Name:

1. If you are ill, leave now and send an email. Your classmates don't want
your germs!
2. NO graphing calculators.
3. ALL backpacks, caps, phones (off), etc. should be placed at the front of
the room ASAP - exams will not be handed out until everyone is in
place. Be sure to keep your student ID with you.
4. Prepare your answer sheet with your name AND eID bubbled in.
5. Check your VERSION number (bottom center of the first page) and
bubble this in on your answer sheet under "Special Codes" beneath the
"A" column. Unless you do this you will NOT get a grade!
6. Tear off and use the cover sheet to protect your answer sheet from
roving eyes.
7. The last page of this exam is blank and may be torn off and used for
scratch paper.
8. There are 8 pages and 55 questions in this exam.
9. There are exam proctors as well as TAs among you, so keep your eyes
on your own paper.
10. Turn in BOTH the answer sheet and the exam in the trays that
correspond to your version. IF YOU PUT YOUR ANSWER SHEET IN THE
WRONG TRAY, IT WILL BE SCORED TO THE WRONG KEY.
Amino Acid PKal PKa2 PKa3
(a-carboxy) (a-amino) (side chain)
Glycine 2.35 9.78
Alanine 2.35 9.87
Valine 2.29 9.74
Leucine 2.33 9.74
Isoleucine 2.32 9.76
Methionine 2.13 9.28
Proline 2.95 10.65
Phenylalanine 2.16 9.18
Tryptophan 2.43 9.44
Serine 2.19 9.21
Threonine 2.09 9.10
Asparagine 2.10 8.84
Glutamine 2.17 9.13
Tyrosine 2.20 9.11 10.13
Cysteine 1.92 10.78 8.33
Lysine 2.16 9.18 10.79
Arginine 1.82 8.99 12.48
Histidine 1.80 9.20 6.00
Aspartic acid 1.99 9.90 3.90
Glutamic acid 2.10 9.47 4.07

Version 1 Cover Sheet

 CH 369 Exam 2 March 5, 2013
Name: eID

Helpful Equations:

Vmax [S] / \ [I]

1 Km 1 1
= —+— a =1+—
0 Km + [S] v0 Vmax j [S] Vmax K1
\
1 ( aK 1 1
Competitive Inhibition: —= +
v00 vm: , [s] v
r \
1 aK m 1 a
'

Noncompetitive/Mixed Inhibition: — = r 1+
v0 \ Vmax " 15.1 Vmax

1 iK 1
Uncompetitive Inhibition: — = m — +--c----
v0 Vmax j [S] Vmax

RT [ion] [ion]
A yt = —ln "'= 0.058 loglo [ion]( at 20°C for Z = 1) AG = RT In '" +ZFA'P
ZF [ion] Out 1outu [ion]

R= 8.3145 J • K-1 • mol -I T (K)= T (°C) + 273 F = 96,485 J • V:' • mol -1

Section I: 16 points (1 point each)

1. In which of the following mechanisms is the first product released before the second substrate binds?
A) random sequential B) ordered sequential C) ping pong

2. Due to the hydrophobicity of the lipid bilayer, small ions like K+ are never able to leave the cell by simple
diffusion.
A) True B) False

3. Ion channels can open in response to which of the following

A) Changes in membrane potential D) A and C
B) Changes in pH E) All of the above
C) Binding of a specific ligand

4. A molecule moves across a membrane from a lower to a higher concentration with the aid of a membrane protein.
This process is known as:
A) chemiosmotic coupling B) diffusion C) active transport D) facilitated transport

5. What type of protein secondary structure predominates in G-protein coupled receptors?

A) a helices B) [3 sheets C) B-type helices D) None predominates

6. What is unique about the nature of a low-barrier H-bond as compared to a typical H-bond?
A) The H-bond forms between 2 electronegative elements.
B) Only an H nucleus is small enough to approach the lone pair electron cloud.
C) The length of the H-bond is shorter and therefore stronger.
D) A low-barrier H-bond results in less energy stabilization than in a typical H-bond.

