-5 -13

3 2 4
-4 - -7 - -11
3 2 3 2 4 3

-23 -34

Multiple Choice Questions

1. L-alanine and D-alanine
A) are present in virtually all proteins.
B) are superimposable isomers of each other.
C) are enantiomers.
D) lack an R group.
E) none of these

2. The isoelectric point, or pI, of an amino acid or a protein is

A) the pH at which the amino acid or protein has no net charge.
B) zero at pH 7.0.
C) the pH at which the amino acid or protein is neither hydrophobic nor hydrophilic.
D) the measure of the hydropathy of an amino acid or protein.
E) none of these

3. By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to:
A) determine a protein’s isoelectric point.
B) determine an enzyme’s specific activity.
C) determine the amino acid composition of the protein.
D) preserve a protein’s native structure and biological activity.
E) separate proteins exclusively on the basis of molecular weight.

4. Which of the following is true about the Edman degradation system of sequencing polypeptides?
I) The Edman degradation system is carried out on a machine called an Edmanator.
II) The Edman degradation system will work on any size polypeptide.
III) In the Edman degradation system the amino-terminal residue is labeled with fluro dinitrobenzene and
the polypeptide is hydrolyzed with 6m HCl to its constituent amino acids.
IV) In the Edman degradation system the amino-terminal residue is labeled with phenylisothiocyanate,
cleaved with trifluroacetic acid, purified and identified in each successive cycle..

A) I and II B) II and IV C)I, II and III D) IV only E) none of these

1 Developed By –Manojit Bhattacharya.

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5. A nonapeptide was determined to have the following amino acid composition: (Lys)2,
(Gly) 2, (Phe) ,2 His, Leu, Met. The native peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB)
and then hydrolyzed; 2,4-dinitrophenylhistidine was identified by HPLC. When the native peptide was
exposed to cyanogen bromide (CNBr), an octapeptide and free glycine were recovered. Incubation of
the native peptide with trypsin gave a pentapeptide, a tripeptide, and free Lys. 2,4-Dinitrophenyl-histidine
was recovered from the pentapeptide, and 2,4-dinitrophenylphenylalanine was recovered from the
tripeptide. Digestion with the enzyme pepsin produced a dipeptide, a tripeptide, and a tetrapeptide. The
tetrapeptide was composed of (Lys) 2, Phe, and Gly. The native sequence was determined to be:

A) Gly–Phe–Lys–Lys–Gly–Leu–Met–Phe–His.
B) His–Leu–Gly–Lys–Lys–Phe–Phe–Gly–Met.
C) His–Leu–Phe–Gly–Lys–Lys–Phe–Met–Gly.
D) His–Phe–Leu–Gly–Lys–Lys–Phe–Met–Gly.
E) Met–Leu–Phe–Lys–Phe–Gly–Gly–Lys–His.

6. All of the following are considered “weak” interactions in proteins, except:

A) hydrogen bonds.
B) hydrophobic interactions.
C) ionic bonds.
D) peptide bonds.
E) van der Waals forces.

7. The most important contribution to the stability of a protein’s conformation appears to be the:
A) entropy increase from the decrease in ordered water molecules forming a solvent shell around it.
B) maximum entropy increase from ionic interactions between the ionized amino acids in a protein.
C) sum of free energies of formation of many weak interactions among the hundreds of amino acids in a
protein.
D )sum of free energies of formation of many weak interactions between its polar amino acids and
surrounding water.
E)stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and the amino
group of another.

8. In the diagram below, the plane drawn behind the peptide bond indicates the:

A) absence of rotation around the C—N bond because of its partial double-bond character.
B) plane of rotation around the Ca—N bond.
C) region of steric hindrance determined by the large C=O group.
D) region of the peptide bond that contributes to a Ramachandran plot.
E) theoretical space between Ä and +180 degrees that can be occupied by the f and y angles in
the peptide bond.
2 Developed By –Manojit Bhattacharya.
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9. In the 〈 helix the hydrogen bonds:
A) are roughly parallel to the axis of the helix.
B) are roughly perpendicular to the axis of the helix.
C) occur mainly between electronegative atoms of the R groups.
D) occur only between some of the amino acids of the helix.
E) occur only near the amino and carboxyl termini of the helix.

10. In an 〈 helix, the R groups on the amino acid residues:

A) alternate between the outside and the inside of the helix.
B) are found on the outside of the helix spiral.
C) cause only right-handed helices to form.
D) generate the hydrogen bonds that form the helix.
E) stack within the interior of the helix.

11. An 〈 helix would be destabilized most by:

A) an electric dipole spanning several peptide bonds throughout the 〈 helix.
B) interactions between neighboring Asp and Arg residues.
C) interactions between two adjacent hydrophobic Val residues.
D) the presence of an Arg residue near the carboxyl terminus of the 〈 helix.
E) the presence of two Lys residues near the amino terminus of the 〈 helix.

