University of Washington

Department of Chemistry
Chemistry 453/457
Summer Quarter 2016
Homework Assignment 3
Due at class on Wednesday 10 August2016. Show calculations as well as answers.
.
1) Sequential binding models for partial cooperativity depend upon the geometric
arrangement of the binding sites and the way in which the binding sites interact in this
geometry as they become occupied by ligands. Consider two macromolecules each of
which have three ligand binding sites. The general formula for the binding polynomial is:
qb
2
3
1 3k1 L 3k1k2 L k1k2 k3 L . The equilibrium constants are defined as in
P
Lectures 10 and 11 and in the Tinoco text pages 180-190.
a. Suppose the macromolecule has its three binding
sites arranged in a linear array as shown to the right.
Only adjacent sites that are occupied can interact.
So for all singly bound molecules k1=k. For doubly bound molecules k1k2=k2, if
the occupied sites are not adjacent and k1k2=fk2 if they are adjacent. For the filled
molecule k1k2 k3 f 2 k 3 . Using these rules write out the expression for the binding
q
polynomial b in terms of f, k, and [L].
P

qb
, obtain an
Nqb L
expression for fB in terms of f, k, and [L]. Assume N=3. Now let k=1.00x106,
[L]=0.00001M and f=1.5. Calculate fB. Compare this answer to the value for fB if
the binding were non-cooperative. Is this mode of binding cooperative or anticooperative? Explain.
c. Repeat the calculation in part b only assume f=0.75. Is this mode of binding
cooperative or anti-cooperative? Explain.
d. Repeat the calculations in parts a-c only now assume the
binding sites are arranged in an equilaterial triangle:
b. Using your answer from part a, and the relationship f B

2) A protein has two structural forms R and T. These structural forms

R T
are in equilibrium as shown in the adjacent diagram with
T . In addition each form of the protein has a single ligand

K
R
RL TL
binding site and when R binds the ligand L, RL is formed and
similarly with T, L, and TL. As the diagram also shows R and RL are in equilibrium with
RL and similarly T and TL are in equilibrium with k TL . R binds L
kR
T
R L
T L
more tightly than T binds L so k R kT .
a)

Define the binding polynomial as qP R T TL RL . Using

the three equilibrium constant expressions given above, express

b)

in terms of kT, kR, K, and [L].

q
Using your result for P from part a, and the relationship
R

d)

qP
obtain an expression for fB in terms of kT, kR, K, and
qP N L
[L]. Calculate fB for K=10, kT=0.1, and kR=1.0.
Using your result from part b, obtain an expression for the ratio
fB
in terms of kT, kR, K, and [L]. Would a log-log plot (i.e. a Hill
1 fB
plot) indicate that the binding in this system is: fully cooperative,
partially cooperative or non-cooperative? Explain your answer.
T 1 .
Suppose the equilibrium R T lies to the right so that K
R

fB

c)

qP
R

Determine an expression for the equilibrium constant L

TL
RL

in

terms of kT, kR, and K. Based on this expression, when T and R bind
L, is the equilibrium between TL and RL shifted to the right or the
left? In other words, is the equilibrium constant L greater than, less
than, or equal to K? Explain. Calculate L using the values for K, kT
and kR provided in part b.
3) The distribution function W(x) for a random walk gives the probability of finding the
walker at a position x. For a random walk composed of N jumps, each of length ,
where the probability of taking a single jump in the +x direction is p and the probability
of taking a jump in the x direction is q=1-p, W(x) has the form:
2
1
x x / 2 2
W x
e
2 2

where the average displacement x N p q and the variance

2

2 x 2 x 4 pqN 2 . See Lecture 12.

a) In Lecture 12 section A we said an unbiased random walk is defined as a walk
where there is no preference for the +x or the x direction so that p=q. Suppose a
single-celled animal executes an unbiased random walk which consists of 20
jumps (i.e. N=20) and that each jump is of length 0.05mm . Calculate the
average displacement x , the mean squared displacement x 2 and the variance

2 for this random walk. Calculate the probability W(x) of finding the cell at
x=0.0 mm after 20 jumps. Do the same calculation for x=0.5mm and at x=1.0mm
b) Repeat the calculation of the probability of remaining at x=0.0mm for N=10,
N=60 and N=100. Comparing your results for parts a and b, does the probability
of remaining at x=0.0mm decrease linearly with N or does it decrease faster than
linearly? Explain.
c) Suppose in response to a glucose gradient the cells motion becomes biased such
that the probability of taking a jump in the +x direction is p=20/38. Now the
single-celled animal executes a biased random walk which again consists of 20
jumps (i.e. N=20) with each jump of length 0.05mm . Calculate the average
displacement x , the variance, and the mean squared displacement x 2 for this
biased random walk. Calculate the probability W(x) of finding the cell at
x=0.0mm after 20 jumps. Do the same calculation for x=0.5mm and x=1.0 mm.
d) Repeat the calculation of the probability of remaining at x=0.0mm for biased
random walks consisting of N=10, N=60 and N=100 jumps, assuming p=20/38
and 0.05mm . Does the probability decrease linearly with N or does it
decrease faster than linearly?
4)Consider the following data for the proteins myoglobin and hemoglobin
Protein
Myoglobin
Hemoglobin

Molecular
Weight (kg)
16.900
64.500

Diffusion
Coefficient
Dx1011m2s-1
11.3
6.9

Specific
Volume V2
(mLg-1)
0.74
0.75

Frictional
ratiof/f0
1.11
1.16

a) Calculate the radii of myoglobin and hemoglobin assuming they are unhydrated
spheres.
b) Calculate the radii and volumes of myoglobin and hemoglobin that would
account for the frictional ratios, assuming they are hydrated spheres.
c) For each protein, calculate 1, the mass of water bound per mass of protein.
Assume the density of water is 1g mL-1.
d) Myoglobin is a oxygen storage protein found in the body tissues. Hemoglobin is
an oxygen transport protein. Hemoglobin is composed of n sub-units each

roughly the size of myoglobin. Based on your answers in part b, how many
myoglobin-like sub-units does hemoglobin contain?

5) A macromolecule has a diffusion coefficient D 6.9 1011 m2 s 1 at T=298K and for a

solvent viscosity of 0.891103 kg m 1s 1 .
a) Assuming the molecular is approximately spherical in solution, calculate
the translational frictional coefficient tr and the radius.
b) Calculate the root-mean-squared displacement of the molecule after 1
millisecond.
c) For the purpose of calculating the translational friction f, many rod-like
polymers can be approximated in solution as a chain of beads, each bead
3 Nd
of diameter d. For such a polymer the frictional coefficient is f
ln N
where N is the number of beads in the polymer chain and is the solvent
viscosity. . Suppose the macromolecule in part a aggregates as a linear,
rod-like hexamer. Calculate the coefficient of translational friction and the
coefficient of translational diffusion. Calculate the rms displacement after
1 millisecond. Assume 0.891103 kg m 1s 1

d) Suppose the molecule in part a forms a hexamer in solution, but the

aggregate is roughly spherical, with a volume equal to six times the
volume of the spherical monomer. Calculate the coefficient of frictional
and the coefficient of translational diffusion. Calculate the rms
displacement after 1 millisecond.
e) Based on your answers in part a-d, can translational diffusion coefficients
be used to detect aggregation? How sensitive are diffusion coefficients to
aggregate geometry?