Chemistry 310: General Biochemistry II

This course is a direct continuation of CH 309. We will continue investigating how protein and nucleic acid structures are suited for their function and concentrate on the regulation of catalyzed reactions. To demonstrate these principles, we will discuss representative allosteric regulatory systems. We then will utilize the ideas we’ve explored to examine the well-studied system of carbohydrate metabolism. Finally, we will discuss chemical information transfer and utilization, as well as the regulation of these processes, as evidenced in DNA replication, RNA transcription, and protein translation. Three class hours and one three hour lab per week. Prerequisite: Chem 309.

The information below was updated for spring 2008

I. Course policies

Lecture MWF 9:00-9:50, Parker 104

lab M 2:00-4:50 or Th 11:00-1:50, Parker 240

Office hours

My official office hours are M 1-2, W 1-3, F 10-12, 1-2.

I will be happy to arrange for a different time to meet with you. To do that you may stop by my office and leave a note if I’m 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 three 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 an independent position supported by credible arguments. Third, you will clearly and effectively present biochemical information both written and oral in a manner appropriate to the relevant audience.

Textbook

Biochemistry by R.H. Garrett and C.M. Grisham, 3rd edition.

This semester we will discuss the material in chapters 13-21 and 28-30. There are many excellent books that cover these topics, and you are certainly welcome to use them if you wish. Ask me if you’re not sure about your book. Excellent textbooks have been written by Berg et al., Voet and Voet, and Mathews and van Holde.

Lecture notes

The lecture notes will be available on the web at the Chem 310 area at http://www2.ic.edu/pasman/. The lecture notes will be provided as .pdf files.

Assignments

Exams: There will be two take-home exams (dates indicated on the syllabus), each worth 100 points. The final will be the American Chemical Society Biochemistry exam, and will be worth 100 points.

Presentation: You are responsible for presenting one research paper in class. Your presentation should take about 20 minutes with 10 additional minutes for questions and answers. Your presentation is worth 100 points. Students who are not presenting will prepare three questions relevant to the presented papers (one question each on the results, methods, and discussion sections of each paper). These questions will be worth 100 points. Copies of your paper should be made available to students at least a week in advance. Also see the paper presentation guidelines below.

Grading

90-100% A

80-89% B

70-79% C

60-69% D

The lab grade will be 25% of the final grade for the course. I do not anticipate using a curve, but I will do so if necessary. I will curve “up” but not “down.” A “Plus” or “minus” grade modification can be assigned.

Attendance and Participation

You are expected to attend class regularly. The material on the exams will be drawn heavily from the material covered in class, and, in general, those who attend class regularly benefit more from 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.

Lab

Lab is mandatory for this class. Lab attendance is mandatory and an unexcused lab absence will result in the removal from the course and assignment of a “W” grade. See lab syllabus and description.

II. Lecture syllabus

Week	Topic	Chapter
1/14	Binding kinetics with more than one substrate, catalysis	13,14
1/21	Enzyme mechanisms of catalysis	14
1/28	Enzyme specificity and regulation, allostery, hemoglobin	15
2/4	Molecular motors	16
	Friday, February 8, exam 1, ch. 13-16
2/11	Introduction to metabolism, glycolysis	17,18
2/18	Glycolysis	18
2/25	Krebs cycle	19
3/3	Electron transport and oxidative phosphorylation	20
3/10	Photosynthesis	21
3/17	Spring break
3/24	Photosynthesis	21
	Friday, March 28, Exam 2, ch. 17-21
3/31	DNA replication, recombination, and repair	28
4/7	Transcription mechanisms	29
4/14	RNA processing, translation	30
4/21	Student presentations	-
4/28	Student presentations	-
	Saturday 5/3, final exam, 9-11A.

III. Lab description

Lab manual

Experiments in Biochemistry, 2nd edition, by S.O. Farrell and L.E. Taylor.

Assignments

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.

Grading

Your lab grade will be determined as follows:

Pre-lab questions 50%

Results analysis 50%

Attendance

You are expected 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.

Academic honesty

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 analyze the results 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.

IV. Lab syllabus

Week	Experiment	Title
1/21	8	Enzyme kinetics of tyrosinase
1/28	6	Affinity chromatography preparation
2/4	6	Affinity chromatography of LDH
2/11	8a	Enzyme kinetics of LDH
2/18	8a	Enzyme kinetics of LDH
2/25	10a	Western blot of LDH
3/3	10a	Western blot of LDH
3/10	11	DNA restriction endonucleases
3/17		Spring break
3/24		Spring break
3/31	11	DNA restriction endonucleases
4/7	13	Polymerase chain reaction
4/14	13	Polymerase chain reaction
4/21	12	Cloning of PCR fragments
4/28	12	Expression of PCR fragments

V. Guidelines for research paper presentations

It is your responsibility to pick and present a paper of your choice, although you should discuss the paper and topic with me in advance. Your paper should address a biochemical problem on the molecular and/or atomic level(s). You are expected to demonstrate knowledge of the topic, methods, and conclusions of the paper. Copies of your paper must be made available to students at least one week in advance.

1. Introduction. You should address the background of the study. The Introduction section of the paper usually addresses:

-Data that are accepted as valid, and form the basis for what is known about the issue at hand.

-The main problem(s) addressed in the paper.

-Reasons why the authors consider the question(s) yet unanswered.

2. Results. You should present the experiments the authors performed. It is a good idea to focus on the experiments that are presented in the Figures. There may not be enough time to present all these experiments. Rather than talk about all the experiments superficially, pick a few key ones that really nail down the issue and discuss each one in depth. You should discuss:

-The key experiments that were performed.

-The results obtained.

-How the experiments were performed (refer to the Materials and Methods section).

-How the results can be interpreted vis-à-vis the issues brought up in the Introduction.

3. Discussion. You should present:

-How the experimental results address/resolve the main question in the paper.

-How the authors interpreted the results.

-What new contributions were made to the question brought up in the Introduction.

-Your opinions regarding the conclusions reached in the paper – do you think the authors’ interpretations were correct, were the results over-interpreted, what aspects of the question remain unresolved?