidative phosphorylation ATP synthase

complex

Suggested References

1 Enzymes Biochemistry Biotechnology and Clinical Chemistry-Trevor Palmer

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

10

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 3 (Code 1T3) Biochemical Research Techniques Learning outcome Students will be able to

1 The theoretical aspects of designing the Experiments and also study the Quality

control mechanism in Biochemistry

2 Understand the Sampling techniques and interpret the data based on the measures

of the central tendency

3 Learn the discrepancies and deviations of the variable based of measures of

dispersion

4 Study the relationship between variables based on correlation and regression

analysis

5 Deduce the probable outcomes of an experiment based on observations

following laws of probability and also assess the significance of the

interpretation through tests of significance such as t-test

6 To understand the importance and applications of computational methods and

statistical softwares in Biology

11

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 3 Biochemical Research Techniques

Unit I Research Methodology

1 Introduction to research methodology History and definition of research role of

theory hypothesis sampling variables randomness selection of problem purpose of

research and research reporting

2 Experimental research Early experimentation experimental groups control groups

variables method of controlling variables designing and validation of experiments

3 Methods and tools in research Research tools and its reliability and validity

quantitative and qualitative studies observation inquiry forms Q methodology data

collection limitations and sources of error

4 Types of data Analysis Descriptive data analysis Inferential data analysis Computer

data analysis

Unit II Biostatistics

Principles and practice of statistical methods in biological research samples and populations Basic

statistics-average statistics of dispersion coefficient of variation confidence limits Probability

distribution normal binomial and Poisson distribution Mean variants standard deviations and

standard error correlation and regression test of statistical significance and analysis of variance and

covariance

Unit III Data Retrieval Scientific Writing and Presentation

1 Information Search amp Data Retrieval Tools for Web Search Data Retrieval Tools

Data Mining of Biological Databases

2 Report Writing Significance of report writing different steps in report writing types

of report layout of research paper

3 Mechanics and precautions of writing research reports for scientific journals popular

magazines seminarssymposia conferencesworkshops poster session

4 Presentationndash Oral amp Written Presentations in classrooms scientific meets amp public

audience Defence of research thesis

Unit IV Computers

Introduction of computer networks- Topologies and designs Basics of computer operating systems-

windows and Linux Introduction to Markup language-Hyper Text Markup Language (HTML) and

Extensive Markup Language (XML) Spreadsheets and Presentation software

Systems Biology-An introduction

Introduction to Metagenomics

Suggested References

1 Fundamentals of Biostatistics Bernard A Rosner Thomson-BrooksCole 2006

2 Research methodology in social behavioural and life sciences Designs models and

methods Herman J Ader and Gideon Mellenbergh (Ed) SAGE Publications

6 Principles of Genome analysis and genomics Primrose SB Twyman RM Blackwell

Science (2002)

7 Biostatistics-A foundation for Health Science Daniel WW John Wiley (1983)

8 Statistical Methods Medhi J Willey Eastern Limited (1992)

12

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 4 (Code 1T4) Plant Biochemistry Learning outcome Students will be able to

1 Detailed knowledge of plant cellular architecture and the mechanism

of photosynthetic systems for photophosphorylation will enable the

students to get a dissected approach for understanding autotrophic food

synthesis mechanism driven by photon energy operative in plants

2 Hormonal pathways driving plant growth mechanisms form the

foundation for in vitro plant propagation setup and understanding of

Plant tissue culture aspects Students would gain an thorough insight of

growth regulatory mechanism of plants through which they will be able

to devise the hormonal concoction required for organogenesis and related

plant tissue culture applications

3 Students will be able to learn metabolic attributes and driving

principles of plant growth through basic carbohydrate lipid and protein

metabolism Also the students will be developing a comprehension of

importance of nitrogen and sulphur metabolism in plants and associated

plant physiological alterations

4 With in depth knowledge about plant physiochemical aspects the

students will get equipped to develop an understanding about effects

caused by biotic and abiotic stress factors on plant metabolism and

growth They can thus impinge upon the ways to tackle such stress

physiological aspects to promote and resolve plant stresses

5 Practical exposure to biochemical analysis of plant physiological

aspects would improve the students application approach towards plant

biochemistry as tool to protect plant diversity

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 8: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

8

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 2 (Code 1T2) Advanced Enzymology Learning outcome Students will be able to

1 Describe structure capacities and the component of activity of

chemicals and interaction with enzymes Learning energy of protein

catalyzed responses and compound restraints and administrative

procedure Enzyme action Enzyme Units Specific action

2 Have a detail and more intricate knowledge of allosteric and other

aspects of enzyme catalysis regulation

3 Have a total comprehension of rate of responses and request of

responses and restraints and their kinetics To gain information on

protein catalysis and isoenzymes and on multienzyme and multienzyme

complexes with specific examples

4 Develop intellectual capacity to relate bioenergetics principles and the

entropy to the law of thermodynamics and Free energy and its

connection to chemical equilibria in consolation to enzyme catalysis

5 Theory related to respiratory mechanisms catalysed by enzymatic

principles of redox biochemistry will help the students to gauge wide

applicability of enzymatic reactions in biological systems Detail

description of Coupled reactions and their role in metabolism and

Chemiosmotic hypothesis of ATP synthesis to understand the

mechanism of energy harnessing mechanism operating in biological

system

9

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 2 Advanced Enzymology

Unit I Kinetics and Regulation of enzyme activity

Review of unisubstrate enzyme kinetics multisubstrate enzyme kinetics Co-operativity

phenomenon Hill and Scatchard plots protein-ligand binding and its measurement detailed

mechanism of catalysis of serine protease carbonic anhydrase and PEP kinase

Metalloenzymes

Unit II Allosteric enzymes and multienzyme systems

Allosteric enzymes sigmoidal kinetics and its physiological significance symmetric and

sequential modes of action and their significance immobilized enzymes and their industrial

applications study of multienzyme complexes with respect to occurrence isolation and their

properties and polygenic nature eg pyruvate dehydrogenase and fatty acid synthase

Unit III Enzyme regulation

General mechanisms of enzyme regulation Feed back inhibition and feed forward

stimulation repression and induction of enzymes reversible and irreversible covalent

modifications of enzymes flexibility and conformational mobility of enzymes convergent

and divergent evolution of enzymes

Unit IV Bioenergetics and oxidative phosphorylation

Energy transformation laws of thermodynamics Gibbs energy free energy change redox

potentials phosphate potential ion electrochemical potential proton electrochemical

potential membrane potential Chemi-osmotic theory mitochondrial respiratory chain order

and organization of carrier proton gradients Characterization of Iron- Sulphur proteins and

Cytochromes Q cycle Respiratory controls and oxidative phosphorylation ATP synthase

complex

Suggested References

1 Enzymes Biochemistry Biotechnology and Clinical Chemistry-Trevor Palmer

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

10

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 3 (Code 1T3) Biochemical Research Techniques Learning outcome Students will be able to

1 The theoretical aspects of designing the Experiments and also study the Quality

control mechanism in Biochemistry

2 Understand the Sampling techniques and interpret the data based on the measures

of the central tendency

3 Learn the discrepancies and deviations of the variable based of measures of

dispersion

4 Study the relationship between variables based on correlation and regression

analysis

5 Deduce the probable outcomes of an experiment based on observations

following laws of probability and also assess the significance of the

interpretation through tests of significance such as t-test

6 To understand the importance and applications of computational methods and

statistical softwares in Biology

11

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 3 Biochemical Research Techniques

Unit I Research Methodology

1 Introduction to research methodology History and definition of research role of

theory hypothesis sampling variables randomness selection of problem purpose of

research and research reporting

2 Experimental research Early experimentation experimental groups control groups

variables method of controlling variables designing and validation of experiments

3 Methods and tools in research Research tools and its reliability and validity

quantitative and qualitative studies observation inquiry forms Q methodology data

collection limitations and sources of error

4 Types of data Analysis Descriptive data analysis Inferential data analysis Computer

data analysis

Unit II Biostatistics

Principles and practice of statistical methods in biological research samples and populations Basic

statistics-average statistics of dispersion coefficient of variation confidence limits Probability

distribution normal binomial and Poisson distribution Mean variants standard deviations and

standard error correlation and regression test of statistical significance and analysis of variance and

covariance

Unit III Data Retrieval Scientific Writing and Presentation

1 Information Search amp Data Retrieval Tools for Web Search Data Retrieval Tools

Data Mining of Biological Databases

2 Report Writing Significance of report writing different steps in report writing types

of report layout of research paper

3 Mechanics and precautions of writing research reports for scientific journals popular

magazines seminarssymposia conferencesworkshops poster session

4 Presentationndash Oral amp Written Presentations in classrooms scientific meets amp public

audience Defence of research thesis

Unit IV Computers

Introduction of computer networks- Topologies and designs Basics of computer operating systems-

windows and Linux Introduction to Markup language-Hyper Text Markup Language (HTML) and

Extensive Markup Language (XML) Spreadsheets and Presentation software

Systems Biology-An introduction

Introduction to Metagenomics

Suggested References

1 Fundamentals of Biostatistics Bernard A Rosner Thomson-BrooksCole 2006

2 Research methodology in social behavioural and life sciences Designs models and

methods Herman J Ader and Gideon Mellenbergh (Ed) SAGE Publications

6 Principles of Genome analysis and genomics Primrose SB Twyman RM Blackwell

Science (2002)

