Biomolecular Structure - Chem 791B/C

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This new course combines two previous courses, Protein Structure and Function and Nucleic Acids Chemistry, into a single, modular course. The overall theme of the course is understanding macromolecular structures in biology. Traditional lectures will present concepts in structure, including the physical basis for structure and stability, molecular interactions, and design. The course will also make extensive use of public domain structural databases and software tools for obtaining and viewing structures, including the WEB. A Friday workshop will include hands-on tutorials.

Most students will sign up for the full 4 credits. If you have already taken one of the earlier courses, or have an interest in only one of the modules, contact one of the instructors for more information.
Prerequisites: Introductory Biochemistry, Sophomore Organic
Course No. 120756/122797
Date Ch* Workshops
Tue 8:30am CRC, 113 		Lectures
Tue/Thu 9:30am, LGRT 113
Jan 28
4

Course organization / Forces ... structure (snowed out!)
30
6

Critical analysis of structures: X-ray crystallography data (Bill Royer)

Feb 4

6
Forces ... structure lecture Critical analysis of structures: NMR derived (Sukumar Mupalla)
6
4

Forces underlying macromolecular structure
11
5
Finding/viewing structure data Conformational properties of proteins - secondary structure
13

Conformational properties (continued)
18
Monday schedule - no class Monday schedule - no class
20
6

Folded conformations of proteins - tertiary structure
25
Viewing structures Tertiary structure (continued)
27
7

Proteins in solution and in membranes
Mar 4
Structure prediction & alignment (...continued, Stacy Ciufo)
6

Mechanisms in protein folding (Lila Gierasch)
11
Viewing structures Protein folding (Lila Gierasch - continued)
13
8

Interactions with ligands and other macromolecules
18
spring break - no class spring break - no class
20

spring break - no class
25
BT
Authoring structural models Survey of protein structural motifs
27

including evolutionary aspects
Apr 1
Case Studies - Proteins Nucleotide Chemistry
3

Base-base interactions
8
DNA/RNA Modeling Helical structures: A,B,Z,...
10

Helix substructure, water, ions
15
Nucleic Acid MOdeling Tool Groove interactions, drugs, triplex structures
17

RNA structures, ribozymes
22
Case Studies - DNA/RNA/proteins DNA twisting, kinking, bending, looping
24

Protein-DNA interactions
29
presentations Student Presentations:
May 1

Ä Present structure of a protein/DNA (coords from PDB)
6
presentations Ä Identify common structural motifs within the structure
8

Ä Relate sequence conservation to structure
13
presentations Ä Relate biochemical data to structure
Ä Summarize structure/ function relationships
Grading3 exams (25% each), individual presentation (15%), exercises (10%)
*Texts: Proteins, 2nd Ed., Thomas E. Creighton (Chapters indicated above)
Introduction to Protein Structure, Carl Branden & John Tooze (BT above)
Nucleic Acids in Chemistry & Biology, G. Michael Blackburn and Michael J. Gait
Instructors:Lynmarie Thompson 1323J LGRT X5-0827 Thompson@Chem.UMass.edu
Craig Martin 1436 LGRT X5-3299 CMartin@Chem.UMass.edu