Biomolecular Structure - Fall 2005

Chem 791A
SPIRE number 72300
Instructors:
Craig Martin CMartin@chem.umass.edu and
Jeanne Hardy hardy@chem.umass.edu
Last updated:
11-28-05

News Flash: Exam II Answer Key is available.

MWF 11:15p-12:05p LGRT 202


Textbook: "Protein Structure & Function," Gregory A. Petsko & Dagmar Ringe, Sinauer Press, 2004.
Summary: The purpose of this course is to introduce students to protein and nucleic acid structure, both in the chemical details leading to specific structures and in how structure leads to function. Quoting from the text:

"Two major revolutions have occurred within the last twenty years that have changed the way biologists think about their experiments... The first was the structural revolution. The second is the genomic revolution."
This course will lay the foundations of the former, which in turn is at the heart of the latter. Sequence determines structure determines function.

Prerequisites: The course will assume little background in protein and nucleic acid structure.

Grading (tentative):

Mid/late October exam 30 pts
Late November exam 30 pts
Class Presentation 30 pts
Early December quiz 10 pts
The early December quiz will be comprehensive and may cover topics in student presentations up to that point (date TBA). Those who present early will have the opportunity to submit potential quiz questions (so start thinking now!). The early bird may get a small bonus...

The following minimal cutoffs will be applied:

A = 90-100 B =80-89 C = 70-79 D = 60-69 F = below 60
What does "minimal" mean? As an example, a total score of 90 or better WILL yield an A in the course. In later adjustments, a score of 88 or 89 (for example) may also yield an A for the course.

Go to Syllabus (updated!)


Resources

Quick Links: Presentations | PDB | PyMOL | Jmol (update) | Molecules | DNA | JmolShell

For the Jmol workshop, go directly to the JmolShell Home Page.
What is Jmol?

For the Nucleic Acids part of the course: go to the CHIME link for Nucleic Acids. Be sure to be read the stuff below about which browser to use.


Brief Syllabus:

Instructors: CM- Craig Martin; JH - Jeanne Hardy; JS - Joanna Swain

Week Dates
Chapters Topics
1 Sept 7 & 9 CM 1-0 to 1-8 Sequence to Structure: primary, secondary, and tertiary structure
2 Sept 12, 14 & 16 JH 1-9 to 1-15 Tertiary structure continued. Folding, protein stability, forces guiding structure
3 Sept 19, 21, 23 JH/JH/CM 1-16 to 1-22 Quaternary structure. Survey of motifs: alpha, beta, and mixed domains. Protein flexibility
4 Sept 26, 28 & 30 JS 5-1 to 5-3 Structure Determination:practical aspects of NMR
5 Oct 3, 5 & 7 JH 5-1 to 5-3 Structure Determination: practical aspects of x-ray crystallography
6 Oct 12 & 14 JH/CM
Tools: Protein Data Bank. Introduction to Protein Explorer, SwissPDB Viewer, jMol, PyMol
7 Oct 17, 19 & 21 CM 2-0 to 2-16 Structure to Function: Recognition, active sites, binding sites, dynamics, catalysis
Active site geometry, how active sites achieve catalysis, redox reactions, cofactors, multi-step enzymes
8 Oct 24, 26 & 28 CM
Nucleic Acid Structure: DNA, RNA, riboproteins, ribozymes, aptamers
9 Oct 31, Nov 2 & 4 JH 3-0 to 3-20 Control of Protein Function: Protein domains, control by pH and redox, effector ligands, cooperativity, allostery, protein switches, motor proteins, et al. Control by degradation, phosphorylation, two-component signaling, protein splicing, glycosylation
10 Nov 7
Nov 9
JH
JH/CM

Control of Protein Function: continued...
Jmol/PyMol workshop - Getting ready for presentations
11 Nov 14 & 16
Nov 18
JH/CM
JH

4-0 to 4-7
Jmol/PyMol workshop - Getting ready for presentations
From Sequence to Function: Sequence alignment, protein profiling, deriving function from sequence, protein evolution, homology modeling
12 Nov 21
Nov 23
JH
CM
4-8 to 4-17 Sequence alignment, protein profiling, deriving function from sequence, protein evolution, homology modeling
Protein superfamilies, strategies for identifying binding sites and catalytic residues.
13 Nov 28 CM 4-8 to 4-17 Protein superfamilies, strategies for identifying binding sites and catalytic residues. Case studies.
13 Nov 30

Student presentations:
13 Dec 2

Student presentations:
14 Dec 5

Student presentations:
14 Dec 7

Student presentations:
14 Dec 9

Student presentations:
15 Dec 12

Student presentations:
15 Dec 14

Student presentations: