[PDF] Bc2013 Syllabus (8/13) - Arts & Science - NYU

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30006_7CHEM_UA882_BiochemII_Lupoli_Spr2020.pdf CHEM-UA 882 Biochemistry II

Spring 2020

Lectures: Monday, Wednesday 11:00-12:15. Silver 206

Recitations: Sections by registration

Required textbook: Miesfield Biochemistry,

Norton. ISBN: 978-0-393-61402

Optional additional textbook:

Cox and Nelson,

Lehninger's Principles of Biochemistry, 7th

Edition, MacMillan, ISBN: 978
-1-464-187957

Handouts and

Journal articles will be posted on NYU Classes to supplement the textbook.

Instructors:

Prof. Tania Lupoli, Room: Silver 703

Email: tjl229@nyu.edu

Prof. Somdeb Mitra, Room: Silver 1001S

Email: sm7274@nyu.edu

Recitation Sections

Section Instructor

Schedule Location

101 Somdeb Mitra

Wednesday 9:30 AM to 10:45 AM

102 Somdeb Mitra

Wednesday

6:20 PM to 7:35 PM

103 Somdeb Mitra

Friday

9:30 AM to 10:45 AM

104 Somdeb Mitra
Friday

12:30 PM to 1:45 PM

General information. This course will introduce students to modern research topics in

Biochemistry and Chemical Biology.

The course

will build on the introductry topics o Biochemistry I and introduce natural and artificial appraoches to regulate gene expression, catalysis and metabolic synthesis.

SCHEDULE OF LECTURES

TL = Tania Lupoli; SM = Somdeb Mitra

Lecture,

Date

Instructor

conducting lecture

Topic

Reading

Miesfeld

(M) /Petsko (P)

Recitation

1. Jan. 27

M TL

Overview of course/DNA

Repair M: Ch 3, Ch

26

2, Jan.

29
W

TL Regulation of Gene Expression

1 [PTM, Antisense,

RNAi,]Gene Regulation

M: Ch 23;

Handouts

3, Feb. 3

M

TL Regulation of Gene

Expression

-2 [Lac, steroid hormones, small molecules that target DNA and histone modification]

M: Ch 23;

Handouts Rec. 1

4, Feb. 5

W

TL Regulation of Gene

Expression

-3 [CRISPR,

TALENS, Small Molecules]

Handouts

5, Feb. 10

M TL

The ribosome and the bacterial

cell wall as an antibiotics target

M: Ch 2.3;

22.1
-22.2;

Handout

Rec. 2

6, Feb. 12

W

TL Protein Structure (overview)

and Folding (Thermodynamics)

M: Ch 4.1-

4.2 Feb. 17 M

President's Day

- No Class

7, Feb. 19

W TL

Cellular protein chaperones

- 1

M: Ch 4.3

Handouts

Rec. 3

8, Feb. 24

M TL

Cellular protein chaperones

- 2 Handouts Rec. 4

9, Feb. 26

W

TL Cellular protein degradation

(proteases)

Handouts

Mar. 2 M

Midterm 1

Lectures 1-

8

10, Mar. 4

W

TL Synthesis of natural products:

PKS

Handouts

11, Mar. 9

M TL

Synthesis of natural products:

NRPS Handouts

12, Mar.

11 W

TL Chemical Genetics (kinase

specificity and targeting

M: Ch 8.3

handouts

Rec. 5

Mar 16

-22

Spring Break

13, Mar.

23 M

SM Chemical proteomics and

PROTACS

M: Ch 5.2;

Handouts

Rec. 7

14, Mar.

25 W

SM Review of basic organic

reactions in biochemistry/

Chemical Logic of Metabolism

Handout

Mar 27 F Midterm 2

Lectures 9-

14

15, Mar.

30 M
SM

Photosynthesis [MT2] M: Ch 12 Rec 8

16, Apr. 1

W SM

Carbohydrate Metabolism M: Ch 14

17, Apr. 6

M SM

Lipid Metabolism

-1

M: Ch 15-

16

Rec 9

18, Apr. 8

W SM

Lipid Metabolism

- 2 M: Ch 16

19, Apr.

13, M

SM

Amino Acid Metabolism 1 M: Ch 17 Rec 10

20 Apr.

15 W

SM/TL

Amino Acid

Metabolism 2

M: Ch 17

21, Apr.

20, M

SM

Nucleotide Metabolism 1 M: Ch 18 Rec 11

22, Apr.

22 W

SM

Nucleotide Metabolism 2 M: Ch 18

23, Apr.

27 M

SM

Metabolic Integration M: Ch 19 Rec 12

24, May.

29, W

SM

Metabolic Integration M: Ch 19

25, May 4

M

TL Protein channels and pumps

(metals)

Ch 6.3;

Handouts

Rec 13

26, May 6

W Metals in Biology [Prof.

Buccella]

Handouts

May 10-

16 FINAL EXAM - comprehensive

Date - subject to verification;

check Albert

M = Monday, W = Wednesday, F = Friday

Grades and Exams: Your course grade will be determined in part by scores on three in-class examinations. Two midterms will each be worth 100 points. The final exam will be cumulative, and will be worth 200 points. Please be aware that an unexcused absence from any exam results in a score of zero for that exam. (Please be sure that your excuses are from NYU student health, explaining specifically what condition prevented you from taking the exam.)

Exam Regrade Policy:

Do not make any marks on the exam. On a separate, hand-signed cover sheet stapled to the 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 within two days of receiving the graded exam.

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 additional 100 points will be awarded for quizzes conducted in recitation sections. Recitations will review the lectures and work on additional problems in peer-led groups. Please be sure that you have an assigned recitation section. Missing three or more recitations for any reason at all will result in an incomplete for the class. Team Presentations. To encourage you to start reading primary scientific literature, we will award another 100 points for a team presentation that discusses a modern research topic related to the course material. Each presentation should be 15 minutes long with 5 minutes for questions and answers and incorporate 4-5 primary research articles published after 1995 . Each presentation should expla in the significance of the work, delve deeply into the methodology and discuss its connection to the class. You will deliver this presentation in the recitaiton section together with your study partner. Each of you will be awarded equal points for the team presentation. The presentations will take place during the last 5 weeks of the class; more information will be provided in the recitation section.

Grading:

Activity Points

Midterm 1 100

Midterm 2 100

Final exam 200

Recitation quizzes 100

Presentations 100

Total 600

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. Academic Integrity and Plagiarism: The instructors for this course have no tolerance for plagiarism in any manifestation. 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. 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

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