Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

170 Chapter 3: Proteins
Problems
Which statements are true? Explain why or why not.
3–1 Each strand in a β sheet is a helix with two amino
acids per turn.
3–2 Intrinsically disordered regions of proteins can be
identified using bioinformatic methods to search genes for
encoded amino acid sequences that possess high hydrophobicity
and low net charge.
3–3 Loops of polypeptide that protrude from the surface
of a protein often form the binding sites for other molecules.
3–4 An enzyme reaches a maximum rate at high substrate
concentration because it has a fixed number of
active sites where substrate binds.
3–5 Higher concentrations of enzyme give rise to a
higher turnover number.
3–6 Enzymes that undergo cooperative allosteric transitions
invariably consist of symmetric assemblies of multiple
subunits.
3–7 Continual addition and removal of phosphates
by protein kinases and protein phosphatases is wasteful
of energy—since their combined action consumes ATP—
but it is a necessary consequence of effective regulation by
phosphorylation.
Discuss the following problems.
3–8 Consider the following statement. “To produce
one molecule of each possible kind of polypeptide chain,
300 amino acids in length, would require more atoms than
exist in the universe.” Given the size of the universe, do you
suppose this statement could possibly be correct? Since
counting atoms is a tricky business, consider the problem
from the standpoint of mass. The mass of the observable
universe is estimated to be about 10 80 grams, give or take
an order of magnitude or so. Assuming that the average
mass of an amino acid is 110 daltons, what would be the
mass of one molecule of each possible kind of polypeptide
chain 300 amino acids in length? Is this greater than the
mass of the universe?
3–9 A common strategy for identifying distantly related
homologous proteins is to search the database using a short
signature sequence indicative of the particular protein
function. Why is it better to search with a short sequence
than with a long sequence? Do you not have more chances
for a “hit” in the database with a long sequence?
3–10 The so-called kelch motif consists of a fourstranded
β sheet, which forms what is known as a β propeller.
It is usually found to be repeated four to seven times,
forming a kelch repeat domain in a multidomain protein.
One such kelch repeat domain is shown in Figure Q3–1.
Would you classify this domain as an “in-line” or “plug-in”
type domain?
β6
β5
β4
β3
C
N
Figure Q3–1 The
kelch repeat domain of
galactose oxidase from
D. dendroides (Problem
3–10). The seven individual
β propellers are color
coded and labeled. The
N- and C-termini are
indicated by N and C.
3–11 Titin, which has a molecular weight of about
3 × 10 6 , is the largest polypeptide yet described. Titin
molecules Problems extend p3.06/3.06 from muscle thick filaments to the
Z disc; they are thought to act as springs to keep the thick
filaments centered in the sarcomere. Titin is composed of a
large number of repeated immunoglobulin (Ig) sequences
of 89 amino acids, each of which is folded into a domain
about 4 nm in length (Figure Q3–2A).
You suspect that the springlike behavior of titin is
caused by the sequential unfolding (and refolding) of individual
Ig domains. You test this hypothesis using the atomic
force microscope, which allows you to pick up one end of
a protein molecule and pull with an accurately measured
force. For a fragment of titin containing seven repeats of the
Ig domain, this experiment gives the sawtooth force-versus-extension
curve shown in Figure Q3–2B. If the experiment
is repeated in a solution of 8 M urea (a protein denaturant),
the peaks disappear and the measured extension
becomes much longer for a given force. If the experiment
is repeated after the protein has been cross-linked by treatment
with glutaraldehyde, once again the peaks disappear
but the extension becomes much smaller for a given force.
(A)
(B)
force (pN)
400
300
200
100
0
N
β7
Figure Q3–2 Springlike behavior of titin (Problem 3–11). (A) The
structure of an individual Ig domain. (B) Force in piconewtons versus
extension in nanometers obtained by atomic force microscopy.
β1
β2
0 50 100 150 200
extension (nm)
C
Problems p3.12/3.11