BMB401 | Fall 2018

BIOCHEMISTRY for the

BIOMEDICAL SCIENCES

AMJAD FAROOQ PhD DIC | Associate Professor

Department of Biochemistry & Molecular Biology

University of Miami Miller School of Medicine

Miami, FL 33136

Address: 1011 NW 15th Street, Miami, FL 33136

Office: Gautier Building #116

Email: profamjadfarooq@gmail.com

Phone: +1-786-763-1294

Website: http://farooqlab.net

Module 0 => INTRDODUCTION

§0.1a Syllabus Outline

§0.1b Basic Concepts

Section 0.1a:

Syllabus Outline

The aims of BMB401 are to:

(1) Provide students with an in-depth understanding of the structure andfunction of biomolecules such as proteins, carbohydrates, lipids, andnucleic acids from a biochemical perspective

(2) Encourage students to apply logic and rationale to understanding variousbiochemical concepts and phenomena rather than resort to rote learning

(3) Equip students with the necessary biochemical foundation to embark on acareer in a wide array of fields such as:

- Medicine- Agriculture- Environment- Nutrition- Nanotechnology- Health industry- Pharmaceutical industry- Forensic science

AIMS and GOALS

BMB401 is a 4-credit course and fittingly divided into FOUR equally-weighted modules:

(1) CARBS and LIPIDS—biochemical properties and cellular functions of carbohydrates and lipids,including an overview of thermodynamics and signal transduction

(2) PROTEINS and ENZYMES—biochemical insights into the structure and function of proteins,including catalysis and kinetics of enzymes

(3) METABOLISM and ENERGY—biochemical insights into various metabolic pathways with particularemphasis on the oxidation of food and nutrients to generate energy for the sustenance of life

(4) DNA and RNA—biochemical insights into how genetic information in the form of DNA and RNA isused to direct protein synthesis and cellular processes

In terms of class structure, the course is comprised of:- 75-min class duration- 29 x lecture classes- 04 x workshop classes- 05 x exam classes- 2850-min contact time (38*75min)—exceeds the 700min/credit requirement!

Slides/videos for each lecture class are available for download at:http://farooqlab.net => BMB401 => Course

COURSE CONTENT: TETRAPARTITE

CLASS SCHEDULE: Fall 2018Module 1: CARBS and LIPIDS

Class Date

1.1 Thermodynamics Wed, Aug 22

1.2 Monosaccharides Fri, Aug 24

1.3 Polysaccharides Mon, Aug 27

1.4 Biological Lipids Wed, Aug 29

1.5 Biological Membranes Fri, Aug 31

1.6 Membrane Transport Wed, Sep 05

1.7 Signal Transduction Fri, Sep 07

1.8 Workshop I Mon, Sep 10

1.9 Exam I Wed, Sep 12

Class Date

2.1 Amino Acids Fri, Sep 14

2.2 Protein Properties Mon, Sep 17

2.3 Protein Structure Wed, Sep 19

2.4 Protein Function Fri, Sep 21

2.5 Enzyme Properties Mon, Sep 24

2.6 Enzyme Catalysis Wed, Sep 26

2.7 Enzyme Kinetics Fri, Sep 28

2.8 Workshop II Mon, Oct 01

2.9 Exam II Wed, Oct 03

Class Date

3.1 Metabolic Pathways Fri, Oct 05

3.2 Glucose Catabolism Mon, Oct 08

3.3 Glycogen Metabolism Wed, Oct 10

3.4 Lipid Catabolism Fri, Oct 12

3.5 Protein Catabolism Mon, Oct 15

3.6 Krebs Cycle Wed, Oct 17

3.7 Oxidative Phosphorylation Mon, Oct 22

3.8 Workshop III Wed, Oct 24

3.9 Exam III Fri, Oct 26

Class Date

4.1 Nucleotide Properties Mon, Oct 29

4.2 Nucleotide Metabolism Wed, Oct 31

4.3 Nucleic Acids Fri, Nov 02

4.4 DNA Replication Mon, Nov 05

4.5 RNA Transcription Wed, Nov 07

4.6 RNA Translation Fri, Nov 09

4.7 Gene Regulation Mon, Nov 12

4.8 Workshop IV Wed, Nov 14

4.9 Exam IV Fri, Nov 16

Module 2: PROTEINS and ENZYMES

Module 3: METABOLISM and ENERGY Module 4: DNA and RNA

Class 0.1: Introduction Mon, Aug 20

Retake Exams: 1 | 2 | 3 | 4 Mon, Dec 03

J: MoWeFr => 5:00pm—6:15pm @ LC120

K: MoWeFr => 6:25pm—7:40pm @ LC120

Exam

Session

Regular Exam[a]

