BCH 400 Spring 2006
_____________________
Exam 1
February 8, 2007
Name:
Notes: pKa of amino acid R-groups: aspartate = 4, glutamate = 4, lysine = 10.5, arginine = 12.5, histidine = 6.0
The pKa of the alpha amino group is 10 and the alpha carboxyl group is 2.0.
Mark the correct answer for questions 1 thru 30 on the provided scantron answer sheet.
Multiple Choice (2 points/question)
1) Which of the following statements is not consistent with the vitalistic view of the biological world? a) Biological molecules can only be derived from living organisms. b) Living organisms are subject to the chemical and physical laws. c) Only living organisms can extract, transform and utilize energy from the environment d) Self replication is a process that can only occur in living organisms. e) None of the above
2) Eduard Buchner is famous for_____________________. a) inventing the Buchner funnel b) synthesizing urea from inorganic starting materials c) inventing the “lock and key” model for enzyme/substrate binding d) showing that fermentation could still occur using extracts from killed yeast e) proving that enzymes were proteins
3) A peptide bond is a specialized name for which type of chemical linkage? a) ester linkage b) phosphodiester linkage c) amide linkage d) ether linkage e) phosphoanhydride linkage
4) Of the related substances below, which represents the monomer? a) chromatin b) deoxynucleic acid c) nucleotide d) chromosome
5) Of the following elements, which is not found in large abundance in the cells of all organisms? a) carbon b) iodine c) hydrogen d) nitrogen e) oxygen
6) Order the following from strongest to weakest: 1) van der Waals interactions, 2) hydrogen bonds, 3) Carbon carbon bonds, 4) ionic bonds, 5) hydrophobic interactions a) 1,2,3,4,5 b) 4,3,2,1,5

c) 3,2,4,1,5 d) 5,3,4,2,1 e) 3,4,2,5,1
7) If the pH of an acetic acid solution is higher than the pKa of acetic acid, the concentration of acetic acid is __________ the concentration of acetate ion a) equal to b) greater than c) less than d) none of the above
8) Which of the following functional groups can not participate in hydrogen bonding? a) amino group b) methyl group c) carbonyl group d) hydroxyl group e) sulfhydryl group
9) A weak acid _________________ in an aqueous environment. a) completely disassociates b) only partially disassociates c) can function as a buffer d) a and c e) b and c
10) Which of the following amino acids has only one chiral carbon? a) glycine b) isoleucine c) threonine d) alanine e) all of the above
11) Which of the following amino acids can function as a buffer at pH 7? a) glutamic acid b) asparagine c) lysine d) alanine e) histidine
12) Which of the following type of protein analyses requires a single pure protein? a) Edmund degradation protein sequencing b) x-ray crystallography c) amino acid analysis d) a and c e) all of the above
13) _________ separates proteins based on charged. a) Affinity chromatography b) Gel permeation chromatography c) Ion exchange chromatography d) Isoelectric focusing e) c and d

14)
Isoelectric focusing is used to determine a protein’s _________________. a) molecular weight b) subunit composition c) pI d) a and c e) none of the above
15) If you cleaved the following peptide (i.e. A-Y-K-M-C-S) with cyanogen bromide (CNBr), which peptides fragments would you obtain? a) A and Y-K-M-C-S b) A-Y and K-M-C-S c) A-Y-K and M-C-S d) A-Y-K-M and C-S e) A-Y-K-M-C and S
16) The number of possible secondary structures is limited by_____________________. a) the number of allowable Phi and Psi angles b) the number of different types of amino acids c) hydrophobic interactions d) the size of the hydration shell e) none of the above
17) What is the order that elements of an unfolded protein come together to form a native conformation? a) domains, native tertiary structure, local 2 o
structures, motifs b) motifs, local 2 o structures, domains, native tertiary structure c) local 2 o
structures, domains, motifs, native tertiary structure d) local 2 o
structures, motifs, domains, native tertiary structure e) none of the above
18) Which of the following is an allosteric modulator of hemoglobin function? a) protons b) CO
2 c) O
2 d) 2,3, bisphosphoglycerate (BPG) e) All of the above
19) Disulfide bonds are introduced into a protein _________________________. a) prior to folding b) during the folding process c) after folding is completed d) none of the above
20) Which of the following is not an essential amino acid? a) histidine b) lysine c) tryptophan d) alanine

e) all of the above
21) _____________ play the most important role in stabilizing alpha-helices, beta-sheets and beta turns. a) Hydrophobic interactions b) Ionic bonds c) Covalent bonds d) van der Waals interactions e) Hydrogen bonds
22) The R-groups of the amino acid residues comprising an alpha helix are oriented________________. a) towards the interior of the helix b) outward away from the helix axis c) randomly throughout the helix d) on a single side of the helix outer surface e) none of the above
23) Fibrous proteins ______________________________. a) are highly water soluble b) exist primarily in the monomeric state c) have diverse functions d) all of the above e) none of the above
24) Hemoglobin has an