7 Biostatistics-A foundation for Health Science Daniel WW John Wiley (1983)

8 Statistical Methods Medhi J Willey Eastern Limited (1992)

12

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 4 (Code 1T4) Plant Biochemistry Learning outcome Students will be able to

1 Detailed knowledge of plant cellular architecture and the mechanism

of photosynthetic systems for photophosphorylation will enable the

students to get a dissected approach for understanding autotrophic food

synthesis mechanism driven by photon energy operative in plants

2 Hormonal pathways driving plant growth mechanisms form the

foundation for in vitro plant propagation setup and understanding of

Plant tissue culture aspects Students would gain an thorough insight of

growth regulatory mechanism of plants through which they will be able

to devise the hormonal concoction required for organogenesis and related

plant tissue culture applications

3 Students will be able to learn metabolic attributes and driving

principles of plant growth through basic carbohydrate lipid and protein

metabolism Also the students will be developing a comprehension of

importance of nitrogen and sulphur metabolism in plants and associated

plant physiological alterations

4 With in depth knowledge about plant physiochemical aspects the

students will get equipped to develop an understanding about effects

caused by biotic and abiotic stress factors on plant metabolism and

growth They can thus impinge upon the ways to tackle such stress

physiological aspects to promote and resolve plant stresses

5 Practical exposure to biochemical analysis of plant physiological

aspects would improve the students application approach towards plant

biochemistry as tool to protect plant diversity

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 9: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

9

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 2 Advanced Enzymology

Unit I Kinetics and Regulation of enzyme activity

Review of unisubstrate enzyme kinetics multisubstrate enzyme kinetics Co-operativity

phenomenon Hill and Scatchard plots protein-ligand binding and its measurement detailed

mechanism of catalysis of serine protease carbonic anhydrase and PEP kinase

Metalloenzymes

Unit II Allosteric enzymes and multienzyme systems

Allosteric enzymes sigmoidal kinetics and its physiological significance symmetric and

sequential modes of action and their significance immobilized enzymes and their industrial

applications study of multienzyme complexes with respect to occurrence isolation and their

properties and polygenic nature eg pyruvate dehydrogenase and fatty acid synthase

Unit III Enzyme regulation

General mechanisms of enzyme regulation Feed back inhibition and feed forward

stimulation repression and induction of enzymes reversible and irreversible covalent

modifications of enzymes flexibility and conformational mobility of enzymes convergent

and divergent evolution of enzymes

Unit IV Bioenergetics and oxidative phosphorylation

Energy transformation laws of thermodynamics Gibbs energy free energy change redox

potentials phosphate potential ion electrochemical potential proton electrochemical

potential membrane potential Chemi-osmotic theory mitochondrial respiratory chain order

and organization of carrier proton gradients Characterization of Iron- Sulphur proteins and

Cytochromes Q cycle Respiratory controls and oxidative phosphorylation ATP synthase

complex

Suggested References

1 Enzymes Biochemistry Biotechnology and Clinical Chemistry-Trevor Palmer

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

10

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 3 (Code 1T3) Biochemical Research Techniques Learning outcome Students will be able to

1 The theoretical aspects of designing the Experiments and also study the Quality

control mechanism in Biochemistry

2 Understand the Sampling techniques and interpret the data based on the measures

of the central tendency

3 Learn the discrepancies and deviations of the variable based of measures of

dispersion

4 Study the relationship between variables based on correlation and regression

analysis

5 Deduce the probable outcomes of an experiment based on observations

following laws of probability and also assess the significance of the

interpretation through tests of significance such as t-test

6 To understand the importance and applications of computational methods and

statistical softwares in Biology

11

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 3 Biochemical Research Techniques

Unit I Research Methodology

1 Introduction to research methodology History and definition of research role of

theory hypothesis sampling variables randomness selection of problem purpose of

research and research reporting

2 Experimental research Early experimentation experimental groups control groups

variables method of controlling variables designing and validation of experiments

3 Methods and tools in research Research tools and its reliability and validity

quantitative and qualitative studies observation inquiry forms Q methodology data

collection limitations and sources of error

4 Types of data Analysis Descriptive data analysis Inferential data analysis Computer

data analysis

Unit II Biostatistics

Principles and practice of statistical methods in biological research samples and populations Basic

statistics-average statistics of dispersion coefficient of variation confidence limits Probability

distribution normal binomial and Poisson distribution Mean variants standard deviations and

standard error correlation and regression test of statistical significance and analysis of variance and

covariance

Unit III Data Retrieval Scientific Writing and Presentation

1 Information Search amp Data Retrieval Tools for Web Search Data Retrieval Tools

Data Mining of Biological Databases

2 Report Writing Significance of report writing different steps in report writing types

of report layout of research paper

3 Mechanics and precautions of writing research reports for scientific journals popular

magazines seminarssymposia conferencesworkshops poster session

4 Presentationndash Oral amp Written Presentations in classrooms scientific meets amp public

audience Defence of research thesis

Unit IV Computers

Introduction of computer networks- Topologies and designs Basics of computer operating systems-

windows and Linux Introduction to Markup language-Hyper Text Markup Language (HTML) and

Extensive Markup Language (XML) Spreadsheets and Presentation software

Systems Biology-An introduction

Introduction to Metagenomics

Suggested References

1 Fundamentals of Biostatistics Bernard A Rosner Thomson-BrooksCole 2006

2 Research methodology in social behavioural and life sciences Designs models and

methods Herman J Ader and Gideon Mellenbergh (Ed) SAGE Publications

6 Principles of Genome analysis and genomics Primrose SB Twyman RM Blackwell

Science (2002)

7 Biostatistics-A foundation for Health Science Daniel WW John Wiley (1983)

8 Statistical Methods Medhi J Willey Eastern Limited (1992)

12

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 4 (Code 1T4) Plant Biochemistry Learning outcome Students will be able to

1 Detailed knowledge of plant cellular architecture and the mechanism

of photosynthetic systems for photophosphorylation will enable the

students to get a dissected approach for understanding autotrophic food

synthesis mechanism driven by photon energy operative in plants

2 Hormonal pathways driving plant growth mechanisms form the

foundation for in vitro plant propagation setup and understanding of

Plant tissue culture aspects Students would gain an thorough insight of

growth regulatory mechanism of plants through which they will be able

to devise the hormonal concoction required for organogenesis and related

plant tissue culture applications

3 Students will be able to learn metabolic attributes and driving

principles of plant growth through basic carbohydrate lipid and protein

metabolism Also the students will be developing a comprehension of

importance of nitrogen and sulphur metabolism in plants and associated

plant physiological alterations

4 With in depth knowledge about plant physiochemical aspects the

students will get equipped to develop an understanding about effects

caused by biotic and abiotic stress factors on plant metabolism and

growth They can thus impinge upon the ways to tackle such stress

physiological aspects to promote and resolve plant stresses

5 Practical exposure to biochemical analysis of plant physiological

aspects would improve the students application approach towards plant

biochemistry as tool to protect plant diversity

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 10: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

10

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 3 (Code 1T3) Biochemical Research Techniques Learning outcome Students will be able to

1 The theoretical aspects of designing the Experiments and also study the Quality

control mechanism in Biochemistry

2 Understand the Sampling techniques and interpret the data based on the measures

of the central tendency

3 Learn the discrepancies and deviations of the variable based of measures of

dispersion

4 Study the relationship between variables based on correlation and regression

analysis

5 Deduce the probable outcomes of an experiment based on observations

following laws of probability and also assess the significance of the

interpretation through tests of significance such as t-test

6 To understand the importance and applications of computational methods and

statistical softwares in Biology

11

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 3 Biochemical Research Techniques

Unit I Research Methodology

1 Introduction to research methodology History and definition of research role of

theory hypothesis sampling variables randomness selection of problem purpose of

research and research reporting

2 Experimental research Early experimentation experimental groups control groups

variables method of controlling variables designing and validation of experiments

3 Methods and tools in research Research tools and its reliability and validity

quantitative and qualitative studies observation inquiry forms Q methodology data

collection limitations and sources of error

4 Types of data Analysis Descriptive data analysis Inferential data analysis Computer

data analysis

Unit II Biostatistics

Principles and practice of statistical methods in biological research samples and populations Basic

statistics-average statistics of dispersion coefficient of variation confidence limits Probability

distribution normal binomial and Poisson distribution Mean variants standard deviations and

standard error correlation and regression test of statistical significance and analysis of variance and

covariance

Unit III Data Retrieval Scientific Writing and Presentation

1 Information Search amp Data Retrieval Tools for Web Search Data Retrieval Tools

Data Mining of Biological Databases

2 Report Writing Significance of report writing different steps in report writing types

of report layout of research paper

3 Mechanics and precautions of writing research reports for scientific journals popular

magazines seminarssymposia conferencesworkshops poster session

4 Presentationndash Oral amp Written Presentations in classrooms scientific meets amp public

audience Defence of research thesis

Unit IV Computers

Introduction of computer networks- Topologies and designs Basics of computer operating systems-

windows and Linux Introduction to Markup language-Hyper Text Markup Language (HTML) and

Extensive Markup Language (XML) Spreadsheets and Presentation software

Systems Biology-An introduction

Introduction to Metagenomics

Suggested References

1 Fundamentals of Biostatistics Bernard A Rosner Thomson-BrooksCole 2006

2 Research methodology in social behavioural and life sciences Designs models and

methods Herman J Ader and Gideon Mellenbergh (Ed) SAGE Publications

6 Principles of Genome analysis and genomics Primrose SB Twyman RM Blackwell

Science (2002)

