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INTRODUCTORY BIOCHEMISTRY
BIOL0280
Second Midterm Examination
April 3, 2014
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your exam after grading it. Please work independently. Read each question carefully before answering.
Unless otherwise indicated, there is only one correct answer for each multiple-choice question. For
multiple choice or matching questions with more than one correct answer, points will be deducted for
missing or incorrect responses. Points are indicated by the question within brackets []. There are no
calculators or other electronic devices needed or allowed on this exam. All hats must be removed
during the exam. Exams will be scanned electronically before being returned.
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1. [2 points] Which of the following reactions can be described as anaplerotic?
A) Oxaloacetate + Acetyl CoA ---> Citrate
B) Malate ---> Oxaloacetate
C) Pyruvate + CO2 ---> Oxaloacetate
D) Both A and C are correct
E) All of the above are correct
Circle the correct answer.
2. [2 points] The enzymes that are unique to the glyoxylate cycle include _________.
A) Aconitase
B) Malate dehydrogenase
C) Fumarase
D) Succinate dehydrogenas
E) Isocitrate lyase
Circle the correct answer.
3. [4 points] Match the cofactors of the pyruvate dehydrogenase complex in the left column with their
corresponding enzyme components and with their roles in the enzymatic steps that are listed in the
right column. For each cofactor, indicate ALL correct answers. Each cofactor might have more than
one correct answer and the roles and components may apply to more than one cofactor.
Cofactor
Enzyme Components and Roles
Coenzyme A ___C,F_______________
A) Pyruvate dehydrogenase E1 component
B) Dihydrolipoyl dehydrogenase E3 component
Thiamine pyrophosphate___A,E______
C) Dihyrdolipoyl transacetylase E2 component
D) Oxidizes the hyrdoxyethyl group
Lipoic acid_____C, G, D____________
E) Decarboxylates pyruvate
F) Accepts the acetyl group from acetyllipoamide
NAD+_______B,I_________________
G) Provides a long flexible arm that conveys
intermediates to different enzyme components
I) Oxidizes FADH2
1 point for indicating all the correct answers for each cofactor, -0.5 for any missing answer, -0.5
for any incorrect answer
4. [2 points] Which of the following answers complete the sentence correctly? Succinate
dehydrogenase:
A) is an iron-sulfur protein like aconitase
B) contains FAD and NAD+ cofactors like pyruvate dehydrogenase
C) is an integral membrane protein unlike the other enzymes of the citric acid cycle
D) carries out an oxidative decarboxylation like isocitrate dehydrogenase
E) is inhibited by mevalonate
Circle the correct answer.
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5. [2 points] A reaction which involves a substrate-level phosphorylation is:
A) isocitrate ---> a-ketoglutarate
B) citrate ---> isocitrate
C) succinyl-CoA ---> succinate
D) succinate ---> fumarate
E) fumarate ---> malate
Circle the correct answer.
6. [4 points] Indicate the order of the following respiratory-chain components from 1-5 with 1 being the
first and 5 being the last. Also indicate with an "X" which components are mobile carriers of
electrons.
Component
Order (1-5)
Mobile Carrier
Cytochrome c
_____3_____
_____x_____
NADH:ubiquinone
oxidoreductase
_____1_____
__________
Cytochrome oxidase
_____4_____
__________
Ubiquinone
_____2_____
_____x_____
7. [4 points] Explain the difference between oxidative phosphorylation and substrate level
phosphorylation in terms of stoichiometry and how ATP is formed.
Oxidative phosphorylation is the process in which ATP is formed as electrons are transferred
from NADH or FADH2 to O2. The energy coupling occurs through a proton and charge
gradient which drives FOF1-ATP synthase. In substrate level phosphorylation, the synthesis
of ATP or GTP from ADP and GDP are coupled by shared intermediates to other chemical
reactions that release sufficient energy to drive the formation of ATP or GTP. Substrate level
phosphorylation has defined stoichiometries because they use a shared intermediate to couple
reactions. Oxidative phosphorylation has a less precise stoichiometry because its driving force
is a gradient of electrons and protons across a membrane. Will accept 4 protons per ATP or
2.5 ATP per NADH or 1.5 ATP per FADH2
1 point for how ATP is formed in ox phos
1 point for how ATP is formed in substrate level phosphorylation
1 point for discussion of stoichiometry with ox phos
1 point for discussion of stoichiometry with substrate level phosphorylation
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8. [2 points] The regulation of the TCA cycle occurs at each of the following enzymes except:
A) citrate synthase
B) isocitrate dehydrogenase
C) aconitase
D) a-ketoglutarate dehydrogenase complex
E) pyruvate dehydrogenase complex
Circle the correct answer.
9. [2 points] Coenzyme Q oxidized by complex III is reduced by:
A) Complex I
B) Complex II
C) Complex III
D) Complex IV
E) Glycerol 3-phosphate dehydrogenase
Circle all correct answer(s) More than one answer may be correct.2 points for all correct, 0.5 point
off for any incorrect or 0.5 point off for any missing answer
10. [2 points] Which of the following statements about the proposed mechanism for ATP synthesis by
ATP synthase is incorrect?
A) The γ subunit acts as a molecular cam-shaft
B) ATP synthase contains sites that change in their affinity for ATP as protons flow through the
complex
C) ATP synthase has two active sites per complex
D) The energy-requiring step is the release of bound ATP
E) ATP synthase does not have more than one active site that is each bound to ATP at the same time
Circle the correct answer.
11. [2 points] The inner mitochondrial membrane contains transporters for which substances?
