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CHEM-UA 881 Biochemistry I

Spring 2015
Lectures: Tuesday, Thursday 4:55-6:10. GCASL C95
Recitations: Sections by registration (see following page)
Required textbook
Matthews, Van Holde, Appling and Anthony-Cahill Biochemistry 4th Edition Pearson,
2013. (MVAA)

Optional additional textbook:


Petsko G and Ringe D Protein Structure and Function, New Science Press. (PR)
This primer presents material that we cover with superb pictures and short but
very clear text. It is an excellent addition to the main textbook.
Faculty:
Kent Kirshenbaum, Department of Chemistry, Room 821 Silver
Email: kent@nyu.edu Telephone: (212) 998-8486
Recitations:

Miguel Perreira
Sabrine Obbad
Jon Kwok

miguel.pereira@nyu.edu
sio206@nyu.edu
jgk298@nyu.edu

Recitation Sections

Section Name
101 Pereira
102 Obbad
103 Pereira
104 Pereira
105 Kwok
106 Pereira

Schedule
Tuesday
2:00 PM to 3:15 PM
Thursday
6:20 PM to 7:35 PM
Tuesday
6:20 PM to 7:35 PM
Thursday
8:00 AM to 9:15 AM
Monday
9:30 AM to 10:45 AM
Thursday
3:30 PM to 4:45

Location
Meyer 261
194 Mercer
Room 308
GCASL 388
Waverly 569
Meyer 261
25W4th C-9

Kirshenbaum office hours:


Silver Building, 8th Floor lab, Monday 4:30-6:00 PM, or by
appointment
General information. This course is a one semester introduction to biochemistry
suitable for majors and professional school requirements. The course introduces
biological macromolecules, including the structure and function of proteins, nucleic
acids, carbohydrates, lipids and membranes. Transport, enzyme mechanisms and
elements of gene action in prokaryotes are discussed. An introduction to
metabolism is presented, emphasizing tools for analysis rather than memorization of
pathways. The course and syllabus for this Spring semester course are designed to
be consistent with the Biochemistry I course offered in Fall by Prof. Kallenbach.
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 150 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.)
Recitation and projects. An additional 150 points will be awarded for non-exam work.
(i) There will be a quiz or problem set to be completed in each recitation, worth a total
of 100 points over the semester (ii) 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. (iii) An additional 50 points are assigned to a project
report, covering an enzyme involved in a metabolic pathway. Detailed instructions for
the report will be provided during the semester.
Activity

Points

Midterm 1

100

Midterm 2

100

Final exam

150

Recitation problem sets and


quizzes

100

Project report

50

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. NYU policy on plagiarism will be enforced with
great vigil. Students who fail to conform to NYUs 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 inform yourself of our policy:
http://cas.nyu.edu/page/academicintegrity
Learning Center Help:
Free peer tutoring, Study Slams, group reviews, workshops, and more.
University Learning Center
www.nyu.edu/ulc
ULC@Academic Resource Center, 18 Washington Place, Lower LevelULC@UHall,
110 East 14th Street, top of stairs by UHall Commons
Soomie Han, J.D.
Assistant Dean
Academic Support Services
Director, University Learning Center
NYU College of Arts & Science

SCHEDULE OF LECTURES
Lecture
Date

Jan. 27 T
1, Jan. 29
R

TOPIC

RECITATION

Snow Day
Overview & Introduction
Matrix of Life

2, Feb. 3 T Bioenergetics
TOOLS: Electrophoresis
3, Feb. 5 R Proteins I Amino acids &
polypeptides
TOOLS: Expression and
purification of proteins
4, Feb. 10
Proteins II Structure and
T
folding
TOOLS: Proteomics
5, Feb. 12
Protein function and
R
evolution
TOOLS: Immunological
methods
6, Feb. 17
Carbohydrates
T
7, Feb. 19
Lipids, membranes and
R
transport
TOOLS: Techniques for
membrane studies
8,Feb. 24 T Enzymes I Kinetics and
mechanism
TOOLS: How to measure rates
Engineering enzymes
Enzymes: II Inhibition and
9, Feb. 26
Regulation
R
Mar. 3 T
MIDTERM 1 - Ch. 2, 3, 5-10
10, Mar. 5
R

READING

Chemical Logic of
Metabolism
TOOLS: Radio-isotopes
Metabolomics

Ch. 1,2

Ch. 3

Rec. 1

Ch. 5

Ch.6
Rec. 2
PR 1-3 to 1-9
Ch.7, 8
PR 1-2 114,1-15, 1-20
Ch. 9

Rec. 3

Ch. 10
PR1-11

Ch. 11
PR 2-6, 2-13

Ch. 11, 12
PR 2-8,
3-11,12,13

Ch. 12

Rec. 4

11 Mar. 10
T

Carbohydrate metabolism
TOOLS: Protein-protein
interactions
12, Mar. 12 Gluconeogenesis
R
13 Mar 24T TCA cycle

Ch. 13
PR 3-18

14 Mar. 26
R

Ch. 15, 18

Oxidative phosphorylation
Coordination of energy
metabolism
Signal Transduction

15, Mar.
31, T
16, Apr. 2, DNA Intro
TOOLS: Manipulating DNA
R
18 Apr. 7 T MIDTERM EXAM II
Ch. 11-15, 18
17 Apr. 9,
DNA replication
TOOLS: PCR
R
18, Apr. 14 DNA restructuring
T
19, Apr. 16 RNA synthesis & processing
R
I
TOOLS: Footprinting
Mapping start sites
20, Apr. 21 RNA synthesis & processing
T
II
TOOLS: DNA microarrays
Chromatin Immunoprecipitation
21, Apr. 23 Protein synthesis I
R
22, Apr. 28 Protein synthesis II
T
23, Apr. 30 Control of gene expression I
R
24, May 5
Control of gene expression II
TOOLS: Mapping complex
T
structures
26, May 7
Review
R
May 13-19 FINAL EXAM comprehensive
Tuesday, 5/14 subject to
verification

Rec. 5

Ch. 13
Ch. 14

Ch. 23

Rec. 6

Ch. 4

Ch. 25
Ch. 26

Rec. 7

Ch. 27

Ch, 27

Rec. 8

Ch. 28
Ch. 28

Rec. 9

Ch. 29
Ch. 29

Ch. 25-29

REVIEW