Biophysics 322, Assignment 1

Abhishek Das, 20131056

August 28, 2015

Problem 1. Tabulate E.Coli Proteins

Solution.

Protein name
Hexokinase
FtsZ
MinD

PDB number
1BDG
1RQ7
3Q9L

Diameter(Ao )
72.35
82.23
63.14

Problem 2. Recalculating the inter-protein spacing in E.coli assuming that

genomic DNA occupies the central one fifth segment of the cell length.
Solution. Considering the E.coli cell to be a spherocylinder of length 2
m and width 1 m,from the assumption in the problem,we have a segment
length of (2-0.4)m = 1.6 m and a height of 1 m.
Height(h) = 1.6m
Radius of cylinder(r) = .5m
V olume of cylinder(Vh ) = r2 h = 1.256m3
V olume of the spherical parts(Vs ) = r3 .4/3 = .523m3
T otal available volume f or proteins(VAvl ) = 1.256 + .523 = 1.779m3
The dry mass of an E.coli cell is about 280 f g.[See Reference]
Mass of total protein content MP = (Dry Mass/2) = 140 f g.
Now the mass of 1 amino acid unit is approximately 100Da.
1Da = 1.6 1024 g.
Considering that 300 amino acids give a protein monomer,the mass of 1
protein is:
M = 300 100Da = 48 1021 g
No of proteins in an E.coli cell is MP /M = 2.9 106
From Problem 1 average protein diameter is 72.5 Ao ,which is negligible when
compared to the dimensions of the cell.
Hence the proteins can be considered as points scattered in the cell.Assuming

the scatter to be even in a cubical cell,we have the volume available for each
protein (V ) as:
V = VAvl /N
Where N is the number of proteins in the cell.
V = 0.61 1024
As we assumed a cubical cell(3-D) inter protein spacing (I) = V 1/3
I = 8.4nm
.
Problem 3.
Solution. The spacing between proteins is 8.4 nm and the average protein
size is 7.2 nm.The relation between them can be written as:
I Dp
Dp being the protein diameter.Thus the proteins are crowded in the cell as
the spacing is comparable to their size.
Problem 4.
Solution. We have the length of a diploid human genome as 6.4109 bp.The
number of bp per nucleosome (n) is 150. So,the number of nucleosomes in
nucleus (N) is
6.4 109
N = l/n =
= 42 106
150
The 150bp are around the nucleosome in 1.67 turns,which gives us 89 bp per
turn.The length of one bp is about 1/3 nm.So,the length of DNA around a
nucleosome is 891/3 = 29.6 nm.As this is the circumference of a nucleosome,the radius can be found using
C = 2r
C
= 4.72nm
2
Considering the nucleosome to be a cylinder,with its height greater than 2
times the width of DNA (due to the circumfereing of nucleosome).Taking
the height to be 5 nm,we have:
r=

V (nucleosome) = r2 h = 349.7nm3
2

Total volume occupied by nucleosomes is

V (N ucleosome) = V (nucleosome) N = 14.69 1019 m3
Considering the nucleus to be a half ellipsoid with a circle of 5 m radius
on the plane and a height of 3 m ,its volume is
V (nucleus) = 0.5 5 5 3 = 157.08m3
The ratio of volume of chromatinized DNA to that of nucleus is:
=

V (N ucleosome)
14.69 1019
=
= 0.009 0.01
V (nucleus)
157.08 1018

That is the nucleus has about 100 times the volume of chromatinized DNA.
Ref erences :
1) BioNumbers Harvard Database
2) Physical Biology of Cell, Garland Science
3) Athale, C. A. Chaudhari, H. (2011) Population Length Variability
and Nucleoid Numbers in E. coli. Bioinformatics 27, 2944-2948.
4) Protein Data Bank