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07
Problem Set 1 (Sizes and Equilibria) due Mon, Sep 13, 2010,
before class
Problem 1.
As we discussed in class and you have by now observed in the drawings of Goodsell,
the cell is crammed full of macromolecules required to carry out metabolism. Over the
course of the semester, you will see that it is important to think about and have some
intuition about sizes and time scales in biology. This problem is designed to help you think
about some of these issues. Shown in Fig.1A below is a typical E. coli cell that is 2 µm in
length and 0.8 µm in diameter. The weight of an E. coli cell in exponential growth in
glucose is 0.95 pg. Fig. 1A also shows the nucleoid and a ribosome. The structure of the
ribosome, the macromolecular machine composed of protein and RNA of molecular weight
of 2.5 MDa, that makes polypeptides in all organisms is shown in Fig. 1B. Its dimensions
are given in one ref as 200 Å in diameter. To solve problem 1, you will have to make an
assumption about the shape of the object in question to calculate a volume.
Figure 1
A. B.
A typical E. coli cell 70S subunit of the ribosome
http://www.proteopedia.org/wiki/index.php/Ribosome gives the three dimension picture
of the ribosome in motion.
Questions:
a. Calculate the volume of the E. coli cell given the available information. It should be
noted, however, that the volume changes with growth conditions.
b. You are given that the ribosome is 30% of the cell mass. How many molecules of the
ribosome are there in the cell?
c. Calculate the volume of the ribosome. It is of interest that most macromolecular
machines found inside the cell are of similar size to the ribosome, however they are
not as abundant.
d. Given the number of ribosomes in the cell, what volume of the cell is composed of
ribosomes?
e. How does the picture in Fig. 1A agree with your calculation?
f. Given the volume of the E. coli cell that you calculated in a. above, at pH 7 how many
protons are in the bacterial cell? Note the bacterial cell is 70% water. As you have
seen from the first few lectures, bacterial cells contain thousands of macromolecules
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including proteins and DNA. Examination of the building blocks of these species
shows that they all have ionizable groups. What does your calculation tell you about
the concentration of H+ and OH‐ in the cell?
g. The genetic information in DNA contains a linear sequence of successive code words
or codons. Each codon is composed of three nucleotides and codes for a single
amino acid, the building blocks of proteins. The molecular weight of E. coli DNA is
2.5 x 109 Da. The average molecular weight of a nucleotide pair is 660 Da and each
nucleotide pair contributes to 0.34 nm of the DNA length. Calculate the length of an
DNA molecule and compare it to the dimensions of the typical E. coli cell. How does
it fit into the cell? How does this calculation fit with the cartoon in Fig. 1A?
Problem 2.
There are a number of common buffers inside all cells that help to maintain pH
homeostasis essential for survival: inorganic phosphate, carbonic acid, and the side chains
of proteins. In the next lecture we will examine hemoglobin (Hb), the protein transporter
of O2 to the cells from the lungs and CO2, the end product of metabolism, from the tissues
back to the lungs. A major regulatory mechanism for loading and unloading O2 from Hb is
the Bohr effect and involves H+ and a contribution from carbonic acid which functions as an
important buffer in the blood. The following equilibria exist in the erythrocytes of your
blood:
Kh = 2.8 x 10‐3 Kd = 1.5 x 10‐4
CO2 + H2O H2CO3 HCO3‐ + H+
Kh is the hydration equilibrium constant for CO2 at 25ºC and Kd is the dissociation constant
for H2CO3 to HCO3‐ and a H+.
Ka = ??
CO2 + H2O H HCO3‐ + H+
Questions:
a. Using this information, calculate the Ka (the acidity constant for CO2): the equilibrium
constant between CO2 and HCO3‐. This information is important in solving the following
problem.
You are walking in front of the Stata center with you Cairn Terrier McEnzyme (“Zymee”).
You have recently developed a nanosensor in your UROP lab that allows you to instantly
measure the pH of your blood. At the start of your walk, the pH was 7.35. All of a sudden
as you pass in front of the construction for the Koch center, an unleashed German shepherd
bounds out of no where and starts chasing you and Zymee. Your fear triggers rapid
breakdown of your glycogen (polymer of glucose) to glucose and the glucose is rapidly
converted to lactic acid. You escape the German shepherd’s jaws by seconds as you jump
into the Stata Center and slam the door shut. You immediately measure the pH of your
blood and despite the lactic acid produced due to anaerobic glycolysis, it remains 7.35. You
then go into the lab in building 18 and draw 10 cc (mL) of your blood and measure the total
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amount of CO2 present in this sample by its acidification to pH 1.0. The analysis reveals
that the sample contained 5.6 cc of CO2. Recall that 1 mole of gas occupies 22.6 L.
b. Why did you acidify your blood to measure CO2? (Think about the equilibria described
above.) Calculate the number of moles and the concentration of CO2 in this blood sample.
c. Given that the pH of your blood had not changed, the blood sample at that time was
actually a mixture of CO2 and HCO3‐ . Calculate from the information in a and b, the
concentrations of CO2 and HCO3‐.
d. Draw the different charged states accessible to phosphate. How does phosphate function
as a buffer inside the cell? Why is it nearly optimal for controlling the physiological pH?
e. What amino acid side chains of proteins can function as buffers? Why?
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