Solutions for problems assigned with Lectures 1 & 2

Garrett & Grisham, pg. 27

3. Escherichia coli cells are about 2 m (microns) long and 0.8 m in diameter.
a. How many E. coli cells laid end to end would fit across the diameter of a pin head?
(Assume a pinhead diameter of 0.5 mm.)

Answer:

E. coli /pinhead di ameter =
0.5 mm/di a.
2 m/E. col i
=
0.5 10
3
m
2 10
-6
m
= 250 E. col i/pi nhead di ameter


b. What is the volume of an E. coli cell? (Assume it is a cylinder, with the volume of a
cylinder given by V=tr
2
h, where t = 3.14.)

Answer:

V = tr
2
h
= 3.14 (
0.8 m
2
)
2
2 m
= 3.14 (0.4 10
6
m)
2
(2 10
6
m)
= 1 18
18
m
3
But, 1 m
3
= (10
2
cm)
3
= 10
6
cm
3
= 10
6
ml = 10
3
L
V = 1 10
-18
m
3
= 1 10
-15
L
= 1 fL (femtoli ter)


c. What is the surface area of an E. coli cell? What is the surface-to-volume ratio of an
E. coli cell?

Note There is a mistake in this answer in the Study Guide.

Answer:
1 -
m
6
10 6 =
2
m
12
10 6
= SA/V
2
m
12
10 6 =
m)
6
10 m)(2
6
10 (0.8 3.14
2
m)
6
10 (0.4 3.14 2 =
dh
2
r 2 = SA

+
3
m
18
10 1
t t


d. Glucose, a major energy-yielding nutrient, is present in bacterial cells at a
concentration of about 1 mM. How many glucose molecules are contained in a typical E.
coli cell? (Recall that Avogadros number = 6.023 x 10
23
.)

Answer:

moles glucose = concentration volume
= 1 mM 1 10
-15
L (from b.)
= 1 10
-18
mol es
# mol ecul es = 1 10
-18
mol es 6.023 10
23
(mol ecule/mol)
= 6 10
5
mol ecul es


e. A number of regulatory proteins are present in E. coli at only one or two molecules per
cell. If we assume that an E. coli contains just one molecule of a particular protein, what
is the molar concentration of this protein in the cell?

Answer:

1 molecule
6.023 10
23
mol ecules/mol e
= 1.7 10
-24
mol e
Mol ar concentrati on =
mol es
volume(in l i ters)
=
1.7 10
-24
mol e
10
-15
L (from b.)
= 1.7 10
-9
M = 1.7 nM


f. An E. coli cell contains about 15,000 ribosomes, which carry out protein synthesis.
Assuming ribosomes are spherical and have a diameter of 20 nm (nanometers), what
fraction of the E. coli cell volume is occupied by ribosomes?

Answer:


volume of one ribosome =
4
3
tr
3
=
4
3
3.14 (10 10
9
m)
3
= 4.2 10
-24
m
3


volume of 15, 000 ribosomes = 4.2 10
-24
m
3
15, 000
= 6.3 10
20
m
3
fractional vol ume = vol ume ri bosome/vol ume E. col i
=
6.3 10
20
m
3
1 10
18
m
3
(from b.)
= 0.063 or 6.3%






g. The E. coli chromosome is a single DNA molecule whose mass is about 3.0 x 10
9

Daltons. This macromolecule is actually a circular array of nucleotide pairs. The
average molecular weight of a nucleotide pair is 660 and each pair imparts 0.34 nm to
the length of the DNA molecule. What is the total length of the E. coli chromosome? How
does this length compare with the overall dimensions of an E. coli cell? How many
nucleotide pairs does this DNA contain? The average E. coli protein is a linear chain of
360 amino acids. If three nucleotide pairs in a gene encode one amino acid in a protein,
how many different proteins can the E. coli chromosome encode? (the answer to this
question is a reasonable approximation of the maximum number of different kinds of
proteins that can be expected in bacteria.)

Answer: The number of moles of base pairs in 3.1 x 10
9
D dsDNA is given by
775
m 2
m 1,550
coli E. length
DNA length
2mm = length
m 1,550 = mm 1.55 = m
3
10 1.55 =
(nm/bp) 0.34 bp/mole mole
6
10 4.55 = length
bp/mole mole
6
10 4.55 = dsDNA molecule 1
bp/mole mole
6
10 4.55
bp) e 660(gm/mol
dsDNA) (gm/mole
9
10 3.0
= =

coli E.


