Transcript Chapter 4 Problem Set

Chap. 4. Problem 1.
Part (a). Double and triple bonds
are shorter and stronger than
single bonds. Because the length
of a peptide bond more closely
resembles that of a double bond,
it suggests that a peptide bond
has some characteristics of a
double bond. Thus, a peptide
bond is predicted to be stronger
than a typical single bond.
Part (b). The conclusion that a
peptide bond resembles a double
bond is further supported by the
fact that the two -carbon
atoms attached to the C-N
peptide bond are always trans to
one another. Rotation about this
bond is apparently impossible. As
shown in Fig. 4-2, peptide bonds
have double bond character due
to resonance of electrons among
the atoms of the bond.
Chap. 4. Problem 4. The folding and unfolding of the
Poly(Glu) and Poly(Lys)  helices
results from changes in the charge
of the side-chains of these amino
acids as a function of pH. As the
pH of the solution containing
Poly(Glu) is raised, the carboxyl
group in the Glu side-chain
dissociates and becomes negatively
charged. This results in charge
repulsion that destabilizes the 
helix. For Poly(Lys), elevation of
pH causes the proton on the amino group of the side-chain to
dissociate. This neutralizes the
charge on the R group and allows
the peptide to fold into an  helix.
These transitions occur over a
narrow range of pH due to the
cooperative effects of R group
ionization on structure along the
length of the  helix.
Chap. 4. Problem 5.
Part (a). Disulfide bonds, being
covalent bonds, have a strong
effect on the stabilization of
protein conformation. Disulfide
bonds have marked effects on the
mechanical strength (tortoise
shell) and stiffness (wheat dough)
of the proteins that contain them.
Part (b). Heating of globular
proteins leads to increased
thermal motion of amino acid
residues and disruption of many
noncovalent interactions. However
disulfide bonds are not broken by
heating. The presence of these
bonds prevents the polypeptide
from becoming completely
randomized and can facilitate the
refolding of the protein when the
temperature is reduced.
Chap. 4. Problem 7.
Part (a). ß turns commonly (but
not always) occur where Gly and
Pro residues are found in the
polypeptide chain. Thus, ß turns
might occur at the residue 6-7
and 19-21 positions of the
peptide shown. Note that Gly is
found in ß turns because it is
small and flexible. Pro is
prevalent in ß turns because
peptide bonds involving the imino
nitrogen of Pro readily assume the
cis configuration (Fig. 4-8).
Part (b). An intrachain disulfide
cross-linkage could occur between
the Cys residues of the peptide
located at positions 13 and 24.
Part (c). On the basis of hydrophobicity (Table 3-1), Asp, Gln,
and Lys might be expected to occur on the external surface of a
globular protein. Ile and Ala would be more likely to occur in the
nonpolar interior of a globular protein. Thr has intermediate
polarity and might be present in either location.
Chap. 4. Problem 9.
A motif (also called a fold) is a recognizable folding pattern
involving two or more elements of secondary structure and the
connections between them. A motif can be an elaborate
structure involving multiple protein segments folded together,
such as a large ß barrel. A domain is a part of a polypeptide
chain that is independently stable or could undergo movements
as a single entity with respect to the entire protein. Obviously,
myoglobin is a complete three dimensional structure. In fact, it
is all three of these terms. The folded structure (a.k.a. the
globin fold) is a motif found in all globins. Myoglobin also
consists of a single domain that can be referred to as the globin
domain.
Chap. 4. Problem 10.
The proteins shown in Panels (a)
and (b) are dominated by ß and
 structure, respectively. Based
on  and  angles, ß
conformation occurs in the upper
left quadrant of a Ramachandran
plot, whereas -helical structure
lies in the lower left quadrant
(see Fig. 4-9). Thus it is most
likely that the Ramachandran
plot shown in Panel (c) belongs to
the protein shown in Panel (a),
and the plot in Panel (d) belongs
to the protein shown in Panel (b).
Chap. 4. Problem 11.
The sequence cleaved by this C. perfringens enzyme occurs in
animal collagens (e.g., Gly-Pro-Y, see text p. 127). This suggests
that the enzyme is a member of the collagenase family. This
group of enzymes breaks down collagen and damages the
connective tissue barriers of the skin and hide, etc. of the host
animal allowing the bacterium to better infect the animal.
Bacterial cells lack collagen, and thus the enzyme is not harmful
to the bacterium itself.
Chap. 4. Problem 13.
Based on visual inspection, Peptide b contains 3 Gly and 2 Pro
residues, which are uncommon in  helices. On the other hand,
Peptide a contains 5 Ala residues which are frequently found in 
helices. These data suggest that Peptide a would be more likely
to form an  helix. This assumption is supported by calculating
the values of ∆∆G˚ for folding of the residues of each peptide
into an  helix using the data in Table 4-2. For Peptide a, ∆∆G˚
for helix formation is 13 kJ/mol, whereas ∆∆G˚ is 41 kJ/mol
for Peptide b. Because Peptide a has the lower value of ∆∆G˚,
it is more likely to be folded into an  helix. Note that ∆∆G˚
values are the differences in free energy change relative to
alanine, that is required for an amino acid to take up the helical conformation.