Biology 493V Syllabus
(3/1/2007)

 

Date

Topic

Homework Due:  (Reading; Problems)

1/8

Introduction

 

1/10

Software & the Protein Data Bank;
Amino Acids: intro and conventions

Chapter 1; download software for class;
Begin phi/psi model for next week!

1/12

Amino acids: pKa’s and chemical properties; Backbone Conformations

supplemental readings: pKa’s (Creighton 1.0-1.3; 1.7); study your amino acids

 

 

 

1/15

Martin Luther King Jr. Holiday

 

1/17

Amino Acids: χ1 and Side-Chain Conformations (hands-on)

eCampus Reading: “On the Other Hand”

Review p. 10; (HW problems TBA)

1/19

Amino Acid Quiz

Side-Chain Conformations, cont’d

Chapter 2 pp. 13-26; Review p. 8-10;
Simple 3D, physical phi/psi model (due)

 

 

 

1/22

Secondary Structures

 

Display & Color exercise due

1/24

Secondary Structures hands-on exercise

Chapter 2 pp.  26-33

1/26

Secondary Structure Motifs

 

 

 

 

1/29

3-D Structure: stabilizing forces

supplemental reading: (Whitford)

1/31

Forces, continued;

3-D Motifs: Alpha Structures

Chapter 3 pp. 35-46
HW Problems Due

2/2

3-D Motifs: Alpha/Beta Structures

Chapter 4 pp. 47-66

 

 

 

2/5

3-D Motifs: Beta Structures

Chapter 5 pp. 67-88

2/7

Exam 1

 

2/9

Protein Classification

eCampus readings: SCOP and CATH

 

 

 

2/12

Determining Structures: X-ray Crystallography

Chapter 18 pp. 373-386

begin Quaternary Structure MiniProject

2/14

X-ray crystallography, continued

eCampus: “Dumb Luck & Crystals” article

2/16

Finish x-ray topics

X-ray HW probs due

 

 

 

2/19

Review “x-ray” HW;

Begin NMR Spectroscopy

Chap. 18 pp. 387-392

2/21

NMR, continued

eCampus:  Wuthrich article

2/23

Mini Projects peer (pre)view

NMR homework problems due
Quaternary Struct. Mini Projects due

 

 

 

2/26

Mini Projects peer review

 

Revised Mini-Project diagrams due

2/28

X-ray vs. NMR: discussion & hands-on

X-ray vs. NMR comparison due

3/2

Fibrous Proteins

Chapter 14: pp. 283-298
X-ray vs. NMR hands-on due
Begin fibrous prot. Mini Project

 

 

 

3/5

Fibrous Proteins, continued
Membrane Proteins

 

3/7

Review HW; Membrane Proteins, continued

Chapter 12 pp. 223-248

3/9

Membrane Proteins; Begin Enzymes

Mini Project Due (Fibrous Proteins)
Chapter 11 pp. 205-215

 

 

 

3/12

Enzymes

Chapter 11 pp. 215-222
Membrane Protein HW problems due

3/14

Enzymes, continued

Trypsin HW problems due

3/16

Guest lecture: Ken Blemings

Protein choices + reference due*

 

 

 

3/19

Exam 2

 

3/21

Begin Immune System Proteins

Chapter 15

3/23

Immune System, continued

Continue collecting references for project

 

 

 

3/24-4/1

Spring Recess

 

 

 

 

4/2

Structure Prediction & Design

Chapter 17 (continued over next few days)

4/4

Structure Prediction & Design

Outline of paper; List of Questions due*

4/6

WVU Holiday

 

 

 

 

4/9

Structure Prediction; hands-on
Begin Protein Folding

Continue work on Major Project

4/11

Protein Folding

Finish Structure Prediction hands-on, TBA

Chapter 6; eCampus:  Silent Mutation article

4/13

Protein Folding

Chapter 6, continued

 

 

 

4/16

Catch-up Day

Rough drafts due today.*

4/18

Work Day; No Class (office hours!)

Pick up rough drafts today.

4/20

Example of a Presentation:  Brazzein, a Sweet-Tasting Protein

Final Draft of Paper Due

 

 

 

4/23

Student Presentations

Papers due*

4/25

Student Presentations

 

4/27

Student Presentations

 

 

 

 

5/4 (FRI)

FINAL EXAM, 11:00am - 1:00pm

Plan your travel NOW—no rescheduling.