The Math and Physics Parts of Undergrad Biochemistry

1. INTRODUCTION
It is known that the following logical sequence is true:
The good part of bio is the chem part, and the good part of chem is the physics part, and
the good part of physics is the math part.
By “telescoping”, or cancelling out all terms except the first and last:
The good part of bio is the chem part, the good part of chem is the physics part, and the
good part of physics is the math part.
we arrive at:
The good part of bio is the math part.
If the above logical sequence is true, then the following excerpt of it is also true:
The good part of bio is the chem part, and the good part of chem is the physics part.
It may also be telescoped to arrive at:
The good part of bio is the physics part.
The following math and physics problems, as well as the image below (intro to Chapter 3,
Thermodynamic Principles: A Review) are taken from Voet and Voet’s (2005) Biochemistry 3rd
ed. (Yes, the authors were married to each other. Until death did them part.) Given their source,
they are trivial and have therefore been left as exercises for the reader. Thanks to my gr12 chem
teacher (Kristy Conners) for giving her old copy from her undergrad days to me. I have
paraphrased the questions to remove any unnecessary bio shit that you would need bio to know,
because we’re not here for that. I am absolutely assuming you know all the math and physics
needed for these though. Just because the good part of physics is the math part doesn’t mean I
didn’t include the wonderful theory questions.

Figure 1. Intro to Chapter 3, Thermodynamic Principles: A Review. No other chapter in the

textbook was given a similar literary treatment, perhaps because they do not deserve one.
 2. PROBLEM SET
1. Under optimal conditions for growth, an E. coli cell will divide around every 20 min.
a) If no cells died, how long would it take a single E. coli cell, under optimal
conditions in a 10-L culture flask, to reach it maximum cell density of 1010
cells/mL?
b) Assuming that optimum conditions could be maintained, how long would it take
for the total volume of the cells alone to reach 1km3? (Assume an E. coli cell is a
cylinder 2 × 10-6m long and 1 × 10-6m in diameter.)
[Chapter 1, #1]

2. Go to a physical library, find the printed academic journals, and pick a title that interests
you. Skim the paper and note its organization. In other words, go touch grass. [Where’s
the math/physics? In whatever paper you pick! Chapter 1, #12, paraphrased obviously]

3. A common funeral litany is the Biblical verse: “Ashes to ashes, dust to dust.” Why might
a bereaved family of thermodynamicists be equally comforted by a recitation of the
second law of thermodynamics? [Chapter 3, #1. I find it funny how Word doesn’t
recognize “thermodynamicists” as a real word, as if such things shouldn’t exist. The
suicide rates of pioneering thermodynamicists would seem to agree.]

4. How many flights of 4-m high stairs must an overweight person weighing 75 kg climb to
atone for the indiscretion of eating a 500-Cal hamburger? Assume that there is a 20%
efficiency in converting nutritional energy to mechanical energy. [Chapter 3, #2. I
assume that this person is a short student athlete on a strict diet, hence their atonement for
such a small hamburger.]

5. In terms of thermodynamic concepts, why is it more difficult to park a car in a small

space than it is to drive it out of such a space? [Chapter 3, #3]

6. It has been said that an army of monkeys, typing at random, would eventually produce all
of Shakespeare’s works. How long, on average, would it take 1 million monkeys, each
 typing on a 46-key typewriter (space included but no shift key) at the rate of 1 keystroke
per second, to type the phrase “to be or not to be”? How long, on average, would it take
one monkey to do so on a computer if the computer would only accept the correct letter
in the phrase and then would shift to its next letter (i.e. the computer knew what it
wanted)? [Chapter 3, #4]

7. Show that the transfer of heat from an object of higher temperature to one of lower
temperature, but not the reverse process, obeys the second law of thermodynamics.
[Chapter 3, #5]

8. Carbon monoxide crystallizes with its CO molecules arranged in parallel rows. Since CO
is a very nearly ellipsoidal molecule, in the absence of polarity effects, adjacent CO
molecules could equally well line up in a head-to-tail or a head-to-head fashion. In a
crystal consisting of 1023 molecules, what is the entropy of all the CO molecules being
aligned head to tail? [Chapter 3, #6]