(Mandatory)

Makeup Exam[b]

(if needed)

Retake Exam[c]

(Optional) Date Time Location

I 1 N/A N/A Wed, Sep 12

3:00pm-4:30pm (ODS)

5:00pm-6:00pm (J)

6:25pm-7:25pm (K)

ODS

LC120

LC120

II 2 1 N/A Wed, Oct 03

3:00pm-4:30pm (ODS)

5:00pm-6:00pm (J)

6:25pm-7:25pm (K)

ODS

LC120

LC120

III 3 2 N/A Fri, Oct 26

3:00pm-4:30pm (ODS)

5:00pm-6:00pm (J)

6:25pm-7:25pm (K)

ODS

LC120

LC120

IV 4 3 N/A Fri, Nov 163:00pm-4:30pm (ODS)

5:00pm-6:00pm (J)

6:25pm-7:25pm (K)

ODS

LC120

LC120

V N/A 4 1 | 2 | 3 | 4 Mon, Dec 033:00pm-4:30pm (ODS)

5:00pm-6:00pm (J)

6:25pm-7:25pm (K)

ODS

LC120

LC120

[a] Each exam will be digitally administered via the Blackboard and last exactly 60min

[b] A makeup exam will be offered in the subsequent session only along with the regular exam—if making up an exam,

students will be required to take the regular exam @ 5:00pm and the makeup exam @ 6:25pm

[c] Only ONE of the regular exams can be retaken during Session V

REGULAR EXAMS: ITINERARY

CLASS SWITCHING

K J switch Not Allowed Students who must make KJ switch on an

occasional basis in order to avoid a conflict

must request permission to do so in-person

or over a phone call at least 24 hours prior to

that class. Requesting permission via email

will automatically result in the request being

denied!

J K switch Allowed JK switch is not only allowed but also

strongly encouraged due to extra seating

available in the latter class. No prior

permission is required.

J/K double-dip Allowed Students willing to attend both classes back-

to-back are welcome and encouraged to do

so provided that the seating is not an issue.

No prior permission is required.

LECTURE CLASSES

- At the end of each of 29 lecture classes, students will be provided with a 4-min quiz

comprised of 10 true/false statements (extra time for those registered with the ODS)—

each of these statements will reflect the ability of students to comprehend and engage

in the lecture material presented during that class

- Students must bring their mobile devices, such as a laptop or tablet, with them to each

class in order to log into the Blackboard and take the quiz

- Students will be awarded one point for every correct answer—ie a maximum score of

10 points/quiz

- At the end of 29 lecture classes, only the top 20 best quiz scores for each student will

be aggregated toward the overall score—with a maximum score of 200 (20*10) points

for the entire Quiz Challenge

- Such strategy will provide ample flexibility—ie students may skip without a penalty up

to a maximum of NINE quizzes due to: [1] excused absences (eg due to sickness,

interviews, and events); [2] classes that overrun allotted time (eg due to technical

issues or extended discussions during the lecture); and [3] any other reasons (which

need not be justified).

- The Quiz Challenge will contribute 20% to the FINAL GRADE in the form of what is

being referred to herein as Exam 0—the other 80% will be contributed by FOUR

regular exams (Exams 1-4)

NON-LECTURE CLASSES

In addition to delivering lectures, the class time will also be used to accomplish the

following two goals of the course:

Workshop Classes—

After the completion of an heptad of lectures within each module of the course, the

students will be provided with a 60-min practice test (simulated exam) to take in

their own time prior to the Workshop class. Each practice test will be comprised of

50-multiple choice questions, which will be representative of what the students can

expect to tackle in the regular exam. In the Workshop class, the students can

discuss their practice test questions or any lecture material that they wish to do so.

