Quiz moved again -> Friday

Class-

I received note from several students that will be taking the GRE next Wednesday morning. Therefore, as voted on in class this morning, we will have the quiz on the Friday of next week.

Cheers,
MSS

Quiz next week moved to Wed

Per the near-unanimous vote of the class, I will move the quiz from next Monday to next Wednesday. If this will cause a problem for you, please let me know immediately.

Cheers,
MSS

HW2 notes

Hi class-

A couple of notes on HW2:

On problem 3, when you look at the description of the structure on the PDB website, there will be three different chains - two for thrombin and one for hirugen (a hiruden mimic). Hirugen will be about 12 residues long.

On problem 4, keep in mind that what is given is the fraction of the total that is folded ([F]/[F]+[U]), not the ratio of folded to unfolded ([F]/[U]).

On problem 6b, assume T = 300 K.

Cheers,
MSS

Talk on how to job interview

Hi class-

I received a note from Prof. Seborg that two ChE almuni will present a talk on "How to Succeed When Interviewing for an Industrial Job" today at 5pm in the Multicultural Center Theater:

The two speakers, Marc Privatera and Christina Borgese, were both AIChE Student Chapter presidents at UCSB. Marc was the UCSB recruiter for Clorox for several years and has had considerable experience interviewing ChE students. Recently, he moved to a biodiesel startup company, Biofuelbox, where he is the chief Technology Officer. Christina is a 2006 graduate who has worked at both Clorox and Biofuelbox.

Cheers,
MSS

Grade distributions thus far

Hi class-

Here are some statistics on grades for the first two quizzes and first homework:

Quiz 1
average +- std dev: 81% +- 11%
max: 96%
min: 52%

Quiz 2
average +- std dev: 73 +- 17%
max: 100%
min: 33%

Homework 1
average +- std dev: 82% +- 14%
max: 100%
min: 18%

Keep in mind that homework assignments count for 35% of your grade and quizzes 25%. In addition, remember that the lowest quiz grade will be dropped.

Cheers,
MSS

Interesting video

Dear class-

I highly suggest you take a look at this wonderful animation, entitled "The Inner Life of the Cell":

http://multimedia.mcb.harvard.edu/anim_innerlife_hi.html

It gives a molecular picture of most of the processes and compartments inside of a cell that we have been discussing. Although some of these are highly dramatized (for example, actin and tubulin assembly), the video does do an excellent job of integrating most of the major cellular processes and might make it easier for you to visualize the topics discussed in class.

Cheers,
MSS

Hints on HW1

Dear class-

Here are some hints on HW1 for the problems.

Problem 1:
In this problem, you are tackling a problem of combinatorics. The problem essentially asks you how many spots there must be in a DNA sequence that are variable (i.e., one of the four possible bases) in order to have 10^10 unique sequences.

Problem 2:
To compute how far proteins are from each other, you want to assume each protein sits in a little cube of volume. The distance between proteins is then V^(1/3). Therefore, to solve this problem, you have to first compute the volume per protein.

Problem 3:
For part b, first sketch out what the Coulombic interaction looks like. Then, sketch what the total LJ + Coulombic interaction would look like for small q, medium q, and large q. At some point, as you increase q, the minimum in the net potential should vanish. What are the mathematical criteria for the vanishing of a minimum? In other words, what two conditions involving the derivatives of a function must apply when a minimum becomes and inflection point? This provides two equations... what are the two unknowns?

Problem 6:
(b) Imagine that the protein is fixed at the origin. What conformations must the ligand give up when it binds?

Problem 7:
(a) To get from heat capacities to entropies and enthalpies, you will have to integrate from a reference temperature. What are the definitions of CP?

(b) To eliminate DeltaS(Tf) from your final expressions, you will need to let T = Tf and DeltaG= the value at the folding temperature, then solve your expression for DeltaS.

(d) You will want to use either the slope or intercept of some line to estimate DeltaH(Tf)

Problem 8
You are going to first want to write all of your equations in terms of K1, K2, K3, K4 where K1=exp(-DeltaG1/RT) and so on and so forth. Next, express the concentrations of the various bound hemoglobin species in terms of equilibrium constants, [O2], and [H]. What constraint governs the total concentration of hemoglobin? Write down a mass balance on concentrations of hemoglobin. Let [H]0 be equal to the total amount. Then, f0 = [H]/[H]0, f1 = [HO2]/[H]0 and so on and so forth.

Problem 9
This problem amounts to finding the probability of one molecular state relative to another one, using Boltzmann populations, P ~ exp(-U/kB T). Be sure to normalize the probabilities such that they sum to one.

That's all the hints for now. Good luck,

MSS




Problem

Hints on problem set 1

Hi class-

If you're having a little bit of trouble getting started with PS1, here are a few hints for some of the more challenging problems.

On problems 6,7, and 9, you are using the Boltzmann population rules that we discussed in class. These may be new concepts for you, but these problems will help you grow comfortable in applying them. When you are working on these problems, you need to start by thinking about states: what are the possible states the system can have (e.g., folded or unfolded, bound or unbound, correct or incorrect nucleotide)?

• Write down a list of all states.
  
• Next, you need to assign a probability to each of the states, and that probability is given by the Boltzmann rule. You need to know the list of all of the states in order to normalize the probabilities, i.e., to ensure that they sum to one over all states.
  
• Keep the following in mind for the Boltzmann rule. If your state consists of multiple possible molecular configurations, you want to use a free energy in the Boltzmann exponential. If it consists of only one, you can use the internal energy.

On problem 8, you will be using concepts from your earlier chemistry courses that should be more than familiar to you. Keep in mind that the equilibrium constant for a reaction relates to the reaction free energy by:

K = exp( - DeltaG0/ R T )

We'll eventually derive this rule in class this week. You will need to know this relationship in order to solve problem 8. Also keep in mind for problem 8 that the total concentration of hemoglobin molecules is constant, [H] + [H(O2)] + [H(O2)2] + [H(O2)3] + [H(O2)4] = const = [H]0. What you are trying to find is f0 = [H]/[H]0, f1 = [H]/[H]1, and so on and so forth.

Cheers,
MSS

Updated course website

Dear class-

I have posted the slides for the first three lectures and my notes for the lecture on thermodynamics on the course website. The thermo notes in particular may be helpful to you in thinking about and digesting today's lecture, and as you are working on the homework.

Cheers,
MSS