Essential Cell Biology 5th edition

A:10 Answers
Figure A4−4
ANSWER 4–5
Figure A4−5
curly
See Figure A4–5.
mild reduction
oxidation
straight
substrate
mirror image
ECB5 EA4.04/A4.04
of substrate
active site
of enzyme
active site
of enzyme
ANSWER 4–6
A. Feedback inhibition from Z that affects the reaction
B → C would increase the flow through the B → X →
Y → Z pathway, because the conversion of B to C is
inhibited. Thus, the more Z there is, the more production
ECB5 EA4.05/A4.05
of Z would be stimulated. This is likely to result in an
uncontrolled “runaway” amplification of this pathway.
B. Feedback inhibition from Z affecting Y → Z would only
inhibit the production of Z. In this scheme, however, X
and Y would still be made at normal rates, even though
both of these intermediates are no longer needed at this
level. This pathway is therefore less efficient than the
one shown in Figure 4−42.
C. If Z is a positive regulator of the step B → X, then the
more Z there is, the more B will be converted to X and
therefore shunted into the pathway producing more Z.
This would result in a runaway amplification similar to
that described for (A).
D. If Z is a positive regulator of the step B → C, then
accumulation of Z leads to a redirection of the pathway
to make more C. This is a second possible way, in
addition to that shown in the figure, to balance the
distribution of compounds into the two branches of the
pathway.
ANSWER 4–7 Both nucleotide binding and
phosphorylation can induce allosteric changes in proteins.
These can have a multitude of consequences, such as
altered enzyme activity, drastic shape changes, and changes
in affinity for other proteins or small molecules. Both
mechanisms are quite versatile. An advantage of nucleotide
binding is the fast rate with which a small nucleotide
can diffuse to the protein; the shape changes that
accompany the function of motor proteins, for example,
require quick nucleotide replenishment. If the different
conformational states of a motor protein were controlled
by phosphorylation, for example, a protein kinase would
either need to diffuse into position at each step, a much
slower process, or be associated permanently with each
motor protein. One advantage of phosphorylation is that it
requires only a single amino acid on the protein’s surface,
rather than a specific binding site. Phosphates can therefore
be added to many different side chains on the same protein
(as long as protein kinases with the proper specificities
exist), thereby vastly increasing the complexity of regulation
that can be achieved for a single protein.
ANSWER 4–8 In working together in a complex, all three
proteins contribute to the specificity (by binding to the safe
and key directly). They help position one another correctly,
and provide the mechanical bracing that allows them to
perform a task that they could not perform individually
(the key is grasped by two of the proteins, for example).
Moreover, their functions are generally coordinated in time
(for instance, the binding of ATP to one subunit is likely to
require that ATP has already been hydrolyzed to ADP by
another).
ANSWER 4–9 The α helix is right-handed. The three
strands that form the large β sheet are antiparallel. There
are no knots in the polypeptide chain, presumably because
a knot would interfere with the folding of the protein into its
three-dimensional conformation after protein synthesis.
ANSWER 4–10
A. True. Only a few amino acid side chains contribute to the
active site. The rest of the protein is required to maintain
the polypeptide chain in the correct conformation,
provide additional binding sites for regulatory purposes,
and localize the protein in the cell.
B. True. Some enzymes form covalent intermediates with
their substrates (see middle panels of Figure 4−39);
however, in all cases, the enzyme is restored to its
original structure after the reaction.
C. False. β sheets can, in principle, contain any number of
strands because the two strands that form the rims of
the sheet are available for hydrogen-bonding to other
strands. (β sheets in known proteins contain from 2 to 16
strands.)
D. False. It is true that the specificity of an antibody
molecule is exclusively contained in polypeptide loops