(1 pt) Write your exam ID ( A) in the blank at the upper ...

Chem 153A, Winter 2009, Final Exam 2A Answer Sheet 1 (Green)

2/11

1. (1 pt) Write your exam ID (A) in the blank at the upper right of your answer sheet.

2. (5 pts) Which of the reactions of a metabolic pathway would you expect to be

regulated? List all that apply:

a. the 1st committed step of the pathway

b. the last step of the pathway

c. a highly spontaneous reaction

d. a rate-limiting reaction

e. a reaction in which [products]/[reactants] is close to Keq

f. a very fast reaction (relative to others in the pathway)

g. a reaction with a large, positive ∆E°'

h. a reaction involving a phosphoryl transfer from phosphoenolpyruvate

i. a reaction that is used in the reverse pathway

3. (3 pts) The reaction X → Y has ∆G°' = -3.7 kJ/mol. If [Y] > [X], which of the

following can be concluded?

a. the reaction will be spontaneous in the direction written

b. the reaction will be spontaneous in the reverse direction

c. the reaction is near equilibrium

d. the reaction is at equilibrium

e. none of the above

4. (2 pts) What metabolite is the first intermediate common to the breakdown of

proteins, polysaccharides, and fatty acids?

5. (3 pts) Given the following reactions:

Explain why the conversion of B→C would be spontaneous in the cell (30 words or

less).

6. (4 pts) Does glucose or ATP act as a nucleophile in the reaction catalyzed by

hexokinase? Briefly explain your answer (15 words or less).

7. (3 pts) Which one of the following sets most likely represents amino acids found in

the active site of glucosephosphate isomerase?

a. Arg, Ser, Met, Val

b. Phe, Val, Ile, Thr

c. Ser, Cys, His, Gln

d. Tyr, Thr, Trp, His

e. Gly, Ala, Cys, Pro


3/11

8. (5 pts) Which of the following catalytic mechanisms are important in the catalytic

mechanism of aldolase:

a. general acid catalysis

b. general base catalysis

c. covalent catalysis

d. electrostatic catalysis

e. metal-ion catalysis

9. (13 pts) Select from the following list of enzymes to answer the questions below:

A. hexokinase

B. glucokinase

C. glucosephosphate isomerase

D. phosphofructokinase-1

E. phosphofructokinase-2

F. phosphoprotein phosphatase

G. aldolase

H. triosephosphate isomerase

I. glyceraldehyde-3-phosphate

dehydrogenase

J. phosphoglycerate kinase

K. phosphoglycerate mutase

L. enolase

M. pyruvate kinase

N. pyruvate dehydrogenase

complex

O. citrate synthase

P. aconitase

Q. isocitrate dehydrogenase

R. α-ketoglutarate dehydrogenase

complex

S. succinyl-CoA synthetase

T. succinate dehydrogenase

U. fumarase

V. malate dehydrogenase

W. flavoprotein dehydrogenase

X. 3-phosphoglycerol

dehydrogenase

Y. ATP synthase

a. Which of these enzymes can bind NADH?

b. Which of these enzymes are phosphorylated as part of their catalytic

mechanism?

c. Which of these enzymes are regulated by phosphorylation?

10. (5 pts) Arrange the following molecules in order of increasing oxidation state.


4/11

11. (14 pts) You are studying a new organism, and based on the sequence, you find what

you think is the gene for pyruvate dehydrogenase complex enzyme 2 (E2). To test

your hypothesis, you change the gene so that all all lysine residues that were in the

enzyme will be arginine instead. You then check the growth of the organism under

anaerobic and aerobic conditions.

a. How would lysine → arginine mutations affect the function of pyruvate

dehydrogenase complex E2? Explain in 25 words or less.

b. If your hypothesis is correct, how will the organism’s growth differ from

normal under anaerobic conditions? Explain why in 15 words or less.

c. If your hypothesis is correct, how will the organism’s growth differ from

normal under aerobic conditions? Explain why in 15 words or less.