2

2 conformation with a heme prosthetic group and therefore is classified as a ______. a) simple monomeric protein b) a conjugated monomeric protein c) a conjugated homomultimeric protein d) a simple heteromultimeric protein e) a conjugated heteromultimeric protein
25) Which is more stable? a) an anti-parallel beta sheet b) a parallel beta sheet

Matching (2 points per match, only one answer per question)
E. B.
C .
A.
D.
26) carbonyl group ____
27) amide group
28) ester linkage
____
____
29) hydroxyl group ____
30) sugar monomer ____

31) Short answer question a) (10 points) Draw the correct structure for the following peptide at pH 3.0: G-P-W-
S-N-E-P-T-L-I b) (5 points) Calculate the overall charge of this molecule at pH 3.0. c) (5 points) Using the pKa’s listed at the top of page one, calculate the pI of the peptide.

BRIEFLY IN THE SPACE PROVIDED ANSWER FOUR OF THE SEVEN QUESTIONS
LISTED BELOW. EACH IS VALUED AT 5 POINTS. YOU MAY ANSWER A 5 TH
QUESTION FOR EXTRA CREDIT. I WILL ONLY GRADE THE FIRST FIVE
ANSWERS SO CIRCLE THE NUMBERS OF THE QUESTIONS FOR WHICH YOU
WANT CREDIT
32) You want to purify ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO), a major photosynthetic protein from spinach. Describe how you would use differential centrifugation to enrich for RubisCO. Describe what g-forces you would use and which fraction would contain the most RubisCO.
32) Describe how oxygen could serve as both a substrate and an allosteric modulator of hemoglobin.
33) Describe how CO
2
and pH act to alter hemoglobin’s affinity for oxygen.

34) Explain how hydrophobic interactions drive protein folding.
35) Explain how the peptide bond limits the number of possible secondary structure in any polypeptide chain.
36) Explain how the prion protein, PrPSc, causes the neurodegenerative Creutzfeld-Jacobs disease.

37) You have a pure protein that you want to characterize. You ran the protein through a gel permeation chromatography column and determined that its native conformation has a molecular weight of 290 kilodaltons. You then analyze the protein by SDS-PAGE. From this analysis you identify 3 subunits designated as alpha, beta and gamma with molecular weights of 80, 50 and 10 kilodaltons respectively. Based on these results tell me how many of each subunit make up the native conformation of your protein. There are multiple possible correct answers, but only give me one.

BCH 400 Spring 2007
Exam 2
February 28, 2007
Name: _____________________
Mark the correct answer for questions 1 thru 30 on the provided scantron answer sheet.
Multiple Choice (2 points/question)
1) Which of the following is a property of a catalyst? a) A catalyst changes the chemical equilibrium b) A catalyst needs to be replenished after each reaction c) A catalyst decreases the activation energy barrier of a reaction d) a and d e) all of the above
2) Which of the following classes of enzyme catalyze intramolecular rearrangements? a) transferase b) lyase c) isomerase d) oxidoreductase e) ligase
3) NADH and NADPH are commonly required by which class of enzyme? a) transferase b) lyase c) isomerase d) oxidoreductase e) ligase
4) Which of the following classes of enzymes catalyzes reactions using Ping Pong kinetics? a) transferase b) lyase c) isomerase d) oxidoreductase e) ligase
5) The term ____________ defines the form of the enzyme that is lacking a required prosthetic group. a) coenzyme b) apoenzyme c) holoenzyme d) allosteric enzyme e) co-substrate
6) A reaction whose rate is dependent on a single reactant is referred to as a ________. a) Zero order reaction b) 1 st
order reaction c) 2 nd
order reaction d) Pseudo 1 st
order reaction e) Pseudo zero order reaction

7) Which of the following does not describe Km? a) K m
= (k
-1
+ k
2
)/k
1 b) K m
= [s] @ ½ V max c) K m
= Michaelis constant d) K m
= k cat
[E t
] e) K m
= -1/ x-intercept
8) The enzyme hexokinase has a K m
of 8 X 10
-6
for glucose, a K m
of 8 X 10
-3
for allose and a
K m
of and a K m
of 1 X 10
-2
for ribulose. Based on these K m
values, for which substrate does hexokinase have the strongest affinity? a) ribulose b) glucose c) allose d) all are the same e) none of the above
9) Catalytic perfection refers to the case where_________________________________. a) the enzyme always catalyzes the same reaction b) the V max
value is obtained c) the k cat
/K m
value is close to the diffusion limit d) the rate of the conversion of ES to E + P is zero e) none of the above
10) Which of the following is also referred to as the turn over number? a) V max b) k cat
/K m c) k cat d) K m e) none of the above
11) In a Lineweaver Burke plot, the y-intercept equals______________. a) 1/V max b) 1/ K m c)
– 1/ K m d) k cat e) none of the above
12) Which of the following statements is true regarding an allosteric enzyme? a) An allosteric enzyme has quaternary structure. b) An allosteric modulator binds distal to the substrate binding site. c) An allosteric enzyme does not follow the Michaelis Menton kinetics. d) a and b e) all of the above
13) The allosteric transition of hemoglobin from the T to the R conformation modulated by oxygen binding occurs through the __________________. a) concerted model b) sequential model

