Introduction to Biochemistry, Cell and Molecular Biology II

Losiana NayakIndian Statistical Institute

http://www.isical.ac.in/~losiana_t/

A field of science concerned with studying the chemical structures and processes of biological phenomena at the molecular level.

A branch of biology dealing with the ultimate physicochemical organization of living matter and especially with the molecular basis of inheritance and protein synthesis.

Ref: http://www.britannica.com/

Molecular Biology

Cell: structural unit of life

cytoplasm

A cell can be distinguished into a outer membrane,

central nucleus and cytoplasm.

Cell membrane

nucleus

Typical structure of a cellRobert Hooke, an English

scientist, first described cells in 1665.

Cell theory consists of three basic points:

1. All living things are made of cells.

2. The cell is the smallest living thing that can perform all the functions of life.

3. All cells must come from preexisting cells. An animal Cell

Plant cells are differentfrom animalcells. Theycontain the

green photosynthetic

pigment chloroplast.

Growth

The answer is cell division, which is of two types

1. Mitosis [Somatic division]2. Meiosis [Genetic division/

Reductional division]

Functions of a cell?

Genetic controlEnergy houseSupportStoragePackagingTransport

Central Dogma of molecular biology

Information Only Goes One Way

The central dogma states that once “information”has passed into protein it cannot get out again. The transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein, may be possible, but transfer from protein to protein, or from protein to nucleic acid, is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein.

Francis Crick, 1958

AT

TA

GC

CG

GC

TA

T

AG

C

CG

GC

TA

AT

Packaging DNA

Histone proteins

Histoneoctomer

B DNA Helix 2 nm

AT

TA

GC

CG

GC

TA

T

AG

C

CG

GC

TA

AT

Packaging DNA

Histone proteins

B DNA Helix

Histoneoctomer

2 nm

AT

TA

GC

CG

GC

TA

T

AG

C

CG

GC

TA

AT

Packaging DNA

Histone proteins

Histoneoctomer

Nucleosome

11 nm

B DNA Helix 2 nm

Packaging DNA

ATA

CG

CG

GC

TA

AT

Histone H1

Packaging DNA

ATA

CG

CG

GC

TA

AT

Histone H1

Packaging DNA

ATA

CG

CG

GC

TA

AT

Protein scaffold

11 nm“Beads on a string”

30 nm

Tight helical fiber

Looped Domains200 nm

Packaging DNA

G

C

A

T

Protein scaffold

Metaphase Chromosome

700 nm

11 nm

30 nm200 nm

2 nm

Looped Domains

Nucleosomes

B DNA Helix

Tight helical fiber

A “Simple” Eukaryotic Gene

Terminator Sequence

Promoter/Control Region

Transcription Start Site

3’5’

RNA Transcript

Introns

Exon 2 Exon 3Int. 2Exon 1 Int. 1

3’ Untranslated Region5’ Untranslated Region

Exons

DNA

Cytoplasm

NucleusG AAAAAA

Export

Degradation etc.G AAAAAA

Eukaryotic Gene Expression

G AAAAAA

RNAProcessing

mRNA

RNA

Transcription

Nuclear pores

Ribosome

Translation

Packaging

ModificationTransportation

Degradation

Stages of Transcription

Transcription can be logically divided into three distinct stages:

1. Initiation2. Elongation3. Termination

Transcription Initiation

Proteins called transcription factors bind to the promoter region of a geneIf the appropriate transcription factors are present, RNA polymerase binds to form an initiation complexRNA polymerase melts the DNA at the transcription start sitePolymerization of RNA begins

5’

3’

3’

5’

Template (antisense) strand

Coding (sense) strand

Transcription

5’

3’

3’

5’

Template (antisense) strand

Coding (sense) strand

5’

RNA

RNAPol.

Transcription

5’

3’

3’

5’

5’

RNAPol.Template

(antisense) strand

Coding (sense) strand

Transcription Termination

There are two types of termination:Rho dependent requires a protein called Rho, that binds to and slides along the RNA transcript. The terminator sequence slows down the elongation complex, Rho catches up and knocks it off the DNA Rho independent termination depends on both slowing down the elongation complex, and an AT rich region that destabilizes the elongation complex

RNAPol.