7. Which of the conditions below represents a steady state?

A) d[S]ldt = 0 B) d[ES]ldt = 0 C) d[P]ldt =0 D) d[S]ldt = cl[P]ldt

Version 1 Page 1
 8. Feedback inhibition is a feature of what type of enzymatic control?
A) Genetic control D) Compartmentalization
B) Covalent modification E) Both B and C are correct.
C) Allosteric regulation

9. Can an enzyme that obeys Michaelis-Menten kinetics be influenced by allosteric effectors?

A) Yes B) No

10. Which of the following is NOT a function of lipid molecules?

A) signaling molecules D) hormone precursors
B) components of proteins E) catalysts
C) vitamins

11. A ligand that binds to a receptor to elicit a biological effect is known as a(n)
A) antagonist B) agonist C) protagonist D) inverse agonist

12. What is the one defming feature of lipids?

A) They all contain flexible hydrocarbon chains. D) They all contain large polar head groups.
B) They are all a type of fatty acid. E) They all can form polymers.
C) They are all primarily hydrophobic.

13. Chymotrypsin catalyzes peptide bond cleavage after large nonpolar residues and will not hydrolyze any other type
of bond.
A) True B) False

14. Which of the following would be a proper expression for the dissociation constant associated with ligand (L)
binding to receptor (R)?
[ Ri[L] [R • 1.1 [Li
A) K d = B) K d = C) K d =
[R • 1,1 [R][L] [R] [R • Li

15. Which of the following amino acids is (are) capable of participating in acid/base catalysis?
A) Thr B) Arg C) Met D) Asp E) Gln F) none of the above G) all of the above

16. Which type of secondary structure present in integral membrane proteins is readily detectable in the primary
structure?
A) membrane-spanning a helix B) membrane-spanning (3 sheet

Section II: 66 points (2 points each)

17. Which of the following statements regarding the free energy changes of an enzyme-catalyzed reaction is TRUE?
A) A large negative AGE„ indicates that all of the transition state molecules will be converted to product.
B) A large negative AGm, indicates a low energy of activation.
C) A large positive AGru, indicates that the reaction will proceed spontaneously in the reverse direction as that in
which it is written.
D) Transition states for the slow reactions have much longer lifetimes than those for fast reactions.
E) Both A and C are true.
F) Both C and D are true.

Version 1 Page 2
18. Which of the following statements about the insulin receptor is FALSE?
A) It is a dimer of dimers.
B) The individual polypeptide chains are connected by disulfide bonds.
C) Insulin binds to the dimer of a subunits.
D) The tyrosine kinase activity resides in the p subunits.
E) The receptor does not undergo a conformational change upon binding insulin because it is already in the
dimer form.
F) Both C and E are false.
G) Both D and E are false.

19. Insulin binds to a receptor that

A) is coupled directly to a G protein. D) migrates to the nucleus to affect transcription.
B) possesses tyrosine kinase activity. E) directly activates MAP kinase.
C) possesses serine/threonine phosphatase activity.

20. What would occur when the action potential for muscle contraction reaches its terminus, if SNARE complexes
were not functioning?
A) Calcium ions would not enter the axon terminus.
B) Acetylcholine would not be packaged into vesicles and would eventually degrade.
C) Muscle contraction would still occur but at a slower rate.
D) Acetylcholine released from the axon terminus would be unable to bind to the receptors on the muscle cell in
order to cause contraction.
E) Membrane fusion would not occur and there would be no release of acetylcholine into the synaptic cleft.

Use the following to answer questions 21-23:

A Lineweaver-Burk plot is shown below for three different enzyme-catalyzed reactions.

