Final exam

Biophysics 2
Enginycria Fisic;\

Barcelona, Ju ne 3 , 20 14

Exam review : June 12, 12h

FUN DAM EN TALS (61')

2h, 00 notes

Basic paramete.r: k B T/le1 = 26m V

Questions
1. (0.5p) E xplain what is the central dogma of biology

2. (D.5p) Comment on the IlHli u different types of RNA present in t he cell and thei r fUllction
3. (O.Sp) Explain how the spatial coordin ates (X -Y- Z) of the DNA or protein probed with
magnetic tWeezer:) is measured. Why does an experimentalist have to wait some time
uutil being able to measure th e fo rce CVCIl when the probe position is properly detected?

Bionumbe rs
4. (0.75 p) Make an estimation of the tiule it would take a human cell t o react to an ex.ternal

signal in the membrane if, instead of changing dir cctJy t he propert ies of membrane pro
teins, the signal would have to diffuse to t he center of the cell, start t he t ranscription of a
gene, produce a protein and th is protein had to cOlne back to the mcmbrane (Disregard
the time it takes for mRNA to reach ribosome, consider that the protein weight:) 150
kDa)
5. (0.75p) T he basic functioning of ATP-sy nthase is the same in both bacteria and humans
except tha.t in bacteria ATP-synthase is in t he extern al membrane. Explain wha.t hi the
source of energy th at allows ATP-synthasc to produce ATP a nd make a.n est imation of
how many protons have to move through the external membrane in bacteria in order to
produce enough energy (via ATP) for th e transcription of a typical protei n (Consider
that most of t he energy necessary to produce a. protein is used in breaking the hydrogen
bonds of dsDNA . Consider that tbe whole process is very efficient.).

6. (1.5p) In the freely-jointed-chain (FJC) model of a polymer we saw that t he cnd-to- end
distance probability fol lowed a C aussian distri bution

(R. N)
,

(_3
_)
27rNl':

'J/2

,"'12m:

( I)

that gave a scaling for t he typical s ize of the poiym,cr witiJ the numh(!]" of segments as
R ..... Nl/2 . On e of the main drawbacks of this formulation is that it docs not consider
excluded-volume efrects. Th is can be taken iut.o acco\ml considering t he polymer as
Ii 3D self-avoiding random walk. There is, however, a Simpler argument proposed by
F lory that gives the eorn,'l:l scaJillg. Tn this, t.he self-avoiding cI[c(;t is considered to be
an interaction energy E ex:: N th at is proportional to the number of :)cgments Nand
the fractional volume of l.hc polymer t/J, i.e., the fraction of t he volume of space Lhat is
actually occupied by tbe polymer.
a.) (0.75p) Following t;he previous cou ~ide ra tions , calcu late t he ellergy, entropy and [rcc
energy of the polymer as a. function of its typical size R.
b (0.75p) Obtain the value of H that corresponds to equilibr ium (minimizing P) an d,
from this, the new scaling o f R vs N.
7. (1.5p) Consider a skeletal muscle cell li ving in a mooi um wh ere t he ex trn.ccl!ular con
centration of potassium is 5m M and sod ium is at 150 Illl\-!. A simple HI! model fo r the
evolution of the membrane pot;cntiaJ is

dV/dt ~ - 1.2mh(V - EN.) - 3n2 (V - Ex)

(2)

where m,lt and n arc gating variables whose rates at l.he resting [)utenl.ial fulfi ll

nOX! = 11.00 = 1/2,111 00 = 1/18 and ENu = 50 mV wit h EI{ u nknown.

a) (0.75p) Describe t he character istics of the sodium and pot assium d HlImcls in terms
of ullits and subunits drawing an schematic of t he possible transitions between

configurations.
b) (0 .75p) Obtain the intracellular concentration of potassium 8l1d sodium (kept by
t he Na/ I< pump) knowing t hat the resting potential of the cell is -60 mV

Midterm exam
Biophysics 2
Enginy(>rin rfsic:a

BaTcclona., March 25, 2014

EXERCISES (4p)
2h , notes a llowed
1. (2p) In the zipper model of melting of DN A, i t is assumed that t he bonds of DNA start
breaking at one end , and it is only possible t o break a bond next to a broken one, so the
DNA spli ts as a zipper , hence the na me of the model. We will as.<Ju me that i:Ul energy (
is m,.-oded Lo lm::ak eat:h bo nd , amI there is a nUll1ucr n of t:Onflg lll"utions ill the broken
state, corresponding to the rotation al degrees of freed om (as opposed to ( = 0 and n = 1
in t hc bou nd state).
a) (0. 5p) W hich is t he probability of fi nd ing the DN A with p broke n bonds '!

b) (0.5p) Write down the pa rtition function of the system

c) (0.5p) Calculate the average number of broken bonds at a give n tem perature

eI) (0.5p) From the result above, calculate the melti ng temperature of DN A
2. (2p) In t h is problem we will try to wr iLe down a model for non~p ro ccss ive molecu lar
motors. For this , we will consider a one-state model, where the probabili ty that the
motor is at pos ition n at time t is given by p(n, t). We will assume, as we d id in class,
tha t the motor has probabilities k+D.t and L D.t. of ju mping to Lne right and to the left,
respectively, in the time interval l::l.t. But now we will consider that the motor can also
detach from t he t rack with probabili ty 66.t .

a) (O.S p) Wri te down the master CCluation for the probability dist.ri bution p(n, t ).

b) (0.5p) Go to the continuum li mit and wri Le the equation satis fied by p(x , t).
c) (0 .5p) Find the general sol ution to th at equatio n if t he in itial condition is a pulse
a t t = 0, x = 0 [for that, you may want. to do a change of va.riables th a.t red uces the
equ ation found in c) to a d iffus ion equation with drift].
d) (0.5p) Find the distance a motor t ravels before detaching (the run length L) , given
by L = V(t} , where V is the avcrage speed of the motor and (t ) the average time
it remains on the track. (For simplicity consider that the detachment kinetics does
not cha nge the value of V ).

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