[PDF] CHEM-UA 881 Biochemistry I - NYU Arts & Science

30006_7Biochem1Spring2020Syllabus.pdf

CHEM-UA 881 Biochemistry I

Spring 2020

Lectures: Tuesday, Thursday 12:30-1:45.

Location: 12 Waverly, Room G08

Recitations: Sections by registration, beginning on week 2 Required textbook: Miesfeld & McEvoy, Biochemistry, Norton. 1 st Edition. You are strongly encouraged to obtain a copy of the textbook that allows access to online "Smartwork5" problems from the publisher's website. Optional additional textbook: Petsko G and Ringe D Protein Structure and Function, New Science Press. This textbook presents material that we cover with superb pictures and short but very clear text. It is an excellent addition to the main textbook.

Instructors:

Prof. Kent Kirshenbaum, Department of Chemistry, Room 821 Silver

Email: kent@nyu.edu

Office Hours: Fridays from 2:00 to 3:30

Prof. Paramjit Arora, Dept. of Chemistry, Room 360 Brown

Email: arora@nyu.edu

Office Hours: Wednesdays, 2:30-4 PM

Clinical Faculty, Recitation Leader:

Dr. Rohini Qamra, Department of Chemistry, Room 1001U Silver

Email: qamrar01@nyu.edu

Office Hours: Fridays 12:30-1:30 PM

Class website: This course is on NYU Classes. Notes, readings, problem sets, study guides, modules and web links as well as answers to problems will all be posted on the web. General information. This course is a one-semester introductio n to biochemistry suitable for majors and meeting professional school requirements. The course introduces the important families of biological macromolecules, including proteins, nucleic acids, carbohydrates, and lipids. The relationship between sequence, structure and function of biopolymers is a central focus. Mechanisms of enzymatic catalysis and signal transduction are featured. There is an emphasis on the flow of information in biological systems at the molecular level, described as "The Central Dogma". A brief introduction to metabolism is prese nted, empha sizing general concepts rather than memorization of pathways.

Recitation Sections

Section Instructor Time Location

101 Dr. Rohini Qamra M 11-12:15 25W4-C10

102 Dr. Rohini Qamra M 12:30-1:45 25W4-C8

103 Dr. Rohini Qamra M 2:00-3:15 25W4-C10

106 Dr. Rohini Qamra M 9:30-10:45 25W4-C13

Grades and Exams: Your course grade will be determined in part by scores on four examinations. There will be three midterm exams and one final. The lowest midterm exam grade will be dropped. As a consequence, you are permitted one absence from a midterm exam for any reason whatsoever. There is no necessity for make-up midterm exams, and none will be given. There will be no excused or unexcused absences for a second mid-term exam. Students who do not take the final exam as scheduled without a documented and approved excuse will result in an automatic grade of 0 for the final.

Exam Regrade Policy:

• Do not make any marks on the exam. • On a separa te, ha nd-signed cover sheet stapl ed to th e exam, list your email address, state the problems that were misgraded, and affirm that no changes to the exam were made after grading. • Submit the regrade request no later t han the subseque nt recitation to the recitation leader. • Arithmetic errors in adding up points will be corrected immediately. Any other regrade request will cause the entire exam to be regraded; therefore, your overall score may increase or decrease. • Oral or late requests for regrading will not be accepted. Recitation Quizzes. An addi tional 20% of the course grade will be awarded for performance in recitati on sections. Recitations will review the lecture s an d work on additional problems in peer-led groups. There will be a short quiz at the beginning of each recitation, featuring questions from that week's homework assignment. Please be sure that you have an assigned recitation section. Missing more than two recitations will result in a reduction of grade.

Activity Points

Two highest midterm exams 50%

Final exam 30%

Recitation: participation, homework problems and quizzes 20%

Total 100%

Academic Integrity and Plagiarism: The instructors for this course have no tolerance for plagiarism in any form. The NYU policy on plagiarism will be enforced with great vigil. Students who fail to conform to NYU's standards on academic integrity will be subject to stringent disciplinary action ("pour encourager les autres"). Inform yourself in advance of proper academic conduct. In brief (and quoting from the College of Arts & Science policy), "Academic honesty means that the work you submit - in whatever form - is original." When in doubt, ask. Please consult: http://cas.nyu.edu/page/academicintegrity Disabilities: New York University provides accommodations for qualified students with disabilities. To ensure that the most appropriate accommodations are provided, students should contact the Moses Center for Students with Disabilities (212-998-4980). Special needs for the lecture or exams should be brought to attention of the instructor by no later than September 25. If accommodations are needed, students must register with CSD (see http://www.nyu.edu/students/communities-and-groups/students-with- disabilities/how-to-register.html for more information). If you wait until the exam date is approaching to register with CSD or to inform the instructor, we may be unable to provide appropriate accommodations. Learning Center Help: Free peer tutoring, Study Slams, group reviews, workshops, and more. ULC@Academic Resource Center, 18 Washington Place, Lower LevelULC@UHall, 110 East 14th Street, top of stairs by UHall Commons.