To calculate the number of different proteins:


360 aa/protein 3 bp/aa = 1080 bp/protei n
# di fferent protei ns =
4.55 10
6
bp
1080 bp/protei n
= 4, 213 proteins



10. Why does the central role of weak forces in biomolecular interactions restrict living
systems to a narrow range of environmental conditions?

Answer: The weak forces such as hydrogen bonds, ionic bonds, hydrophobic interactions, and
van der Waals interactions can be easily overcome by low amounts of energy. Slightly elevated
temperatures are sufficient to break hydrogen bonds. Changes in ionic strength, pH,
concentration of particular ions, etc., all potentially have profound effects on macromolecular
structures dependent on the weak forces.

11. Describe what is meant by the phrase "cells are steady-state systems".

Answer: Life is characterized as a system through which both energy and matter flow. The
consequence of energy flow in this case is order, the order of monomeric units in biopolymers,
which in turn produce macromolecular structures that function together as a living cell.






Garrett & Grisham, pg. 75

1. An enzymatic hydrolysis of fructose-1-P


Fructose1P +H
2
O fructose+P
i

was allowed to proceed to equilibrium at 25C. The original concentration of fructose-1-P
was 0.2 M, but when the system had reached equilibrium the concentration of fructose 1-
P was only 6.52 x 10
-5
M. Calculate the equilibrium constant for this reaction and the
standard free energy of hydrolysis of fructose 1-P.

Answer:


For fructose1P+H
2
O fructose+P
i

The equilibrium constant, Keq, is given by

K
eq
=
[f ructose]
eq
[P
i
]
eq
[ f ructose1 P]
eq

At 25C or 298

K (273 + 25), [fructose-1-P]eq = 6.52 x 10
-5
M. Initially [fructose-1-P] = 0.2 M. The
amount of the fructose produced is given by: 0.2 M - 6.52 x 10
-5
M.
And, since an equal amount of [Pi] is produced, Keq may be written as follows:
mol / kJ 9 . 15 G
ln613 K 298 K) J/mol 314 . 8 ( G
RTlnK G
M 613 K
10 52 . 6
) 10 52 . 6 2M . 0 )( 10 52 . 6 2M . 0 (
K
eq
eq
5
5 5
eq
= A
= A
= A
=


=









3. The standard state free energy of hydrolysis of acetyl phosphate is G = -42.3
kJ/mol.

AcetylP +H
2
O acetate+P
i

Calculate the free energy change for the acetyl phosphate hydrolysis in a solution of 2
mM acetate, 2 mM phosphate and 3 nM acetyl phosphate.

Answer:
kJ/mol -24.8 = G
) 10 (3
) 10 (2 ) 10 (2
ln K 20) + (273 K) l 8.314(J/mo + ol) 42,300(J/m = G
P] - [acetyl
] P [acetate][
ln K 20) + (273 K) l 8.314(J/mo + G = G
[Reactant]
[Product]
RTln + G = G
9 -
3 - 3 -
i
initial
initial
A


A
A A
A A






6. For the process A B, Keq(AB) is 0.02 at 37C. For the process B C, Keq(BC) is 1000
at 37C.
a. Determine Keq(AC), the equilibrium constant for the overall process


A C, from Keq(AB)
and Keq(BC).
b. Determine standard state free energy changes for all three processes, and use G(AC)
to determine Keq(AC). Make sure that this value agrees with that determined in part a, of
this problem.

Answer:


For A B and B C,
K
eq
(AB) =
[B]
eq
[A]
eq
, and K
eq
(BC) =
[C]
eq
[B]
eq
By solving for [B]
eq
in the above two equations we find:
[B]
eq
= K
eq
(AB) [ A]
eq
=
[C]
eq
K
eq
(BC)
This equation can be rearranged to give:
[C]
eq
[ A]
eq
= K
eq
(AC) =K
eq
(AB) K
eq
(BC) =0.021000 or,
K
eq
(AC) =20

The standard free energy change is calculated as follows:
mol / kJ 8 . 17 ) BC ( G
ln1000 K 310 ) molK / J ( 314 . 8 ) BC ( RTlnK ) BC ( G
mol / kJ 1 . 10 ) AB ( G
02 . ln0 K 310 ) K mol / J ( 314 . 8 ) AB ( RTlnK ) AB ( G
eq
eq
= A
= = A
= A
= = A


or
mol / 72kJ . 7 ) AC ( G
ln20 K 310 ) K mol / J ( 314 . 8 ) AC ( RTlnK ) AC ( G
eq
= A
= = A

l mo / 70kJ . 7 mol / 8kJ . 17 mol / 1kJ . 10 ) AC ( G
) BC ( G ) AB ( G ) AC ( G
= = A
A + A = A




8. Write the equilibrium constant, Keq, for the hydrolysis of creatine phosphate and
calculate a value for Keq at 25C from the value of G' in Table 3.3.