7 Biostatistics-A foundation for Health Science Daniel WW John Wiley (1983)

8 Statistical Methods Medhi J Willey Eastern Limited (1992)

12

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 4 (Code 1T4) Plant Biochemistry Learning outcome Students will be able to

1 Detailed knowledge of plant cellular architecture and the mechanism

of photosynthetic systems for photophosphorylation will enable the

students to get a dissected approach for understanding autotrophic food

synthesis mechanism driven by photon energy operative in plants

2 Hormonal pathways driving plant growth mechanisms form the

foundation for in vitro plant propagation setup and understanding of

Plant tissue culture aspects Students would gain an thorough insight of

growth regulatory mechanism of plants through which they will be able

to devise the hormonal concoction required for organogenesis and related

plant tissue culture applications

3 Students will be able to learn metabolic attributes and driving

principles of plant growth through basic carbohydrate lipid and protein

metabolism Also the students will be developing a comprehension of

importance of nitrogen and sulphur metabolism in plants and associated

plant physiological alterations

4 With in depth knowledge about plant physiochemical aspects the

students will get equipped to develop an understanding about effects

caused by biotic and abiotic stress factors on plant metabolism and

growth They can thus impinge upon the ways to tackle such stress

physiological aspects to promote and resolve plant stresses

5 Practical exposure to biochemical analysis of plant physiological

aspects would improve the students application approach towards plant

biochemistry as tool to protect plant diversity

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 11: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

11

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T 3 Biochemical Research Techniques

Unit I Research Methodology

1 Introduction to research methodology History and definition of research role of

theory hypothesis sampling variables randomness selection of problem purpose of

research and research reporting

2 Experimental research Early experimentation experimental groups control groups

variables method of controlling variables designing and validation of experiments

3 Methods and tools in research Research tools and its reliability and validity

quantitative and qualitative studies observation inquiry forms Q methodology data

collection limitations and sources of error

4 Types of data Analysis Descriptive data analysis Inferential data analysis Computer

data analysis

Unit II Biostatistics

Principles and practice of statistical methods in biological research samples and populations Basic

statistics-average statistics of dispersion coefficient of variation confidence limits Probability

distribution normal binomial and Poisson distribution Mean variants standard deviations and

standard error correlation and regression test of statistical significance and analysis of variance and

covariance

Unit III Data Retrieval Scientific Writing and Presentation

1 Information Search amp Data Retrieval Tools for Web Search Data Retrieval Tools

Data Mining of Biological Databases

2 Report Writing Significance of report writing different steps in report writing types

of report layout of research paper

3 Mechanics and precautions of writing research reports for scientific journals popular

magazines seminarssymposia conferencesworkshops poster session

4 Presentationndash Oral amp Written Presentations in classrooms scientific meets amp public

audience Defence of research thesis

Unit IV Computers

Introduction of computer networks- Topologies and designs Basics of computer operating systems-

windows and Linux Introduction to Markup language-Hyper Text Markup Language (HTML) and

Extensive Markup Language (XML) Spreadsheets and Presentation software

Systems Biology-An introduction

Introduction to Metagenomics

Suggested References

1 Fundamentals of Biostatistics Bernard A Rosner Thomson-BrooksCole 2006

2 Research methodology in social behavioural and life sciences Designs models and

methods Herman J Ader and Gideon Mellenbergh (Ed) SAGE Publications

6 Principles of Genome analysis and genomics Primrose SB Twyman RM Blackwell

Science (2002)

7 Biostatistics-A foundation for Health Science Daniel WW John Wiley (1983)

8 Statistical Methods Medhi J Willey Eastern Limited (1992)

12

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 4 (Code 1T4) Plant Biochemistry Learning outcome Students will be able to

1 Detailed knowledge of plant cellular architecture and the mechanism

of photosynthetic systems for photophosphorylation will enable the

students to get a dissected approach for understanding autotrophic food

synthesis mechanism driven by photon energy operative in plants

2 Hormonal pathways driving plant growth mechanisms form the

foundation for in vitro plant propagation setup and understanding of

Plant tissue culture aspects Students would gain an thorough insight of

growth regulatory mechanism of plants through which they will be able

to devise the hormonal concoction required for organogenesis and related

plant tissue culture applications

3 Students will be able to learn metabolic attributes and driving

principles of plant growth through basic carbohydrate lipid and protein

metabolism Also the students will be developing a comprehension of

importance of nitrogen and sulphur metabolism in plants and associated

plant physiological alterations

4 With in depth knowledge about plant physiochemical aspects the

students will get equipped to develop an understanding about effects

caused by biotic and abiotic stress factors on plant metabolism and

growth They can thus impinge upon the ways to tackle such stress

physiological aspects to promote and resolve plant stresses

5 Practical exposure to biochemical analysis of plant physiological

aspects would improve the students application approach towards plant

biochemistry as tool to protect plant diversity

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 12: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

12

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

Paper 4 (Code 1T4) Plant Biochemistry Learning outcome Students will be able to

1 Detailed knowledge of plant cellular architecture and the mechanism

of photosynthetic systems for photophosphorylation will enable the

students to get a dissected approach for understanding autotrophic food

synthesis mechanism driven by photon energy operative in plants

2 Hormonal pathways driving plant growth mechanisms form the

foundation for in vitro plant propagation setup and understanding of

Plant tissue culture aspects Students would gain an thorough insight of

growth regulatory mechanism of plants through which they will be able

to devise the hormonal concoction required for organogenesis and related

plant tissue culture applications

3 Students will be able to learn metabolic attributes and driving

principles of plant growth through basic carbohydrate lipid and protein

metabolism Also the students will be developing a comprehension of

importance of nitrogen and sulphur metabolism in plants and associated

plant physiological alterations

4 With in depth knowledge about plant physiochemical aspects the

students will get equipped to develop an understanding about effects

caused by biotic and abiotic stress factors on plant metabolism and

growth They can thus impinge upon the ways to tackle such stress

physiological aspects to promote and resolve plant stresses

5 Practical exposure to biochemical analysis of plant physiological

aspects would improve the students application approach towards plant

biochemistry as tool to protect plant diversity

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 13: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

13

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1T4 Plant Biochemistry

Unit I Plant Cell and Photosynthesis

Structure of plant cell Structure of plant cell membrane and cell wall

Structure of chloroplast system Photosynthetic pigments and their functions Photo system

I amp II Photosynthetic electron transport and photophosphorylation

Calvin cycle(C3 plants) Hatch slack pathway (C4 plants) Crassulacean acid metabolism

Unit II Plant hormones and Tissue culture

Plant hormones Biosynthesis structure and biochemical mode of action of auxins

gibberellins cytokinins abscisic acid and ethylene Other plant growth regulators

Plant tissue culture Plant cell organs and culture Somaclonal variation protoplast isolation

fusion and culture of protoplasts Application of plant tissue culture

Unit III Plant respiration and Metabolism

Plant respiration Carbohydrate lipid and Protein metabolism Cyanide sensitive and

insensitive respiration

Nitrogen metabolism Development and structure of root nodules Role of nod factors in

nodule development Structure of plant nitrogenase system Symbiotic nitrogen fixation and

and its regulation Formation and assimilation of ammonia

Sulphur metabolism Sulphate activation Reduction of active sulphate Oxidation of

inorganic sulphur incorporation of sulphur into amino acids

Unit IV Biochemistry of plant growth amp stress physiology

Biochemistry of seed and bud dormancy Biochemistry of seed germination factors affecting seed germination Structure and function of Phytochrome and Cryptochrome Photoperiodism and Vernalization Hormonal regulation of flowering Responses of plant to biotic (pathogens and insects) and abiotic (water temperature and salt) stresses Mechanism of resistance to biotic stress and tolerance to abiotic stress

Suggested References

1 Plant physiology -Taiz amp Ziger

2 Biochemistry and molecular Biology of plant-Buchanan

3 Plant physiology -M Devlin

4 Plant pathology- George N Agriose

5 Plant breeding- BD Singh

6 Germination of seed- AM Mayer amp A Mayber

7 Introduction of Plant Physiology -William Hopkins

8 Introduction to plant - Godwin amp merser

9 Plant physiology - Mohit Warma

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 14: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

14

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 1

1P 1 Protein Biochemistry and Enzymology

1 Estimation of protein by UV Spectrophotometer by E280E260 method

2 Estimation of Riboflavin by Arnoldrsquos fluorimetric method

3 Estimation of Thiamine by thiochrome method

4 Separation of proteins by PAGE

5 Seperation of proteins by SDS gel electrophoresis

6 Western Blotting

7 Purification of proteins by isoelectric precipitation

8 Molecular weight determination

9 Fractionation of cells by differential centrifugation

10 Assay of marker enzymes

11 To study the essentiality of co-enzymes in enzyme catalyzed reaction

12 Fractionation of human plasma proteins by precipitation

13 Assay of acid and alkaline phosphatase

14 Effect of environmental factors such as pH temperature and inhibitors on alkaline

phosphatase

15 Measurement of initial velocity

16 To study kinetics of enzyme using Lineweaver-Burk Eadie-Hofstee and Hanes Plots

1P 2 Biochemical Research Techniques and Plant Biochemistry

1 Absorption of water by live amp dead seeds

2 Changes in carbohydrate protein content during germination

3 Induction of proteinases amylases and lipase during germination

4 Induction of vitamin C synthesis during germination

5 Isolation and characterization of trypsin inhibitor

6 Assay of peroxidase catalase phenol oxidase ascorbic acid oxidase

7 Isolation of plant DNA amp RNA

8 Estimation of carotene ascorbic acid phenols and tannins in fruits and vegetables

9 Development of callus culture from meristems and leaves

1S1 Seminar

InstitutionalEducational tour For minimum 08 days

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 15: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