9. The U.S. Patent Office has received, and continues to receive, numerous applications for
perpetual motion machines. Perpetual motion machines have been classified as those of
the first kind, which violate the first law of thermodynamics, and those of the second
kind, which violate the second law of thermodynamics. The fallacy in a perpetual motion
machine of the first kind is generally easy to detect. An example would be a motor-driven
electrical generator that produces energy in excess of that input by the motor. The fallacy
in a perpetual motion machine of the second kind, however, is usually more subtle. Take,
for example, a ship that uses heat energy extracted from the sea by a heat pump so as to
power a steam engine that drives the ship as well as the heat pump. Show, in general
terms, that such a propulsion system would violate the second law of thermodynamics.
[Word count of this question=150. If you thought this was a bitch to read, I had to type it
out by hand, reading the physical textbook, because I couldn’t find a pdf of it. Chapter 3,
#7]

10. How many sequences can you make of the letters G, D, Y, C, and L, where no letter is
repeated, but all letters are used? [Chapter 4, #3, paraphrased]
11. Calculate the ratio of the volume of a hemoglobin molecule (65 kg/mol) to that of the
four O2 molecules it binds. [32g/mol] Also calculate the ratio of the volume of a typical
office (4 × 4 × 3 m) to that of a typical office worker (70 kg) that occupies it. Assume
that the molecular volumes of hemoglobin and O2 are in equal proportion to their
molecular densities and that the office worker has a density of 1.0 g/cm3. Compare the
magnitude of these ratios. [Chapter 8, #12]

12. State the rotational symmetries of each of the following objects: a) a starfish, b) a square
pyramid, c) a rectangular box, and d) a trigonal bipyramid, in the proper mathematical
notation, not e.g. “five-fold”. [Chapter 8, #16.]

13. Find the coefficients of (H+M)n for n = 0, 1, 2, and 3. [Chapter 8, #24, paraphrased]

14. Consider a protein with 10 sulfurs. Any 2 sulfurs can bond to each other. If the protein is
broken and reformed, what is the probability that all of the sulfurs will bond with the
same sulfur as before if the protein has
a) 5 sulfur-sulfur bonds?
b) 3 sulfur-sulfur bonds instead?
[Chapter 9, #2, paraphrased]

15. The Adair equation describes what happens if there are multiple ways for a protein to
bind with a molecule. Given below is the case where the protein has 4 spots that the
molecule can bind to. Show that it can be simplified to a hyperbola for k1 = k2 = k3 = k4:
[Chapter 10, #14, paraphrased, don’t worry about what the variables mean. Hint: why did
I include the bio context for this?]

[S ] 3[S ]2 3[S ]3 [S ]4
+ + +
k1 k1 k2 k1 k 2 k 3 k1 k2 k3 k4
Y=
4 [S ] 6 [S] 4[ S] [S ]
1+ + + +
k 1 k1 k2 k1 k2 k3 k 1 k 2 k3 k 4
16. Estimate the thickness of the surface layer formed by Benjamin Franklin’s teaspoon of oil
on Clapham pond (1 teaspoon ≈ 5 ml and 1 acre = 4047m2). [Chapter 12, #4. This is a
real thing that actually happened.]
17. One Curie (Ci) of radioactivity is defined as 3.70×1010 disintegrations/s, the number that
occurs in 1 g of pure 226Ra. A sample of 14CO2 has a specific radioactivity of 5 μCi/μmol.
Given that 4C has a half-life of 5715 years, what percentage of its atoms are 14C? [Chapter
16, #3]

18. Given that 2n = 10,000, find ⌊n⌋. [Chapter 18, #1, paraphrased]

19. A membrane 100 × 10-10 m thick has a membrane potential of 100 mV. What is the
magnitude of this potential difference in V/cm? [Chapter 20, # 6, paraphrased]

20. Why is chlorophyll green when it absorbs in the red and blue regions of the spectrum?
[Chapter 24, #1]

21. Calculate the energy in a mole of 680 nm light waves/particles, in kJ/mol.

22. The two ends of a 2340 unit long DNA double helix are stuck to each other, forming a
circle. When this circle is constrained to lie in a plane, the DNA has a twist (T) of 212.
When released, the DNA takes up its normal twist of 10.4 units/turn. Indicate the values
of the linking number (L), writhing number (W), and twist for both the constrained and
unconstrained states of this DNA circle. [If all bio math is trivial, why wouldn’t you
know how to solve it, even if it includes ribbon theory (topology/differential geometry
that you can blame Gauss for)? Chapter 29, #5, paraphrased]

23. Explain why the number of vertices in an icosadeltahedron always ends in the numeral
“2” (e.g. 12 for T =1). [Chapter 33, #3, paraphrased]

24. Sketch an icosahedral facet of a T = 9 icosadeltahedron, including subdivisions. [Chapter

33, #4, paraphrased because the original question sounded like it was asking you to draw
 the entire icosadeltahedron, which would be brutal, and the solutions manual only gives a
single facet anyways]

3. WORKED SOLUTIONS
These were all typed out by hand, referencing the physical solutions manual because I couldn’t
find a pdf of it either. Why not scan/take pictures of the manual itself? Because it talks about the
bio stuff I took out for your convenience.

