Syllabus | Fall 2016

BMB401 | 3-Credit

BIOCHEMISTRY for the

BIOMEDICAL SCIENCES

AMJAD FAROOQ PhD DIC

Department of Biochemistry

Miller School of Medicine

University of Miami

Miami, FL 33136

Office: Gautier Building #116

Email: profamjadfarooq@gmail.com

Phone: 786-763-1294

Website: http://farooqlab.net

The aims of BMB401 are to: (1) Provide students with an in-depth understanding of the structure and

function of biomolecules such as proteins, carbohydrates, lipids, and nucleic acids from a biochemical perspective

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

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

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

AIMS and GOALS

BMB401 is divided into FOUR parts*: (1) CARBS and LIPIDS—biochemical properties and cellular functions of

carbohydrates and lipids, including an overview of thermodynamics and biochemical signaling

(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 particular emphasis 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 is used to direct protein synthesis and cellular processes

*Each part is equally weighted and comprised of six 75-min lectures—ie a total of

24 lectures during the semester—slides for each lecture are available for download @ http://farooqlab.net

COURSE CONTENT

CLASS SCHEDULE Part 1: CARBS and LIPIDS

Lecture Date Topic

1.1 Aug 22 (Mon) Thermodynamics

1.2 Aug 24 (Wed) Monosaccharides

1.3 Aug 29 (Mon) Polysaccharides

1.4 Aug 31 (Wed) Lipids

1.5 Sep 07 (Wed) Membrane Transport

1.6 Sep 12 (Mon) Biochemical Signaling

Lecture Date Topic

2.1 Sep 14 (Wed) Amino Acids

2.2 Sep 21 (Wed) Protein Sequence

2.3 Sep 26 (Mon) Protein Structure

2.4 Sep 28 (Wed) Protein Function

2.5 Oct 03 (Mon) Enzyme Catalysis

2.6 Oct 05 (Wed) Enzyme Kinetics

Lecture Date Topic

3.1 Oct 10 (Mon) Metabolic Pathways

3.2 Oct 17 (Mon) Glucose Catabolism

3.3 Oct 19 (Wed) Glycogen Metabolism

3.4 Oct 24 (Mon) Noncarb Metabolism

3.5 Oct 26 (Wed) Citric Acid Cycle

3.6 Oct 31 (Mon) Oxidative Phosphorylation

Lecture Date Topic

4.1 Nov 02 (Wed) Nucleotides

4.2 Nov 09 (Wed) Nucleic Acids

4.3 Nov 14 (Mon) DNA Replication

4.4 Nov 16 (Wed) RNA Transcription

4.5 Nov 28 (Mon) RNA Translation

4.6 Nov 30 (Wed) Gene Regulation

Part 2: PROTEINS and ENZYMES

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

Sec-J Mon/Wed @ 5:00pm—6:15pm # LC170

Sec-K Mon/Wed @ 6:25pm—7:40pm # LC170

CLASS ATTENDANCE (Exam 0)

- Of the 24 lectures, students are required to attend all!

- Absence due to sickness, or otherwise, must be supported by a document

- For each lecture, class attendance will be digitally registered—students will be required to log into the Blackboard to confirm their physical presence at the end of each lecture

- Students must bring their mobile devices—such as a laptop or tablet—with them to each lecture so that they can register their attendance

- Students will be awarded 4 points for every lecture that they attend—ie 96 points for all 24 lectures

- A bonus of 4 points will be awarded to all students–such that they can potentially obtain a perfect attendance score of 100 points at the end of the semester

- Class attendance 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)

FORMAT of REGULAR EXAMS (Exams 1-4)

- Each of the four parts (Part 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 Part 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 usually administered about a week after the completion of each part 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 (or a later) scheduled exam session (eg Sessions II-V)

- Each exam will be comprised of 50 multiple-choice questions 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)

- Students registered with ODS—for an additional 50% time request (but no other requirements)—are expected to take each exam along with the rest of the class at each scheduled exam session