The differences in growth match what you expect based on your hypothesis. But

when you extract the cell contents from the mutated organism and check for the

enzyme’s activity, you find that pyruvate can be converted into acetyl-CoA at normal

rates. Further, you find a build-up of one of the intermediates of the citric acid cycle.

d. Why does the organism’s growth differ as expected, but pyurvate is converted

normally? Explain in 15 words or less.

e. Which citric acid cycle intermediate do you find in excess?

12. (9 pts) You perform a carbon-labeling experiment to see how quickly a cell

metabolizes glucose. Rather than labeling only one carbon of glucose, you label all

carbons. Assuming all intermediates are used in catabolic processes, what fraction of

the labeled carbons will be expelled as CO2 by the end of the first, second, and third

rounds of the citric acid cycle? Show your reasoning.

13. (3 pts) We learned that pyruvate carboxylase is virtually inactive in the absence of

acetyl-CoA. Why is this feature of its regulation important to the cell? Explain in 30

words or less.


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14. (4 pts) Given the following reaction:

NADH + H+ + FMN → NAD

+ + FMNH2

a. Which compound becomes reduced?

b. Which enzyme (that we’ve studied) catalyzes this reaction?

15. (14 pts) Given the following types of redox centers:

A. Coenzyme Q

B. Cu ion

C. FAD

D. FMN

E. Iron-sulfur cluster

F. Heme a

G. Heme b

H. Heme c

I. NAD+

a. For each of the listed complexes or components of the electron transport

chain, list the redox centers it contains. (That is, those that are permanently

bound.) You may use the same type of redox center for more than one

complex.

b. Starting with succinate and ending with O2, list in order the types of redox

centers that carry electrons directly through the transport chain. (You may use

each type more than once, but if the same type is used in several steps that

occur in a row, you only need to list that center once for that portion of the

chain. Multiple blanks are provided, but you may not need all of them.)

16. (12 pts) True or False?

a. In the malate-aspartate shuttle, glutamate and oxaloacetate are interconverted.

b. In the malate-aspartate shuttle, glutamate and oxaloacetate cross the

membrane using the same transporter.

c. The ∆G of ATP synthesis via substrate-level phosphorylation isn’t the same as

that for oxidative phosphorylation, because one involves overcoming a barrier

to combining ADP and Pi, while the other involves overcoming a barrier to

releasing the bound ATP.

d. The proton motive force is caused by a combination of the concentration and

charge differences that are produced across the inner mitochondrial

membrane.

e. The γ subunit of ATP synthase predominantly binds the T-state (ATP-bound

state) of an α-β dimer.

f. The hetero-hexamer (trimer of α-β subunit dimers) of ATP synthase does not

rotate during ATP synthesis.

Chem 153A, Winter 2009, Final Exam 2A Answer Sheet 2 (Purple)

6/11

17. (1 pt) Write your exam ID (A) in the blank at the upper right of your answer sheet.

18. (9 pts) We learned that water is essential for life, and that many of the reasons for this

stem from its unusual properties. List three unusual properties of water and briefly

explain how each contributed to the evolution and viability of life.

19. (5 pts) Below is the open-chain structure of one isomer of altrose. On the backbone

provided, draw the cyclic form, and circle the anomeric carbon. What is the full

name of the sugar you have drawn?

O

20. (5 pts) Shown below is the titration curve of an unknown peptide. Which of the

following could be the sequence of this peptide? There may be more than one correct

answer.