14) Which of the following amino acids function in proton transfer reactions in the active site of many enzymes? a) aspartate b) glutamate c) histidine d) a and b e) all of the above
15) When the product of a biosynthetic pathway functions as an allosteric inhibitor of an early enzyme in the pathway, this type of regulation is referred to as _____________. a) covalent modification b) feedback inhibition c) feedforward inhibition d) zymogenic regulation e) a and b
16) According to the induced fit theory for enzyme function, ___________________. a) the enzyme’s affinity for the substrate is greater than its affinity for the transition state b) conformational changes occur within the active site to convert S to the transition state c) formation of the transition state is not dependent on the formation of the ES complex d) none of the above
17) Which of the following classes of inhibitors is structurally related to the enzyme’s substrate? a) uncompetitive inhibitors b) noncompetitive inhibitors c) competitive inhibitors d) a and c e) none of the above
18) Which of the following coenzymes function in acyl transfer reactions? a) lipoamide b) coenzyme A c) pyridoxal phosphate d) a and b e) b and c
19) Which of the following coenzymes is a cosubstrate? a) NAD+/NADH b) Lipoamide c) Pyridoxal phosphate d) Biotin e) None of the above
20) ________ bind reversibly to the enzyme and often participate in stabilizing substrate binding. a) Activator ions b) Metalloenzyme metal centers

21)
Which of the following coenzymes form Schiff’s base intermediates with amino acid substrates? a) NAD+/NADH b) Lipoamide c) Pyridoxal phosphate d) Thiamin pyrophosphate e) None of the above
22) Which of the following substances function in oxidation/reduction reactions? a) NAD+/NADH b) FMN c) Ubiquinone d) Cytochromes e) All of the above
23) Which of the following carbohydrates functions as an energy store in human liver and muscle tissue? a) starch b) chitin c) glycogen d) a and c e) none of the above
24) Sugar residues in a ___________ polymer are rotated 180 o
relative to the next sugar residue. a) starch b) cellulose c) glycogen d) a and c e) none of the above
25) Cellulose can not be utilized as a food source by humans because humans lack the enzyme required to cleave ______________. a)

1

4 glycosidic linkages b)

1

6 glycosidic linkages c)

1

4 glycosidic linkages d) a and b e) none of the above
26) Which of the following carbohydrate polymers is a major component of dental plaque? a) cellulose b) chitin c) dextran d) glycogen e) none of the above

27) Complex carbohydrates are covalently attached to ___________ residues during N-linked glycosylation of proteins. a) lysine b) arginine c) asparagine d) histidine e) glutamine
28) The carbohydrate determinants of the ABO blood antigens are the result of _______. a) N-linked glycosylations b) O-linked glycosylations c) S-linked glycosylations d) All of the above e) None of the above
29) Which of the following carbohydrate exist as branched polymers? a) starch b) cellulose c) chitin d) a and b e) b and c
30) What types of interactions are responsible for the stabilization of cellulose polymers in cellulose cables? a) ionic interactions b) H-bonding c) Hydrophobic interactions d) All of the above e) None of the above
Short answer Questions
31) (10 points total) a) (6 points) Draw the Fischer and Haworth projections for beta-D-glucose. Make sure to include all hydrogens and hydroxyl groups. b) (2 points) Circle the anomeric carbon. c) (2 points) Determine the number of possible stereoisomers for both the open chain and cyclized forms.

0.18
0.16
0.14
0.12
0.1
0.08
0.06
0.04
0.02
0
-5
32) (15 points total) You have purified the ichyase enzyme from baboons’ seat pads and have to characterize its kinetic properties. You have performed a number of experiments and plotted the data on the Lineweaver Burke plot shown below. a) (5 points) From the Lineweaver Burke plot below, determine the K m
and V max
. Make sure to include the correct units for each in your answer. Show all of your work for partial credit. b) (5 points) On the graph below, draw the Lineweaver Burke plot that would occur if you added an uncompetitive inhibitor to your enzyme reaction. c) (5 points) Describe how the addition of the noncompetitive inhibitor affects the K m
and
V max of the baboon ichyase. Describe why these changes occur.
0.2
0
-4 -3 -2
0
0
0
-1 0 1
1/(umoles/liter)
2
0
3 4 5

BRIEFLY IN THE SPACE PROVIDED ANSWER THREE OF THE FIVE QUESTIONS
LISTED BELOW. EACH IS VALUED AT 5 POINTS. YOU MAY ANSWER A 4 TH
QUESTION FOR EXTRA CREDIT. I WILL ONLY GRADE THE FIRST FOUR
ANSWERS SO CIRCLE THE NUMBERS OF THE QUESTIONS FOR WHICH YOU
WANT CREDIT
33) Below is the structure of sucrose. Based on this structure describe why sucrose is not a reducing sugar.
CH
2
OH
H
OH
O
H
H
OH
H OH
O
CH
2
OH
O
H OH
H
CH
2
OH
OH H
34) How do the histidine and aspartic acid residues in active site of serine proteases help facilitate the active site serine’s role in catalysis?