Exam Classes—

Each module of the course will culminate with an exam class wherein students will

be presented with a 60-min regular exam comprised of 50-multiple choice

questions in order to assess and grade their ability to understand and comprehend

the biochemical knowledge on their own without help from anyone; unless there is

a technical issue (eg login or device failure), students must NOT raise their hands

to ask for any help whatsoever with exams questions—and—they are expected to

understand and comprehend the biochemical language used to set up the

question and select the correct response exclusively on their own.

REGULAR EXAMS: The Format

- Each of the four modules (Modules 1-4) of the course will be assessed by a separate exam—ie there will be a total of FOUR regular exams (Exams 1-4), with Exam 1 corresponding to the content of Module 1 and so forth

- To accommodate the needs of all students, a total of FIVE exam sessions (Sessions I-V) will be made available during the semester

- Each exam will be administered immediately after the completion of each module of the course—students unable to take an exam, due to sickness or otherwise, will be provided with an alternative opportunity to do so at the next scheduled exam session (eg Sessions II-V)

- Each exam will be comprised of 50 multiple-choice questions with a maximum score of 200 (50*4) points and designed to be completed in 60 minutes—an additional 30 minutes will be provided to students who are registered with the Office of Disability Services (ODS)

- Unless there is a requirement for the provision of a separate room, students registered with ODS are expected to take each exam along with the rest of the class at each scheduled exam session

REGULAR EXAMS: MAKEUP and RETAKE

- Should one miss a regular exam, they will be provided with an opportunity in the subsequent exam session to undertake the makeup exam—students will be required to take BOTH the regular exam and the makeup exam back-to-back in a single session (2 x 60min)!

- Additionally, all students will be provided with an opportunity to retake any ONE of the regular exams (Exams 1-4) during Exam Session V—so that they can redeem themselves should they perform poorly (or below their expectations) in one of the regular exams

- For a regular exam that is attempted TWICE (ie retaken), the higher score from either attempt will be carried forward toward the FINAL GRADE—iestudents will not be penalized for making a lower score on a retake exam!

- The opportunity to retake an earlier exam is a PRIVILEGE extended to all students—but it is ultimately each student’s responsibility to make additional time available for studying as well as retaking an exam

REGULAR EXAMS: INSTRUCTIONS

- All students are expected to abide by the Honor Code—students should not

receive or provide help from any source during an exam and any irregularities

witnessed must be reported to the proctor(s) and to the Honor Council

- All personal devices such as cell phones and calculators must be switched off and

put away—ditto for personal belongings such as bags that must be neatly tucked

away under the desk

- Each of the FOUR exams will be administered electronically, or digitally, via the

Blackboard—detailed instructions on taking digital exams are provided at:

Blackboard => Assessments => Regular Exams

- Each exam will require the installation of Respondus Lockdown Browser on each

student’s digital device such as a laptop or a tablet—it is the student’s

responsibility to thoroughly familiarize with the use of Respondus browser so that

inadvertent errors can be avoided during an exam

- Unless there is a technical issue (eg login or device failure), students must NOT

raise their hands to ask for any help whatsoever with exam questions—and—they

are expected to understand and comprehend the biochemical language used to

set up the question and select the correct response exclusively on their own

GRADING SCHEME

SCORE = (Exam0 + Exam1 + Exam2 + Exam3 + Exam4)

- The FOUR regular exams (Exams 1-4) along with the overall quiz score (Exam 0) will each carry a maximum of 200 points—ie the final SCORE will be =< 1000 points

- All exams (Exams 0-4) will be weighted equally—ie each exam will account for 20% toward the final SCORE (=< 1000 points)

- The final letter grades will be assigned from the final SCORE (=<1000 points) according to the distribution shown on the right—though these boundaries may be slightly altered depending on the mean value of the final SCORE for all students

- A projected GRADE based on the student’s current (or cumulative) score will be dynamically made available via the Blackboard right from the get-go—ie as soon as the quiz is submitted after the completion of Class 0!