a. Asp-Gly-Ser-Ser-Gln-Glu-Tyr-Cys-Arg-Val

b. Ala-Glu-Tyr-Arg-Cys-Val-Ser

c. Asp-Gly-Ser-Ser-Gln-Thr-Glu-Tyr-Cys-Arg-Val

d. Trp-Tyr-His-Glu-Glu-Arg-Thr-Cys-Asn-Asn-Lys-Ser

e. DDEMRCTSP

f. ACDEFGILMNPQRSTVWXY

g. DDLQNRSASYNCW

h. KKGEFMNRTSSCYQ


7/11

21. (10 pts) For each of the following amino acid pairs, name the most likely interaction

that would occur between their side chains:

a. Asn and Glu

b. Arg and Glu

c. Met and Phe

d. Ala and Ser

e. Tyr and Thr

22. (16 pts) The dihedral angles for the structure of hexokinase are plotted below. In

addition, the angles are listed for a portion of the structure:

No. ϕ (°) ψ (°)

No. ϕ (°) ψ (°)

373 -55.3 -56.3 389 -63.7 -38.4

374 -66.0 -36.0 390 -122.6 136.1

375 -66.1 -40.0 391 -96.4 138.3

376 -58.4 -29.4 392 -130.0 113.3

377 -69.6 -36.1 393 -152.1 166.2

378 -72.7 -29.8 394 -120.6 129.8

379 -72.8 -51.3 395 -106.3 127.7

380 -53.2 -40.0 396 -89.7 117.1 381 -61.4 -44.7 397 -111.4 154.3

382 -65.5 -37.3 398 -170.6 163.9

383 -64.5 -36.1 399 134.6 134.8

384 -73.6 -40.9 400 -56.5 -43.3

385 -61.6 -39.1 401 -59.6 -57.3

386 -87.8 -1.9 402 -56.8 -43.6

387 59.1 4.7 403 -75.8 -22.2

388 -78.9 139.8 404 -111.4 -19.8

a. What kind of plot is shown?

b. What does the shading on the plot indicate? Explain the darkest, medium, and

white gradations (15 words or less).

c. Provide an explanation for the position of the spot indicated by the arrow (20

words or less). Hint: Each spot corresponds to an amino acid in the

sequence; consider how they differ.

d. On the provided peptide backbone, draw arrows to the bonds about which the

ϕ and ψ dihedral angles are measured (and label them ϕ or ψ). Circle the

bonds about which there is no rotation.

e. In the full listing of ϕ and ψ values for hexokinase, position 1 has the

following values: ϕ = NA, ψ = -53.5°. Why is no ϕ value assigned? Explain

in 15 words or less.

Position Position


8/11

23. (21 pts) The pentose phosphate pathway is used by the cell to generate NADPH and

5-carbon sugars. It branches off from the glycolytic pathway, but can convert its

intermediates back into glycolytic intermediates if needed. (Note that the conversion

of C to glycolytic intermediates has the stoichiometry 3C → 2D + E.)

a. Name intermediates A, C, D, and E.

b. What is the cellular role of NADPH?

c. How does NADPH differ structurally from NADH (5 words or less)?

d. Name the class and subclass of enzyme 1.

e. Although enzyme 2 could be classified by same names as enzyme 1, give a

different class and subclass name for enzyme 2 that would still be correct.

f. Generating NADPH through the pentose phosphate pathway reduces the

number intermediates passing through glycolysis and subsequent pathways.

What glycolytic intermediate is sacrificed, and how much NADPH is

produced as a result (of losing one intermediate molecule)? Show your

reasoning.

g. Based on your answer to part f, and assuming the complete, aerobic

metabolism of the intermediate, calculate how much ATP is sacrificed (that is,

not synthesized) per NADPH produced. Use the ‘new’ P/O values and

assume the malate-aspartate shuttle is present. Show your work.


9/11

24. (30 pts) You want to study the kinetics of hexokinase.

a. Write the equation for the reaction catalyzed by hexokinase.

To begin your kinetic experiments, you first need to make the buffer. You want to

keep the reaction mixture at pH 7.2, and the following buffers are available to you:

Buffer name pKa

Acetic acid 4.8

Citric acid 5.4

MES 6.2

Bis-Tris 6.5

PIPES 6.8

Sodium phosphate 7.2

HEPES 7.6

Glycylglycine 8.2

Tris 8.3

CHES 9.5

b. Sodium phosphate is not a good buffer to use for this reaction. Which one of

the other buffers listed above would be the best to use? Explain your selection

in 25 words or less.

c. Why isn’t sodium phosphate a good buffer to use? Explain in 15 words or

less. Hint: It isn’t because of phosphate’s pKa.