35) Describe why the value k cat
/K m
is a better predictor of how well a particular a substance functions as a enzyme substrate than does K m
alone.
36) Describe the steady state and initial velocity assumptions of Michaelis Menton kinetics.
37) Describe why a transition state analog for a specific enzyme can function well as an inhibitor. To which class of inhibitor would a transition state analog belong?

BCH 400/600
Spring 2007
Exam 3
Name________________________
For questions 1 thru 35 mark your correct answer on the exam and the scantron answer sheet.
There is only one correct answer per question.
Multiple Choice
1) Which of the following does not belong to the acyl-lipid class? a) phospholipids b) triacylglycerols c) waxes d) carotenoids e) sphingolipids
2) A fatty acid that contains 18 carbons with a single double bond positioned between the ninth and tenth carbon is referred to as _______________________. a) Oleic acid b) C18:1 delta 9 c) C18:1 omega 9 d) a and b e) all of the above
3) Which of the following fatty acids would be a solid at room temperature? a) Stearic acid b) Oleic acid c) Linoleic acid d) Linolinic acid e) a and b
4) Intrinsic membrane proteins _______________within a lipid bylayer. a) can only diffuse in one dimension b) can only diffuse in two dimension c) can only diffuse in three dimensions d) do not diffuse and are anchored in place e) none of the above
5) Lipid anchored proteins can be tethered to the membrane through a covalent linkage with which of the following types of molecules? a) palmityl group b) farnesyl group c) geranylgeranyl group d) myristryl group e) all of the above
6) Which of the following types of membrane transporters does not show saturable kinetics? a) pores b) channels c) facultative passive transporters d) a and b e) b and c

7) Steroids belong to which terpene class? a) monoterpenes b) sesquiterpenes c) diterpenes d) triterpenes e) tetraterpenes
8) Which of the following plays a critical role in determining the duration of signaling in a Gprotein mediated signal transduction pathway? a) Cytsolic effector enzyme activity b) The G-protein GTPase Kcat c) Second messenger turnover d) a and b e) b and c
9) The TCA cycle is organized as a ___________ pathway. a) linear b) closed loop c) spiral d) b and c e) none of the above
10) Which of the following pathways is amphibolic? a) glycolysis b) glycogen synthesis c) gluconeogenesis d) TCA cycle e) b and c
11) In vivo, the concentrations of metabolic pathway intermediates are
________________________. a) at equilibrium b) at steady state c) present at concentration close to the Km value for their respective enzymes d) a and c e) b and c
12) What is the mass action ratio? a) Ratio of the products over the reactants when the reaction is at equilibrium. b) Ratio of the actual product concentrations over the actual reactant concentrations c) Q d) a and c e) b and c
13) Which of the following contribute to the large release of energy when a phosphoanhydride linkage is cleaved? a) electrostatic repulsions b) resonance instabilities c) entropic considerations d) a and c e) all of the above

14) Which of the following types of transporters functions to transport solutes against the solutes concentration gradient? a) Pores b) Channels c) facultative passive transporters d) active transporter e) all of the above
15) _________ refers to the process by which lactic acid is removed from muscle tissue and is transported to the liver where it is converted to glucose, which is subsequently transported back to the muscles for use as an energy source. a) The Pasteur Effect b) Lactic acid fermentation c) Oxidative phosphorylation d) The Cori Cycle e) The Bohr Effect
16) Fructose 2,6 bisphosphate_____________________. a) is converted to glyceraldehyde-3-phosphate and dihydroxyacetone phosphate during glycolysis b) is an allosteric activator of phosphofructokinase-1 c) is an allosteric inhibitor of fructose 1,6 bisphosphatase d) a and b e) b and c
17) The use of high levels of high fructose corn syrup is problematic in relation to maintaining one’s weight because_____________________. a) fructose contains more calories than sucrose b) fructose can by-pass the enzymatic steps that regulate rates of glycolysis c) fructose is not absorbed well by the body d) fructose is rapidly converted to ethanol e) all of the above
18) What is the net number of moles of ATP produced from one mole of glucose through glycolysis under anaerobic conditions? a) 1 b) 2 c) 10 d) 24 e) Unknown
19) Which of the following enzymes catalyze a reversible near equilibrium reaction of glycolysis? a) hexokinase b) pyruvate kinase c) PEP carboxykinase d) aldolase e) a and d

