University of Santo Tomas

College of Science
Department of Chemistry

CHM 4111
PROTEINS: Structure and Function

1. Describe the four levels of protein structure. Do all proteins exhibit all four levels?
2. A protein is subjected to end group analysis by dansyl chloride. The liberated dansylamino acids are found
to be present with a molar ratio of two parts Ser to one part Ala. What conclusions can be drawn about the
nature of the protein?
3. Treatment of a polypeptide by 2-mercaptoethanol yields two polypeptides that have the following amino
acid sequences:
1. Ala-Phe-Cys-Met-Tyr-Cys-Leu-Trp-Cys-Asn
2. Val-Cys-Trp-Val-Ile-Phe-Gly-Cys-Lys
Chymotrypsin-catalyzed hydrolysis of the intact polypeptide yields polypeptide fragments with the
following amino acid compositions:
3. (Ala, Phe)
4. (Asn, Cys2, Met,Tyr)
5. (Cys, Gly, Lys)
6. (Cys2, Leu,Trp2,Val)
7. (Ile, Phe,Val)
Indicate the positions of the disulfide bonds in the original polypeptide.
4. A polypeptide was subjected to the following treatments with the indicated results. What is its primary

structure?
I. Acid hydrolysis:
1. (Ala,Arg, Cys, Glx, Gly, Lys, Leu, Met, Phe,Thr)
II. Aminopeptidase M:
2. No fragments
 III. Carboxypeptidase A _ carboxypeptidase B:
3. No fragments
IV. Trypsin followed by Edman degradation of the separated products:
4. Cys-Gly-Leu-Phe-Arg
5. Thr-Ala-Met-Glu-Lys

5. Explain why the conformational freedom of peptide bonds is limited.

It is limited due to the planar structure of a polypeptide, but also because of the resonance structure that
puts a double bond between the nitrogen and the now-not-carbonyl carbonyl carbon. You can't rotate a
double bond, and some of that character is in that spot due to resonance.
6. Summarize the features of an α helix and a parallel and antiparallel β sheet.
 In parallel beta-sheets the strands all
run in one direction, whereas in
antiparallel sheets they all run in
opposite directions. In mixed sheets
some strands are parallel and others
are antiparallel. In the classical Pauling-
Corey models the parallel beta-sheet
has somewhat more distorted and
consequently weaker hydrogen bonds
between the strands.

Beta-sheets are very common in

globular proteins and most contain less
than six strands. The width of a six-
stranded beta-sheet is approximately
25 Angstroms. No preference for
parallel or antiparallel beta-sheets is
observed, but parallel sheets with less
than four strands are rare, perhaps
reflecting their lower stability. Sheets
tend to be either all parallel or all
antiparallel, but mixed sheets do occur.

The Pauling-Corey model of the beta-

sheet is planar. However, most beta-
sheets found in globular protein X-ray
structures are twisted. This twist is left-
handed as shown below. The overall
twisting of the sheet results from a
relative rotation of each residue in the
strands by 30 degrees per amino acid in
a right-handed sense. Parallel sheets are less twisted than antiparallel and are always
buried. In contrast, antiparallel sheets can withstand greater distortions (twisting and beta-
bulges) and greater exposure to solvent. This implies that antiparallel sheets are more
stable than parallel ones which is consistent both with the hydrogen bond geometry and
the fact that small parallel sheets rarely occur

 * Hydrogen bonding btwn neighboring polypeptide chains

* Each strand has 2-residue repeat
* Parallel: chains extend in same direction
* Anitparallel: chains run in opposite directions
*** Parallel less stable than antiparallel
7. What properties do fibrous proteins confer on substances such as hair and bones?
Fibrous proteins, which are elongated molecules that often have 1 dominant type of secondary structure,
are responsible for the mechanical properties (ex., high tensile strength) of hair, bones, etc.
8. Describe the features of the amino acid sequences that are necessary to form a coiled coil or a left-handed
triple helix.
Collagen is a triple helix
* 1/3 of residues are Gly; ~15-30% are Pro or Hyp
*Repeating triplets: Gly-X-Y (X often Pro; Y often Hyp)
*3 Left-handed parallel chains wrap= right-handed helical structure
*3 residues per turn
9. How can you differentiate between regular and irregular secondary structures?
Unlike regular secondary structure, successive residues in irregular secondary structure do not have
the same backbone configuration.
10. Explain why knowing a protein’s amino acid sequence is required to determine its tertiary structure. Why do
turns and loops most often occur on the protein surface?
11. Which side chains usually occur on a protein’s surface? In its interior?
12. Describe some of the common protein structural motifs.
13. What is the effect of the following changes on the O2 affinity of myoglobin and hemoglobin?
 (a) A drop in the pH of blood plasma from 7.4 to 7.2.
(b) A decrease in the partial pressure of CO2 in the lungs from 6 kPa (holding one’s breath) to 2 kPa
(normal).
(c) An increase in the BPG level from 5 mM (normal altitudes) to 8 mM (high altitudes).
14. Studies of oxygen transport in pregnant mammals have shown that the O2-saturation curves of fetal and
maternal blood are markedly different when measured under the same conditions. Fetal erythrocytes contain
a structural variant of hemoglobin, HbF, consisting of two γ and two β subunits (γ2β2), whereas maternal
erythrocytes contain HbA (α2β2).
(a) Which hemoglobin has a higher affinity for oxygen under physiological conditions, HbA or HbF?
Explain.
(b) What is the physiological significance of the different O2 affinities?
(c) When all the BPG is carefully removed from samples of HbA and HbF, the measured O2-saturation
curves (and consequently the O2 affinities) are displaced to the left. However, HbA now has a greater
affinity for oxygen than does HbF. When BPG is reintroduced, the O2-saturation curves return to
normal, as shown in the graph. What is the effect of BPG on the O2 affinity of hemoglobin? How can the
above information be used to explain the different O2 affinities of fetal and maternal hemoglobin?