You make the buffer, to a final concentration of 100 mM. You add 1 mL of your

buffer to a reaction vial, then add 10 mM glucose, 10 mM ATP, and 0.5 nM

hexokinase.

d. What are the initial concentrations of the protonated and deprotonated forms

of the buffer? Show your work.

e. What additional compound must you add in order for the reaction to begin?

You begin the reaction, taking measurements every minute. You produce the

following curve:

(Problem continued on following page.)


10/11

(Problem 23 continued)

f. Which of the following can you determine based only on this data? There

may be several correct answers.

A. [S]

B. [ES]

C. Km

D. Vo

E. Vmax

F. kcat

G. Keq

H. reaction rate

I. catalytic efficiency

J. Whether this enzyme exhibits

sigmoidal kinetics

g. You let the reaction run to completion. What is the final ratio of [ADP] to

[ATP] in the reaction vial? Show your work. (The ∆G°' for this reaction is -

16.7 kJ/mol. Assume the experiment is carried out at 25°C.) Hint: You don’t

need the quadratic formula.

h. What is the final concentration of ADP in the reaction vial? Calculate this

from your answer in part g, and show your work.

i. What is the final pH of the reaction solution? Assume that any effect of

equilibration by water is negligible. (Assume all equilibration is done by the

buffer.) Show your work.

25. (14 pts) Given the enzyme catalyzed reaction:

a. What assumption must be made about this reaction in order for Km to

approach the Kd of the enzyme-substrate complex?

b. Briefly define ‘first-order’ as it applies to rate constants (15 words or less).

c. Of the rate-constants above, which are first-order?

d. Write two different expressions for the Kd of the enzyme substrate complex.

e. Under what condition is ES at steady state? Write an expression using

concentrations and rate constants.

26. (8 pts) True or False?

a. The transition state of a reaction cannot be isolated.

b. The activation energy of a reaction is the difference between the free energy

of the reactants and the free energy of the highest-energy transition state.

c. The activation energy of a reaction determines whether the reaction will be

spontaneous in the forward direction.

d. Two names of catalytic mechanisms – preferential binding of an intermediate,

and preferential binding of a transition state – refer to the same thing.


11/11

27. (21 pts) The following is the first paragraph of a scientific publication from 1966:

The brain in sheep, as in non-ruminant mammals, appears dependent on

glucose as the substrate for oxidation, yet the blood glucose concentration of

adult sheep is only about 2.5 mM (50 mg/100 ml.) compared with about 5

mM (100 mg/100 ml.) in rats, dogs, men and pigs. If the availability of a

substrate is less in one species than in another, and a tissue were to utilize

the substrate at comparable rates in both species, then one might look for an

inter-species difference in enzyme affinity for this substrate. So we have

estimated the apparent Km for glucose of hexokinase in brain, also liver,

muscle and adiposa, of sheep and rats.

In the paper, the authors describe how they purify hexokinase from the listed tissues

of sheep and rats, and then they analyze the kinetics of the enzymes. They are able to

purify hexokinase from each tissue, and they purify glucokinase from rat liver. The

sheep liver contains no glucokinase.

a. What does the absence of glucokinase from the sheep’s liver mean for energy

storage in sheep? Explain in 15 words or less.