SCHEDULE OF LECTURES

Lecture,

Date

Lecturer

Topic Reading Recitation

1. Jan 28 T

KK Overview & Introduction: The

Central Dogma,

Biopolymers,

Sequence/Structure/Function

Ch. 1

No recitation

2. Jan 30 R

KK Bioenergetics &

Thermodynamics

Sec. 2.1, 2.2

Water as a Biomolecule

3. Feb. 4 T

PA Proteins I - Amino Acids &

Polypeptides

Sec. 4.1

Rec. 1

4. Feb. 6 R

PA Proteins II - Secondary

Structures

Sec. 4.2

5. Feb. 11 T

KK Proteins III - Tertiary and

Quaternary Structure;

Protein Folding & Misfolding

Sec. 4.3 Rec. 2

6. Feb. 12 R

KK Proteins IV: Methods.

Purification, Structure

Determination, Antibodies

Ch. 5

7. Feb. 18 T

PA Proteins V: Functions.

Transport, Hemoglobin,

Allostery, Motor Proteins

Sec. 6.1, 6.2,

6.4

Rec. 3

8. Feb. 20 R

PA Proteins VI: Introduction to

Enzymes,

Structure/Function

Relationships

Sec. 7.1, 7.2

Feb 21 F

Midterm 1 Lectures 1-7

9. Feb. 25 T

PA Proteins VII: Enzyme

Mechanisms & Kinetics

Sec. 7.3, 7.4

Rec. 4

10. Feb. 27 R

PA Proteins VIII: Enzyme

Regulation: Inhibition and

Allostery

Sec. 7.5

11. Mar. 3 T

KK Lipids & Membranes

Sec. 15.1-15.3

Rec. 5

12. Mar. 5 R

KK Membrane Proteins,

Membrane Transport, Cell

Signaling

Sec. 15.4, 6.3,

8.1-8.3

13. Mar. 10 T

PA

Carbohydrates I 13.1 Rec. 6

14. Mar. 12 R

PA

Carbohydrates II:

Polysaccharides and

Glycoproteins

13.2, 13.3

15. Mar. 24 T

PA

Metabolism I TBD Rec. 7

16. Mar. 26 R PA Metabolism II TBD

Mar. 27 F

Midterm 2 Lectures 8-14

17. Mar. 31 T

PA

Metabolism III TBD Rec. 8

18. Apr. 2 R

PA Nucleic Acids I: DNA

Structure

Sec. 3.1, 3.2

19. Apr. 7 T

KK

Nucleic Acids II: Methods Sec. 3.3 Rec. 9

20. Apr. 9 R

KK Nucleic Acids III: Replication

& Repair

Chap. 20

21. Apr. 14 T

KK Nucleic Acids IV:

RNA Structure & Functions

Sec. 21.1 Rec. 10

22. Apr. 16 R

KK Nucleic Acids V: RNA

Synthesis & Processing

Sec. 21.2, 21.3

23. Apr. 21 T

KK Protein Synthesis I: The

Genetic Code

Sec. 22.1 Rec. 11

24. Apr. 23 R

KK Protein Synthesis II:

Translation & the Ribosome

Sec. 22.2

Apr. 24 F

Midterm 3

Lectures 15-

22

25. Apr. 28 T

PA Protein Synthesis III: Post-

translational Modifications &

Trafficking

Sec. 22.3 Rec. 12

26. Apr. 30 R

PA Control of Gene Expression

I: Prokaryotes

Sec. 23.1, 23.2

27. May 5 T

KK Control of Gene Expression

II: RNA interference &

Eukaryotic Gene Regulation

Sec. 21.4, 23.3 Rec 13

28. May 7 R

KK Review & The Future of

Biochemistry:

Synthetic Biology,

Crispr/Cas, Gene Editing

and the Fate of the Human

Species

May 18

FINAL EXAM - comprehensive

12pm-1:50pm; check

Albert for confirmation

T = Tuesday, R = Thursday, F = Friday