21. If the reactions catalyzed by E2 and E3 represent the same reaction in the presence and absence of an inhibitor,
what type of inhibition would thereby be indicated?
A) competitive B) noncompetitive C) mixed D) uncompetitive

22. Which enzyme has the highest Vmax value?

A) El B) E2 C) E3

23. Which enzyme has the highest KM value?

A) El B) E2 C) E3

24. Calculate the intracellular concentration of Na+ when the extracellular concentration is 120 mM and the
membrane potential is -50 mV at 20°C.
A) 16.5M B) 0 C) 16.5 mM D) 1.14 mM E) 114 mM

Version 1 Page 3
25. The presence of an inhibitor causes both the slope and the y-intercept of a Lineweaver-Burk plot to increase
compared to those values in its absence. Which of the following types of inhibitors might be present?
A) competitive E) Either A or B
B) noncompetitive F) Either A or C
C) uncompetitive G) Either B or D
D) mixed

26. Which of the following would be likely to form a bilayer in a solution containing only the lipid indicated?
A) fatty acids F) B and E
B) glycerophospholipids G) B, D and E
C) triacylglycerols H) B, C, D and E
D) cholesterol I) All of the above
E) sphingolipids

27. The action of phospholipase C results in the formation of 2 second messengers. Which of these is lipid soluble?
A) diacylglycerol B) phosphatidylinositol bisphosphate C) inositol trisphosphate D) cAMP

28. Which of the sterol-based molecules below would be the LEAST soluble in an aqueous environment?
OH

Choksterel

cn,
CH
HO
Testosterone Estradiol

Cortisol Aldosterone

A) A B) B C) C D) D E) E

29. Which of the following lipids are isoprene derivatives (structures are labeled according to answer choices)?
0
O 0 CH 3
H 3C
H 3C 0

CH 3
A) B) 6-10

OH

C)
A) sphingomyelin D) Both A and B
B) ubiquinone E) Both B and C
C) retinol F) All of the above

30. How many acyl groups are attached to a sphingosine backbone in order to form a sphingomyelin molecule?
A) 0 B) 1 C) 2 D) 3

31. Which of the following cases would NOT be likely to obey Michaelis-Menten kinetics?
A) A transaminase reaction D) B and C
B) An allosteric enzyme E) All of the above
C) A multi-step reaction

Version 1 Page 4
32. The GTPase activity of the alpha subunit of the G-protein is similar to the activity of which class of enzymes?
A) lyases B) hydrolases C) oxidoreductases D) transferases E) ligases

33. At what point on this reaction coordinate diagram of covalent catalysis has the covalent bond with the enzyme
been fully formed?

Free energy
(G)

Products

Reaction coordinate

A) A B) B C) C D) D

34. The compound DFMO (below, bottom) is an inhibitor of ornithine decarboxylase, which eliminates CO2 from
ornithine (below, top). After carboxyl elimination from DFMO, the fluorine atom is also eliminated and the
molecule attaches to an active site Cys or Lys residue. Which of the following best describes inhibition of
ornithine decarboxylase by DFMO?
O

COO-

C HE,
NH 2
DEMO
A) reversible competitive inhibitor C) irreversible inhibitor
B) reversible mixed inhibitor D) suicide substrate

35. Which of the following could participate in proton transfer?

A) Asp and Glu F) A and B
B) His G) B and C
C) Lys and Arg H) A, B and C
D) Cys and Ser I) All of the above
E) Tyr

36. What would be the velocity of the reaction: A + B -3 C when [A] = 5µM and [B] = 11 [Link] and the rate constant
of the reaction is 600 M - l•s-1 ?
A) 3.3 x 10-8 M/s B) 3.3 x 104 M/s C) 0.033 M/s D) 273 M/s E) 1.3 x 10 4 M/s

37. Based on the reaction below, how would the enzyme catalyzing this reaction be classified?
0 0- 0
\
H3 N"-C-H C -H

H -C -H -1111"- H NI-14+

N CH N CH

I
HC
I
NH HC
I NH
A) Oxidoreductase B) Hydrolase C) Lyase D) Ligase E) Transferase

Version 1 Page 5
38. In the simple enzyme-catalyzed reaction below, which of the rate constants would be first order?
ki k2
E+S ES E+P
k-
A) lc, B) k-1 C) k2 D) A and B E) B and C

39. Kidney cells include two antiport proteins, a H+/Na+ exchanger and a C1 -/HCO3 exchanger. What is the source of
free energy that drives the transmembrane movement of all these ions?
A) ATP hydrolysis C) primary active transport
B) Transfer of phosphoryl group D) secondary active transport

40. Signal transduction can be mediated by two different types of receptors that use different pathways of activation.
What do they share in common?
A) They are both transmembrane proteins.
B) The process begins with a conformational change induced by ligand binding.
C) They all interact with G proteins.
D) A and B are both true.
E) All of the above are true.

