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May 10, 2011

Chem 120B Final Exam

Definitions and Useful Formulas:

Coming soon...

Questions on this exam concern a protein embedded in a lipid bilayer. This

channel protein can allow some, but not all, solute molecules to cross from
one side of the bilayer to the other. As indicated below, molecules of type A can
navigate the channel in either direction.

ch

el
a nn

id
lip

er
ay
l
i
b

A
In the following questions, sketches of the bilayer and protein will sometimes depict
a side view, i.e., a cross-section perpendicular to the membrane. Other sketches will
show a view from above the membrane.

1. A lipid bilayer divides two dilute solutions, numbered 1 and 2. In solution #1, N0
molecules of AB are dissolved, all of which dissociate into separate molecules A and
B. In solution #2, N0 molecules of AC are dissolved; some, but not all, of the AC
molecules dissociate into separate molecules A and C. Only molecules of type A can
move freely through the channel, as depicted below (in side view).
solution #1

channel

A
...

lipid bilayer

...

A C

solution #2

The two solutions have identical volume V = M 3 , which we imagine dividing into
M microscopic cells of a lattice:
M cells
single-cell partition
function qA

l
B

single-cell partition
function qB

A C

single-cell partition
function qAC

lipid bilayer
single-cell partition
function qA
single-cell partition
function qC

A
C

M cells

The partition function of an A molecule, when it is confined to a single lattice cell,

is qA (regardless of whether it resides in solution #1 or #2). Similarly, molecules of
type B, C, and AC have single-cell partition functions qB , qC , and qAC .
3

(1)

We will denote the number of A molecules in solution #1 as NA ; the

(1)
(1)
(2)
corresponding density is A = NA /V . Similarly, solution #2 contains NA
(2)
(2)
molecules of type A at density A = NA /V . Since the other species (B, C, and
AC) are restricted to one solution or the other, we will denote their numbers more
simply as NB , NC , and NAC , and their densities in the relevant solutions as B , C ,
and AC .

2. This question focuses on motion of the protein channel within the plane of the
lipid bilayer. We will caricature this motion as occurring on a two-dimensional
lattice, as shown below in top view.

prob. 1/4

prob. 1/4

l
prob. 1/4

prob. 1/4

x
Time is divided into intervals t sufficiently long that motion during one interval
is uncorrelated from motion during a different interval. In each interval, the
protein hops a distance into an adjacent lattice cell. Hops to the right occur with
probability 1/4. Leftward, upward, and downward hops also occur with probability
1/4.
Let r(t) r(0) be the displacement vector of the protein after time t = n t. Its
square magnitude is
R2 (t) = |r(t) r(0)|2 = [x(t) x(0)]2 + [y(t) y(0)]2 ,
where x(t) and y(t) are the x and ycomponents of the position vector r(t) at
time t.
The lipid bilayer has a total area of L2 , which the protein cannot leave.
Imagine that the protein is initially anchored (perhaps via another molecule in the
membrane), disallowing motion outside a single lattice cell. During a time interval
of duration t, the probability p0 that the protein detaches from this anchor is very
small, p0 1.

3. Consider fluctuations in which the protein channel alternates between open and
closed states, as drawn below (in side view).
closed
(x < x*)

open
(x > x*)

The coordinate x characterizes the size of the gap within the protein. It may
range between a minimum value of 0 and a maximum value of 2x . Between these
extremes, the reversible work required to open a gap of size x is
w(x) =

x,
2x x,

0 < x < x
x < x < 2x

w(x)

e x*

0
0

x*

2x*