C383 Practice Final Exam
Last Name______First Name: ______
Please make sure there are 16pages to this exam, including a page of data and a scratch page.
Part A is composed of 25 multiple choice problems worth 2 points each. Circle the letter next to the correct answer. Multiple answers for the same question receive no credit.
Part B is composed of 17 short answer problems worth 3 points each.
Part C is composed of five problems worth 55 points total.
Score:
Multiple Choice: ______/50
Short answers______/51
Question 43 ______/10
Question 44 ______/10
Question 45 ______/10
Question 46 ______/12
Question 47 ______/15
Bonus ______/2
Total:______/160
Part A.(2 points each) Questions 1-8 focus on the most recent material.
1. ______Preparing a fatty acid to be catabolized through -oxidation involves all of these except
A.expenditure of 2 ATP equivalents.
B.attachment to carnitine.
C.crossing from the matrix into the cytosol through a translocase.
D.attachment to Coenzyme A
2. ______Ketone body formation
A.produces a water-insoluble fuel for brain cells.
B.occurs only under starvation conditions.
C.takes place in the cytosol.
D.allows acetyl CoA to be made into net glucose.
E. is favored when the citric acid cycle is inhibited.
3. ______Which statement concerning fatty acid synthesis is false?
A.Fatty acid synthesis from acetyl CoA requires ATP hydrolysis.
B.Fatty acid synthesis requires acetyl CoA to leave the matrix in the form of citrate.
C.Fatty acid synthesis takes place on a multifunctional enzyme complex.
D.Fatty acid synthesis is regulated at the carnitine transporter.
4. ______Cholesterol is transported from peripheral tissues to the liver as
A.chylomicrons.
B.VLDLs.
C.IDLs.
D.LDLs.
E. HDLs.
5. ______The most common route for a nitrogen atom removed from a branched amino acid in muscle tissue to formation of urea is
A.branched AAglutamate glutamine carbamoyl phosphate urea
B.branched AAalanine aspartate glutamine urea
C.branched AAaspartate alanine glutamate glutamine urea
D.branched AA alanine glutamate carbamoyl phosphate urea
E. branched AA glutamate arginine carbamoyl phosphate urea
6. ______Which of the following can be produced through the pentose phosphate pathway?
A.ATP
B.pyruvate
C.NADPH
D.more than one of the above
7. ______Each of these amino acids is paired with its degradation intermediate except
A.serine pyruvate
B.lysine succinyl CoA
C.asparagine oxaloacetate
D.arginine alpha-ketoglutarate
8. ______Proline biosynthesis starts with the metabolic intermediate
A.oxaloacetate
B.-ketoglutarate
C.pyruvate
D. 3-phosphoglycerate
9. ______Which of these cofactors is NOT a one carbon carrier?
A. THF
B. TPP
C. SAM
D. biotin
10. ______Glycine has pKa values of 2.1 and 9.0. For which pH would it BEST serve as a buffer?
A. 11
B. 8.3
C. 5.5
D. 3.1
E. 2.3
11. ______The net charge of aspartate in a solution at pH 7 is:
A. -1
B. -0.5
C. +0.5
D. +1
E. +1.5
12. ______The aggregation of nonpolar molecules or groups in water is thermodynamically favorable due to the
A. increased entropy of the water molecules.
B. decreased enthalpy of the system.
C. increased entropy of the nonpolar molecules when they associate.
D. very strong van der Waals forces among the nonpolar molecules or groups.
13. ______Pyruvate dehydrogenase complex can be categorized as this type of enzyme:
A. Oxidoreductase
B. Transferase
C. Hydrolase
D. Lyase
E. Isomerase
14. ______An enzyme inhibitor causes an increase in the apparent KM value, but not the apparent Vmax value. It must be
A.a competitive inhibitor.
B.an irreversible inhibitor.
C.an uncompetitive inhibitor.
D. a mixed inhibitor.
E. a mechanism based inhibitor.
.