15

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash I (Code 2T1) Immunology

Learning outcome Students will be able to

1 Remember and Understand basic concepts of Immunology Molecular details of

various receptors and effectors involved in evoking Immune responses

2 Mechanism and pathways of immunity with essential details about immunoglobulin

structures and mechanism of action

3 Appreciate and assess the various immunological techniques used for public health

Applications of immunology based techniques in public health and immunization

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 16: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

16

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T1 Immunology

Unit I The Immune system Immunoglobulins and TCR

History of Immunology Innate Immunity effector mechanisms involved PAMPs PRRs

Phagocytosis Lysis blocking extra cellular killing etc Biochemistry and biology of TLRs

Inflamatory processes inflamamasomes interrelationship between innate and adaptive

immunity

Immunoglobulins and TCR

Immunochemistry Antigen antibody reaction its kinetics and thermodynamics Structure

functions of immunoglobulins Ig genes and their expression Generation of Ab diversity

BCR TCR Organization and re-arrangement of TCR genes TCR diversity

Unit II

Anatomy of Immune system

Immunological cells tissues and organs Maturation activation and differentiation of B and

T cells MHC genes and their polymorphism Structure and function of MHC molecules

Clonal selection theory Cell surface molecules Ig super family integrins selectins

chemokine receptors and other accessory molecules Cytokines and chemokines

Unit III

Immune response by T and B lymphocytes

Cellular and molecular mechanisms of Ab production humoral and cell mediated immunity

Antigen processing and presentation T and B cell interaction Super antigens

Unit IV

Immunological Techniques

Immunochemical techniques including immunodiffusion RIA EIA agglutination

immunoflorescence immunoelectron microscopy immunoelectrophoresis HLA typing

leukocyte migration inhibition technique delayed hypersensitivity technique cytotoxicity

assay Monoclonal Abrsquos hybridoma and other technologies Abzymes

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 17: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

17

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash II (Code 2T2) Clinical Biochemistry

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts in Clinical Biochemistry and

recent automations introduced in it

2 Comprehend basics of Endocrine system and hormones involved for regulation of

various biochemical functions of target organs

3 Illustrate compare and appreciate functions and biochemical attributes of Liver and

implications in Clinical Biochemistry

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 18: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

18

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T2 Clinical Biochemistry

Unit I Automation in clinical biochemistry gastric and blood disorders

Automation in Clinical Biochemistry- Instrumental concept Selection of Instrument Quality

assurance Control of pre-analytical and analytical variables External and internal quality

control measurements

Gastric disorders Disorders of gastric function method of evaluation pancreatic diseases

Steatorrhoea Malabsorption syndrome test for their evaluation

Blood Disorder Review of mechanism of coagulation and fibrinolysis abnormalities in

blood coagulation variation of plasma proteins abnormalities of blood formation anemia

haemoglobinopathies clinical significance of fecal and urine analysis

Unit II Endocrinology I Insulin and glucagon Various types of hyperglycemia Diabetes mellitus Ketonemia

ketonuria Experimental diabetes Hypoglycemia Polyurea Glucose tolerance test

Thyroid Iodine metabolism Hypo and Hyper thyroidism BMRand other test for

evaluation of thyroid function

Parathyroid Calcium and phosphorus metabolism Abnormalities of Parathyroid function

and methods of evaluation

Unit III Endocrinology II

Adrenal Addisonrsquos disease and pheochromocytoma Disorders of steroid metabolism Test

for evaluation of adrenal functions

Pituitary Pituitary hormones Clinical syndromes and their evaluation

Unit IV Liver disorders

Liver disorders Jaundice fatty liver and liver function tests Renal function test

Cerebrospinal fluid Composition in health and disease Lipid profile in health and disease

Elements of Clinical Enzymology Isoenzymes in health and disease

Clinical significance of GOT GPT Creatine kinase LDH etc

Biochemical diagnosis of disease by enzymatic evaluation

Suggested References 1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th EdText book of Medical Physiology - By Guyton

3 Text book of Physiology -By Burn amp levy

4 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

5 Biochemistry with clinical correlation- By Thomas Devli

6 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

7 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

8 Biochemistry - By Lehninger

9 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

10 Biochemistry ndashBy Stanford

11 Basic Medical Biochemistry A Clinical approach- By Smith

12 Principles of Internal Medicines- By HarrisonT R

13 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

14 Practical Biochemistry ndashBy David Plummer

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 19: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

19

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash III (Code 2T3) Cell Biochemistry

Learning outcome Students will be able to

1 Gain knowledge about fundamentals of cell division cycle and decision making

ability of the cells to proceed for duplication with regulatory aspects

2 Cell communication ability and control of cell cycle brough about by internal and

external molecular effectors

3 Understand basic concept of Cancer Biology and stem cells

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 20: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

20

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T3 Cell Biochemistry

Unit I Cell cycle and regulation

Review of cell cycle divisional control regulatory proteins cyclincdk complexes positive

and negative regulation inhibitory molecules restriction points regulation of DNA

synthesis regulation of degradation check points cell cycle arrest role of cyclically

activated protein kinases transcriptional regulation

Unit II Cell communication I

General principles of cell communication extra cellular signals and their receptors autocrine

signaling and role of gap junctions types of cell receptors relay of signal and intracellular

signal proteins regulated proteolysis dependent signaling pathways (Notch Wnt hedgehog

NFKB)

Unit III Cell communication II

Informational transactions in eukaryotic cells- cyclic AMP facet Study of G-proteins

signaling through G-protein linked cell surface receptors signaling through enzyme linked

cell surface receptors Calcium messenger system signaling via GMP

Unit IV Cancer

Causes and types of cancer viral carcinogenesis tumor suppressors oncogenes and signal

transduction growth and spread of cancer molecular basis of cancer therapy molecular

markers

Programmed cell death and its regulation in normal physiology regulation and execution of

mammalian apoptosis cytokine signaling and role of apoptosis in tumor genesis

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The Cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

11 The Cell- G M Cooper

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 21: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

21

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

Paper ndash IV (Code 2T4) Molecular Biology

Learning outcome Students will be able to

1 Remember and understand the fundamental concepts of Molecular Biology and the

experiments involved in it

2 Relate the concepts of Molecular Biology in the development of Biochemical

research techniques

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 22: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

22

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2T4 Molecular Biology

Unit I Eukaryotic and Prokaryotic chromosomes

Chromatin structure Histones DNA nucleosome morphology and higher level organization Functional

states of chromatin and alterations in chromatin organization Chromosome organization Metaphase

chromosomes centromere and kinetochore telomere and its maintenance Holocentric chromosomes

Heterochromatin and euchromatin position effect variegation Chromosomal domains (matrix loop domains)

and their functional significance

Organization of nuclear and organellar genomes C-value paradox Repetitive DNA-satellite DNAs and

interspersed repeated DNAs Transposable elements LINES SINES Alu family and their application in

genome mapping

Concept of a gene Conventional and modern views Fine structure of gene split genes pseudogenes non-

coding genes overlapping genes and multi-gene families

Unit II Replication and Recombination

Replication Review of replication in bacteria plasmid and viruses Models of DNA replication DNA

replication in eukaryotes Eukaryotic DNA polymerases and their roles origin of replication Autonomously

Replicating Segments (ARS) in yeast elongation lagging strand synthesis and termination

Recombination DNA recombination Homologous site specific and transposition

Homologous recombination Holliday Model Messelsson -Radding Model Rec BCD pathway

Site specific recombination Lambda phage ingration and excision rearrengementof immunoglobulin genes

Transposition Prokaryotic transposition Insertion sequences and mere complex transposons (eg Tn3)

conservative and replicative transposition Eukaryotic transposable elements yeast and Drosophila transposons

retroviruses and retrovirus like elements

Unit III Transcription

Review of prokaryotic transcription transcription in eukaryotes Eukaryotic RNA polymerases and their

subunit structure Class I II and III promoters Upstream elements enhancers and silencers General

transcription factors Class I II III genes and their functions elongation factors TBP structure and its role in

transcription mediators Structure of transcription activators zinc fingers homeodomains helix loop helix

bZIP beta barrels

Unit IV Viruses

General properties of viruses (size shape composition of viral capsid spikes envelope and nucleic acids)

Viral classification in brief Baltimore classification Structure and composition of DNA viruses (Herpes virus

amp Adenovirus) and RNA viruses (HIV)

Tumor viruses (HBV HTLV HPV) structure and mechanism of oncogenesis

Structure and life cycle of Lambda and M13 bacteriophages

Laboratory diagnosis of viral diseases

Mechanism of action of Antiviral drugs (Acyclovir Foscarnet Nevirapine Saquinavir Oseltamivir)

