Phys 103 FYS, Homework 1 Solutions

NB: These solutions are written out in full, probably entirely excessive, super-overkill
detail. For instance, I’ve done all the unit conversions explicitly when normally you could
simply write down the result. Your homework is not required to be this tedious, but it
doesn’t hurt either.

1 Estimating the number of E.Coli in the human gut.

1.1 Problem
Estimate the number of E.Coli cells in the human gut. You can base your estimate on the
fact that there is about 1kg of E.Coli in our stomachs at any given time and that a typical
E.Coli cell is 1mm in radius. Also, note that all living matter has roughly the density of
water. How does this compare to the total number of our own cells?

1.2 Solution
An E.Coli is also approximately 1µm in length, so we can say that its volume is is 1µm3 .
Given that it has the density of water - 1g/cm3 , we can compute the mass of one bacterium:
1 gram gram
 
−12
Mecoli = Vecoli × ρwater = 1 µm3 × = 1 × 10 (1)
cm3 bacterium
So the number of E.Coli in our gut is:
!
1 bacterium
Ngut = 1 kg × = 1015 bacteria (2)
10−12 gram

We can run the same analysis using human cells, except noting that our cells are consid-
erably larger. Wikipedia says “a typical human cell size is 10 µm and a typical cell mass is
1 nanogram”. So doing the same thing with a human cell and human weight (rounded up
to 100 kg).

1 gram gram
 
Mhcell = Vhcell × ρwater = (10 µm)3 × 3
= 1 × 10−9 (3)
!
cm hcell
1 cell
Nhcell = 100 kg × = 1014 human cells (4)
10−9 gram

So there are ten times as many E.Coli cells in the human gut than there are human cells in
the entire person.

1
2 Estimating the fraction of a cell occupied by DNA
2.1 Problem
Estimate the fraction of the total volume of an E. coli cell taken up by its genomic DNA,
which is about 5 million base pairs long. Remember from class that the distance between
two base pairs is 0.33nm, and consider the DNA to be a tube 2nm in diameter. Estimate
this fraction for a bacterial virus, like the one discussed in class, whose DNA is 20,000 base
pairs long and it is folded up in the viral capsid some 40nm in diameter. Which organism
has a more tightly packed genome?

2.2 Solution
The length of the genome can be computed from the number of base pairs (5 × 109 bp) and
the distance between base pairs (0.33nm):
!
1 nm
Lgenome = 5 × 106 bp × = 5/3 × 106 nm (5)
3 bp

The volume of a cylinder with that length and diameter 2nm is (π = 3):
2
Vgenome = πrgenome Lgenome = 3 × (1nm)2 × (5/3 × 106 nm) = 5 × 106 nm3 (6)

We decided in problem 1 that the volume of a single E.Coli is 1 µm3 so the fraction of volume
occupied by the genome is:

Vgenome 5 × 106 nm3

fgenome = = = 5 × 10−3 = 0.5% (7)
Vecoli 1 µm3
For the virus, we have:
 
Vgenome 2
πrgenome Lgenome 2
πrgenome Ngenome 13 nm
bp
fgenome = = = 4 3
= (8)
Vvirus Vgenome 3
πrvirus
 
1 nm
π(1nm)2 × (2 × 104 bp) × 3 bp 5
= 4 = = 62.5% (9)
3
π(20 nm)3 8

The virus has a far shorter genome but it is packed more tightly.

2
3 Estimating the number of proteins in an E.Coli cell.
3.1 Problem
Estimate the number of proteins in an E. coli cell. Measurements reveal that 15% of the E.
coli mass is protein. To estimate the mass of a typical protein think of it as a sphere 5nm
in diameter, whose density is approximatelythat of water.

3.2 Solution
The number of proteins in an E.Coli cell is equal to their total mass divided by the weight of
a typical protein. If the protein is a sphere of diameter 5nm with the density of water then
its mass is:
4 1 gram
 
Mprotein = Vprotein ρwater = ( π(2.5 nm)3 ) × = 6 × 10−20 gram (10)
3 cm3
The number of proteins is then given by (recall the mass of an E.Coli from Problem 1):

0.15Mecoli 1.5 × 10−13 gram

Nprotein = = = 2.5 × 106 (11)
Mprotein 6 × 10−20