Homework for section 2

Web site with a good overview of forces
Classic paper by Dill
please look at this pdf for Biochemical Thermodynamis . Pages 10-18 is most important.
A good web site for a biophysics class at Urbana
a good pdf for the interactions between concentration and potential
text book Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. The Mitochondrion.

8 - Thermodynamics (one homework for the two lectures)
web ref Look especially at Explaining Chemical Equilibria and Le Chatelier's Principle
important handouts: sketch of lecture &handout & homework

A nice treatment of the balance of concentration and voltage effects in semipermeable membranes: Donnan effect

9- pKs and stat. mech
Homework (PDF here)class notes

Reading and figure
web ref here
chemwiki on acids and bases

10: Hydrogen bonds; Lennard Jones Interactions & Molecular Volume & Packing
Homework (PDF here)Classnotes

Please read this for background.
There will be a review after class of thermodynamic homework today if needed.

Good web definition of van der waals forces
web site for hydrogen bonds
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
TIBS (2001) 26 521. More hydrogen bonds for the (structural) biologist.

These is the most important for the hydrogen bond class
Angew. Chem. Int. Ed. 2002, 41, 48-76. The hydrogen bond in the solid state.

11-: 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

Another link to a lecture
Rashin and Honig
on Born model of ion solvation

ppt 2: Second class discussion of our proteins and projects. 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? Second presentation template.

Homework (PDF here)

Creighton. Page 153-162 (Handout)
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

a clever way to measure hydrophobicity from membrane insertion PDF
Tables for size and residue burial statistics from Jena Library Hydrophobicity Scales.
Good web site for introduction to partion coefficients

13:Sums of small force
Homework (PDF here)
You will need the class handouts Creighton Page 163-167 to do this homework

Pictures of proton transfer models

14-Electrochemistry and pKs-Thermodynamic boxes
homework. one page summary

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).


15: Electron tunneling. Handout for et; basis of 2 state systems ; A great example from cyclobutadiene isomerization:

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 September 19, 2017