Suggested References

1 Molecular Biology of Gene Watson

2 Gene 7 Benjamin Lewin

3 Cell amp Molecular Biology Devlin

4 Biochemistry Lehninger Nelson amp Cox

5 Biochemistry Voet amp Voet

6 Molecular Biology David Frifelder

7 Molecular biology-Lodish Baltimore

8 Genetics-Russell

9 Genetics 1and 2-CBPower

10 Molecular biology-Watson

11 Molecular biochemistry ndashRobert Weaver

12 Microbiology by Davis

13 Virology by Luria

14 Understanding Viruses-Teri Shors Jones and Bartlett Publishers Massachusetts edition 2009

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 23: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

23

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 2

2P1 Clinical Biochemistry And Immunology

1 Determination of serum and urine Creatinine by Jaffrsquos method

2 Determination of serum Bilirubin by Malloy amp Evllyn method

3 Determination of serum Chloride by Schales amp Schales method

4 Estimation of blood urea by Nesslerisation method

5 Estimation of Serum amylase (EC3211)

6 Estimation of Serum Cholesterol by Single Step Method (Libermann amp Burchard)

7 Determination of Serum Uric Acid by Henry Carawayrsquos method

8 Determination of Icteric Index SGOT SGPT and alkaline phosphatase activity

9 Routine Urine Analysis

10 Quantitative Estimation of T3 T4 and TSH

11 To determine Urinary VMA (3-methoxy 4 ndashHydroxyl Vanillin Mandellic Acid)

12 Glucose Tolerance Test

2P2 Cell And Molecular Biology

1 Use of Simple Compound and Phase Contrast Microscopes

2 Isolation culture and cell counting of lymphocytes

3 Adherent cell line Trypsinization cell count subculturing

4 MTT assay

5 Isolation of DNA from Bacteria and Blood

6 Assessment of purity of DNA by 260280 ratio

7 Isolation of plasmid DNA Mini Prep Midi Prep and Maxi Prep

8 Restriction digestion of DNA

9 Ligation of DNA

10 Separation of DNA fragments by Electrophoresis

11 Southern Blotting amp Northern Blotting

2S1 Seminar

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 24: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

24

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash I (Code 3T1) Advanced Molecular Biology

Learning outcome Students will be able to

1 Understand the concepts of Eukaryotic Transcription regulation mechanisms with details

of enzymes involved eukaryotic transcription process

2 Post transcriptional and translational modifications and regulatory aspects of it

3 Describe the expression of genes and the regulatory RNAs involved in it

4 Appreciate epigenetic ways of gene expression regulation

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 25: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

25

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T1 Advanced Molecular Biology

Unit I Regulation of eukaryotic gene expression at transcriptional level

Overview of transcription by RNA Polymerases I II and III

Anatomy of a protein-coding gene

Basal transcription by RNA polymerase II Subunits of Pol II general transcription factors

Activators How the initiation complex is assembled How initiation occurs

Speeding up the process Enhancers TAFs and how they work

Regulated transcription transcription factors Zinc-fingers (Sp1 the first such factor identified)

Leucine zippers Basic helix loop helix Homeodomains DNA binding domains Activating domains

RNA Elongation HIV TATTAR

RNA polymerase III and regulation of 5S rRNA

Unit II Regulation of eukaryotic gene expression at post translational translational and post-

translational levels

Regulation at tpst-transcriptional level Effect of cap and polyadenylation on splicing trans and

alternative splicing RNA editing mRNA stability and transport

Regulation at Translational level Global regulation through eIF2 and eIF4EeIF4E-BP Specific

regulation through 5 UTRs using RNA structure eg ODC Specific regulation through 5

UTRprotein interactions eg ferritin in eukaryotes and ribosomal proteins in prokaryotes Specific

regulation through 3 UTRs eg 15-LOX

Regulation at post-translational level Control of the level of active proteins regulation of proteolysis

Unit III Regulatory RNAs

Historical background RNA interference as regulatory mechanism in eukaryotes Slicer and dicer

synthesis and function of RNAi molecules in plants chromatin remodeling in human disease and

diagnosis

Unit IV Epigenetics

Background chromosomal inheritance taking fission yeast as an example DNA methyltransferases

DNA methylation maintenance histone modification and regulation of chromatin structure bivalent

histones DNA demethylation histone demethylation

Suggested References

1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd

Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 26: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

26

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash II (Code 3T2) Biotechnology

Learning outcome Students will be able to

1 Remember and Understand fundamental concepts of Genetic Engineering

2 Illustrate and compare different techniques involved in Genetic Engineering

3 Understand the concepts of Prokaryotic and Eukaryotic Transformation and PCR

4 Describe the expression of heterologous genes and the vectors involved in it

5 Appreciate technology involved in industrial products of Protein engineering and

fermentation technology Remember and Understand the design and functioning of

different types of Bioreactors and Downstream processing Evaluate the application of

different types of Bioreactors including immobilization reactor system and its kinetics

6 Comprehend tools important in Bioinformatics analysis for simplified application of

nucleic acid and protein sequence data

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 27: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

27

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T2 Biotechnology

Unit I rDNA technology Genomic and cDNA libraries DNA manipulation enzymes isolation of specific genes

Gene cloning REs vectors-plasmids cosmids phage vectors M13 phage vectors phagemids expression

vectors with strong promoters inducible vectors produce fusion proteins and their isolation Eucaryotic

expression system shuttle vectors YAC BAC insertion of DNA and its ligation to carrier DNA introduction

of DNA in cells gene synthesis gene libraries

Application of recombinant DNA technology in medicine agriculture industry and environmental sciences

Unit II Gene control systems in bacteria and bacteriophage lambda

Mechanism of induction and repression constitutive expression various control mechanisms positive

regulation negative regulation attenuation operon hypothesis with special reference to malgal ara and

histidine operons Regulatory mechanisms in bacteriophage lambda

Regulation of gene expression at various levels (transcription post transcriptional and translational)

DNA-protein interactions Lambda family of repressor trp repressor

Unit III Biochemical engineering Biochemical Engineering Bioreactors and related equipment and

instrumentation types of bioreactor (Batch semi batch CSTF recycle etc) reactor analysis reactor design

reactor for recombination proteins

Fermentation technology Fermentation technology microbial culture reaction genetic modification use of

mutants recombinant DNA technology and application in fermentation technology microbial growth kinetics

sterilization fermentation process kinetics analysis of rate pattern and kinetic groups fermentation process

types control of environmental variables recovery of fermentation products isolation and purification and use

of immobilization techniques

Unit IV Bioinformatics and Drug Designing Introduction to Bioinformatics Applications of Bioinformatics Bioinformatics resources

Biological Databases Overview to Biological Databases Nucleotide Databases (GenBank DDBJ ENA) Protein sequence

databases (Uniprot Swiss prot Prosite Pfam Prodom) Protein structure databases (PDB SCOP CATH)

Sequence analysis Sequence similarity search BLAST FASTA CLUSTAL

Genomics Introduction to Genomics Comparative Genomic Databases Objective of Genome Comparisons Genome

Alignments

Proteomics Overview of Proteomics Experimental Techniques Bioinformatics Approaches Protein-Protein Interaction

Databases and software

Softwaresrsquo for Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Virtual Screening Homology Modeling and Chimera Generation

Suggested References 1 Molecular Biology of the Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation - Gerhard Krauss Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Genes IX Benjamin Lewin Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCB McGraw-Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis 2005

Molecular Biotechnology Principles and Applications of Recombinant DNA Bernard R

GlickhttpwwwamazoncomMolecular-Biotechnology-Principles-Applications-

Recombinantdp1555814980ref=sr_1_6s=booksampie=UTF8ampqid=1323503937ampsr=1-6 - (Author)Publisher

Amer Society for Microbiology 4 edition (December 31 2009)

11 Principles of gene manipulation and genomics S B Primrose Richard M Twyman Publisher Wiley-Blackwell 7

edition (February 17 2006)

12 Principles of Fermentation Technology P F Stanbury (Author) S Hall (Author) A Whitaker (Author) Publisher

Butterworth-Heinemann 2 edition (February 19 1999)

13 1 Bioinformatics A practical guide to the analysis of genes and proteins Baxevanis AD and Ovellette BFF

Wiley-Interscience (2002)

14 2 Molecular and Biotechnology A comprehensive desk reference RA Meyes (Ed) VCH Publishers Inc (1995)

15 3 Textbook of Biotechnology Das HK Wiley Dreamtech India Pvt Ltd (2004)

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 28: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

28

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

Semester 3

Paper ndash III (Code 3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Learning outcome Students will be able to

1 To understand key principles of toxicology including various factors affecting toxicity and toxicity assessment

2 To evaluate analyse disposition of toxicants and factor affecting to disposition of toxicants

3 The know how of toxicokinetics and biotransformation 4 To critically analyse and interpret non-organ directed toxicity To

study effect of environmental toxicity on human beings

5 To develop an understanding of the genetic toxicology and

Developmental Toxicology for scientific research practices

6 Critical evaluation of relationship between target organ toxicity for

experimental designs

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 29: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

29

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Core Elective 1

3T3 A) Toxicology (Biochemical And Environmental Toxicology)

Unit I General principles of Toxicology

Definition Different facets of toxicology and their interrelationships Classification of toxic

agents Desired and undesired effects

Various factors affecting toxicity vehicles formulation factors biological half life volume

and concentration dose dosage forms routes of administration entry genetic status etc