15. ______Triacylglycerols are not found in cell membranes because they are
A. not amphipathic.
B. amphipathic.
C. not abundant in cells.
D. charged at biological pH.
16. ______If a membrane transport protein sends compound A out of the cell while bringing compound B into the cell with the hydrolysis of ATP, this transporter would be
A. a secondary active transporter.
B. an active symporter.
C. a passive symporter.
D. an active antiporter.
17. ______Which of these signal transduction components is a second messenger?
A. glucagon
B. G-protein coupled receptor
C. cAMP
D. protein kinase A
E. receptor tyrosine kinase
18. ______Because hemoglobin is tetrameric
A. it binds oxygen more tightly than myoglobin.
B. it’s oxygen binding curve is a rectangular hyperbola.
C. it cannot be regulated by allosteric control.
D. it can bind oxygen cooperatively.
E. None of the above.
19. ______Which statement is false concerning the fate of glucose-6-phosphate in a muscle cell?
A. G-6-P can be incorporated into glycogen.
B. G-6-P can enter the pentose phosphate pathway.
C. G-6-P can be converted to glucose.
D. G-6-P can enter glycolysis.
20. ______The net effect of the eight steps of the citric acid cycle is to
A. completely oxidize an acetyl group to carbon dioxide.
B. convert pyruvate to acetyl CoA.
C. produce a citrate molecule
D. produce 2 ATP for every pass through the cycle.
E. More than one of the above
21. ______The standard reduction potential for the reaction of oxaloacetate and NADH to produce malate and NAD+ is
A. -0.149 V
B. 0.149 V
C. -0.481 V
D. 0.481 V
22. ______In humans, a full rotation of the ATP synthase rotor requires _____ protons and forms ___ ATP.
A. 3, 8
B. 8, 3
C. 10, 2
D. 2, 10
23. ______Which of the following enzymes is not allosterically regulated?
A. phosphofructokinase
B. pyruvate dehydrogenase complex
C. glyceraldehyde-3-P dehydrogenase
D. pyruvate kinase
E. isocitrate dehydrogenase
24. ______Which of the following is not a tissue-specific role for liver:
A. ketogenesis
B. urea production
C. glycogen synthesis
D. lactate recycling
E. alanine recycling
25. ______Which of the statements concerning a near-equilibrium reaction is TRUE?
A. The concentrations of reactants and products are nearly equal under cellular conditions
B. The enzyme catalyzed reaction is most likely regulated.
C. The standard free energy of the reaction must be near zero.
D. The flux through the reaction is affected by changes in reactant concentration.
Part B:(3 points each) Questions 26-30 focus on the most recent material.
26. From the following list, choose one enzyme type that fits each description below: oxidoreductase, transferase, hydrolase, lyase, isomerase, ligase.
______glucose-6-phosphate glucose + phosphate
______dihydroxyacetonephosphate (DHAP) glyceraldehyde-3-P (GAP)
______Protein kinase A
27. List three ways in which fatty acid degradation and fatty acid synthesis differ.
28. Which of the following compounds are glucogenic? Circle every compound that is glucogenic, and put an X through compounds that are not.
ketone bodies Odd chain fatty acidlysine
Even chain fatty acidalanineglycerol
29.Put these intermediates of cholesterol synthesis in order, and circle the one that is formed in the regulated step: mevalonate, acetyl CoA, squalene.
30.Circle the one letter abbreviation of the THREE amino acids that are major carriers of nitrogen from peripheral tissue to the liver. If you circle more than three, you will get zero points.
G R Q A D E
31. What is the pH of an acetate/acetic acid solution (pKa= 4.7) in which acetic acid is 80% in its deprotonated form?
32. Draw the product of the transamination of alanine.
33. Draw the ala-lys dipeptide at its isoelectric point.
34. Give an example of a protein that has each of these functions:
Structural protein: ______
Catalyst: ______
Oxygen-binding protein: ______
35. Calculate the free energy change when glucose is phosphorylated by ATP to form glucose-1-phosphate.
36. If this Michaelis-Menton graph were produced using a [E]T of 30 nM, estimate kcat and KM:
Kcat = ______KM = ______
37. Draw the structure of -D-galactose, the C-4 epimer of glucose.
38. What is the net change in high energy bonds in the reaction below?Predict the standard free energy of this reaction to be positive, negative, or near zero.
