Chap. 3 Problem 1
See Fig. 3.1a & 3.2 for basic
information about structure
classifications. More on the definitions
of primary, secondary, tertiary, and
quaternary structure can be found in
the text on p. 61-68. Examples of
secondary structures are the  helix, ß
sheet, and ß turns. Secondary
structures are stabilized primarily by
H-bonds. All three types of noncovalent
interactions (H-bonds, ionic
interactions, and van der Waals forces)
stabilize tertiary and quaternary
structure. The hydrophobic effect also
is generally important in the folding of
protein structure elements.
Chap. 3 Problem 2
Molecular chaperones and chaperonins
play important roles in the folding of
newly synthesized proteins in cells. By
binding to an unfolded protein and
promoting folding, its aggregation and
targeting to the proteasome for
degradation are prevented. Although
many proteins can fold spontaneously,
chaperones reduce the time required
for folding and decrease the likelihood
that the protein will become trapped in
a partially folded state. Molecular
chaperones (e.g., Hsp70, Fig. 3.16) act
as monomers to promote folding,
whereas chaperonins (e.g., GroELS, Fig.
3.17) are large multisubunit machines.
Both chaperonins and molecular
chaperones use ATP to catalyze folding.
Fig. 3.17a
Chap. 3 Problem 3
Enzymes accelerate chemical
reactions by stabilizing and thereby
lowering the energy of the transition
state (Fig. 3.20). The active site is
where the substrate binds and the
chemical reaction occurs. The
turnover number (kcat) is the rate
constant for the reaction. It is
equivalent to the number of substrate molecules that can be converted
to product at a single active site per second. The Km is a reflection of
an enzyme’s affinity for the substrate and is mathematically equal to
the substrate concentration at which the reaction rate is 1/2 Vmax (Fig.
3.22b, below). The lower the Km, the higher the affinity of the enzyme
for substrate. The Vmax of an enzyme-catalyzed reaction is the reaction
rate attained when the active sites of all enzyme molecules are bound to
substrate (saturation conditions). The rate constant is a proportionality
constant that when multiplied by the concentration of the ES complex,
gives the reaction rate, V. V becomes equivalent to Vmax when [ES] =
[Etotal].
1/2 Vmax
Chap. 3 Problem 6
Many cellular proteins are
degraded by a large protein
complex known as the proteasome
(p. 85-88). Ubiquitin is a protein
tag that targets proteins to the
proteasome for degradation (Fig.
3.29). Degradation requires
polyubiquitination as shown in the
figure. The degraded protein is
cleaved to small peptides, and the
ubiquitin monomers are recycled.
Proteasome inhibitors that block
degradation of tumor suppressor
proteins are being investigated as
cancer therapeutics.
Chap. 3 Problem 7
Cooperativity refers to a change in
ligand binding affinity or enzymatic
activity in a protein or enzyme that
results from conformational changes
caused by the binding of a regulatory
molecule. Binding of regulatory
molecules fine tunes the activity of
the protein often by changing its
affinity for ligand/substrate. Enzymes
and binding proteins that exhibit
cooperativity have distinctive sigmoidal
shaped activity/binding curves (Fig.
3.30 hemoglobin). Protein
phosphorylation and proteolytic
cleavage also are used to modulate the
function and activity of proteins and
enzymes. Ultimately these
modifications change the conformation
and activity of the protein.