## Tuesday, October 5, 2010

### Week 9 Session Notes - sorry for late upload

Point 9.1

Using a set number of degrees of freedom – we don’t overanalyse, we save ourselves a huge amount of mathematics etc

Elasticity comes from entropy. Entropy determines the elasticity of an object

Rubber band force pulling it back becomes less at high temperature

Elastic energy cost increases with temperature

Shape of curve determines elastic energy (equation 9.4 assumes circular curve)

Approximate a curve as a bunch of little circular segments

Figure 9.4

C) still a coil

d) unwinds and becomes straight

slope of A = entropic elasticity

figure 9.5

gives 4 different models to describe 9.4’s regime A and part of B

talked about reasons why we’d stretch out dna and other things

1D chain model – chain containing segments that pointed either left or right. Only two parameters occurring are temperature (which is fixed), and the persistence length (length of segment)

3D chain – segments can point in any direction. Adds two degrees of freedom (the two extra dimensions)

Elastic rod model – 3dfjc model plus an energy cost for every bend. Each segment cares about what’s going on with its neighbours

Figure 9.7

Find it weird that the structure become more ordered at higher temperatures, as opposed to denaturing. Does show however that at low temperatures it is denatured, and for all we know, it may denature again at a higher temperature.

Cold denaturing – loss of electrostatics, lowering of disulfide bonds

Long protein can be approximated as an infinitely long coil

Short protein – ends can’t be stabilised as easily, due to fraction of residues that can’t become part of the helix

Figure 9.8

Rotation determines fraction of helices

Double conc = double rotation

One helical rotation turns light to the left, the handedness of rotation turns light to the right.

CD

Figure 9.9

Effects of changing degree of cooperativity

In long chains, hard to tell if cooperativity matter

In short chains though, makes a hell of a difference

Cooperativity allows for sharp transitions

Figure 9.10

HbO2 -><- Hb + O2

Keq = [Hb][O2]/[HbO2]

Y = [HbO2]/([Hb] + [HbO2] = fraction bound

Bad to have myoglobin.....20% oxygenation difference in tissue

Haemoglobin has 4 binding sites....effective value of 3 due to its binding nature

Small fraction have 1, 2 or 3 bound