Below is the author’s kinetic plot for the brain hexokinase of sheep (filled circles) and

rat (open circles). The solid lines reflect the initially purified enzymes. The dashed

lines reflect the enzymes after additional purification. ‘S’ represents [glucose].

b. What kind of plot is this?

c. What does the plot tell you about the

difference(s) between sheep and rat

hexokinase? Explain in 15 words or less.

d. Would you expect this result based on the

blood glucose concentrations given in the first

paragraph in the paper? Explain why in 20

words or less.

e. What is different between the two samples

(original and higher purity = solid and dashed

lines) that results in the change shown in the

plot. Be specific. (10 words or less).

f. Why do the authors report “apparent Km” values for the enzymes, instead of

the actual Km values? Explain in 15 words or less.

g. True or False? Sheep hexokinase and rat hexokinase are not isozymes.

Name (Last, First): ______________________________________ First two letters of last name: ___ ___

Student ID Number: _____________________________________

Chemistry and Biochemistry 153A, Winter 2009 Final Exam 2, ID:_________

Page 2 (21 points)

2. ______________________________

3. _______

4. ______________________________

5.

6.

7. _______

Page 3 (23 points)

8. ______________________________

9. a. ______________________________

b. ______________________________

c. ______________________________

10. ______ ______ ______ ______ ______

increasing oxidation state

I have read and agree to all instructions and guidelines for this exam.

Signed: Date:

Total score

Scores

/ 26

Page 4:

/ 30

Page 5:

/ 23

Page 3:

/ 21

Page 2:

(30 words or less)

Answer Sheet 1

(Green)

(15 words or less)

Chemistry and Biochemistry 153A, Winter 2009 Final Exam 2 – Answer Sheet 1 (Green)

Page 4 (26 points)

11. a.

b.

c.

d.

e. __________________________________

12.

13.

Page 5 (30 points)

14. a. _____________________

b. _________________________________

15. a. Complex I: _________________

Complex II: _________________

Complex III: __________________

Complex IV: ______________________

Flavoprotein dehydrogenase: __________________

Cytochrome c : ______________________

16. a. True False

b. True False

c. True False

d. True False

e. True False

f. True False

b. suc. → _____ → _____ → _____ → _____ → _____ → _____ → _____ → _____ → _____→ O2

(25 words or less)

(15 words or less)

(15 words or less)

(15 words or less)

(30 words or less)

fraction of carbons expelled by end of: 1st _______; 2

nd _______; 3

rd _______ round of TCA cycle

Name (Last, First): ______________________________________ First two letters of last name: ___ ___

Student ID Number: _____________________________________

Chemistry and Biochemistry 153A, Winter 2009 Final Exam 2, ID:_________

Page 6 (20 points)

18. (1) __________________, ____________________________________________

(2) __________________, ____________________________________________

(3) __________________, ____________________________________________

19.

O

20. _

sugar name:

_______________________________________

Page 7 (26 points)

21. a. ______________________ b. ______________________ c. ______________________

d. ______________________ e. ______________________

22. a. ______________________

b.

c.

d.

e.

Page 8 (21 points)

23. a. A: _____________________________

C: _____________________________

D: _____________________________

E: _____________________________

b. ________________________________

c. ________________________________

d. ________________________________

e. ________________________________

f.

g.

Total score

/ 21

Page 11:

/ 52

Pages

9, 10:

Scores

/ 21

Page 8:

/ 26

Page 7:

/ 20

Page 6:

Answer Sheet 2

(Purple)

(property) (contribution to life)

20. ____________________________________

(15 words or less)

(15 words or less) (20 words or less)

Chemistry and Biochemistry 153A, Winter 2009 Final Exam 2 – Answer Sheet 2 (Purple)

Pages 9 & 10 (52 points)

24. a. ______________________________________________________________ e.____________

b.

c.

d.

f. _____________________________________

g.

h.

i.

25. a. ________________________________ b.

c. __________________

d. ________________________________

e. _________________________________________________________________________________

26. a. True False

b. True False

c. True False

d. True False

d.

e.

Page 11 (21 points)

27. a.

b. ________________________________

c.

f.

(25 words or less)

(15 words or less)

(15 words or less)

(15 words or less)

(15 words or less)

(20 words or less)

(10 words or less)

g. True

False (15 words or less)

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