- Grades of “Incomplete (I)” will NOT normally be given, and “Retroactive Withdrawals” will not be supported—the only reason for an incomplete grade might be due to an accident or a serious illness that befalls a studentwith an otherwise good standing

950 A+ 1000

900 A < 950

850 A- < 900

800 B+ < 850

750 B < 800

700 B- < 750

650 C+ < 700

600 C < 650

550 C- < 600

0 F < 550

Biochemistry—

Schaum’s Easy

OutlinesFirst Edition (2011)

Philip Kuchel • Gregory Ralston

TEXTBOOK—First Choice (One-Semester)

Highly Recommended—but

all the material needed will

be comprehensively covered

in the lecture slides!

Highly streamlined—144 pages!Cheap—about $10!

BiochemistryFirst Edition (2016)

T A Brown

TEXTBOOK—Second Choice (Two-Semester)

Recommended—but all the material needed will be

comprehensively covered in the lecture slides!

Highly focused—500 pages!Economical—under $100!

Fundamentals of

BiochemistryFifth Edition (2016)

Donald Voet • Judith Voet • Charlotte Pratt

TEXTBOOK—Third Choice (Four-Semester)

Recommended—but all the material needed will be

comprehensively covered in the lecture slides!

Overly detailed—1000 pages!Expensive—over $200!

TEXTBOOK—To textbook or not!

- All the material is being comprehensively covered in the lectures slides

- Accordingly, a textbook is recommended but it is not absolutely necessary

unless one requires further explanation/commentary on the material

presented in the lecture slides

- Students should review the lecture slides first and then decide for

themselves whether they feel the need for a textbook as an additional

supplement—some students may find that the slides are much easier to

understand than the textbook, while others may prefer to use the textbook!

- It should however be noted that the Voet textbook essentially covers a four-

semester biochemistry course (12 credits)!

- On the other hand, the lecture slides represent a curation of the most

fundamental biochemical concepts that can be easily digested within the

context of a one-semester course

- The material covered in the lecture slides amounts to more than about 50%

of the content of Voet textbook but in a streamlined manner!

HELP LINES

For any questions, queries, or concerns vis-à-vis BMB401, Professor Farooq can bereached as follows (in the order of his strong preference):

(1) Class—First-and-foremost, students are advised to get hold of Professor Farooqeither before (Sec-J) or after (Sec-K) each class on Mon|Wed|Fri

(2) Office—With an open-door policy, students are most welcome to stop by ProfessorFarooq’s office—Gautier Bldg #116 @ the Medical campus—anytime without aprior appointment though they are advised to call in advance to check hisavailability

(3) Phone—Students are also strongly encouraged to call Professor Farooq anytime @786-763-1294—an exclusive number established for the BMB401 students (noother phone number must be used!)—to discuss class material or any othermatters that require his prompt attention

Please keep the following points in mind:- Communication via email must be avoided at all costs- When communicating with Professor Farooq, students are advised to address

him as such—students should avoid uncourteous salutations such as “HiDoctor” or “Hi Professor”!

Exercise 0.1a

- What are the four modules of BMB401?

- What is Exam 0? What %age of overall score does Exam 0 carry?

- What is a retake exam? Can one retake any exam? If so, when?

- Can one switch between Sections J and K? Is prior permission required?

- What is the total number of class quizzes available? What is the minimum number of class quizzes that one must take without forfeiting a score?

- What is the best way to contact Professor Farooq? Should email be used as a communication channel?

Section 0.1b:

Basic Concepts

Common Functional Groups and Linkages I

Common Functional Groups and Linkages II

(Carbamoyl)

Phosphorus Compounds

Phosphoryl

group R

Phosphate

group R

Hydrogen

phosphate

(HPO42-) H

Inorganic

phosphate

(PO43-)

Under physiological conditions (pH ~ 7), inorganic phosphate (PO4

3-), often denoted as Pi in textbooks, only exists in the protonated form called hydrogen phosphate (HPO4

2-)—ieif a textbook calls for Pi as one of the

reactants, it has to be in its protonated form!

