Homework for section 2
Web
site with a good overview of forces
8-Thurs Sept 21 > hand in Oct 10
Thermodynamics
web ref Look
especially at Explaining Chemical Equilibria and Le Chatelier's Principle
reading & homework
9-Thurs Sept 28 Thermodynamics
Same homework
& reading used for lecture 8.
10-Thurs Oct 5: Dr Koder will talk about where protein structures come from. Please hand in a brief summary of his class
11-Tues Oct 10: Hydrogen
bonds; Lennard Jones Interactions & Molecular Volume & Packing
Please read this
for background.
There
will be a review after class of thermodynamic homework today if needed.
Homework-11. (PDF
here)
Good web definition here
;
a movie of He coming together
A powerpoint view of torsion
here
Amino acid hydrophobicity, volume,
surface area
TIBS
(2003) 28 593-597" Atom depth in protein structure and function Pintar et
al.
Biochemistry
(2001) 40 15280-15289 Packing is a key selection factor in the evolution
of protein hydrophobic cores. Chen and Sites
Packing m&ms here
Angew. Chem.
Int. Ed. 2002, 41, 48-76. The hydrogen bond in the solid state.
TIBS (2001) 26
521. More hydrogen bonds for the (structural) biologist.
12-Thurs Oct 12: Solvation
of ions
Homework (PDF
here)
You will need the class handout to do this homework.
Bockris & Reddy: Modern Electrochemistsry
Vol 1 pg 45-58
Science
1999 July 2; 285: 100-102 The Cavity
and Pore Helices in the KcsA K+ Channel: Electrostatic Stabilization of Monovalent
Cations Benoît Roux and Roderick MacKinnon
13-Tues Oct 17: Hydrophobicity
Homework (PDF
here)
Creighton. Page 153-162
Science (1983) 222 p 1087-1093 Wolfenden Waterlogged Molecules
Science (1994) 265 p 936-937 On the probability of finding a water moldcule
in a nonpolar cavity. PDF
Radzicka, A., and Wolfenden, R. (1988) Comparing the polarities of the amino
acids: Side chain distribution coeffients between the vapor phase, cyclohexane,
1-octonal, and neutral aqueous solution, Biochemistry 27, 1664-1670. PDF
Biophysical
Chemistry (2003) 105 179-182 Hydrophobicity-getting into hot water
Lesk
14-Tues Oct 19: pKs and
stat. mec
Reading and figure
Homework (PDF
here)
web ref
here
15-Thurs Oct 24: Electrochemistry and pKs-Thermodynamic boxes
Rich, P. R., and Bendall, D. S. (1979) A mechanism for the reduction of cytochromes
by quinols in solution and its relevance to biological electron transfer reactions,
FEBS Lett. 105, 189-194. (PDF
here)
homework
16-Thurs Oct 26:Sums of small forces Creighton
Page 163-167
Homework (PDF
here) You will need the class handout to do this homework.
17-Tues Oct 31 Your second
short talk. Describe the reaction your protein carries out. Focus on the energetics,
the free energy difference between reactants and products under standard conditions
and in the cell. What forces are most important in helping your protein work.
What's the input energy that drives the reactions in your protein?
If you send me a powerpoint label as 'gunner.hr2.ppt' changing for your name
and protein
No homework for today (hand in Homework 14,15)
Reading from previous incarnations of this class.
Acc.Chem.Res 2001, 34, 939-946 The depth of chemical time and the power of enzymes as catalysts Wolfenden and Snider
Protein folding reading
Daggett and Fersht: The present view of
the mechanism of protein folding
Dobson Protein folding and misfolding
Nauli, Kuhlman, Baker Computer-based redesign
of a protein folding pathway
Ferguson and Fersht Early events in protein
folding
Last revised