20) Which of the following hormones causes the breakdown of glycogen? a) epinephrine b) insulin c) glucagons d) a and b e) a nd c
21) Which protein is responsible for the formation of the primer molecule required for glycogen synthesis? a) glycogen phosphorylase b) glycogen synthase c) glycogenin d) 1,6 glucosidase e) All of the above
22) Which of the following pyruvate dehydrogenase cofactors is directly involved in the decarboxylation of pyruvate? a) thiamin pyrophosphate b) lipoamide c) NAD+ d) Coenzyme A e) FAD+
23) Which of the following pyruvate dehydrogenase cofactors is required for the shuttling of the
2 carbon intermediate from the E1 subunit of pyruvate dehydrogenase to coenzyme A? a) thiamin pyrophosphate b) lipoamide c) NAD+ d) Coenzyme A e) FAD+
24) Which gluconeogenic enzyme is also an anapleurotic reaction for the TCA cycle? a) fructose 1,6 bisphosphatase b) Pyruvate carboxylase c) PEP carboxykinase d) Glucose 6 phosphatase e) All of the above
25) Which of the following organs can perform gluconeogenesis? a) Adipose tissue b) liver c) heart d) muscle e) brain

Epinephrine receptor
Adenyl cylase
Protein Kinase A
(inactive)
Protein Kinase A
(active) cellular response cAMP
Matching (2 points each) Match the specific component from the signal transduction pathway above with its function below. PUT YOUR ANSWERS ON YOUR SCANTRON
SHEET!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
26) ____Epinephrine d) effector enzyme
27) ____ G-protein e) second messenger
28) ____ Adenylate cyclase
29) _____ cAMP
30) _____ Protein Kinase a) Transducer b) primary signal c) cytosolic effector enzyme

Matching (2 points each) Match the description with the letter depicting the correct TCA cycle enzyme name listed below. PUT YOUR ANSWERS ON YOUR SCANTRON
SHEET!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
31) _____ Catalyzes the conversion of pyruvate to acetyl-CoA
32) _____ Donates electrons directly to the electron transport chain through the reduction/oxidation of a FAD+
33) _____ Is an important regulatory TCA enzyme that catalyzes an oxidative decarboxylation reaction and is allosterically inhibited by NADH and allosterically activated by ADP and Ca
2+
.
34) _____ Catalyzes a substrate level phosphorylation reaction.
35) _____ Catalyzes the only reaction in the TCA cycle that generates a carbon-carbon bond. a) citrate synthase b) pyruvate dehydrogenase c) isocitrate dehydrogenase d) succinate dehydrogenase e) succinyl-CoA synthetase
36) (10 points) The next page contains the structures of all of the intermediates of glycolysis from glucose to pyruvate. You need to do the following:
A.
(5 points) For the regulated enzymatic reactions of glycolysis, write the name of the reaction substrates, the name of the reaction products next to the correct structure and the name of the enzyme.
B.
(5 points) For the enzymatic reaction that utilizes the cofactor NAD+ as a substrate, write the name of the reaction substrates, the name of the reaction products next to the correct structure and the name of the enzyme.

H
HO
H
H
CHO
C
C
OH
H
C OH
C OH
CH
2
OH
H
C
O
H C OH
CH
2
OPO
3
--
--O
3
PO
C
O
H C OH
CH
2
OPO
3
--
-O
C
O
H C OH
CH
2
OPO
3
--
-O
C
O
H C OPO
3
--
CH
2
OH
H
HO
H
H
CHO
C OH
C H
C OH
C OH
CH
2
OPO
3
--
HO
H
H
CH
2
OPO
3
--
C O
C H
C OH
C OH
CH
2
OPO
3
--
HO
H
H
CH
2
OH
C O
C H
C OH
C OH
CH
2
OPO
3
--
CH
2
OPO
3
--
C O
CH
2
OH
-O O
C
C OPO
3
--
CH
2
-O
C
O
C O
CH
3

Short answer (5 points each) You are required to answer 4 questions. You may answer a 5 th question for extra credit. Please be complete, but BRIEF!!!!! I will not grade more than 5 answers. So circle the question number to make sure it is clear which questions you want me to grade.
37) In a multi-enzyme pathway containing the enzymes A, B and C, at which enzymatic step of the pathway is flux being regulated if enzyme B has a metabolic control coefficient of 1 and enzymes A and C have very small metabolic control coefficients? Explain why.
38) Describe how the Kcat of a G-protein functions as a timer for the duration of signal transduction.
39) A specific glucose transporter is classified as a secondary active transporter. Explain how the ability of the glucose transporter to transport glucose against the glucose concentration gradient is dependent on the function of a Sodium/Potassium ATPase synporter.

40) Describe how glucagon signaling results in covalent modifications that reciprocally activate glycogen breakdown and inhibit glycogen synthesis.
41) Describe the Pasteur Effect and how this relates to rates of glycolysis in tumor tissues.
42) Hexokinase and glucokinase both catalyze the same reaction (i.e. glucose + ATP  glucose-6-phosphate
+ ADP). Describe how glucokinase can function in the storage of glucose in the liver for glycogen synthesis without competing with hexokinase.

