Essential Cell Biology 5th edition

Questions
171
of the enzyme but cannot undergo the reaction catalyzed
by it, what effects would you expect the addition of X to
the reaction to have? Compare the effects of X and of the
accumulation of P.
QUESTION 4–15
Which of the following amino acids would you expect
to find more often near the center of a folded globular
protein? Which ones would you expect to find more often
exposed to the outside? Explain your answers. Ser, Ser-P (a
Ser residue that is phosphorylated), Leu, Lys, Gln, His, Phe,
Val, Ile, Met, Cys–S–S–Cys (two cysteines that are disulfidebonded),
and Glu. Where would you expect to find the most
N-terminal amino acid and the most C-terminal amino acid?
QUESTION 4–16
Assume you want to make and study fragments of a protein.
Would you expect that any fragment of the polypeptide
chain would fold the same way as it would in the intact
protein? Consider the protein shown in Figure 4−20. Which
fragments do you suppose are most likely to fold correctly?
QUESTION 4–17
Neurofilament proteins assemble into long, intermediate
filaments (discussed in Chapter 17), found in abundance
running along the length of nerve cell axons. The C-terminal
region of these proteins is an unstructured polypeptide,
hundreds of amino acids long and heavily modified by the
addition of phosphate groups. The term “polymer brush”
has been applied to this part of the neurofilament. Can you
suggest why?
QUESTION 4–18
An enzyme isolated from a mutant bacterium grown at
20°C works in a test tube at 20°C but not at 37°C (37°C is
the temperature of the gut, where this bacterium normally
lives). Furthermore, once the enzyme has been exposed
to the higher temperature, it no longer works at the lower
one. The same enzyme isolated from the normal bacterium
works at both temperatures. Can you suggest what happens
(at the molecular level) to the mutant enzyme as the
temperature increases?
QUESTION 4–19
A motor protein moves along protein filaments in the cell.
Why are the elements shown in the illustration not sufficient
to mediate directed movement (Figure Q4–19)? With
reference to Figure 4−50, modify the illustration shown
here to include other elements that are required to create a
unidirectional motor, and justify each modification you make
to the illustration.
Figure Q4−19
QUESTION 4–20
Gel-filtration chromatography separates molecules
according to their size (see Panel 4−4, p. 166). Smaller
molecules diffuse faster in solution than larger ones, yet
smaller molecules migrate more slowly through a gelfiltration
column than larger ones. Explain this paradox.
What should happen at very rapid flow rates?
QUESTION 4–21
As shown in Figure 4−16, both α helices and the coiled-coil
structures that can form from them are helical structures,
but do they have the same handedness in the figure?
Explain why?
QUESTION 4–22
How is it possible that a change in a single amino acid in a
protein of 1000 amino acids can destroy protein function,
even when that amino acid is far away from any ligandbinding
site?
QUESTION 4−23
The curve shown in Figure 4−35 is described by the
Michaelis–Menten equation:
rate (v) = V max [S]/(K M + [S])
Can you convince yourself that the features qualitatively
described in the text are accurately represented by this
equation? In particular, how can the equation be simplified
when the substrate concentration [S] is in one of the
following ranges: (A) [S] is much smaller than the K M ,
(B) [S] equals the K M , and (C) [S] is much larger than the K M ?
QUESTION 4−24
The rate of a simple enzyme reaction is given by the
standard Michaelis–Menten equation:
rate = V max [S]/(K M + [S])
If the V max of an enzyme is 100 μmole/sec and the K M is
1 mM, at what substrate concentration is the rate
50 μmole/sec? Plot a graph of rate versus substrate (S)
concentration for [S] = 0 to 10 mM. Convert this to a plot of
1/rate versus 1/[S]. Why is the latter plot a straight line?
QUESTION 4−25
Select the correct options in the following and explain your
choices. If [S] is very much smaller than K M , the active site
of the enzyme is mostly occupied/unoccupied. If [S] is very
much greater than K M , the reaction rate is limited by the
enzyme/substrate concentration.
QUESTION 4−26
A. The reaction rates of the reaction S → P, catalyzed by
enzyme E, were determined under conditions in which only
very little product was formed. The data in the table below
were measured, plot the data as a graph. Use this graph to
estimate the K M and the V max for this enzyme.
B. To determine the K M and V max values more precisely,
a trick is generally used in which the Michaelis–Menten
equation is transformed so that it is possible to plot the
data as a straight line. A simple rearrangement yields
1/rate = (K M /V max ) (1/[S]) + 1/V max
which is an equation of the form y = ax + b. Calculate
1/rate and 1/[S] for the data given in part (A) and then plot
ECB5 Q4.19/Q4.19