41. The Ne/glucose transporter is an example of

A) a uniporter E) secondary active transport
B) a symporter F) B and D
C) simple diffusion G) A and C
D) primary active transport H) B and E

42. Which of the following is FALSE regarding the catalytic mechanism of chymotrypsin?
A) Ser195 functions as a covalent catalyst
B) His57 functions as a base catalyst
C) His57 functions as an acid catalyst
D) The function of the oxyanion hole is best explained by the induced fit model of substrate binding.
E) Asp 102 stabilizes the transition state through low-barrier H-bonds.

43. Which of the following statements regarding catalytic efficiency is TRUE?

A) It reflects both substrate binding and catalytic events.
B) The quantitative measure is Km/kcat.
C) It is the apparent first order rate constant for ES formation.
D) It increases with KM.
E) It decreases with kat.

44. In the catalytic mechanism of chymotrypsin, what is represented by the two hills in the reaction coordinate?
A) His 57 acting as a base catalyst twice in the mechanism
B) Water entering the active site
C) The tetrahedral intermediates, where oxygen acts as a nucleophile attacking the carbonyl carbon
D) His 57 acting as an acid catalyst, donates a proton to the nitrogen of the scissile peptide bond
E) The departure of the C-terminal portion of the cleaved peptide

45. Glutamate acts as a neurotransmitter in the brain. The Glu transporter also transports 3 Na+ and 1 H+ along with
Glu and 1 K+ in the opposite direction. What is the net charge imbalance across the cell membrane for each Glu
transported at physiological pH?
A) +4 B) +3 C) +2 D) +1 E) 0

Version 1 Page 6
46. Bacteria of the genus Lactobacillus produce lactobacillic acid, a 19-carbon fatty acid containing a cyclopropane
ring (see structure below). Would you expect that the melting point of this fatty acid would be closer to the
melting point of stearate (18:0) or oleate (18:1)?
H H
\C/
/ \
\/.\/,\/CH-CH coo-

A) closer to oleate B) closer to stearate

47. Which of the following is a second messenger?

A) cortisol B) epinephrine C) insulin D) cAMP E) G protein

48. What factor(s) are important in the high selectivity of the K+ channel?
A) The pore is lined with negatively-charged carboxyl groups to coordinate the positive ion.
B) A network of Tyr residues ensures that smaller ions like Na+ will be excluded.
C) A loop connecting two of the helices constricts the pore to make it specific for K.
D) Coordinated H2O molecules restrict the size of the cation that can be transported.
E) A and B are factors.
F) A, B and C are factors.
G) All of the above are factors

49. The height of the activation barrier determines:

A) The free energy change of the reaction.
B) The rate of the reaction.
C) The probability that the reaction will be spontaneous.
D) A and C
E) A, B and C

Section III: 18 points (3 points each)

50. Calculate AG at 37°C when Cal' ions move from the endoplasmic reticulum ([Ca 2+] = 1 mM) to the cytosol
([Ca2+] = 0.1 M) at a membrane potential of -50 mV (cytosol face negative).
A) -33.4 kJ/mol B) -28.6 kJ/mol C) -15.1 kJ/mol D) +28.6 kJ/mol