EXAM 4
BCH 400/600
April 16, 2007
Name____________________________________
Mark the correct answer for questions 1 thru 40 on the provided scantron answer sheet.
Multiple Choice (2 points/question)
1) In an electron transport chain, electrons are donated from an electron donor with a _____ to an electron acceptor with a _______. a) more negative reduction potential, more positive reduction potential b) more positive reduction potential, more negative reduction potential c) positive charge, negative charge d) none of the above
2) The most ATP is produced when electrons are donated to the mitochondrial electron transport chain through which protein complex? a) Fatty acyl-CoA dehydrogenase b) Complex I c) Complex II d) Complex III e) Complex IV
3) Cytochrome C ___________________________________. a) is a water soluble electron carrier that donates electrons to Complex IV b) is a water soluble electron carrier that donates electrons to complex III c) is a water soluble electron carrier that donates electrons to Complex I d) a and c e) b and c
4) Which of the following protein complexes do not pump protons out of the mitochondrial matrix and into the mitochondrial inner membrane space? a) Complex I b) Complex II c) Complex III d) Complex IV e) None of the above
5) If the electron transport chain is uncoupled from ATP synthesis, the energy generated through the electron transport chain is _______________. a) converted to other high energy phosphate containing molecules b) converted to free electrons c) lost as light d) lost as heat e) none of the above
6) Which of the following protein complexes donate electrons directly to the plastoquinone pool? a) Complex II b) Fatty acyl-CoA dehydrogenase c) Glycerol-3-phosphate dehydrogenase complex d) Succinate dehydrogenase e) All of the above

7) Which of the following contributes most to the proton motive force generated through the mitochondrial electron transport chain? a) the charge differential across the inner mitochondrial membrane b) the chemical differential across the inner mitochondrial membrane c) the ATP/ADP ratio d) a and b e) All of the above
8) Which of the following protein complexes functions in the transfer of electrons from cytosoliclly derived
NADH to the mitochondria electron transport chain? a) Glycerol-3-phosphate dehydrogenase complex b) Succinate dehydrogenase c) Malate/Aspartate shuttle d) a and c e) all of the above
9) What is the term that refers to the process where a photon causes the oxidation of a photosystem chlorophyll? a) resonance energy transfer b) heat loss c) fluorescence d) charge separation e) Q cycle
10) In regards to the light reactions of photosynthesis, the proton gradient required for ATP production is generated across _________________. a) the inner chloroplast membrane b) the outer chloroplast membrane c) the thylakoid membrane d) the inner mitochondrial membrane e) the outer mitochondrial membrane
11) Which of the following is a photosynthetic antennae pigment? a) Chlorophyll b) Carotenoids c) Phycobilins d) All of the above e) None of the above
12) While the enzyme RuBisCO utilizes CO
2
as a substrate, CO
2
is also required by RuBisCO for what other purpose? a) activation of RuBisCO b) inhibition of RuBisCO c) transketolase activity d) to alter the pH of the enzyme
13) When RuBisCo utilizes oxygen instead of CO
2
as a substrate, the process is referred to as________________.

a) photosynthesis b) C3 photosynthesis c) CAM photosynthesis d) C4 photosynthesis e) photorespiration
14) Protons are concentrated in the thylakoid lumen by which of the following components of the photosynthetic electron transport chain? a) photosystem I b) oxygen evolving complex of photosystem II c) the Q cycle transfer of electron from plastoquinone to the cytochrome bf complex d) a and b e) b and c
15) Which of the following activate RuBisCO activity? a) light b) elevated Mg2+ concentration in the chloroplast stroma c) decreased levels of oxidized ferradoxin d) elevated pH of the stroma e) all of the above
16) The oxygenase reaction of RuBisCO generates _______________. a) 3-phosphoglycerate b) glyceraldehyde-3-phosphate c) phosphoglycolate d) a and b e) a and c
17) Which of the following enzymes is involved in the regeneration of ribulose-1,5,-bisphosphate during the
Calvin Cycle? a) transketolase b) RuBisCO c) aldolase d) a and c e) all of the above
18) Which of the following represents a mechanism by which photorespiration is avoided by the spatial separation of the CO
2 concentrating pathway and the CO
2
fixation by RuBisCO? a) Calvin Cycle b) CAM photosynthesis c) C4 photosynthesis d) Photophosphorylation e) None of the above
19) Which of the following lipoprotein classes functions to transport dietary fat to the liver and other tissues? a) VLDL b) IDL

c) LDL d) Chylomicrons e) HDL
20) Which of the following lipoprotein classes functions to transport cholesterol from the tissues back to the liver? a) VLDL b) IDL c) LDL d) Chylomicrons e) HDL
21) Aspirin _________________________. a) specifically inhibits COX I b) specifically inhibits COX II c) inhibits both COX I and COX II d) none of the above
22) Free fatty acids are carried through the blood stream _________________. a) as free fatty acids b) in lipoproteins c) bound to serum albumins d) as triacylglycerides e) none of the above
23) Acetyl-CoA carboxylase catalyzes the ATP dependent carboxylation of acetyl-CoA to form malonyl-CoA.
What cofactor (other than Coenzyme A) is required for acetyl-CoA carboxylase function? a) pyridoxal phosphate b) thiamin pyrophosphate c) biotin d) NADH e) NADPH
24) In mammals, the enzyme activities of fatty acid synthesis ____________. a) exist as individual soluble enzymes b) exist as a single multifunctional polypeptide chain
25) In mamaals, the enzymes required for beta-oxidation are localized _________________. a) in the cytosol b) within the mitochondria
26) What enzyme controls the amount of cholesterol produced in humans? a) acetyl-CoA carboxylase b) HMG-CoA synthase c) HMG-CoA reductase d) Thiolase e) Mevalonate kinase
27) What cofactor provides reducing power required for fatty acid biosynthesis? a) pyridoxal phosphate b) thiamin pyrophosphate c) biotin d) NAD+

