BIOL/CHEM 3361.

002

EXAMPLE EXAM I QUESTIONS

There will be several short answer questions that you can answer on the back of the Scantron sheet.
These will include drawing the structures of one or more amino acids.

2. Lysine
a. has an epsilon amino group
b. can be acetylated on its side chain
c. is abbreviated L
d. a and b
e. a and c

3. The energy of a charge-charge interaction is:

a. less in water than acetic acid
b. angle-dependent
c. inversely proportional to the distance between the charges squared
d. independent of the strength of the charges
e. approximately 2 kJ/mol

4. All of the statements about the classification of these amino acids are correct EXCEPT:
a. Aspartic acid and asparagine are acidic amino acids.
b. Alanine and valine are neutral, nonpolar amino acids.
c. Serine and glutamine are polar, uncharged amino acids.
d. Lysine and arginine are basic amino acids.
e. Tyrosine and phenylalanine are aromatic amino acids.

5. Enthalpy change, ΔH, is:

a. the sum of heat absorbed and work.
b. not a thermodynamic state function.
c. a measure of disorder in a system.
d. determined by pressure change at a constant temperature.
e. equal to the heat transferred at constant pressure and volume.

6. What makes carbon such an abundant element in biomolecules?

a. It can form up to five bonds by sharing its electrons.
b. It forms only single bonds.
c. It provides low bond energy.
d. It forms stable covalent bonds by electron pair sharing.
 e. It does not usually bond to other carbons, allowing a more diverse combination of
elements.

7. At physiological pH, the ratio of positively to negatively charged amino acid residues in
proteins in general is approximately
a. 3:1
b. 2:1
c. 1:1
d. 1:2
e. 1:3

8. If the side chain pka of an Asp residue is shifted to 4.5 by the microenvironment, what fraction
of the residue will exist as the conjugate base at pH 5.5?
a. 0.09
b. 0.25
c. 0.50
d. 0.82
e. 0.91

9. Which of the following properly ranks the non-covalent interactions in order of increasing
strength?
a. ionic, hydrogen bond, van der Waals
b. van der Waals, hydrogen bond, ionic
c. van der Waals, ionic, hydrogen bond
d. hydrogen bond, van der Waals, ionic
e. cannot be determined since ionic interactions and hydrogen bonds often vary in
strength

10. Assuming typical pKas for its residues, what charge is carried by the peptide FREEENERGY
at pH 8?
a. +0.5
b. +1.0
c. -2.0
d. -1.5

11. Which of the following peptides would have the largest extinction coefficient at 280 nm?
a. PAVYWC
b. WNAWMG
c. PFWPGA
d. SFAFTT
e. YMHGYH

12. The tetrameric structure of hemoglobin is an example of which level of protein structure?
a. 1st
b. 2nd
 c. 3rd
d. 4th
e. 5th

13. For the reaction below at 25º C, Gº = -18 kJ/mol. What is Keq for this reaction? R is 8.31
J/Kmol
AC+D
a. 2.6 x 104
b. 2.6 x 104 M
c. 1.4 x 103
d. 1.4 x 103 M
e. 1.7 x 103 M-1

14. For the reaction below at 25º C, Gº = -52 kJ/mol and Hº = -12 kJ/ mol. What is Sº for
this reaction? R is 8.31 J/Kmol
AC+D
a. +134 J/K mol
b. -134 J/K mol
c. - 24 J/K mol
d. +37 J/K mol
e. - 37 J/K mol

15. If the conjugate [base]/[ acid] ratio for a weak acid is 1000/1, what is the pH of the solution?
a. pI + 1
b. pKa + 2
c. pKa + 3
d. pI - 2
e. pKa - 3

16. An interaction between two subunits of a protein was determined to have a ΔG°’= -57.05
kJ/mol. What is the Keq for the reaction at 25°C?
a. 1.02
b. 1.32
c. 10-10
d. 1010
e. cannot determine from given information

17. Which of the following proteins would emerge first from a CM-cellulose column run at pH
6.5?
a. A (Mr 23,500; pI 7.0)
b. B (Mr 125, 200; pI 7.5)
c. C (Mr 93,650; pI 8.3)
d. D (Mr 54,500; pI 9.1)
e. E (Mr 12,300; pI 10)

18. Pure liquid water consists of H2O molecules:

 a. held in a rigid three-dimensional network.
b. with local preference for linear geometry.
c. with large numbers of strained or broken hydrogen bonds.
d. which do not switch H-bonds readily.
e. all are true.

19. Based upon the following reactions, what would be the ΔG°’ for the formation of ATP from
phosphoenolpyruvate and ADP?

ATP > ADP + Pi ΔG°’ = -31.5 kJ/mol

phosphoenolpyruvate > pyruvate + Pi ΔG°’ = -62.2 kJ/mol

a. -93.7 kJ/mol
b. -30.7 kJ/mol
c. +30.7 kJ/mol
d. +93.7 kJ/mol
e. cannot determine from given information

21. Estimate the pH of the resulting solution prepared by mixing 1.0 mole of solid disodium
phosphate (Na2HPO4) and 1.25 mole of hydrochloric acid. The pKa values for phosphoric acid
are 2.1, 7.2, 12.4.
a. pH < 2.1
b. pH = 2.1
c. 2.1 < pH < 7.2
d. pH = 7.2
e. 7.2 < pH < 12.4

22. A Van’t Hoff Plot with a negative slope indicates:

a. spontaneous reaction
b. non-spontaneous reaction
c. endothermic reaction
d. exothermic reaction
e. favorable entropy

23. Molecules of a given protein have all EXCEPT:

a. a fixed amino acid composition.
b. a defined amino acid sequence.
c. a sequence read from C-terminal end to N-terminal end.
 d. an invariant molecular weight.
e. a nucleotide sequence from which they are encoded.

24. H-bonding by water is cooperative. This means:

a. a water molecule cannot H-bond with a non-water molecule
b. a water molecule can form four H-bonds
c. a water molecule with two H-bonds is likely to form additional H-bonds
d. H-bonds forged by a water molecule are 0.274 nm
e. H-bonds in solution water are constantly breaking and being reformed

25. Reverse phase chromatography:

a. separates proteins based on hydrophobicity
b. can use a decreasing salt gradient to elute bound proteins
c. can use an increasing non-polar solution gradient to elute bound proteins
d. is commonly used to separate peptides
e. all of the above

26. The optimal distance for a van der Waals interaction is:
a. a lot less than the sum of the van der Waals radii
b. slightly less than the sum of the van der Waals radii
c. the sum of the van der Waals radii
d. slightly more than the sum of the van der Waals radii
e. a lot more than the sum of the van der Waals radii

27. Two-dimensional gel electrophoresis separates proteins based on ________, and is typically
________.
a. size and pI, analytical
b. size and pI, preparative
c. size and hydrophobicity, analytical
d. size and hydrophobicity, preparative
e. none of the above

28. (2.5 pts) Explain how hydrophobic interactions make the entropy of a system more favorable.

1 pt if there was a reasonable description of hydrophobic interactions

1.5 pts if it was noted that the entropy of a system becomes more favorable because when
hydrophobic interactions occur LESS water molecules are organized at the surface of the
hydrophobic molecule

29. (10 pts) Define the following terms

a. pKa
pKa = -log Ka where Ka is the acid dissociation constant
OR
pKa is the pH at which the concentration of the conjugate base is equal to the concentration of
the acid

[If only write pKa = -log Ka then only get 2 pts]

b. pI
pI is the pH at which the amino acid or protein has a net charge of zero

[If mention isoelectric point get 1 pt; if mention average of two pKa values get 1 pt]

c. ΔG°’
The free energy change at standard state conditions and pH 7.0. This means that all reactants and
products are at a starting concentration of 1 M, except [H+] which is at 10-7M.

[If mention standard state and pH 7 without reference to 1 M concentrations get 2 pts; if mention
free energy get 0.5 pts]
d. Amphipathic
Molecule containing both polar and non-polar parts

[If suggest only applies to amino acid or protein the get 2 pts]