Course Syllabus

 

C3501/W4501 — Biochemistry: Structure and Metabolism

 

Fall 2007

 

Dr. Liang Tong, 701 Fairchild Bldg, [email protected], 854-5203

Dr. Brent Stockwell, 614 Fairchild Bldg, [email protected], 854-2948

 

Class room: Math 207

Class time: Tuesday and Thursday 2:40-3:55 pm

 

Recitations: TBA

 

Course Description and Prerequisites

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.

 

Reading Material

Required

  1. Berg, Tymoczko and Stryer, “Biochemistry, 6th Ed.,” Freeman and Co., New York, 2006.

 

Optional

  1. McMurry and Begley, “The Organic Chemistry of Biological Pathways,” Robert and Company, Englewood, Colorado, 2005.

 


 

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