e) NADPH
28) Which of the following converts the most nitrogen gas to ammonia? a) UV irradiation b) Lightning c) The Haber Process (chemical synthesis of ammonia) d) Nitrogen fixing bacteria e) a and b
29) Which of the following enzymes function in the biological assimilation of ammonia? a) glutamate dehydrogenase b) glutamine synthetase c) glutamate synthase d) all of the above
30) Which of the following is not an essential amino acid? a) isoleucine b) leucine c) lysine d) methionine e) alanine
31) Transamination reactions are essential for ammonia assimilation. What cofactor is required to catalyze transamination reactions? a) pyridoxal phosphate b) thiamin pyrophosphate c) biotin d) NAD+ e) NADPH
32) Which enzyme is shared between the IPP and ketone body biosynthetic pathways? a) thiolase b) HMG-CoA synthase c) HMG-CoA reductase d) a and b e) all of the above
Matching – Match the correct enzyme name with the letter on the figure.
33) _____ enoyl-ACP reductase

A
B
C
D
34)_____

-ketoacyl-ACP reductase
35)_____

-ketoacyl-ACP synthase
36) _____

-hydroxyacyl-ACP dehydrase
Matching – Match the correct enzyme name with the letter on the figure.
D
A
37) _____ enoyl-CoA hydratase
38) _____ thiolase
39) _____

-hydroxyacyl-CoA dehydrogenase
40) _____ acyl-CoA dehydrogenase
C
B

Short answer (5 points each) You are required to answer 4 questions. You may answer a 5 th question for extra credit. Please be complete, but BRIEF!!!!! I will not grade more than 5 answers. So circle the question number to make sure it is clear which questions you want me to grade.
41) If only three protons are required to power the F
0
F
1
ATP synthase to produce one molecule of ATP, explain why does the text book say that four protons are required for the synthesis of one molecule of ATP?
42) Explain how dinitrophenol functions as a chemical uncoupler of the electron transport chain and oxidative phosphorylation. Discuss how it was used in the past as a weight loss drug.
43) Explain how excess LDL in the blood leads to cardiovascular disease.
44) Explain why referring to the Calvin cycle as the “dark reactions” of photosynthesis is misleading and incorrect?

45) Explain why four photons are required for the oxygen evolving complex of photosystem II to convert water to oxygen.
46) Explain why the breath of a diabetic person sometimes smells of acetone.
47) Explain how nitrogen fixing bacteria protect the oxygen sensitive enzyme nitrogenase from becoming inactivated by oxygen.

48) Why is the Atkin’s diet so effective at causing people to loose weight?

BCH400/600
Spring 2007
Exam 5
Name__________________________________
For questions 1 thru 25 mark the correct answer on the exam sheet. There will be only one correct answer for each question.
Multiple Choice (2 points each)
1) Which of the following protein modifications target a protein for degradation? a.
Phosphorylation b.
ubiquitination c.
zymogen activation d.
subunit aggregation e.
all of the above
2) Specific amino acids associated with the ______ of a protein determine its half life. a.
C-terminal b.
N-terminal c.
All of the above
3) Ubiquitin is covalently attached to a protein through an amide linkage to which specific amino acid? a.
aspartate b.
glutamate c.
lysine d.
arginine e.
histidine
4) What part of the 26S proteosome complex recognizes an ubiquitinated protein? a) 20S proteosome core b) 19S cap c) E3 subunit d) E2 subunit e) All of the above
5) What part of the 26S proteosome complex contains the protease function? a) 20S proteosome core b) 19S cap c) E3 subunit d) E2 subunit e) All of the above
6) What is the fate of excess amino acids in animals and humans? a.
they are recycled for the synthesis of new proteins b.
they are stored for future use c.
they are catabolized to free ammonia and carbon skeletons d.
a and b e.
a and c
7) Fish dispose of toxic ammonia by ____________________.