MAKEUP and RETAKE EXAMS

- Should one miss a regular exam, zhe 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—ie students 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!

zhe a gender-neutral pronoun used herein for she/her and he/him

REGULAR EXAM 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 under the EXAMS folder @ the Blackboard

- 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 each student’s responsibility to thoroughly familiarize with the use of Respondus browser so that inadvertent errors can be avoided during an exam

- Students wishing to review the questions/answers after the administration of a

particular exam must do so in-person with Professor Farooq at his office in Gautier Bldg #116 (Medical campus)

GRADING SCHEME

FINAL SCORE (%) = (Exam0 + Exam1 + Exam2 + Exam3 + Exam4) / 5 - The FOUR regular exams (Exams 1-4) along with the class attendance score (Exam

0) will each carry a maximum of 100 points

- All exams (Exams 0-4) will be weighted equally—ie each exam will account for 20% toward the FINAL SCORE

- The final letter grades will be assigned from the

FINAL SCORE 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

- 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 student with an otherwise good standing

95 A+ 100

90 A < 95

85 A- < 90

80 B+ < 85

75 B < 80

70 B- < 75

65 C+ < 70

60 C < 65

55 C- < 60

50 D+ < 55

45 D < 50

0 F < 45

EXAM SESSIONS

Exam

Session

Regular Exam[a]

(Mandatory)

Makeup Exam[b]

(if needed)

Retake Exam[c]

(Optional)

Date

Time

Location

I Exam 1.1 N/A N/A SEP 19 (Mon) 5:00pm-6:15pm (J)

6:25pm-7:40pm (K)

LC170

II Exam 2.1 Exam 1.2 N/A

OCT 12 (Wed) 5:00pm-6:15pm (J)

6:25pm-7:40pm (K)

LC170

III Exam 3.1 Exams 2.2 N/A

NOV 07 (Mon)

5:00pm-6:15pm (J)

6:25pm-7:40pm (K)

LC170

IV Exam 4.1 Exams 3.2 N/A

DEC 05 (Mon) 5:00pm-6:15pm (J)

6:25pm-7:40pm (K)

LC170

V N/A Exams 4.2 Exam 1.3

Exam 2.3

Exam 3.3

Exam 4.3

TBD 5:00pm-6:15pm (J)

6:25pm-7:40pm (K)

LC170

[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—students will be required to take

BOTH the regular exam and the makeup exam back-to-back in a single session (2 x 60min)!

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

HELP LINES

For any questions, queries, or concerns vis-à-vis BMB401, Professor Farooq can be reached as follows (in the order of his strong preference): (1) Class—First-and-foremost, students are advised to get hold of Professor Farooq

either before or after each class on Mondays or Wednesdays

(2) Office—With an open-door policy, students are most welcome to stop by Professor Farooq’s office—Gautier Bldg #116 @ the Medical campus—anytime without a prior appointment though they are advised to call in advance to check that he is not out of office

(3) Phone—Alternatively, students are strongly encouraged to call Professor Farooq anytime @ 786-763-1294—an exclusive number established for the BMB401 students (no other phone number must be used!)—to discuss class material or any other matters that require his prompt attention

(4) Email—As a last resort, and only if absolutely necessary, students are also welcome to email Professor Farooq but only at profamjadfarooq@gmail.com—messages sent to any other email address will be automatically DELETED!

When communicating with Professor Farooq, students are advised to address him as such—students should avoid uncourteous salutations such as “Hi Doctor” or “Hi Professor”!

Biochemistry First Edition (2016)

T A Brown

TEXT BOOK (First Choice)—not yet released!

Recommended—but all the material needed will be

comprehensively covered in the lecture slides!

Highly focused—500 pages! Economical—only $80!

Fundamentals of

Biochemistry Fifth Edition (2016)

Donald Voet • Judith Voet • Charlotte Pratt

TEXT BOOK (Second Choice)

Recommended—but all the material needed will be

comprehensively covered in the lecture slides!

Overly detailed—1000 pages! Expensive—over $250!