51. In unstimulated T cells, a transcription factor called NFAT (nuclear factor of activated T cells) resides in the
cytosol in a phosphorylated form. When the cell is stimulated, the cytosolic Ca 2+ concentration increases and
activates a phosphatase called calcineurin. Activated calcineurin hydrolyzes a phosphate from NFAT, allowing it
to be localized to the nucleus where it there stimulates the expression of genes needed for T cell activation. Based
on your understanding of the cell signaling pathway involved, order the steps of this activation process.
1)There is an influx of Ca2+ from the endoplasmic reticulum into the cytosol
2) G protein activates phospholipase C
3) Extracellular ligand binds to G protein coupled receptor
4) Extracellular ligand binds to receptor tyrosine kinase
5) Phosphatidylinositol bisphosphate is hydrolyzed
6) Ca2+ ions bind to calmodulin
7) Calcineurin activates NFAT
8) Ca2+-calmodulin complex binds to calineurin
A) 3, 1, 2, 5, 6, 7, 8 D) 3, 2, 1, 5, 6, 8, 7
B) 4, 1, 2, 5, 6, 8, 7 E) 3, 2, 5, 1, 6, 8, 7
C) 4, 2, 5, 1, 6, 7, 8 F) 4, 2, 5, 1, 6, 8, 7

Version 1 Page 7
52. Which of the following boxed areas are most likely to be part of the membrane spanning portion of the protein,
glycophorin A.
A
LSTIEVAMETIIITSSSVSK S YRS S QTND11EKRDTYAATPRAIEE
VSEISVRTVICPPEEETGERVQLATIEESEPEVILIEGVMAGVIG
1ILLISYGIR.R[Link]K SP SDITY PtPSDTDVPIISSVEIENPETSIDQ
0 E
A) A B) B C) C D) D E) E

53. A patient suffers from premature zymogen activation, so that the pancreatic enzymes are activated in the pancreas
rather than the small intestine -- causing damage to the pancreas. Which of the following would be the most
effective in preventing these effects?
A) chymotrypsin inhibitor B) trypsin inhibitor C) elastase inhibitor

54. Aspartate aminotransferase (AspAT) catalyzes the following reaction:

aspartate + a—ketoglutarate---> oxaloacetate + glutamate
The AspAT enzyme has two active-site arginines, Arg 386 and Arg 292, which interact with the a-carboxylate
and P-carboxylate groups on the aspartate substrate, respectively. Investigators studied the mechanism of AspAT
in more detail by constructing mutant AspAT enzymes in which either or both of the essential arginines were
replaced with a lysine residue. The kinetic parameters for the wild-type (normal) enzyme and mutant enzymes are
shown in the table below:
Enzyme KM aspartate (mM) licat (s 1)
Wild-type AspAT (Arg 292 Arg 386) 4 530
Mutant AspAT (Lys 292 Arg 386) 30 180
Mutant AspAT (Arg 292 Lys 386) 9 117
Mutant AspAT (Lys 292 Lys 386) 300 0.06

Of the mutant forms which has: 1) the best turnover number and which 2) has the best catalytic efficiency?
A) 1) Lys 292 Arg 386; 2) Lys 292 Arg 386 D) 1) Arg 292 Lys 386; 2) Lys 292 Arg 386
B) 1) Arg 292 Lys 386; 2) Lys 292 Lys 386 E) 1) Lys 292 Arg 386; 2) Arg 292 Lys 386
C) 1) Lys 292 Lys 386; 2) Arg 292 Lys 386 F) 1) Lys 292 Lys 386; 2) Lys 292 Lys 386

55. An enzyme has a KM of 3 mM in the absence of a competitive inhibitor in a solution of 2 mM substrate and a V..
of 15 nM/s. What concentration of a competitive inhibitor with K1 of 3 mM is required to achieve an initial
velocity of 5 nM/s?
A) 0.1 mM B) 0.4 mM C) 0.7 mM D) 1.0 mM E) 1.3 mM

Version 1 Page 8
a

Version 1 Page 9
Answer Key

1. C
2. B
3. E
4. C
5. A
6. C
7. B
8. C
9. A
10. E
11. B
12. C
13. B
14. A
15. D
16. A
17. C
18. E
19. B
20. E
21. C
22. C
23. B
24. C
25. G
26. F
27. A
28. A
29. E
30. B
31. E
32. B
33. B
34. C
35. F
36. A
37. C
38. E
39. D
40. D
41. H
42. D
43. A
44. C
45. C
46. A
47. D
48. B
49.B

31. E
52. C
53. B
Version 1 Page 9
54. E
55. D

Vcrion 1 PL we 10