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1.   Enzymes increase the rate of a reaction by
     a. decreasing the activation energy
     b. increasing the overall free energy of the reaction
     c. increasing the activation energy
     d. a and b
     e. b and c

2.  Which of the following is true about Km ,the Michaelis constant?
     a. Km= (k2+k3)/k1
     b. it is the [S] when V = Vmax/2
     c. it is dependent on pH, temperature and ionic strength
     d. all of the above
     e. none of the above

3.  Which of the following is demonstrates the allosteric characteristic of Hb
     a. the oxygen binding curve is sigmoidal
     b. the oxygen binding curve is hyperbolic
     c. sensitive to BPG and exhibits the Bohr effect
     d. b and c
     e. a and c

4. At equilibrium
     a.  G = 1
     b.  G = 0
     c.  G < 1
     d.  G > 1
     e. all of the above

5. Which one is NOT true of SDS-gel electrophoresis?
     a. it can provide large amounts of purified proteins in their native state
     b. it separates proteins on the basis of net charge
     c. it separates proteins on the basis of mass
     d. a and b
     e. all of the above

6.  Which of the following affects the hemoglobin binding affinity for O2?
     a. pH
     b. H+
     c. BPG
     d. [CO2]
     e. all of the above

7.   Enzymes bind to substrates to form:
     a. activation energy
     b. product
     c. ES complex
     d. active sites
     e. reactants

8. Competitive inhibition can be overcome
     a.  by a sufficiently high [S]
     b. by a sufficiently low [S]
     c. by adding more enzyme
     d. by dilution
     e. none of the above

9.  Disadvantages of Sanger's method for N-terminal analysis include
     a. the reagents react with several R groups, giving false results
     b. it is not very sensitive
     c. it destroys the entire protein
     d. a and b
     e. all of the above

10.  The phenomenon that a molecule with a net charge will move in an electric field is called:
     a.  isoelectric focusing
     b.  electrophoresis
     c.  chromatography
     d.  net charge
     e.  autoradiography

11. Substrates are held in the active site of an enzyme by
     a. hydrogen bonds
     b. ionic bonds
     c. action of coenzymes
     d. shape of the active site
     e. all of  the above

12. Proteins can be purified in active form on the basis of which characteristics?
     a.  size
     b.  size,  solubility
     c.  size, solubility, charge
     d.  size, solubility, charge, specific binding affinity
     e.  none of the above

13. Which factors affect hemoglobin's ability to bind oxygen
     a. CO2
     b.  pH
     c.  BPG
     d.  a and b
     e.  all of the above

14. An inhibition characterized by rapid dissociation of the enzyme-inhibitor complex is
     a.  reversible inhibition
     b. irreversible inhibition
     c. feedback inhibition
     d. a and c
     e. b and c

15.   Which of the following is true about the Lineweaver-Burk plot ?
     a. its slope = Vmax / Km
     b. its intercept with y-axis = 1 / Vmax
     c. it is a plot of V versus [S]
     d. its intercept with x-axis = 1 / Km
     e. none of the above

16.  Myoglobin and hemoglobin have a decreased affinity for CO because:
     a. the heme group naturally has a stronger affinity for oxygen
     b. the distal histidine creates steric hinderance
     c. CO is more stable when it binds to the heme group at an angle
     d. O2 is more stable when it binds to the heme group linearly
     e. myoglobin and hemoglobin does not have decreased affinity for CO

17. The amino-terminal residue (N-terminus) of a protein can be identified by labeling it with
     a. fluorodinitrobenzene
     b. dabsyl chloride
     c. CNBr
     d. a and b
     e.  all of the above

18. CnBr cleaves after
     a. cys
     b. met
     c. his
     d. a and b
     e. all of the above

19.  Enzymes are controlled by
     a. calmodulin, a regulatory protein
     b. phosphorylation of serine
     c. phosphorylation of threonine
     d. proteolytic activation
     e. all of the above

20. Competitive inhibition can be overcome
     a.  by a sufficiently high [S]
     b. by a sufficiently low [S]
     c. by adding more enzyme
     d. by dilution
     e. none of the above

21. Which of the following is/are method(s) of separating proteins?
     a. gel-filtration chromatography
     b. salting out
     c. according to net charge by ion - exchange chromatography
     d. affinity chromatography
     e. all of the above

22. The linear binding of carbon monoxide to hemoglobin and myoglobin
     a. is made possible by the steric interaction of the proximal his
     b. is made possible by the steric interaction of the distal his
     c. is prevented by the steric interaction of the distal his
     d. is prevented by the steric interaction of the proximal his
     e. is prevented by the steric interaction of both proximal and distal his

23. Hundreds of proteins have been sequenced by
     a.  Edman degradation
     b.  recombinant DNA technology
     c.  electrospray mass spectrometry
     d.  a and b
     e.  all of the above

24. The primary structure of HbA and HbS
     a. are identical; the difference is in the tertiary and quaternary structures
     b. differ by 1 amino acid residue
     c. differ by 2 amino acid residues
     d.  differ by 1 amino acid residue per subunit
     e. differ by several amino acid residues

25. Decreasing pH causes:
     a. hemoglobin and myoglobin to increase their oxygen affinity
     b. hemoglobin to increase its oxygen affinity; myoglobin is not affected by pH
     c. hemoglobin to decrease its oxygen affinity; myoglobin is not affected by pH
     d. myoglobin to increase its oxygen affinity; hemoglobin is not affected by pH
     e. myoglobin to decrease its oxygen affinity; hemoglobin is not affected by pH

26. The change in Gibbs free energy,  G,
     a. is directly proportional to the change in standard free energy,  Go
     b. = 0 at equilibrium
     c. can only be calculated when the reactants and products are present at 1M
     d. < 0 when the reaction is nonspontaneous
     e. indicates the rate and direction of the reaction

27. Fetal hemoglobin (HbF) has a greater affinity for O2 than adult hemoglobin (HbA) because
     a. Hb loses its affinity for O2 as we age
     b. the   chains of HbF, unlike the  -chains of HbA, are able to interact, increasing the protein' O2
          affinity
     c. HbF binds BPG more strongly than does HbA
     d. HbF binds BPG less strongly than does HbA
     e. both b and c contribute

28. Which of the following is true about the change in free energy ( G)?
     a. a reaction can occur spontaneously only if delta G is negative
     b. a system is at equilibrium and no net change can take place if  G=0
     c. a reaction cannot occur spontaneously if  G is positive
     d. an input of free energy is required to drive a reaction with positive  G
     e. all of the above

29. A non-competitive inhibitor of an enzyme
     a. increases Km without necessarily affecting Vmax
     b. decreases Km without  necessarily affecting Vmax
     c. increases  Vmax without  necessarily affecting Km
     d. decreases Vmax without  necessarily affecting Km
     e. decreases both Km and Vmax

30. Enzymes
     a. alter reaction equilibria
     b.  accelerate reactions by stabilizing transition states
     c. are highly specific
     d. have immense catalytic power
     e. all of the above

31. Which of the following is true ?
     a. in competitive inhibition, the x- intercept of the plot of 1/V versus 1/[S] and the slope are the same in
          the presence and absence of inhibitor
     b. in noncompetitive inhibition, Vmax is decreased, so the y-intercept is also decreased
     c. the hallmark of noncompetitive inhibition is that it can be overcome by a sufficiently high [S]
     d. a and b
     e. none of the above

32. All the following are true about  G EXCEPT:
     a. reactions occur spontaneously only if   G is negative
     b.  G of a reaction is path dependent
     c.  G provides no information about the rate of the reaction
     d. G is the change of free energy of a system
     e. A system is at equilibrium if  G = 0

33. The order of emergence of molecules in gel electrophoresis is:
     a.   the same as gel filtration chromatography - Large molecules travel more rapidly than small
     b.  the same a gel filtration chromatography - Small molecules travel more rapidly than large
     c. opposite of gel filtration chromatography.  In electrophoresis, small molecules travel more rapidly
          than large, and in gel filtration, large molecules travel more rapidly than small
     d.  opposite of gel filtration chromatography.  In electrophoresis, large molecules travel more rapidly
          than small, and in gel filtration, small molecules travel more rapidly than large
     e.  identical, because these are two names for the same technique
 

34.                      a specific protein whose activity is altered by increased pH

35.                           a specific protein whose activity is altered by binding a metal

36.                           a specific protein whose activity is altered by binding a nucleotide

Part II.  [50 pts]  Short answer.  Choose 10. 5 points each

1.  One of the first steps in protein sequencing is determining the number of different polypeptide chain
subunits comprising the protein.  Briefly describe the methods used for this analysis.  Be sure to mention AT
LEAST two different approaches used.

2.  Indicate the correct answer, and EXPLAIN:  The catalytic activity of an enzyme will
     a. increase with increasing temperature
     b. increase with decreasing temperature
     c. be unaffected by temperature
     d. be greatest within some particular temperature range
     e. any of the above might be true; it depends on the enzyme

3.  Why is it necessary to fragment a purified polypeptide before amino acid sequencing?

4.  Why is it necessary to fragment a polypeptide in more than one fashion, and sequence each set of fragments.
Illustrate this approach using a theoretical example.

5.  Briefly describe two different techniques for isolating (purifying) and characterizing a polypeptide.  What
characteristics can, and which can not be inferred from the two techniques you chose?

6. Sketch a kinetic plot (V x [S]) of an enzyme + a competitive inhibitor.  Sketch the corresponding
Lineweaver-Burk plot.  Explain the effect of the inhibitor - why does it affect the kinetics in this way?

7. Sketch a kinetic plot (V x [S]) of an enzyme + a non-competitive inhibitor.  Sketch the corresponding
Lineweaver-Burk plot.  Explain the effect of the inhibitor - why does it affect the kinetics in this way?

8, 9. [10 points] Compare the concerted and sequential models of allosteric cooperativity  [Bonus .. 1 pt:   Is it
important to this discussion what the number of allosteric components (binding sites) per protein unit is?
Explain why or why not.] 10. Under what circumstances will an enzyme's kinetic V x [S] plot be hyperbolic, and when sigmoidal?  Explain.

11,12.  [10 points] Describe and explain the biochemistry underlying the familiar pattern of oxygenated and
deoxygenated blood circulating through our (and all animals which use blood to circulate gasses) circulatory
system.  Specifically: a) describe the O2-binding properties of hemoglobin and myoglobin in the lungs; b) in
tissues such as muscles; c) what causes the differences in these two extreme  ends  of  the circulatory system.
Note: O2 partial pressure is only part of the story.

13. Under what circumstances, if any, can a substrate and an inhibitor bind a enzyme simultaneously.  What is
the significance of this?
 

EXTRA CREDIT: Write your own question and answer it.  HINT: this is you opportunity to show what you
know.  Do not ask yourself a question if you aren't sure of the answer.  Ask the question you were sure would
be on the exam, so you studied the material, and then somehow it was left off!  Your score will depend on the
quality of the question as well as the answer - up to a possible maximum of 5 pts.