css.php

Home » Section 2: Forces and Folding: Homework section II

Section 2: Forces and Folding: Homework section II

Homework for section 2

Web site with a good overview of forces 
A classic paper by Dill (you can find this paper on Dropbox as dill-Biochem1990.pdf)
please look at this pdf for Biochemical Thermodynamics. Pages 10-18 is most important (you can find this pdf on Dropbox as Biochemical Thermodynamics.pdf).
A good web site for a biophysics class at Urbana
Good textbook 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)

Use the Dropbox folder that we made for you to submit homework. 
Due Date : October 10, 2019

Homework link
web ref Look especially at Explaining Chemical Equilibria and Le Chatelier’s Principle 



9: pKs and stat. mech

Use the Dropbox folder that we made for you to submit homework. 
Due Date : October 10, 2019


Homework link
Look  figure
web ref here
chemwiki on acids and bases



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.

10: Solvation of ions

Use the Dropbox folder that we made for you to submit homework. 
Due Date : October 29, 2019


Homework link 

You will need the class handout to do this homework. 
Bockris & Reddy: Modern Electrochemistry 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 BenoĆ®t Roux and Roderick MacKinnon
Rashin and Honig on Born model of ion solvation
 


11-: Hydrophobicity

Use the Dropbox folder that we made for you to submit homework. 
Due Date : October 29, 2019


Homework link

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 molecule in a nonpolar cavity PDF Radzicka, A., and Wolfenden, R. (1988) ( You can find this article in Dropbox as wolf.wat_.94.pdf). Comparing the polarities of the amino acids: Side chain distribution coefficients 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
Good web site for an introduction to partition coefficients


12: Hydrogen bonds; Lennard Jones Interactions & Molecular Volume & Packing

Use the Dropbox folder that we made for you to submit homework. 
Due Date : November 5, 2019

Homework link

Please read this for the 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.

This is the most important for the hydrogen bond class
Angew. Chem. Int. Ed. 2002, 41, 48-76.(you can find this paper on Dropbox as angew.chem_.02.steiner-hydrogen-bonds
.pdf)  The hydrogen bond in the solid state.

13: Sums of small force

Use the Dropbox folder that we made for you to submit homework. 
Due Date : November 5, 2019


Homework link
You will need the class handouts Creighton Page 163-167 to do this homework


14: Electrochemistry and pKs-Thermodynamic boxes

Use the Dropbox folder that we made for you to submit homework. 
Due Date : November 19,2019


Homework link. 

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: 

Use the Dropbox folder that we made for you to submit homework. 
Due Date : November 19,2019


THE LAST HOMEWORK!

Handout for etbasis of 2 state systems (you can find this article as feynman.pdf in Dropbox) ; 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

Need help with the Commons? Visit our
help page
Send us a message
Skip to toolbar