Chemistry 791B Fall 2001
9/6/01 Working course outline: updates found at
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.
Instructor: Lynmarie Thompson (thompson@chem.umass.edu, 5-0827)
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 exercises/homework
25% for final presentation
Prerequisites: Introductory Biochemistry, Sophomore Organic
|
Date |
Topic |
Assignment |
|
|
Sept 6 |
Thursday |
Forces underlying structure |
B & T Chapter 1, Creighton Ch 4 |
|
Sept 11 |
Tuesday |
Backbone conformations: secondary structure |
B & T Chapter 2 |
|
Sept 13 |
Thursday |
RNA/protein: Ribosome Wayne Decatur |
Review translation (any biochemistry text) |
|
Sept 18 |
Tuesday |
Motifs, topology diagrams |
B & T Chapter 2 |
|
**Sept 19 |
Wed 4 pm LGRT 101 |
MCB seminar: Peter Moore, Chemistry, Yale University |
|
|
Sept 20 |
Thursday |
Tertiary structures: Alpha |
B & T Chapter 3 |
|
Sept 25 |
Tuesday |
CRC: Protein Explorer |
Assignment 1: due 10/2 |
|
Sept 27 |
Thursday |
Tertiary structures: Alpha/beta |
B & T Chapter 4 |
|
Oct 2 |
Tuesday |
CRC: Protein Explorer Rasmol refcard |
Assignment 2: due 10/11 |
|
Oct 4 |
Thursday |
Tertiary structures: beta |
B & T Chapter 5 |
|
Oct 9 |
Tuesday |
CRC: Homology modeling Kelcy Newell |
Tamm paper |
|
**Oct 9 |
Tues 4 pm LGRT 101 |
MCB seminar: Lukas K. Tamm, University of Virginia "Structure, Folding and Insertion of b-Barrel Membrane Proteins" CANCELLED |
|
|
Oct 11 |
Thursday |
Protein Folding Lila Gierasch |
B & T Chapter 6 Crieghton 7.4-7.5 |
|
Oct 16 |
Tuesday |
CRC Workshop: Presentation topics |
|
|
Oct 18 |
Thursday |
Solving structures: NMR Joanna Swain |
G. Wider (2000) Biotechniques 29, 1278. |
|
**Oct 22 |
Mon 4 pm LGRT 101 |
MCB seminar: Venki Ramakrishnan, MRC, Cambridge "Decoding the Message: Structural Basis for tRNA Selection by the Ribosome" |
|
|
Oct 23 |
Tuesday |
CRC Workshop Eric Martz |
|
|
Oct 25 |
Thursday |
CRC Workshop Eric Martz |
(turn in pdb id and copy of primary reference) |
|
Oct 30 |
Tuesday |
CRC: Chime presentations Craig Martin |
Exam 1, due 11/6 9:30am Q2Mono, Q2Dimer |
|
Nov 1 |
Thursday |
Craig Martin |
B & T Chapter 7 |
|
Nov 6 |
Tuesday |
CRC: Homology modeling Kelcy Newell |
Exam 1 due 9:30am! |
|
Nov 8 |
Thursday |
Craig Martin |
B & T Chapter 8, 9, 10 |
|
Nov 13 |
Tuesday |
Membrane proteins |
B & T Chapter 12-13 |
|
Nov 15 |
Thursday |
Membrane proteins |
|
|
Nov 20 |
Tuesday |
Solving structures: x-ray Bill Royer |
Ch 18 & Crystallography Made Crystal Clear |
|
**Nov 20 |
Tues 4pm LGRT 101 |
MCB seminar: Bill Royer, UMass Worcester "Structural diversity in quaternary assembly and allosteric mechanisms of cooperative hemoglobins" |
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Nov 22 |
Thursday |
No class -Thanksgiving |
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Nov 27 |
Tuesday |
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Nov 29 |
Thursday |
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Dec 4 |
Tuesday |
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Dec 6 |
Thursday |
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Dec 11 |
Tuesday |
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Dec 13 |
Thursday |
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** Plan to attend these seminars of special interest if at all possible.
Other ribosome papers of interest: Muth et al, Polacek et al