HPO42- PO4

3- + H+

pK = 12

O O

|| ||

R1—C—O—C—R2Anhydride[without hydride(H-)—two acyl

groups bonded together via an O

atom]

Comparison of Complex Bonds

O

||

R2—C—O—R1Ester[acyl group bonded to an R

moiety via an O atom]

O

||-O—P—O—R1

|

O-

Phosphoester[phosphoryl group bonded to

an R moiety via an O atom]

Thioester[acyl group bonded to an R

via an S atom]

O

||-O—C—S—R1

O O

|| ||

—O—P—O—P—O—

| |

O- O-

Phosphoanhydride[two phosphoryl groups bonded

together via an O atom]

(1) (2)

(3)

(4)

(1) Phosphoanhydride

(2) Phosphoanhydride

(3) Phosphoester

(4) N-glycosidic

ATP

O

||

R2—O—P—O—R1

|

O-

Phosphodiester[phosphoryl group bonded to

two R moieties via O atoms]

Mono- and Dicarboxylic Acids

1:1

Formate

(Methanoate)

-

2:1

Acetate

(Ethanoate)

-

3:1

Propionate

(Propanoate)

-

4:1

Butyrate

(Butanoate)

-

5:1

Valerate

(Pentanoate)

-

2:2

Oxalate

(Ethanedioate)

--

3:2

Malonate

(Propanedioate)

- -

4:2

Succinate

(Butanedioate)

--

5:2

Glutarate

(Pentanedioate)

- -

Monocarboxylate Anions

Dicarboxylate Dianions

Atomic Distances

- In biochemistry, the atomic distances are usually expressed in the units of Angstrom (Å):

1 Å = 10-10 m

but 1 nm = 10-9 m

and 1 pm = 10-12 m

thus 1 Å = 0.1 nm = 100 pm

- Knowledge of the metric system is central to understanding biochemistry!

Anders Ångström(1814-1874)

The Metric System Prefixes

Kilo 103 Thousand

Mega 106 Million

Giga 109 Billion

Tera 1012 Trillion

Peta 1015 Quadrillion

Exa 1018 Quintillion

Milli 10-3 Thousandth

Micro 10-6 Millionth

Nano 10-9 Billionth

Pico 10-12 Trillionth

Femto 10-15 Quadrillionth

Atto 10-18 Quintillionth

Biological Polymers

Polypeptide

Polysaccharide Polynucleotide

- Biological molecules are subject to natural selection—thus imparting upon living organisms an inherent ability to adapt to environmental pressures

- Such natural selection usually occurs at genomic level—iemutations in the DNA sequence—but often manifests itself in the form of altered proteins and other molecules

“Adapt” and “adopt” are not synonymous:

Adapt—“to change/adjust”—eg the ability to adapt to environment is a key to success!

Adopt—“to take on/up”—eg the protein adopts a 3D fold under physiological conditions!

Natural Selection

Common Latin Jargons

in vitro “in glass” — studies conducted in a test tube

in vivo “in living (body)” — studies carried out inside living organisms

ex vivo “outside living (body)” — studies executed on cultured cells outside an organism

in situ “on site” — studies performed on site (in place); eg examining an organ while it is still attached to the body after it has been sacrificed

in silico “in silicon (computer)” — studies performed on a computer (microchips are largely comprised of silicon—a semiconductor metal)

vide infra “look below” — see below

vide supra “look above” —see above

ad nauseum “to nausea (sickness)” — something that is repetitively discussed or mentioned to the point of sickness!

Hypothesis vs Theory vs Law

Hypothesis

A plausible statement/opinion/observation that needs to be tested

thoroughly

—eg the enzyme is only active in the presence of Mg2+ ions

Theory

A principle that has been thoroughly tested and applied

—eg theory of evolution

Law

A fundamental rule that is universally true

—eg law of gravitation

Exercise 0.1b

- What are the common functional groups in organic chemistry?

- What is an organic anhydride? What is the difference between a phosphodiester bond and a phosphoanhydridelinkage?

- Write out the chemical structures of simple monocarboxylate anions and dicarboxylate dianions?

- Express one Ångstrom (Å) in the units of meter (m). How many Ås are there in one nanometer (nm)?

- Write the names of three common biopolymers