1. a) The number of cells in 10L of saturated culture is:

10L × 103 mL/L × 1010 cells/mL = 1014 cells.
2n = 1014 where n is the number of doublings.
n = 14/log2 = 46.5
b) Volume of an E. coli cell = π × (10-6m /2)2 × 2 × 10-6m = 1.57 × 10-18m3
Number of bacteria in 1km3

2. N/A [Don’t tell me you need a worked solution for how to TOUCH GRASS.]

3. Both are statements of the drive towards randomness of all spontaneous processes,
including death.

4. Since climbing the stairs will produce negligible frictional heat,

∆ U =w=Fh=mgh
where h is the height climbed. But,
J
∆ U =500 Cal × 4184 × 0.20=418,400 J
Cal
2 −2
∆ U 418,400 kg × m × s
h= = =569 m
mg 75 kg ×9.8 m/ s
Therefore,
 569 m
Flights of stairs= =142 flights
4 m/ flight
5. There are only a limited number of configurations that constitute an “acceptably” parked
car in a small space. [I added the quotation marks.] In contrast, there are a much larger
number of configurations that constitute a car which has been pulled out of a small
parking space. Hence, there is a greater entropy increase associated with pulling the car
out of the parking space than there is associated with parking it. Since there is no
enthalpy change associated with the position of the car (assuming a level parking lot),
pulling a car out of a parking space is a more spontaneous process (lesser ΔG) than in
parking the car.

6. The phrase has 18 characters. There are 4618 different 18-character phrases possible. Half
would be typed, on average, before the desired phrase was generated. This would take
1,000,000 monkeys, each typing 1 key/s,
18
46 6 23 16
× 10 =4.25 ×10 s=1.35 ×10 years
2
This is well over the 2.0×1010 year estimate for the universe’s age [from 2004 when the
textbook and its associated solutions manual were written, I can’t be arsed to search the
current estimate.]

7. Since q is positive for heat absorbed, the entropy change associated with losing an
amount of heat q at T1 and absorbing it at T2 is:

−q q ( T 1−T 2 ) q
∆ S= + =
T1 T2 T1 T2

For T1 > T2, ΔS >0, a spontaneous process. For T1 < T2, ΔS <0, a nonspontaneous
process.

8. Each CO molecule in the crystal can have only 2 orientations: the C to the left or the C to
the right. Hence, there are only 2 ways of lining up all of the CO molecules head-to-tail:
all Cs to the left or all Cs to the right. The total number of ways of lining up 1023
23
molecules is 210 . The probability, W, of randomly having all head-to-tail molecules is
23
therefore 2/210 so that
 −23
10 J −0.96 J
S=k B lnW =1.3807 × =
K ( ln 2−10 ln2 )
23
K

9. The answer here is similar to that of #7. [#5 in the textbook chapter] The perpetual
motion machine of the second kind proposed transfers heat, q, at the temperature of the
sea, T1, to boiling water at temperature T2 where T1 > T2. For such a process,

−q q ( T 1−T 2 ) q
∆ S= + = <0
T1 T2 T1 T2

where ΔS refers to the entire system, that is the ship and the ocean. Since the 2nd law of
thermodynamics states that ΔS > 0 for real processes, the proposed engine cannot operate
as advertised.

10. The first residue can be one of five letters, the second one of the remaining four, etc.
N=5 × 4 × 3× 2 ×1=5 !=120

11. The ratio of the masses of hemoglobin, which is approximately equal to the ratio of their
volumes, is
65 kg /mol ×1000 g /kg
=508.
4 ×32 g/mol
The volume of the office worker is
g g m 3
70 kg × 1000 ×1 3 ×1 =0.070 m
kg cm 100 cm
3

Hence the ratio of the volumes of the office and the office worker is
4×4×3
=686
0.070
These ratios are similar in magnitude, which would surprise many biochemists.