Principles of selective toxicity comparative morphology comparative biochemistry

comparative cytology

Toxicity assessment acute subchronic chronic exposure determination of ED50 and LD50

values tests for mutagenecity carcinogenicity genotoxicity Ames test

Unit II Disposition of Toxicants

Factors affecting disposition of toxicants absorption distribution biotransformation

elimination

Absorption through gastro-intestinal tract lungs skin

Distribution storage in tissues blood-brain barrier passage across placenta redistribution

Biotransformation Phase I and II reactions metabolic interrelationship antidotal therapy

Excretion urinary fecal exhalation other routes

Toxicokinetics classic and physiologic

Unit III A) Non ndashorgan directed toxicity

Chemical carcinogenesis definition mechanism

Genetic toxicology definition health impacts and mechanism of induction of genetic

alterations

Developmental toxicology definition principles mechanism and pathogenesis of

developmental toxicity

B) Environmental Toxicology

Air pollution definition air pollutants health effects and risk assessment of air pollution

Introduction to Ecotoxicology

Unit IV Target organ toxicity

Skin skin as a barrier dermatitis acne urticaria

Toxic responses of the blood blood as a target organ toxicology of erythron leukon and

platelets

Toxic responses of the liver physiology and pathophysiology factors in liver injury

mechanism of liver injury

Toxic responses of the respiratory system lungs structure and functions pulmonotoxic

agents pathogenesis of chemical induced damage acute and chronic responses of lungs to

injury

Suggested References

1 Casarette and Doullrsquos Toxicology by Klaassen CD

2 Biochemical Toxicology of Environmental Agents by Bruine D

3 Detoxification mechanisms by Williams RT

4 Selective Toxicity by Albert A

5 Developmental Toxicology by Hood RD

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 30: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

30

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash III (Code 3T3 B) Nutrition (Nutritional Biochemistry) (Core Elective 1)

Learning outcome Students will be able to

1 Capably describe the biochemical techniques that are relevant for the investigation of nutrient metabolism

2 Understand key principles of energy expenditure thermogenic effects Energy requirements and role of dietary fibers in nutrition

3 To read interpret and discuss protein energy malnutrition disorders of mineral metabolism for scientific research

4 To develop an understanding of the observational and experimental character of science in nutritional biochemistry

5 To communicate role of clinical nutrition and food allergies in scientific communication frameworks such as written reports and open discussion

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 31: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

31

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T3 B Nutrition (Nutritional Biochemistry) (Core Elective 1)

Unit I Basic Concepts

Basic Concept Energy content of foods Measurements of energy expenditure Direct amp

Indirect calorimetry Definition of BMR and SDA and factors affecting these Thermogenic

effects of foods Energy requirements of man and woman and factors affecting energy

requirements

Role of dietary fibers in nutrition

Unit II Nutritional Disorders

Protein Energy Malnutrition (PEM) Aetiology Clinical features Metabolic disorders

and Management of Marasmus and Kwashiorkor diseases

Disorders of Mineral Metabolism Hypercalecemia Hypocalcaemia Normocalcemia

Hyperphosphatemia

Unit III Starvation and Antinutrients

Starvation Techniques for studying starvation protein metabolim in prolonged fasting

protein sparing treatments during fasting Concept of high protein low calorific weight

reduction diets

Antinutrients Naturally occurring food borne toxicants protease inhibitors hemagglutins

hepatotoxins allergens oxalates toxins from mushrooms animal food stuffs and sea foods

Unit IV Clinical Nutrition and Food Allergies

Clinical Nutrition Role of diet and nutrition in the prevention and treatment of diseases

dental caries Fluorosis Atherosclerosis amp Rheumatic disorders Inherited metabolic

Disorders Phenylketonuria Maple Syrup disease amp Hemocystinuria

Food Allergies Definition role of antigen host and environment types of

hypersensitivities diagnosis and treatment of allergy

Suggested Reading 1 Basics of clinical nutrition author- yk joshi jaypee publication

2 Nutrition for the community Gully baba publishing house

Essentials of human nutrition author-jim mann amp stewart truswell oxford university press

3 Introduction to human nutrition

edited by- professor michael gibney (ucd institute of food and health) professor susan lanham-new

(university of surrey) professor aedin Cassidy (university of east anglia) professor hester vorster (north-

west university south africa) httpwwwnutritionsocietyorgpublicationstextbooksintroduction-to-

human-nutritionsthashtdyscawhdpuf

4 Nutrition and metabolism

edited by- professor susan lanham-new (university of surrey) professor ian macdonald (university of

nottingham) professor helen roche (unviersity college dublin) -

httpwwwnutritionsocietyorgpublicationstextbooksnutrition-and-metabolismsthashiusrjtiudpuf

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 32: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

32

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Foundation Course 1 Biomolecules and Basic Metabolism

Unit I Carbohydrates and metabolism

Classification of carbohydrates Structure occurrence and biological importance of

monosaccharides oligosaccharides and polysaccharides

Introduction to Metabolism glycolysis glucogenesis and gluconeogenesis TCA cycle and its

amphibolic role energetics of carbohydrate metabolismAlternate pathways HMP shunt Enter-

Doudoroff glucuronate and glyoxylate pathways Corirsquos cycle

Unit II Lipids and metabolism

Classification of lipids Fatty acids Saturated and unsaturated fatty acids Essential fatty acids

Glycerophospholipids Glycolipids properties and functions

Metabolism Oxidation of fatty acids even and odd numbered unsaturated and branched chain fatty

acids

Degradation and biosynthesis of triacylglycerols and phospholipids energetic of beta- oxidation

Cholesterol biosynthesis catabolism and regulation

Unit III Proteins and metabolism

Classification of amino acids and proteins Protein structures primary secondary tertiary and

quarternary structure General metabolic reaction of amino acids transamination oxidative

deamination minor pathways of amino acid degradation transdeamination amino acid oxidase non

oxidative deamination

Degradation and biosynthesis of amino acids glycogenic and ketogenic amino acids Urea cycle

pathway and regulation

Unit IV Minerals and metabolism

Major and minor and ultra trace minerals their occurrence functions toxicity and interaction with

other nutrients

Iron metabolism and regulation

Calcium and phosphorus metabolism and regulation

Suggested Reading

1 Biophysical Techniques- Upadhyay Upadhyay and Nath

2 Principles of Biochemistry- Lehninger David L Nelson and Michael M Cox

3 Enzymes- Malcolm Dixon and Edwin Webb

4 Harperrsquos Biochemistry- Harper

5 Biochemistry- Western and Todd

6 Cell and Molecular Biology-Gerald Karp

7 Fundamentals of Biochemistry-Donald Voet Judith G Voet and Charlotte W Bratt

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 33: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

33

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

Paper ndash IV (Code 3T4 ) Bioresearch Techniques I (Subject centric core 1)

Learning outcome Students will be able to

1 Understand key principles of how flow cytometer work including data

analysis for their applications

2 Improve on skillful process of the animal cell culture techniques and

experimental demand of knowledge including an appreciation of the

need for good experimental design and scientific research practices

3 To incline intellectual curiosity in DNA and RNA techniques and

related fields that extends well beyond the course

4 To develop practical laboratory skills in the field of DNA and RNA

techniques

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 34: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

34

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3T4 Bioresearch Techniques I (Subject centric core 1)

Unit I Flow cytometry

Principles of flow cytometry Instrument overview principle of fluorescence sample preparation

data analysis and applications of flow cytometry Overview Fludics Generation of Scatter and

fluorescence ( Optical bench optical filters signal detection Treshold) Data Analysis (Data

Collection and Display gating data analysis for subsetting applications Data analysis for ther

applications) Sorting Lasers and Alignment (Working of lasers and laser alignment)

Unit II Animal cell culture techniques

Animal cell Culture Cell culture (adherent and suspension) basic equipment cell culture media-

Components sterility buffering capacity growth requirements supplementation of serum antibiotic

and antimycotic agents preparation of medium advantages and limitations of Primary cell culture

clonal cell lines basic technique a of animal cell subcultuing disaggregation method for quantitation

of cells in culture counting chamber counters cell viability determination cytotoxicity assay and its

applications cell apoptosis assay and its applications 3 D cultures

Unit III DNA techniques

Isolation Sequencing Restriction Nucleases Gel Electrophoresis DNA probes Nucleic acid

hybridization Southern blotting DNA fingerprinting and DNA typing DNA Library

DNA sequencing Sanger and Maxam Gilbert

Restriction Mapping DNase foot printing DMS foot printing knockouts

PCR RFLP RAPD AFLP SNP

Unit IV RNA techniques

Isolation Hybridization Northern Blotting in vitro labeling with radioisotopes and chemical

markers

Mapping and quantifying transcripts S1assay primer extension run off transcription

Transcription rate measurement in vivo Nuclear run on transcription reporter gene N transcription

si RNA technology gene silencing techniques its applications microarrays ribozyme technology

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp Francis

2005

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 35: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

35

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 3

3P1 Biotechnology And Molecular Biology

1) Fermentation

i) Isolation of microorganisms from soil demonstrating synthesis capability of desired product

Gram staining (Desired property to be decided by the instructor) and screening

ii) Optimization of the lab scale production of the desired product Effect of temperature pH

substrate concentration

iii) Growth curve Estimation of cell number substrate utilization andor product formation

2) Polymerase Chain Reaction

i) PCR amplification from genomic DNA

ii) Nested PCR

iii) Random Amplification of Polymorphic DNA (RAPD)

3) Restriction Fragment Length Polymorphism (RFLP)

3P2 A Biochemical And Environmental Toxicology

1 Qualitative detection of various toxicants in biological samples

Phenothiazine derivatives Organochlorine compounds (Fujiwara test) Phenol Methanol Arsenic (As)

Antimony (Sb) Selenium (Se) Mercury (Hg) Bismuth (Bi) Fluoride (F) Boron (Bo) Gutzeit test for

Antimony (Sb) and Arsenic (As) Spot test for metal toxicants

2 Quantitative determination of Salicylate Paracetamol (acetaminophen) Sulphonamide in biological

samples

3 Enzyme assay in toxic conditions

GOT (AST) GPT (ALT) Acid phosphatase Alkaline phosphatase Acetyl cholinesterase etc

4 Construction of dose-response curves

5 Determination of LD50 value of a toxicant

6 Induction of hepatotoxicity diabetes skin lesions teratogenesis

7 Assay of biomarkers of environmental pollution toxicity

OR

3P2 B) Nutritional Biochemistry

1 Determination of Calcium in food samples

2 Determination of Inorganic Phosphorous in food samples

3 Determination of Iron in food samples

4 Determination of beta carotene in carrots by column chromatography

5 Determination of Ascorbic Acid in food

6 Estimation of Amylase activity

7 Determination of Total Lipids By Sulphophospho vanillin Method

3S1 Seminar

InstitutionalEducational tour For minimum 08 days

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 36: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

36

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash I (Code 4T1) Advanced Clinical Biochemistry

Learning outcome Students will be able to

1 Analyse evaluate and generate information from a wide variety of sources regarding the key principles of aging and Neurological disorders

2 Analyse the effects of obesity on physiological functions including gene regulation

3 Critically interpret molecular and metabolic diseases and develop new knowledge domain about them

4 To develop effective creative and innovative solutions to current research problems in Reproductive Disease and Reproductive Biochemistry

5 To develop practical laboratory skill for Assisted Reproductive Technology program

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 37: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

37

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T1 Advanced Clinical Biochemistry

Unit I Aging and Neurological Disorders

Current view and theories of aging auto immune connection and HLA association processes of

aging and biochemical alteration DNA damage protein oxidation and axonal transport in aging

nutritional intervention as anti-aging therapy

Alzheimerrsquos disease Causes symptoms diagnosis pathogenesis genetics APP ApoE PS2 tau

protein risk factors and therapeutic approaches

Progeria Parkinsonrsquos disease Causes symptoms diagnosis pathogenesis genetics and therapeutic

approaches

Unit II Obesity

Theories lipid metabolism adipose tissue anomalies

Genetic basis of familial obesity effects of neuropeptides and leptin in nutrient partitioning

Obesity related derangements in metabolic regulation Therapeutic approaches

Unit III Molecular and Metabolic Diseases

Human gene map genetic diversity polymorphism genetic linkage chromosomal disorder

Monogenetic Disorders Autosomal dominant autosomal recessive X-linked Multifactorial

disorders Genetic heterogeneity Allelic heterogeneity Pathogenesis of genetic disease

Galactosemia Hemophilia Sickle cell anemia Muscular dystrophy Hypercholesterolemia Gout

Turnerrsquos syndrome

Unit IV Reproductive Biochemistry

Overview of reproductive system and reproduction biochemistry of reproductive disorders (male amp

female) Influence of various factors in reproduction with special reference to role of prostaglandins

and gonadotrophins Mechanism and methods of birth control and possible biochemical

consequences thereof Biochemical markerrsquos in infertility disorders Techniques involved in assisted

reproductive technology (ART) Culture media and cell culture techniques in ART programme

Suggested References

1 Clinical Biochemistry ndash Metabolic and Clinical aspects By-William J Marshall amp Stephen

K Angert

2 Harperrsquos Biochemistry - 27th Ed

3 Text book of Medical Physiology - By Guyton

4 Text book of Physiology -By Burn amp levy

5 Biochemistry ndashBy L Stryer (Freeman amp CoNY)

6 Biochemistry with clinical correlation- By Thomas Devli

7 The Metabolic Basis of Inherited Disease 5th Ed-By John Stanbury

8 Teitz Fundamentals of Clinical Chemistry ndashBy CABurtis amp Ashwood

9 Biochemistry - By Lehninger

10 Lehningerrsquos Biochemistry ndashBy Nelson amp Cox

11 Biochemistry ndashBy Stanford

12 Basic Medical Biochemistry A Clinical approach- By Smith

13 Principles of Internal Medicines- By HarrisonT R

14 Practical Biochemistry Principles amp Techniques- By Wilson amp Walker

15 Practical Biochemistry ndashBy David Plummer

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 38: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

38

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash II (Code 4T2) Advanced Immunology

Learning outcome Students will be able to

1 Understand details of lymph node microanatomy and learn the B and T cells encounter with antigens and study its development

2 Gain insight into antigen presentation and autophagy on a detailed molecular level

3 Understand immunology of mucosal surfaces and the interplay between commensal flora and the immune system in the gut

4 In-depth knowledge of the cellular and molecular basis for autoimmune disease and allergies

5 Basic knowledge of tumor immunology and the development of novel recombinant antibodies for treatment of cancer and autoimmune disease

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 39: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

39

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T2 Advanced Immunology

Unit I Introductory Immunobiology

Complement system Alternative and Classical pathway of complement activation

Immune networks Homeostasis in the immune system-termination of normal immune

responses network hypothesis

In vivo immunity to viruses bacteria fungi protozoa worms etc

Unit II Immunological tolerance and Autoimmunity

Immunologic tolerance T lymphocyte tolerance- central and peripheral Apoptosis in

Lymphocytes-pathways and biochemical mechanisms effector mechanisms Tolerance

induced regulatory T cells B lymphocyte tolerance- Central and Peripheral Homeostasis in

the immune pathogenesis and therapeutic approaches to autoimmunity

Unit III Tumor and Transplantation Immunology Hypersensitivity

General features of tumor immunity tumor antigens Immune response to tumor and

evasion Immunotherapy Types of hypersensitivity Effector mechanisms of immunologic

tissue injury and disease

Unit IV Immunodeficiency and Vaccinology

MHC and disease susceptibility immune deficiency disorders Active immunization

(immune prophylaxis) passive immunization adjuvants modern approaches to vaccine

development role of vaccines in the prevention of disease

Suggested References

1 Cellular and Molecular Immunology- 5th Edition Abul K Abbas Andrew Litchman

2 Immunology-5th Edition Richard A Goldsby Thomas J Kindt Barbara A Osborne

Janis Kuby

3 Immunology- 6th Edition Ivan Roitt Jonathan Brostoff David Male

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 40: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

40

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 A) Toxicology (Clinical Research)

Learning outcome Students will be able to

1 Have knowledge about assessment and management of ethical clinical trial

programs

2 Demonstrate competency in biopharmaceutical clinical trial research designs and

regulatory affairs

3 Demonstrate competencies in evaluating clinical research data and

communicating results Manage innovative products through the discovery

processes and into the clinical trial phases

4 Identify and classify different types of trial designs when reading a trial report

understand the essential of GLP roles and responsibilities of stakeholders in

clinical trials

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 41: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

41

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 A) Toxicology (Clinical Research)

Unit I Pre-Clinical Research

Animal studies acute amp chronic toxicity of drugs regulations for number amp types of

animals protocols for animal experimentation Biochemical amp histopathological studies of

animals after drug administration Mechanism amp cause of death Routine toxicity studies amp

special toxicity studies carcinogenicity mutagenicity amp teratogenicity to be given special

emphasis

Unit II Phases of Clinical Research

Phases of clinical research number of volunteers in phase I amp types of patients in phase II to

IV Importance of these investigations Post marketing surveillance (PMS) amp

pharmacovigilence in case of clinical investigations after marketing authorization

Importance of ethical committee protocol design documentation in clinical trials Bio

Availability and Bio Equivalence studies Pharmacokinetics Pharmacodynamics Genomic

studies

Unit III Good lab practices

Good Clinical Practices Good Manufacturing Practices and Good Laboratory Practices

Principles of ICH-GCP History GCP declaration of Helsinki Belmont report Nuremberg

code Tuskgee trial Schedules Y and its amendments ICMR Guidelines Composition

functions amp operations of IRBIEC ethics of clinical trials Health Authorities- CDSCO US-

FDA EMEA and other

Unit IV Roles and Responsibilities of different stake holders in Clinical Research-

Sponsor CRO SMO Ethics Committee Investigator CRA CRC Patients and other

Departments in Clinical Research- Operations Business Development Regulatory

Pharmacovigilance Data Management Centralized Monitoring Quality Finance Important

documents in Clinical Research and importance of documentation in Clinical Research

Stages in clinical trial-Feasibilities PSSV SIV SMV and Close-out visits Audits and

Inspections

Suggested reading

1 Clinical Research Coordinator Handbook Norris Deborrah Plexus Publications

20040601

2 Clinical Research Methodology and Evidence-Based Medicine Babu Ajit N

Anshan 20080530

3 Conducting Clinical Research Judy Stone Biblio Distribution 2006

4 Essentials of clinical research Stephen P Glasser (Edt) Springer Verlag 2008

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 42: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

42

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

Paper ndash III (Code 4T3 B) Nutrition (Applied Nutritional Biochemistry)

