Chem C130/MCB C100A - Biophysical Chemistry - Fall 2005 -Aathi's Discussion Section

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CHEM130A/MCB100A Course Website

Discussion Sections:

102: 71 Evans Hall 9-10AM Friday CCN: 11483
109: 285 Cory Hall 11-12PM Friday CCN: 12914

Office Hours:

3-4PM Monday 155 Donner Hall
9-10AM Wednesday 113 Donner Hall
10AM-11AM Friday 113 Donner Hall

In-Section Quiz +Exams:

Quiz-1 091605 - Chptrs 1 and 2 of JK's book -closed book
Quiz-2 100705 Solutions- Chptr 4 of JK's book - open book
Quiz-3A 110405 Solutions - Chptrs 6 and 7 of JK's book - open book
Quiz-3B 110905 Solutions - Chptrs 6 and 7 of JK's book - open book
Quiz-3C 111105 Solutions - Chptrs 6 and 7 of JK's book - open book
Practice-exam1 113005 Solutions
Quiz-4 120205 Allostery, co-operativity, enzyme kinetics - Closed Book
Practice-exam2 120505


Section Notes

Section 1 (09-02-05)
Fun Papers:
Van der Waals forces in the gecko
Why Nature Chose Phosphates
Hydrophobic effect at different length scales
Section 2 (09-09-05)
Errata: In thinking about complexity of organisms I got you to think about power law dependencies of complexity on the number of genes, which I think is fine.However, I had incorrectly ignored alternative splicing. While yeast(S.cerevisiae) has only ~250 introns and just a couple of cases known of alternate splicing the human genome has just far too many(no one has a good estimate).
Errata: The orbitals involved in the octahedral coordination in Mg(II) are six sp3d2 hybridised orbitals
Section 3 (09-16-05)
Quiz 1
Fun Papers:
Bacteriorhodopsin-the movie
Everything you always wanted to know about WATER but were afraid to ask

Section 4 (09-23-05)
Fun Papers:
Invention of the Genetic Code A great historical narrative of the brilliant yet wrong predictions on the genetic code - an exercise in systematic counting

Section 5 (09-30-05)
Fun Papers:
The Paracelcus Challenge Can two proteins with greater than 50% sequence identity have completely different folds?
SCOP fold statistics

Section 6 (10-07-05)
Quiz 2

Section 7 (10-14-05)
Energy&Entropy a quick look -1
Energy&Entropy a quick look -2
Energy&Entropy a quick look -3

Section 8 (10-21-05)
How to make sense of the heat capacity in an adiabatic reaction (problem 4B in Mid Term)

Frequently Asked Questions

How do I calculate factorials on the TI 30X IIS calculator? (101405)
In brief: To find for example 69! the keys you would press are
69 PRB > > = =
Basically the PRB key pulls down a menu of nPr, nCr, !, RAND . You use your scroll keys to get to !. Then press Enter (=) to select !. Press Enter (=) again to get the answer.
For some pictures to illustrate the above, check pg 78 in this link

What do I need to know in Chptr6 for the Mid Term Exam-2? (101505)
Multiplicity concepts and how they relate to spontaneous evolution of a system. Essentially till pg 28 of Chptr6

About the bond energy for covalent bond: in textbook equ5.33, it wrote: U= k/2(r-r0)^2 on professor's note on the web p.9, it wrote: V= +V0 + k(r-ro)^2 Are they same and how they related to each other? (101505)
These are basically the same relations. I believe John used the version in 5.33 simply to illustrate that it is a harmonic (spring like) potential. U=Uo +k*(r-ro)^2 is the general form of the two. In this case the spring constant = k/2 (F=-dU/dr=spring constant*displacement from equilibrium) Do not get confused by the inconsistent use of k and k/2 as the constants.

why the stabilization energy at optimal bond length (V0)is negative? (101505)
The stabilization energy is negative if the two particles are attractive. The stabilization energy is simply the work done by you in bring the two particles together from infinite initial separation. If the particles attract each other then you have done negative work.