Chem 791A SPIRE number 72300 |
Instructors: Craig Martin CMartin@chem.umass.edu and Jeanne Hardy hardy@chem.umass.edu |
Last updated: 11-28-05 |
MWF 11:15p-12:05p LGRT 202
"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." |
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 following minimal cutoffs will be applied:
A = 90-100 | B =80-89 | C = 70-79 | D = 60-69 | F = below 60 |
Go to Syllabus (updated!)
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.
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: |