5’RNA

RNAPol.

5’RNA

RNAPol.

5’ RNA

Termination (Rho Independent)

Terminator

RNAPol.

5’RNA

Termination (Rho Dependent)

Terminator

ρ

RNAPol.

5’ RNA

ρ

RNAPol.

5’RNA

Help, rhohit me!

ρ

Products of Transcription

Transcription produces three major RNA products:

1.Ribosomal RNA (rRNA) - Several rRNAs are vital constituents of ribosomes

2.Transfer RNA (tRNA) - The molecule that physically couples nucleic acid codons with specific amino acids

3.Messenger RNA (mRNA) - The nucleic acid messenger that carries encoded information from genes on DNA to the protein manufacturing ribosomes

Requirements for Translation

Ribosomes - rRNA and ProtiensmRNA - NucleotidestRNAAminoacyl-tRNA Synthetase, L Amino AcidsATP - For energy

Small subunit

EAP

Large subunit

GAG...C-AGGAGG-NNNNNNNNNN-AUG---NNN---NNN---NNN---NNN---5’mRNA

3’

Ribosome Structure

Aminoacyl-tRNAbinding site

Exit site

Peptidyl-tRNAbinding site

AELarge

subunitP

Small subunit

Translation - Initiation

fMet

UACGAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

AERibosome P UCU

Arg

Aminoacyl tRNAPhe

Leu

Met

SerGly

Polypeptide

CCA

Translation - Elongation

GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

AERibosome P

PheLeu

Met

SerGly

Polypeptide

Arg

Aminoacyl tRNA

UCUCCA

Translation - Elongation

GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

AERibosome P

CCA

Arg

UCU

PheLeu

Met

SerGly

Polypeptide

Translation - Elongation

GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

AERibosome P

Translation - Elongation

Aminoacyl tRNA

CGA

Ala

CCA

Arg

UCU

PheLeu

Met

SerGly

Polypeptide

GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

AERibosome P

Translation - Elongation

CCA

Arg

UCU

PheLeu

Met

SerGly

Polypeptide

CGA

Ala

GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

AERibosome P

Translation - Termination

CGA

PheLeu

Met

SerGly

PolypeptideAla

Arg

Val

CGAGAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’STOP

A

EP

Translation - Termination

CGA

PheLeu

Met

SerGly

PolypeptideAla

Arg

ValCGA

GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

STOP

3’

5’

5’

3’

Transcription And Translation In Prokaryotes

Ribosome

Ribosome5’

mRNA

RNAPol.

AN OVERVIEW OF METABOLISM

CARBOHYDRATE METABOLISMLIPID METABOLISM

PROTEIN METABOILSMENERGY METABOLISM

WHAT IS METABOLISM?

A Continuous gradual process of biological systems that includes both building and breaking of macronutrients for the purpose of growth, reproduction and senescence.

WHAT IT INCLUDES?

GENESIS

ANABOLISM

LYSIS

CATABOLISM

METABOLISM

FATS POLYSACCHARIDES PROTEINS

Fatty acids Glucose Aminoacids

Glycerol Other Sugers

Acetyl Co A CO A

ATP ADP

O2 e CITRIC

OXIDATIVE ACID

PHOSPHORYLATION CYCLE

2CO2

Signal transduction pathway?Signal means any communication that encodes a messageSignal Transduction involves conversion of a signal from extracellular environment to functional changes within the cellA Signal transduction pathway is a series of steps that enable signal transmission through physical barriers like cell membrane, organelle membrane and nuclear membrane

General process of a STPExtracellular signal is present outside a cell: typically a hormone, neurotransmitter or growth factorSignal binds to a receptor causing a change in receptor conformation, thus transmitting a signal to the interior of the cellThe signal precipitates many enzyme catalyzed protein interactions, ultimately causing changes in the cell’s functions (ex. glucose uptake, cell division, transcription)

Reference

Biochemistry by Lubert StryerCell and Molecular Biology by De Roberties and De Roberties

Some Slides are taken from

Timothy G. Standish, Ph. D.