Bio200b: Biological Molecules
Robert Fairman
rfairman@haverford.edu
Sharpless 311, x4205
Office hours: by appointment
|
Date |
Lecture |
Readings |
Lab |
|
January 17 |
Review of Functional Groups An introduction to basic building blocks in biology |
ECB Ch. 2 and Panels 2-1, 2-2, 2-5 |
Lab 1: Survey of web-based resources for macromolecular structures |
|
19 |
Protein function & structure Protein folding & stability |
ECB Ch. 4, pp. 119-143 Supplementary reading: G&G Ch. 5 |
|
|
24 |
Anfinsen experiment Hemoglobin: structure, function, allostery (globin evolution if time) |
Blackboard postings ECB pp 60, 209-210 G&G pp 398-409 V&V pp 190-191 |
Lab 2: Enzyme assay of salivary a-amylase |
|
26 |
Hemoglobin (cont'd) Introduction to enzymes |
ECB Ch. 3, pp
91-100 Supplementary reading: G&G Ch. 10.1-10.3 |
|
|
31 |
Enzyme kinetics, mechanism |
ECB Ch. 3, pp 101-105, 145-149 |
Experiment 3: Structural studies of hemoglobin using Protein Explorer |
|
February 2 |
Cell signaling and communication |
ECB Ch. 16, pp 533-546, 557-569 |
|
|
7 |
Integration of signaling and metabolism Basic chemical underpinnings in energy utilization |
ECB Ch. 16, pp 557-569 M&M, pp 192-196, 478-488 Suppl. reading available ECB Ch. 3, pp 83-91, 106-116 |
Experiment 4: Fibrin clot formation See Ch. 12
(G&G) pp 396-397 for additional background |
|
9 |
Glycolysis and citric acid cycle |
ECB Ch. 13 |
|
|
TAKE
HOME EXAM, AVAILABLE FEB. 2 & DUE FEB. 9 |
|||
|
Date |
Lecture |
Readings |
Lab |
|
14 |
Oxidative phosphorylation |
ECB Ch. 14, pp. 453-476 |
Experiment 5: Fibrin clot fractionation by SDS-PAGE |
|
16 |
Photosynthesis |
ECB Ch. 14, pp. 476-493 |
|
|
21 |
DNA structure and replication |
Rev. ECB Ch. 5, pp. 169-177 ECB Ch. 6, pp. 195-208 |
Experiment 6: Analysis of fibrin clot fractionation |
|
23 |
DNA recombination & repair Review of prokaryotic transcription |
ECB Ch. 6, pp. 209-224 ECB Ch. 7, pp. 234-236 ECB Ch. 8, pp. 267-272 |
|
|
28 |
Prokaryotic gene regulation |
ECB Ch. 8, pp. 272-275 G&G Ch. 24, pp. 762-776 |
Experiment 7: Gel shift analysis of lac repressor/lac operator complex |
|
March 2 |
IN
CLASS EXAM |
||
REQUIREMENTS
A. EXAMS - There will be two exams, the first will be a take-home exam and the second will be an in-class exam. Each exam will consist of multiple choice, short answer, and essay questions and is worth 35% of your quarter grade for the lecture component of the course.
Take-home exam: The exam has been designed to be about 2 hours long (however you will be allowed 3 hours). The exam is due on February 9 at 5 PM. The exam will be assessed a 10% penalty for each day that it is late.
In-class exam: Any essay questions will be a take-home component of this exam, and must be turned in with the remainder of the exam on March 3.
B. PROBLEM SETS - There will be four problem sets to assist you in studying for the exams. Two will be graded, and the remaining two must be turned in for full credit. The graded problem sets will each be worth 10% and the ungraded problem sets will each be worth 5%. The problem sets are due in class on the following dates:
Problem set 1: material thru hemoglobin lecture, due 1/31
Problem set 2: enzymes and cell signaling, due 2/9
Problem set 3: metabolism and photosynthesis, due 2/21
Problem set 4: from DNA structure to end of course, due 3/3
Problem sets will be assessed a 10% (1 pt) penalty for each day that they are late.
C. TEXTS - We will continue to use Essential Cell Biology (ECB; by Alberts, et al.). However, we will be exploring concepts in biochemistry more in depth this quarter and you'll find that Garrett & GrishamÕs Principles of Biochemistry with a Human Focus will be a particularly useful reference tool. Suggested readings from Garrett & Grisham (G&G) have been included in your syllabus above; you will find that they will complement the lectures and, on a few occasions, be more in depth, than ECB. Exams will be based only on lectures and ECB readings. Three copies of Garrett & GrishamÕs textbook will be on reserve in Sharpless library and some of the suggested readings will be posted on Blackboard. Handouts or postings on Blackboard from other texts will also be available.
D. LECTURE NOTES - Lecture notes will be posted on the Blackboard course web site after the material has been covered. The links will be available through the syllabus.
E. BIOLOGY QUESTION CENTER - The Bio Question Center will continue to be available this semester. The schedule will be announced in class and posted on Blackboard as it becomes available.
F. GUIDED LEARNING GROUP - The GLG will also be available again this semester. Meeting times to be announced in class and posted in Blackboard.