12. Amino acid residues commonly found in the middle of  turn are:
A) Ala and Gly.
B) hydrophobic.
C) Pro and Gly.
D) those with ionized R-groups.
E) two Cys.

13. The 〈 -keratin chains indicated by the diagram below have undergone one chemical step. To alter
the shape of the 〈 -keratin chains—as in hair waving—what subsequent steps are required?

A) Chemical oxidation and then shape remodeling

B) Chemical reduction and then chemical oxidation
C) Chemical reduction and then shape remodeling
Shape remodeling
3D)Developed and then chemical oxidation
By –Manojit Bhattacharya.
E) Shape remodeling and then chemical reduction
 Page
14. Which of the following statements is false?
A) Collagen is a protein in which the polypeptides are mainly in the 〈 -helix conformation.
B) Disulfide linkages are important for keratin structure.
C) Gly residues are particularly abundant in collagen.
D) Silk fibroin is a protein in which the polypeptide is almost entirely in the  conformation.
E) 〈 -keratin is a protein in which the polypeptides are mainly in the 〈 -helix conformation.

15. Which of the following binding constants has the highest affinity?
7 -1
A.) Ka= 1.0 x 10 M
-9
B) Kd= 1.0 x 10 M
-9
C) Kd = 1.5 x 10 M
8 -1
D) K a = 2.0 x 10 M
E) None of these, they are all the same

Essay questions (a total of 70 points)

16. ( 5 points) Fumaric acid and Maleic acid are trans and cis isomers of a four carbon dicarboxylic acid.
Maleic acid has pKa values of 1.83 and 6.02, Fumaric acid has pKa values of 3.02 and 4.44. The equilibria
can be represented by the this short hand notation, where M represents maleic and F represents fumaric:
- -2 - -2
MH2  MH  M and FH2  FH  F

The following energy diagram represents the relative stabiltiy of each form of malic acid and fumarate.
Fill in the diagram by placing the short hand symbols that are used in the equilibria expression above
on the lines that represent the reaction coordinate.
Acid Dissociation Reaction for Maleic and Fumaric
Acids
40

35

30
Free Energy (kJ)

25
ee Energy (kJ)

20

15

10

0
Reaction coordinate

4 Developed By –Manojit Bhattacharya.

17. (5 points) Why does maleic acid have a pKa
2 value that is much higher than the pKa
2 value for
fumaric acid?
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18. (5 points) Match the following protein terms:

A) Chaperonins _____
1. catalyzed by peptidyl prolyl isomerase
B) Disulfide interchange _____ 2. catalyzed by protein disulfide isomerase
3. prevents denaturation of proteins due to
C) Hsp-70_____ increased temperature
4. elaborate protein complexes that hydrolyze
D) Peptide bond hydrolysis_____ ATP in the process of folding proteins
5. catalyzed by chymotrypsin
E) Peptide bond isomerization_____

19. (15 points) Draw the structure for the following peptide at pH 7. Then, calculate the pI for this peptide.
Use pKa=8 for the amino terminus group and pKa =3.4 for the carboxy terminus group. You know all of
the other pKa values for the R groups.

RQPE

5 Developed By –Manojit Bhattacharya.

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20. (20 points) Eight diseases were presented in class. These diseases all in involved the same
protein, but because there are different types of the protein present in different tissues, different
symptoms occur with each disease. Describe the disease that your group presented. Fully describe the
protein that is involved and the cause, treatment and symptoms of the disease.

6 Developed By –Manojit Bhattacharya.

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21. (10 points) The following peptide was cleaved with trypsin and the resulting peptides were
separated by cation exchange chromatography. What are the peptide fragments? What is their order of elution
for these peptides at pH 6 from a cation exchange column. For all of the peptides, the N terminus amino group
pKa is 8 and the C terminus carboxyl pKa is 3.4.

THERQCKIESCANWIN

1. Write about the methods employed in detection of Amino acids, Peptides and
Proteins? [16]
2. Describe the role of hydrophobic forces in tertiary structure. [16]
3. Justify the statement - “Information of final structure of protein lies in its primary
structure”. [16]
4. Describe DNA binding proteins in detail. [16]
5. (a) What are proteases.
(b) Describe different classes of proteases with examples.
(c) Explain the action of serine proteases in details. [5+6+5]
6. Explain the make up of photosynthetic center and their action with respect to their
structure. [16]
7. Explain the steps involved in Protein engineering by directed Mutagenesis and gene
cloning? [16]
8. Describe the basic principles with respect to protein design. [16]

22. (10 points) What amino acid(s) best fit(s) each of these descriptions?
A. This amino acid is rarely found in collagen, but it found in keratin.

B. What two amino acids are found in collagen, but rarely found in keratin?

C. What amino acid is oxidized by one of the treatments that is used to remove disulfide bonds?

D. What three amino acids can be detected by their absorbance of UV light?

E. Give an example of an amino acid that has a side chain that is negatively charged at pH 6.

7 Developed By –Manojit Bhattacharya.