Bio200b:  Biological Molecules        Spring 2004

 

Robert Fairman

rfairman@haverford.edu

Sharpless 311, x4205

 

Date

Lecture

Readings

Lab

January

19

Review of functional groups

 

 

Handout

Ch. 2 (Lodish) pp. 14-22

Review Ch. 1 (GG)

  Experiment 1:

Graphics exercise exploring structure of hemoglobin

 

 

  Project 1:

Protein structural analysis

21

 

Amino acids and the peptide bond

 

Ch. 4 (GG) pp 68-81, 85-88

 

23

 

Protein structure & motifs

 

 

Ch. 5 (GG) pp. 113-137

Supplementary reading:

Ch. 3 (L) pp. 51-60

26

 

Protein stability & folding

 

 

Ch. 1 (GG) pp. 13-18

Ch. 5 (GG) pp. 136-151

Supplementary reading

Ch. 2 (L) pp. 22-26

 

 

  Experiment 2:

Fibrin clot formation

See Ch. 12 (GG) pp 396-397 for additional background

28

 

Hemoglobin:

Structure/function relationships

Ch. 12 (GG) pp. 402-405

30

 

Hemoglobin:

Regulation and allostery

 

Ch. 12 (GG) pp. 405-411

February

2

Hemoglobin:

Principles in molecular evolution

Ch. 6, Section 3: Chemical Evolution (Voet & Voet, 2nd Edition)

 

 

  Experiment 3:

Fibrin clot analysis by SDS-PAGE

4

 

Enzymes:

Catalysis

 

Ch. 10 (GG) pp. 320-332

6

 

Enzymes:

Regulation

 

Ch. 10 (GG) pp. 334-358

9

 

Enzymes:

Mechanism

 

Ch. 11 (GG)

 

 

  Experiment 4:

Bioinformatics studies of globin sequences

11

 

Metabolism:

Basic concepts

 

Ch. 3 (GG) pp. 51-66

Ch. 14 (GG) pp. 438-448

13

 

Metabolism:

Glycolysis

 

Ch. 15 (GG)

Supplementary reading:

Ch. 16 (L) pp. 616-622

Mid-Quarter Exam Due:  Monday, February 16 at 5:00 PM

 

  Experiment 5:

Lactate dehydrogenase: purification and concentration determination

February

16

 

Metabolism:

Citric acid cycle

 

Ch. 16 (GG)

Supplementary reading:

Ch. 16 (L) pp. 622-630

18

 

Metabolism:

Oxidative phosphorylation

 

Ch. 17 (GG)

Supplementary reading:

Ch. 16 (L) pp. 632-648

20

 

Photosynthesis

 

 

Ch. 18 (GG)

Supplementary reading:

Ch. 16 (L) pp. 649-664

23

 

Carbohydrate structure

 

 

Ch. 7 (GG) pp. 205-231

 

 

  Experiment 6:

Lactate dehydrogenase: measurement of specific activity

25

 

Glycoproteins and Proteoglycans

 

Ch. 7 (GG) pp. 232-239

Supplementary reading:

Ch. 22 (L) pp. 989-993

27

 

DNA building blocks

Structural hierarchy Š from the double helix to chromatin

Ch. 8 (GG) pp. 241-253, pp. 275-281

Supplementary reading:

Ch. 4 (L) pp. 101-108

March

1

DNA replication

 

 

Ch. 23 (GG) pp. 722-736

Supplementary reading:

Ch. 4 (L) pp. 111-113

 

 

Discussion

 

Project 2:

Protein misfolding & disease

3

 

Central Dogma:

Transcription and RNA polymerase

Ch. 24 (GG) pp. 761-769

5

 

Central Dogma:

Prokaryotic transcriptional regulation

Ch. 24 (GG) pp. 769-776

  Final Exam Due:  Thursday, March 18 at 5:00 PM

REQUIREMENTS

 

A. EXAMS - There will be two timed take-home exams.  Each exam will be worth 35% of your quarter grade for the lecture.  The penalty for turning an exam in late will be 3 points for missing the deadline.  The last exam will not be cumulative but will only cover the material presented subsequent to the mid-quarter exam.  You should expect  the exam to take about 2 hours (however we will allow you 3 hours).

 

B. PROBLEM SETS - There will be three graded problem sets and appropriate study guides to assist you in preparing for the exams.  They will be graded on a scale of 7-10.  The penalty for turning in an assignment late will be 1 point for missing the deadline and an additional point for each extra day that it is late.  The graded problem sets will be collectively worth 30% of your quarter grade for the lecture component of the course and are due on the following dates at 5:00 PM:

                  Problem Set 1: proteins and hemoglobin                           Due Feb. 6th (Fri)

                  Study Guide 1: enzymes

                  Problem set 2: metabolism:                                                          Due Feb. 23rd (Mon)

                  Study Guide 2: photosynthesis

                  Study Guide 3: carbohydrates

                  Problem set 3: DNA structure, replication,

                                                      central dogma                                                      Due Mar. 5th (Fri)

 

C. TEXTS - We will use Garrett & GrishamÕs Principles of Biochemistry with a Human Focus as a primary text but supplementary readings will be given from Lodish's Molecular Cell Biology as well to help provide a cohesive connection to other quarters.  You will not be held responsible for the supplementary reading material on exams.

 

D. LECTURE NOTES - My notes will be available on the Blackboard course web site.  You will find links to my notes, and other suggested readings, from the Bio200 web page as we move through the semester.  The links will be available through the syllabus.

 

E. LABORATORY - This quarter's laboratory will focus on techniques important for protein structure, function, and purification.  In addition, the proteins selected for study will help to reinforce important concepts learned in lecture such as in the lectures on metabolism and enzyme catalysis through studies of lactate dehydrogenase.  As such, you may find questions in the exams that will be drawn from the pre-lab lectures and experimental findings.

 

F. BIOLOGY QUESTION CENTER - The Bio Question Center will be available again this semester.  The schedule will be posted on the Web as it becomes available.  Currently, we expect that the Question Center will be available on Wednesdays and Sundays.  Please contact Emily Nietrzeba (email:  enietrze) regarding any questions.

 

G. GUIDED LEARNING GROUP - The GLG will also be available again this semester.  You may contact Katie Hart (email:  khart) for any questions about scheduling.

 

H. LAB TA's - TBA