Biomolecular Structure - Chemistry 791B Fall 2002
The overall goal of this course is to understand macromolecular structures in biology. Traditional lectures will present concepts in structure, including the physical basis for structure and stability, molecular interactions, and design. We will also have computer workshops using Protein Explorer and other public domain software for manipulating macromolecules in three dimensions. Finally, each student will present an oral presentation taking the class on a WEB-based tour of the structure of a chosen biomolecule, illustrating principles learned throughout the course, and relating them to the biological function.
Instructor: Lynmarie Thompson (thompson@chem.umass.edu, 5-0827, LGRT 403E)
Meetings: Tu/Thu 9:30-10:45 in GSM 51 or CRC
Text: Introduction to Protein Structure (2nd ed), by Carl Branden & John Tooze,
plus selected readings from other sources including
Proteins: Structures and Molecular Properties, by T. Creighton
Crystallography Made Crystal Clear, by Gale Rhodes
Grading: 50% (25% each) for 2 take-home exams (to be completed independently -- NO DISCUSSIONS)
25% for class participation & homework, 25% for final presentation
Prerequisites: Introductory Biochemistry, Sophomore Organic Chemistry
|
Date |
Topic |
Assignment |
|
|
Sept 5 |
Thursday |
Forces underlying structure |
B & T Ch 1, Creighton Ch 4 |
|
Sept 10 |
Tuesday |
Forces underlying structure - continued |
|
|
Sept 12 |
Thursday |
Secondary structure, Motifs, Topology diagrams |
B & T Chapter 2 |
|
Sept 17 |
Tuesday |
Tertiary structures: alpha |
B & T Chapter 3 |
|
Sept 19 |
Thursday |
CRC: Protein Explorer |
Assignment 1: due 9/24 |
|
Sept 24 |
Tuesday |
Tertiary structures: alpha/beta |
B & T Chapter 4 |
|
Sept 26 |
Thursday |
CRC: Protein Explorer Rasmol refcard |
Assignment 2: due 10/1 |
|
Oct 1 |
Tuesday |
Tertiary structures: beta |
B & T Chapter 5 |
|
Oct 3 |
Thursday |
CRC: Chime presentations |
Download Chimeshell |
|
Oct 8 |
Tuesday |
Protein Folding |
B & T Chapter 6 |
|
**Oct 8 |
Tues 4 pm 319 Morrill |
MCB seminar: Andrew Miranker, Yale University "Causes and Consequences of Protein Misfolding in Type II Diabetes and End Stage Renal Failure" |
|
|
Oct 10 |
Thursday |
CRC: Chime presentations |
Presentations scheduled (turn in pdb id and primary reference) |
|
Oct 15 |
Tuesday |
Protein Folding |
TIBS review, Creighton 7.4-7.5 |
|
**Oct 15 |
Tues 4 pm 319 Morrill |
MCB seminar: David Christianson, Univ of Pennsylvania "Zinc Enzymes and Membrane Function: Structures and Mechanisms of Carbonic Anhydrase XII and LpxC" |
|
| Oct 17 | Thursday |
Solving structures: NMR Joanna Swain |
Assigned paper |
|
Oct 22 |
Tuesday |
CRC Workshop: |
Assignment 3: due 10/29 |
|
Oct 24 |
Thursday |
CRC Workshop: ConSurf Eric Martz |
|
| Oct 29 | Tuesday |
CRC: Homology modeling Kelcy Newell
|
Homology modeling paper |
|
Oct 31 |
Thursday |
CRC: Homology modeling Kelcy Newell |
Exam 1 distributed |
|
Nov 5 |
Tuesday |
Craig Martin |
B & T Chapter 7 |
|
Nov 7 |
Thursday |
Craig Martin |
B & T Chapter 8, 9, 10 Exam 1 due 9:30am! |
|
Nov 12 |
Tuesday |
B & T Chapter 12-13 |
|
|
Nov 14 |
Thursday |
Membrane proteins |
MPLinks |
|
Nov 19 |
Tuesday |
CRC Workshop |
|
|
Nov 21 |
Thursday |
Solving structures: x-ray William Royer UMass Medical School |
Ch 18 & Crystallography Made Crystal Clear |
|
Nov 26 |
Tuesday |
Signal transduction modules |
Exam 2 distributed B&T Chapter 13 |
|
Nov 28 |
Thursday |
No class -Thanksgiving |
|
|
Dec 3 |
Tuesday |
Protein structure prediction and evolution |
B&T Chapter 17 |
|
Dec 5 |
Thursday |
Protein engineering |
Exam 2 due 9:30am! papers: engineering |
|
Dec 10 |
Tues |
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Dec 12 |
Thursday |
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** Plan to attend these seminars of special interest.