a.
converting it to uric acid, which is subsequently secreted b.
converting it to urea, which is subsequently secreted c.
releasing it directly to the environment d.
all of the above e.
none of the above
8) The enzyme of the urea cycle are localized within ________________. a.
the mitochondria b.
the cytosol c.
the chloroplast d.
a and b e.
all of the above
9) Which amino acid participates as a pathway intermediate in the urea cycle? a.
lysine b.
arginine c.
glutamine d.
histidine e.
tyrosine
10) In humans, the urea cycle functions primarily in the ___________. a.
muscle tissue b.
heart c.
brain d.
liver e.
adipose tissue
11) What is the preferred fuel molecule utilized by the brain? a.
fatty acids b.
proteins c.
glucose d.
glycogen e.
all of the above
12) Which of the following fuel molecules could be utilized by muscle tissue for energy? a.
fatty acids b.
glucose c.
ketone bodies d.
glycogen e.
all of the above
13) Muscle tissue gets rid of toxic ammonia _________________. a.
by running the urea cycle in its cells b.
through the glucose/alanine cycle c.
through the Cori cycle d.
through the Bohr Effect e.
none of the above
14) The heart utilizes what fuel molecule as its preferred fuel source?

a.
fatty acids b.
proteins c.
glucose d.
glycogen e.
all of the above
15) What hormone is secreted in response to high blood glucose levels? a.
glucagon b.
epinephrine c.
insulin d.
a and b e.
none of the above
16) After a period of starvation when blood glucose levels begin to rise, which organ system gets first access to that glucose? a.
liver b.
heart c.
brain d.
muscle e.
adipose tissue
17) Which form of DNA is the predominate form found in biological systems? a.
A-DNA b.
B-DNA c.
cDNA d.
Z-DNA e.
All of the above
18) Which of the following nucleotides contains a pyrimidine base? a.
adenosine triphosphate b.
guanosine triphosphate c.
cytidine triphosphate d.
a and b e.
none of the above
19) A nucleoside consists of __________________. a.
a pentose sugar b.
a nitrogenous base c.
one or more phosphate groups d.
a and b e.
all of the above
20) Which of the following stabilizes a DNA double helix? a.
H-bonding between complementary bases b.
Hydrophobic environment of helix interior c.
Van der waals force between stacked bases d.
Mg2+ ions associating with the sugar phosphate backbone e.
All of the above
21) DNA replication is said to be________________.

a.
a semi-conservative process b.
a semi-discontinuous process c.
a bi-directional process d.
a and b e.
all of the above
22) Which of the following enzymes function to remove supercoils from a double stranded DNA molecule? a.
DNA polymerase b.
Topoisomerase c.
DNA ligase d.
DNA helicase e.
3’-5’ exonuclease
23) Where in the cell does DNA replication occur a) within the nucleus b) within the mitochondria c) within the chloroplast d) a and b e) all of the above
24) Which of the following are components of nucleosomes? a.
histones b.
DNA c.
H1 protein d.
a and b e.
all of the above
25) During DNA replication a new nucleotide is integrated into the growing nucleic acid polymer through a
_______________ linkage a.
phosphoanhydride b.
amide c.
phosphodiester d.
ionic e.
none of the above

Problems 26 thru 30 Match the correct letter on the diagram below with the correct enzyme name (2 points each) MARK THE CORRECT ANSWER BELOW AND ON YOUR SCANTRON ANSWER SHEET
26) ______ replication fork
27) ______ RNA primers
28) ______ Okazaki fragments
29) ______ leading strand
30) ______ lagging strand a b c d a e
Problems 31 thru 35 Match the correct letter on the diagram below with the correct enzyme name (2 points each) MARK THE CORRECT ANSWER BELOW AND ON YOUR SCANTRON ANSWER SHEET b d e c a
31) _______________ fatty acid synthesis
32) _______________ TCA Cycle
33) _______________ gluconeogenesis
34) _______________ aneorbic fermentation
35) _______________ isoprenoid biosynthesis

36) (10 points) Draw the correct structure of the single stranded RNA molecule (including the correct sugar, nitrogenous bases, and the phosphodiester backbone) that has the following sequence. 5’-C-G-U-A-3’. All bases need to be in the anti-conformation.

Short answer (5 points each) You are required to answer 4 questions. You may answer a 5 th question for extra credit. Please be complete, but BRIEF!!!!! I will not grade more than 5 answers. So circle the question number to make sure it is clear which questions you want me to grade.
37) Which is worse, taking this exam or having a sharp stick poked in your eye?
38) Describe why DNA replication is describe as a semi-discontinuous process.
39) Describe two mechanisms that cells use to prevent mutations from occurring within their genome.
40) Describe why hydrogen bonding between complementary bases within the helix interior of a double stranded DNA molecule is stronger than typical hydrogen bonds.

41) Describe the glucose-alanine cycle.
42) List three modes by which enzyme activity is regulated.
43) Describe how to sequence DNA using the Sanger Method (aka - the dideoxynucleotide chain termination method)?

44) In “Bizzaro World,” DNA replication occurs in a dispersive manner instead of a semi-conservative manner.
You are the Bizzaro equivalent of Messelson or Stahl. You first grow Bizzaro bacteria in
15
N-labeled nucleotides and then transfer the culture to normal medium containing
14
N-labeled nucleotides. You separate the “heavy labeled” DNA from the “light-labeled” DNA by centrifugation from bacteria harvest before the media switch and then again after one round of DNA replication. Describe the results of your experiments.