Chemistry 309: General Biochemistry I
The information below was updated in fall 2008
A. Course policies
TWThF 11:00 Ð 11:50, Parker 104
Office hours
My official office hours are Monday 10-12 and 1-2, and Thursday 10-11 and 12-2.
I will be happy to arrange for a different time to meet with you. To do that you can stop by my office and leave a note if IÕm not there, send me an email, or leave me a telephone message.
Office 230 Parker Hall; email zpasman@ic.edu; phone 245-3435.
Learning goals
Consistent with the Illinois College and the Chemistry Department mission statements (see the Illinois College catalog), you are expected to accomplish two broad learning goals in this course. First, you will learn to understand biochemical terms, concepts, and theories, and be able to interpret major scientific events, reports, and ideas from a biochemical perspective. Second, you will design, conduct, and interpret the results of experiments to solve biochemical problems, thereby developing independent positions supported by credible arguments.
Textbook
Biochemistry by R.H. Garrett and C.M. Grisham, 3rd edition, which should be at the bookstore.
This semester we will cover chapters 1-15. There are many excellent books that cover the same topics, and you are certainly welcome to use them if you wish. Ask me if youÕre not sure about your book. Great textbooks have been written by Voet and Voet, Mathews and van Holde, and Berg et al. (Stryer).
Lecture notes.
The lecture notes will be available on the web at the Chem 309 area at http://www2.ic.edu/pasman/. The lecture notes will be provided as pdf files.
Assignments
There will be four exams (dates indicated on the schedule below), each worth 100 points. The lab grade will be 25% of the final grade for the course.
Grading
90-100% A
80-89% B
70-79% C
60-69% D
+ and Ð grades are available. I do not anticipate using a curve, but I will do so if necessary. I will curve ÒupÓ but not Òdown.Ó
Attendance and Participation
You are expected to attend the lectures regularly. Material on the exams will be drawn heavily from the material covered in class, and, in general, regular attendance contributes to success in the course. Class participation is expected in the form of debating and answering questions. You are encouraged to ask questions during lectures.
Academic Honesty
I will prosecute any case of academic fraud or dishonesty that I can document. Academic dishonesty, simply put, is representing work as your own when it is not. Also, see the Illinois College honor code. If, in your judgment, an issue might be subject to academic honesty considerations, ask me for clarification as soon as possible, that is, before you might appear as if you acted dishonestly.
|
Week |
Material |
Chapter |
|
8/25 |
Introduction, biomolecules, cell organization, chemistry of water |
1,2 |
|
9/1 |
Chemistry of water, aqueous buffers, thermodynamics |
2,3 |
|
9/8 |
The three laws of thermodynamics |
3 |
|
9/15 |
Amino acids, protein function |
4 |
|
|
Wednesday, September 17, exam 1, Ch. 1-3 |
|
|
9/22 |
Protein structure and folding |
5,6 |
|
9/29 |
Protein structure and folding |
5,6 |
|
10/6 |
Protein structure and folding |
5,6 |
|
10/13 |
Carbohydrate structure and function |
7 |
|
|
Wednesday, October 15, exam 2, Ch. 4-7 |
|
|
10/20 |
Structure and function of lipids, fall break |
8 |
|
10/27 |
Membrane structure, transport across membranes |
9 |
|
11/3 |
Nucleic acids function, DNA structure |
10,11 |
|
11/10 |
DNA and RNA structure |
10,11 |
|
|
Wednesday, November 12, exam 3, Ch. 8-11 |
|
|
11/17 |
Enzyme kinetics and specificity |
13 |
|
11/24 |
Enzyme regulation, Thanksgiving break |
13,15 |
|
12/1 |
Catalytic mechanisms |
14,15 |
|
|
Thursday, December 11, 9-11, exam 4, Ch. 13-15 |
|
Experiments in Biochemistry, 2nd edition, by S.O. Farrell and L.E. Taylor.
For each experiment, you are responsible for the following:
(1) Answers to the pre-lab questions for the appropriate experiment, due before the lab period.
(2) Analysis of results, due by 5PM on the day following the lab period.
Your lab grade will be determined as follows:
Pre-lab questions 50%
Results analysis 50%
You are required to attend each lab session. Usually, it will be not be possible to make up the lab because of the preparation and supervision time involved, and you should make every effort to be in lab. If you cannot be in a particular lab session, please contact me beforehand.
During the lab period you are going to work in groups of 3-5, and results obviously will be shared within your group. You also may do the results analysis in groups, if you wish. You are expected, however, to work out the pre-lab questions on your own. If, in your judgment, an issue might be subject to academic honesty considerations, ask me for clarification as soon as possible.
|
Week |
Experiment |
|
9/1 |
1. Use of pipettors |
|
9/8 |
2. Preparation of buffers |
|
9/15 |
3. Beer's law and standard curves |
|
9/22 |
4a. Purification of LDH I |
|
9/29 |
no lab scheduled |
|
10/6 |
4a. Purification of LDH II |
|
10/13 |
3a. Protein concentration of LDH fractions |
|
10/20 |
Fall Break |
|
10/27 |
5. Separation and identification of amino acids |
|
11/3 |
5a. Purification of LDH by ion exchange chromatography I |
|
11/10 |
5a. Purification of LDH by ion exchange chromatography II |
|
11/17 |
6a. Purification of LDH by affinity chromatography I |
|
11/24 |
Thanksgiving break |
|
12/1 |
6a. Purification of LDH by affinity chromatography II |