56
Questions
number of Na+ ions that the cell loses due solely to spontaneous translocation across
the phospholipid bilayer. State any assumptions you make. (The electrical permittivity
in a vacuum is 8.9 × 10−12 C2 m−2 N−2, the relative electrical permittivity of a phospho
lipid bilayer is 5, and the charge on a single electron is −1.6 × 10−19 C.)
2.9 The complete oxidation of a single molecule of glucose to carbon dioxide and water in
principle involves a total free energy change equivalent of −2870 kJ mol−1 (the minus
sign indicates that energy is released, as opposed to absorbed), whereas that for ATP
hydrolysis to ADP and inorganic phosphate (the opposite of ATP synthesis) is equiva
lent to 18 kBT per molecule.
a
If the TCA cycle synthesizes a total of 38 ATP molecules from every molecule of
glucose, what is the energetic efficiency?
b
If ATP synthesis occurs inside a mitochondrion whose volume is comparable
to a bacterial cell and the concentration of glucose it utilizes is 5 mM, calcu
late the theoretical rise in temperature if all glucose were instantly oxidized in a
single step. Comment on the result in light of the actual cellular mechanisms for
extracting chemical energy from glucose.
2.10 At one point in the TCA inside a mitochondrion in a eukaryotic cell cycle, NAD+
is reduced to NADH oxaloacetate−, and the free energy of NADH is coupled to the
pumping of a proton across the inner membrane against the proton motive force.
a
How much free energy in units of kBT per molecule is required to pump a single
proton across the inner membrane?
b
Write down this full electrochemical for the reduction of NAD+ by oxaloacetate−
and calculate the standard free energy change for this process in units of kBT per
molecule. Stating any assumptions, calculate how many protons NADH pump
across the inner membrane in a single TCA cycle.
c
Inside a mitochondrion, the pH is regulated at 7.5. If all nicotinamide is present
either as NAD+ or NADH, calculate the relative % abundance of NAD+ or NADH
in the mitochondrion. Comment on the result.
2.11 The definition of a cell as outlined in this chapter is as being the minimal structural
and functional unit of life that can self-replicate and can exist “independently.” But
in practice, a cell is not isolated, for example, there are pores in the membrane that
convey molecules in/out of the cell. Does this alter our notion of independence? Are
there more robust alternative definitions of a cell?
2.12 There are ~1015 cells in a typical human body, but only ~1014 of them are human. What
are the others? Does this alter our view of the definition of a “human organism”?
2.13 If you go to the Protein Data Bank (www.pdb.org), you can download “pdb”
coordinates for many, many molecular structures, the following PDB IDs being
good examples: 1QO1 and 1AOI. You can install a variety of free software tools (e.g.,
RasMol, but there are several others available) and open/display these pdb files.
a
Where appropriate, use the software to display separate strands of the DNA
double helix red and blue, with nonpolar amino acids residues yellow and polar
amino acid residues magenta.
b
Using the software, find out what is the maximum separation of any two atoms
in either structure.
2.14
a
What are the attractive and repulsive forces relevant to single biomolecule
interactions, and how do they differ in terms of the relative distance dependence
and magnitude?
b
What forces are most relevant to protein folding of a protein, and why?
2.15 The average and standard deviation of heights measured from a population of adult
women of the same age and ethnic background were 1.64 and 0.07 m, respectively.
Comment on how this compares to the expected variation between the sets of genes
from the same population.
2.16 A 10 mL of culture containing a virus that infects bacteria was prepared from a cul
ture of growing E. coli bacteria at the peak of viral infection activity, and 1 mL of the
culture was divided into 10 volumes of 100 μL each. Nine of these were grown with