39. The net ATP production for anaerobic glycolysis starting from glucose is ______ATP.
40. Would each of the following structures be more likely in the core or on the surface of a globular protein?
Amphipathic -sheet:______
Nonpolar -helix: ______
Irregular loop: ______
41. The oxidation of malate is the last step of the citric acid cycle. The reaction has a large positive standard free energy, but occurs spontaneously in the cell. Explain.
42. Does insulin upregulate or down regulate each of the following pathways?
Glycogen synthesis ______
Fatty acid synthesis: ______
Glycolysis ______
43. The enzyme aldolase catalyzes the following reaction:
Fructose-1,6-bisphosphate dihydroxyacetone phosphate + glyceraldehyde 3-phosphate
When this reaction was run under standard conditions, the free energy of the reaction was determined to be +23.8 kJ/mol. Under normal cellular conditions, typical concentrations of these substances are 0.15 mM fructose 1,6-bisphosphate, 4.3 x 10-6M dihydroxyacetone phosphate, and 9.9 x 10-5 M glyceraldehyde 3-phosphate.
A. What is G0’ for this reaction?
B. What G for this reaction?
C. Is this reaction spontaneous or nonspontaneous under cellular conditions? Explain.
D. If the reaction under cellular conditions were to proceed toward equilibrium, would the concentration of reactants or the concentration of product increase? Explain.
44. What is the yield of ATP when one molecule of phosphoenolpyruvate is completely oxidized to CO2 by a mammalian cell homogenate? Assume that glycolysis, the citric acid cycle, and oxidative phosphorylation are fully active. Give a full and clear accounting of reduced cofactors and ATP equivalents to credit. A one-number answer will receive no credit.
Bonus (2pts): What was the most interesting thing that you learned in Biochemistry?
45. S-acetonyl-CoA (shown below) has by synthesized and tested as an inhibitor of citrate synthase.
A. Write the reaction catalyzed by citrate synthase.
B. Why is the name of this enzyme not “citrate synthetase”?
C. The Lineweaver-Burke plot of this enzyme with and without the inhibitor is shown below. What type of inhibitor is it? Explain.
D. Based on these data, how would you expect this inhibitor to affect pyruvate carboxylase? How would this affect gluconeogenesis?
46. Drawing figures. In the spaces below, draw an appropriately shaped figure, including necessary axis labels.
A. A titration curve for lysine, with a side chain pKa of 10.5.
B. A DNA melting curve for a poly(AT) sequence and a poly(GC) sequence (indicate which is poly(AT) and which is poly(GC))
C. A plot of initial velocity versus substrate concentration for a Michaelis-Menton enzyme.
D. The same plot as (C), but the enzyme is treated with a competitive inhibitor
E. a pH profile for an enzyme with two key ionized residues: a cysteine with pKa 4.2 and a Histidine with pKa 8.2
F. Saturation curve for myoglobin and hemoglobin (indicate which is which)
47. A. A molecule of glutamate that you eat can eventually be transformed into part of a glucose molecule that you store in your liver. Circle the pathways/cycles below that are part of this overall transformation. Cross out any that are not.
citric acid cycle, gluconeogenesis, pentose phosphate pathway, glycogen synthesis, glycolysis
B. Trace the metabolic path of this glutamate molecule through the intermediates it becomes on the way to being glucose. Draw the structure of glutamate and -D-glucose in the boxes. Indicate the order of transformation by writing “1”, “2”, etc next to each appropriate structure. Cross out the one molecule not involved in this pathway.
C. The nitrogen atom of glutamate must be removed by oxidative deamination, and is incorporated into a molecule that is excreted. Draw the structure of this molecule.
pKa values for amino acids:carboxy terminus of polypeptide: 3.5
amino terminus of polypeptide: 9.0
Sidechains: Asp 3.9Cys 8.4Arg 12.5
Glu 4.1Tyr 10.5His 6.0Lys 10.5
G = RT ln + ZF G = -nFEo’
R = 8.314 J/ mol . K F = 96,485 J/V . mol
pH = pKa + log [A-]/[HA] v = (Vmax[S])/KM + [S]
Scratch paper: Nothing written on this page will be graded.
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