Course Syllabus
C3501/W4501 — Biochemistry:
Structure and Metabolism
Fall 2007
Dr. Liang Tong, 701 Fairchild Bldg, lt133@columbia.edu, 854-5203
Dr. Brent Stockwell, 614 Fairchild Bldg, bs2198@columbia.edu, 854-2948
Class room: Math 207
Class time: Tuesday and Thursday 2:40-3:55 pm
Recitations: TBA
In
this course, we will cover subject matter in biochemistry, organic chemistry and
structural biology. We will discuss the structure and function of both proteins
and small molecules in biological systems. Proteins are the primary class of
biological macromolecules and serve to carry out most cellular functions. Small
organic molecules function in energy production and creating building blocks
for the components of cells and can also be used to perturb the functions of
proteins directly.
The
first half of the course will cover protein structure and enzyme kinetics. The
second half of the course will explore how small molecules are used
endogenously by living systems in metabolic and catabolic pathways; this course
will focus on the mechanistic organic chemistry involved in metabolic pathways. The course is intended to provide a
foundation of structural biology, bio-organic chemistry and biochemistry and to
expose students to some emerging areas of research.
There
will be eight quizzes, one midterm and one final. Grades will be
assigned based on class participation, quizzes, the midterm and the final.
Prerequisites: one year of college-level biology and one year of organic
chemistry, or the instructor’s permission.
Required
Optional
|
Date |
Lecture # |
McMurry chapter (optional) |
Stryer Chapter (required) |
Topic |
|
|
|
|
|
Part 1:
Proteins in Biology |
|
Sept. 4 |
1 |
|
1, 4 |
Introduction |
|
Sept. 6 |
2 |
|
1, 8.2,
15.1-3 |
Thermodynamics and biochemical interactions |
|
Sept. 11 |
3 |
|
2 |
Amino acids, the building blocks of proteins |
|
Sept. 13 (Q) |
4 |
|
2 |
The three-dimensional structures of proteins I |
|
Sept. 18 |
5 |
|
2 |
The three-dimensional structures of proteins II |
|
Sept. 20 (Q) |
6 |
|
3 |
Experimental methods for studying proteins |
|
Sept. 25 |
7 |
|
8 |
Enzyme kinetics |
|
Sept 27(Q) |
8 |
|
9 |
Enzyme mechanism |
|
Oct. 2 |
9 |
|
10 |
Enzyme regulation |
|
Oct. 4 (Q) |
10 |
|
7, 14 |
Functional diversity of proteins |
|
Oct. 9 |
11 |
|
11, 12 |
Lipids, membranes, carbohydrates |
|
Oct. 11 |
12 |
|
6 |
Protein sequence analysis and other topics |
|
Oct. 16 |
|
|
|
Mid-term |
|
|
|
|
|
Part 2: Small
Molecules in Biology |
|
Oct. 18 |
1 |
1,2 |
|
Review of organic chemistry in biology |
|
Oct. 23 |
2 |
4 |
16 |
Glycolysis |
|
Oct. 25 |
3 |
4 |
16 |
Glycolysis continued |
|
Oct. 30 (Q) |
4 |
4 |
17 |
The TCA cycle |
|
Nov. 1 |
5 |
4 |
17 |
The TCA cycle |
|
Nov. 8 (Q) |
6 |
|
18 |
Oxidative phosphorylation |
|
Nov. 13 |
7 |
|
18 |
Oxidative phosphorylation
|
|
Nov. 15 (Q) |
8 |
|
26 |
Biosynthesis of membrane lipids and steroids |
|
Nov. 20 |
9 |
|
26 |
Biosynthesis of membrane lipids and steroids |
|
Nov. 27 |
10 |
|
24 |
Amino acid metabolism |
|
Nov. 29 (Q) |
11 |
|
27 |
Integration of metabolism |
|
Dec. 4 |
12 |
|
Articles on Courseworks |
Cell death |
|
Dec. 6 |
13 |
|
35 |
Drug discovery |
Q: A quiz will be given at the
end of the lecture on that day