12. a) C5 b)C4 c)D2 d)D3

13. Using Pascal’s triangle, the coefficients are:
1, 1 for n = 0 1, 2, 1 for n = 1 1, 3, 3, 1 for n = 2 1, 4, 6, 4, 1 for n = 3
[The above is my own solution, not from the solutions manual. It brute-forces these
instead of using Pascal’s triangle, which sounds awful, but makes sense for the
biochemical context of H and M being molecules that combine to make bigger molecules,
but we’re not here for that]

14. a) All 10 sulfurs can bond with each other. There is a 1/9 chance that a particular S can
pair with its proper mate, a 1/7 chance that a particular S of the remaining ones can pair
with its proper mate, etc. Therefore, the probability of all 10 sulfurs randomly pair with
their respective proper mates is:
1 1 1 1 1 1
× × × × =
9 7 5 3 1 945
b) First, the unbonded sulfurs must be chosen. Order is irrelevant, hence this is 10C4
10 ! 10 × 9× 8 ×7 × 6× 5 ×4 ×3 ×2 ×1
¿ = =210
4 ! 6 ! (4 × 3 ×2 ×1)(6 ×5 × 4 ×3 × 2× 1)

Of the remaining sulfurs, there is a 1/5 chance that one will bond with its proper mate,
1/3 chance of a particular S left bonding with its mate, etc. Hence, the probability of
randomly forming 3 particular S-S bonds among 10 sulfurs is:
1 1 1
× =
210 5 ×3 ×1 3150

15. The numerator and denominator can be factored to yield

( )
3
[S] [S]
1+
k1 k1
Y=

( )
4
[ ] S
1+
k1

[S]
¿
(k ¿¿ 1+[S ])¿

The graph of this function is a hyperbola. QED [The solutions manual doesn’t explain
that it describes a hyperbola because it’s a rational function. Because this equation is yet
another example of biochemical combinatorics, the coefficients of each [S] are, once
 again, from Pascal’s triangle. This is why they can be factored into binomials, as
demonstrated above.]

16. According to Franklin, about 1 teaspoon of oil spread over about half an acre. Since
V
x=
A
Where x = thickness of the oil layer, V = volume of oil, and A = area of the oil, then
3
3 m
5 cm × 0.01
cm −9
x= 2
=2.5× 10 m
4047 m
[The solutions manual, being American, gives the answer in Å, or angstroms, which are a
non-SI unit where 1 Å = 10-10 m.]

17. The first-order rate constant for the disintegration of 14C is:
−4
0.693 10
k= =1.21 ×
5715 years y
−4
10 1y 1d 1h
¿ 1.21 × × × ×
y 365 d 24 h 3600 s
−12
¿ 3.85 ×10 /s
Thus, one mole of 14C should have
−12
23 10 12
6.02 ×10 ×3.85 × =2.31× 10 disintegrations /s
s
A sample with 5 μCi/μmol has 5 Ci/mol
10 11
¿ 5 ×3.70 ×10 =1.85× 10 disintegrations /s
Therefore, the percentage of its C atoms which are 14C is
11
1.85× 10
12
×100=8 %
2.31× 10

18.
 nlog 2=10,000
log 10,000 4
n= = =13.3
log 2 0.301
⌊ 13.3 ⌋ =13

19. 100mV potential difference across a 100 × 10-10 membrane corresponds to

0.1 V
=100,000 V /cm
−10 100 cm
100× 10 m×
m

20. Chlorophyll absorbs red and blue light and therefore transmits green light, the colour we
see.

21. 680 nm corresponds to 680 × 10-9 m.

Nhc
E=
λ
23
6.02 ×10 −34 8m
× 6.626 ×10 J ∙ sec ×2.998 ×10
mol s
¿ −9
=176 kJ /mol
680 ×10 m

22. L = T + W. For the constrained DNA circle, W = 0, hence L = T = 212. For the
unconstrained DNA circle, L = 212 since this quantity is invariant,
2340units
T= =225
10.4 units/turn

And W = L – T = 212 – 225 = -13.

23. An icosadeltahedron has 60T subunits that are clustered around 12 pentagonal vertives
with the remainder being clustered around hexagonal vertices. Hence, it has
 60 T−5× 12
=10(T −1)
6
hexagonal vertices and
10 ( T −1 ) +12=10 T + 2

vertices of any kind. This latter number always ends in the numeral “2”. [The solutions
manual neglects to acknowledge Euler’s Polyhedral Formula, which sucks imo bc it’s
one of my favourite formulas]

24.