Learning outcome Students will be

1 Capable of describing biochemical pathways relevant in nutrient metabolism 2 Capable of using selected biochemical techniques relevant in nutritional

biochemical research 3 Critical reading of scientific articles in nutritional biochemistry 4 Capable of discussing research questions relevant to nutritional biochemistry 5 The ability to ask critical questions and discuss nutritional biochemical research

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 43: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

43

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T3 B) Nutrition (Applied Nutritional Biochemistry)

Unit I Clinical nutrition

Role of a dietician role and responsibilities of a dietitian nutrition counseling professional

ethics and obligations

Diet therapy-Rationale for diet therapy (normal diet modifications of the diet to the light

diet soft diet full liquid diet clear liquid tube feeding) Routes for diet therapy-enteral and

parental use of biochemical parameters in the planning of diets use of computers in the

planning of diets

Unit II Nutritional Counseling and Dietetics

Nutritive value of different food groups and changes due to cooking in various food groups

Storage of foods food quality and factors affecting food quality Control of food quality Use

of additives Classification and applications

Unit III Community Nutrition

Opportunities in community Nutrition Assessing Community Resources assessing target

population program planning Assessing communityrsquos nutritional resources Food insecurity

food assistance programs world hunger and food insecurity Principles of nutrition education

and policy making national nutrition agenda

Unit IV Applied Nutrition and Public Health Concept of Health Nutrition and Public Health Nutrition Demographic trends in India and

the significance of certain indices of Health and Nutrition situation of a community IMR

MMR TFR Birth rate Death rate Life expectancy etc) Major nutritional problems in

developing countries Dietary surveys-methods ways of interpretations and analysis

recommendations based on survey findings Assessment of nutritional status biochemical

and anthropometry

Suggested Reading

Clinical nutrition

edited by- professor marinos elia (university of outhampton) professor olle ljungqvist

(karolinska institutet amp oumlrebro university hospital) dr outham outhamp (university of

outhampton professor susan lanham-new (university of surrey) - see more at

httpwwwnutritionsocietyorgpublicationstextbooksclinical-

nutritionsthashw12tfscqdpuf

Public health nutrition

edited by- professor michael gibney (ucd institute of food and health) professor barrie

margetts (university of southampton) dr john kearney (dublin institute of technology)

professor lenore arab (university of california los angeles)

httpwwwnutritionsocietyorgpublicationstextbookspublic-health-

nutritionsthash8pvhu1m0dpuf

Staying healthy with nutrition author- elson m Hass buck levin

American dietetic association complete food and nutrition guide Roberta larson duyff

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 44: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

44

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

MSc Biochemistry CBCS syllabus Effective from 2015-16

SEMESTER 4

Foundation 2 Basic Enzymology

Unit I

Introduction to Enzymology Nomenclature and classification of enzymes History sources of

enzymes (Animal Plant and microorganisms) Protein amp nonprotein nature of enzymes with

examples enzymes as biological catalysts and their importance principle of assay of enzymes and

measurement of activity effect of experimental conditions on measurement of activity such as time pH temp

substrate definition of enzyme unit Stability of enzymes and half life of enzymes Effect of environmental

factors on stability of enzymes Concept of Zymogens and active enzyme with examples effect of activators

and inhibitors on enzyme activity Role of coenzymes and cofactors on enzyme catalysis with examples

Unit II Production amp purification

Method os screening of sources for desired enzymes Availability of the sources for procurement

of enzymes Natural and synthetic Media for microbial enzyme production effect of inducers and

environmental factors on enzyme production by microorganisms

Methods of isolation of enzymes form the source purification of enzyme by dialysis salt and solvent

precipitation chromatography gel filtration Purification by affinity chromatography methods of

determination of purity and nature of of enzymes by simple PAGE SDSPAGE and 2 D electrophoresis

Unit III Enzyme Kinetics

Lock amp key model and Koshland model of enzyme active site Determination of active site of enzyme

Michelis Mentain equation kinetics of reversible irreversible and nonreversible enzymes Line Weaver burk

plot and Eddie Hofstie Plot Determination of kinetic constants and activation energy Effect of competitive

and non-competitive inhibitors on enzyme activity Allosteric enzyme and sigmoidal kinetics

Unit IV Applications of enzymes

Structure and function of multienzyme complex systems such as PDH KGH B oxidation spiral and glycolysis

Advantages of soluble and membrane bound enzymes Futile cycles in Biochemistry

Methods of immobilization of enzymes advantages and disadvantages of immobilization Application of

Immobilized enzymes in agriculture cosmetics detergent dairy brewing and food industries with examples

such as lactase pectinase proteinase invertaselipase etc Application of enzymes in nanotechnology

biosensors etc

Suggested references

1 Enzymology and Enzyme Technology 2014 by SM Bhatt (S Chand)

2 Enzyme Technology 2006 by Ashok Pandey (Editor) Colin Webb (Editor) MARCELO

FERNANDES (Editor) Springer

3 Biocatalysts and enzyme technology 2012 Klaus Buchholz

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 45: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

45

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

Learning outcome Students will be able to

1 Learn describe and build up knowledge domain regarding the latest and most advanced Bioresearch techniques available for biochemical research

2 Be aware select appropriately apply technology platforms and Perform techniques for analysis of DNA and protein expression

3 Evaluation of data and controls related to research techniques 4 Create thought-provoking questions related to the laboratory equipment

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 46: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

46

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4T4 Bioresearch Techniques II (Subject centric core 2)

UNIT I

Biochemical methods I- Co-immunoprecipitation BiFC bimolecular fluorescence

complementation affinity electrophoresis Pull down assays label transfer yeast two hybrid

screens phage display

UNIT II

Biochemical methods II- In-vivo crosslinking of protein complexes using photo-reactive

amino acid analogs Tandem affinity purification (TAP) Chemical cross-linking SPINE

(Strepprotein interaction experiment) Quantitative immunoprecipitation combined with

knock-down (QUICK) Proximity ligation assay (PLA) in situ

UNIT III

Biophysical and theoretical methods I

Bio-Layer Interferometry

Dual polarisation interferometry (DPI)

Static light scattering (SLS)

Dynamic light scattering (DLS)

Surface plasmon resonance

UNIT IV

Biophysical and theoretical methods II

Fluorescence polarizationanisotropy

Fluorescence correlation spectroscopy

FRET BRET

2D-FT NMR spectroscopy

Proteinndashprotein docking

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Suggested References

1 Molecular Biology of The Cell Alberts 5th Edition 2007 NCBI Publication

2 Principles of Biochemistry Lehninger WH Freeman

3 Biochemistry of Signal Transduction and Regulation-shy‐ Gerhard Krauss

Wiley VCH 3rd Revised Edition

4 Molecular Cell Biology Lodish 6th Edition WH Freeman amp Company

5 The cell Cooper 2nd Edition ASM Press

6 Gene IX Benjamin Lewin

Published by Pearson Prentice Hall

7 Cell and Molecular Biology Gerald Karp

8 Molecular Biology Robert Weaver 1st Edition WCBNMcGraw-shy‐Hill

9 Molecular Biology of the Gene Watson 6th Edition Pearson Publication

10 Gene Regulation A Eukaryotic Perspective David Latchman 5 illustrated Taylor amp

Francis 2005

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 47: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

47

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4

4P1 Advanced Clinical Biochemistry and Immunology and Toxicology and Nutrition

1 Demonstration of dialysis using blood filtrate (Protein Separation)

2 Immunology

a Quantitative Estimation of Antibody

b Precipitation Techniques Double Immunodiffusion Single (Radial)

Immunodiffusion

3 Electrophoretic Techniques Immuno-electrophoresisRocket Immunoelectrophoresis

Immuno-diffusion

4 To assay cathepsin D ATPase (NaKCaMg) Lipid peroxidase enzymes

5 Assay of Acetylcholine esterase activity in rat brain

6 Assay of monoamine oxidase

7 Fractionation of tissues and assay of proteins

8 Assay of ornithine amino transferase

9 Glutathione Estimation

10 Organ tissue morphology histopathology

11 Assay of toxicant biotransformation enzyme-cytochrome P450

12 Test for teratogenecity carcinogenecity Ames test

13 To perform pair wise alignment of sequences using BLAST program

14 To design primers for the given gene sequences

15 To perform multiple sequence alignment and generate phylogenetic tree

16 To retrieve and visualize the three dimensional structures of proteins

17 To retrieve metagenomic sequences and primer designing to develop STS marker

OR

18 Determination of Triglycerides

19 Proximate Analysis of Food Samples

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar

Page 48: SEMESTER I SYLLABUS for M. Sc. BIOCHEMISTRY Choice Based ... · 1992 Edition: Second Edition 4. Protein Engineering Protocols (Methods in Molecular Biology) Kristian Müller (Editor),

48

--------------------------------------------------------------------------------------------------------------------------------------RTM Nagpur University MSc Biochemistry syllabus Effective from 2020-21 Including Foundation course amp Subject centric course at Semester III and Semester IV

SEMESTER 4 Project

Learning outcome Students will be able to

1 Plan and develop experimental design projects from concept through to professional

prototype

2 Apply theoretical knowledge conceptual skills and techniques to the development of

solutions for biochemical problems

3 Apply initiative and judgment in planning problem solving and decision making in

practice or future study

4 Design a research project and submit in a form of thesis they will present their results of

the thesis to an audience of peers and faculty and be able to defend their results during

final evaluation

4PROJ PROJECT

4S1 Seminar