Answer: For the reaction:
7
eq
298 314 . 8
) 10 (-43.3
RT
G
eq
eq
eq 2 eq
eq i eq
eq
i 2
10 3.89 = K
e = e = K
: write can we , -RTlnK = G From
O] [H phosphate] [creatine
] [P [creatine]
= K
l -43.3kJ/mo = G , P + creatine O H + phosphate creatine
3

10. Calculate the free energy of hydrolysis of ATP in a rat liver cell in which the ATP,
ADP, and Pi concentrations are 3.4, 1.3, and 4.8 mM, respectively.

Answer: For [ATP] = 3.4 mM, [ADP] = 1.3 mM, and [P
i
] = 4.8 mM, calculate the G of hydrolysis
of ATP.
mol / kJ 7 . 46 G C, 37 At
mol / kJ 1 . 46 G
10 4 . 3
) 10 )(4.8 10 (1.3
ln K ) 5 2 273 ( 10 8.314 + 3.3) Table (From mol / 5kJ . 30 G
] ATP [
] P ][ ADP [
RTln G G
3 -
3 - 3 -
3 -
i
= A
= A


+ = A
+ A = A

11. Hexokinase catalyzes the phosphorylation of glucose from ATP, yielding glucose-6-P
and ADP. Using the values of Table 3.3, calculate the standard-state free energy change
and equilibrium constant for the hexokinase reaction. (The glucose to glucose-6-P
reaction is not in Table 3.3. Use G'= -13.9 kJ/mol for glucose-6-P hydrolysis.)

Answer:


Hexokinase catalyzes the following reaction:
glucose + ATP glucose -6-P + ADP
This reaction may be broken down into the following two reactions:
glucose +P
i
glucose -6-P + H
2
O (1) and,
ATP+ H
2
O ADP+P
i
(2)


From Table 3.3, we find that G'= -13.9 kJ/mol for glucose-6-P hydrolysis.
Thus, the reverse reaction, namely reaction (1), must have G' = +13.9 kJ/mol.

From Table 3.3, we also find that ATP hydrolysis has G' = - 30.5 kJ/mol.
The overall G' for phosphoryl transfer from ATP to glucose is:

AG' = +13.9 +( 30.5) = 16.6kJ/mol and,
K
eq
= e

AG'
RT
= e

(16.610
3
)
8.314310
= 626.9



Segel pg 205

1.
K
eq
= 0.43

AG = -RTln K
eq


Using calories, not Joules,
RT = 1.987 cal/molK x 298 K = 592 cal/mol

AG = -592 cal/mol x ln(0.43)

AG = 500 cal/mol


2.
GTP + ATP ADPG + PP
i
; K
eq
= 1.0

a. AG = AG + RTln
] ][ [
] ][ [
ATP GTP
PPi ADPG


= -RTln(1) + (592 cal/mol)ln
] 10 ][ 10 [
] 10 ][ 10 [
3 4
5 5




= 0 + -4.09 kcal/mol = -4.09 kcal/mol

b. Spontaneously to the right.


10.
ATP cAMP + PP
i
; K
eq
= 0.065
ATP AMP + PP
i
; AG = -8 kcal/mol

So

ATP AMP + PP
i
; AG = -8 kcal/mol
cAMP + PP
i
ATP; AG = -RTlnK
eq
= -RTln )
065 . 0
1
( = -1618 cal/mol
______________

cAMP AMP ; AG = -8000 cal/mol + -1618 cal/mol = -9618 cal/mol



12.
G-6-P G-1-P ; K
eq
=
19
1
= 0.053 =
] 6 [
] 1 [
P G
P G




Initial: [G6P] = 1 M
Final: [G6P] = 1 X, [G1P] = X

0.053 =
X
X
1


X =
053 . 0 1
053 . 0
+
= 0.05
a. [G6P] = 1 0.05 = 0.95 M, [G1P] = 0.05 M;
] 1 [
] 6 [
P G
P G
= 19

b. [G6P] = 0.095 M, [G1P] = 0.005 M;
] 1 [
] 6 [
P G
P G
= 19

c. [G6P] = 0.0095 M, [G1P] = 0.0005 M;
] 1 [
] 6 [
P G
P G
= 19

etc.