A) NAD+
B) glycerol 3 phosphate
C) ATP
D) aspartate
E) Acetyl CoA
Circle all correct answer(s) More than one answer may be correct. 2 points for all correct, 1 point
off for each incorrect or missing answer
12. [2 points] Which statement about the cyclic pathway in Photosystem I is correct?
A) It involves NADPH formation
B) It uses electrons produced by Photosystem II
C) It generates O2
D) It leads to ATP production via cytochrome b6f complex
E) It uses plastaquinone
Circle the correct answer.
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13. [5 points] Assign each function or product from the right column to the appropriate structure or
pathway in the left column. Please indicate all correct answers and each statement may have more
than one correct answer.
Chlorophyll ______C__________
A) O2 generation
B) Glyceraldehyde 3-phosphate synthesis
Light Harvesting Complex ___C___
C) Light absorption
D) NADPH synthesis
Photosystem I ______(E),C,D__________
E) Separation of electrons
Photosystem II _____A, (E), C__________
Calvin cycle ____B__________
1 point for indicating all the correct answers for each cofactor, -0.5 for each missing answer, -0.5
for each incorrect answer. Answer E was confusing for many students so it was not required to
get the question completely correct.
14. [2 points] Many chlorophyll molecules absorb light and direct it to the reactive center. The transfer
of this absorbed energy is called:
A) fluorescence transfer
B) redox transfer
C) resonance exciton transfer
D) electron transfer
Circle the correct answer.
15. [2 points] What statement is incorrect about RuBisCO?
A) Ribulose 1,5-bisphosphate and carbon dioxide are both substrates
B) It contains both a carboxylase and oxygenase activity
C) It releases 2 molecules of glyceraldehyde 3-phosphate as product
D) It is found in the chloroplast stroma
E) It makes up 50% of soluble protein in chloroplasts
Circle the correct answer.
16. [2 points] The process of photorespiration is suppressed in:
A) C3 plants
B) C4 plants
C) CAM plants
D) Both B and C are correct
E) A, B, and C are correct
Circle the correct answer.
17. [2 points] Which is an output of the reductive phase of the Calvin Cycle (Stage 2)?
A) Ribulose 1,5-bisphosphate
B) 3-phosphoglycerate
C) Glyceraldehyde 3-phosphate
D) ATP
E) NADPH
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Circle the correct answer.
18. [4 points] The following is the sequence of reactions of gluconeogenesis from pyruvate to
phosphoenolpyruvate:
A
B
C
D
Puruvate -------->oxaloacetate -------->malate -------->oxaloacetate -------->phosphoenolpyruvate
Match the letter(s) indicating the reactions of the gluconeogenic pathway with the following
statements. Please indicate all correct answers and each statement may have more than one correct
answer.
Occur in the mitochondria
Letter
____A,B______
Occur in the cytosol
____C,D______
Consumes CO2
____A________
Requires ATP
_____A_______
1 point for indicating all the correct answers for each cofactor, -0.5 for each missing answer, -0.5
for each incorrect answer
19. [4 points] Indicate which of the conditions listed in the right column increase the activity of the
glycolysis, gluconeogenesis, glycogen synthesis, or glycogen breakdown pathways (indicate all
correct answers for each pathway and each condition may be used for more than one pathway)
Glycolysis ___A,B,C,F___________
A) increase in AMP
B) increase in F2,6BP
Gluconeogenesis _D,E,G__________
C) increase in insulin
D) increase in glucagon
Glycogen Synthesis _C,F________
E) starvation
F) fed state
Glycogen Breakdown _D,E,A_______
G) increase in acetyl-CoA
1 point for indicating all the correct answers for each pathway, -0.5 for each missing answer, -0.5
for each incorrect answer
20. [2 points] In the condensation step of the fatty acid synthase enzyme, the addition of two carbon
units to the growing fatty chain involves
A) hydrolysis of ATP
B) oxidation of NADPH
C) reduction of NADP+
D) decarboxylation of malonyl-CoA
E) synthesis of ATP
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Circle the correct answer.
21. [5 points] Place the following incomplete list of reactions or relevant locations during B-oxidation
of fatty acids in the proper order. Indicate the letter next to the order with 1 being the first step and 5
being the last step.
Reaction and locations
A) acyl CoA import into mitochondrion
Order
1) _____C_____________
B) thiolysis
2) _____E_____________
C) activation of fatty acid with ATP
3) _____A_____________
D) hydration
4) _____D____________
E) reaction with carnitine
5) _____B____________
22. [2 points] Acetyl-CoA carboxylase in animals is regulated by all the following except
A) Phosphorylation triggered by glucagon
B) allosterically by citrate
C) allosterically by palmitoyl-CoA
D) allosterically by ATP
E) allosterically by malonyl-CoA
Circle the correct answer.
23. [2 points] Indicate whether the statements below are true or false
T / F
The second bypass reaction of gluconeogenesis is catalyzed by FBPase-1
T / F
The second and third bypass reactions of gluconeogenesis produce ATP
Circle either T or F for each statement
24. [4 points] If glycogen synthase can add a glucose residue to a growing glycogen molecule only if
the glucose chain is at least 8 residues long, how does a new glycogen molecule start? Be sure to
describe any enzymes and substrates involved in the process and exactly how the glycogen chain is
started.
The primer required to start a new glycogen chain is formed by the enzyme glycogenin, which
has a glucose residue covalently attached to one of its tyrosine residues. Glycogenin uses UDPglucose to add approximately 8 glucose residues to itself to generate a primer that glycogen
synthase can extend.
2 points for mentioning glycogenin, 1 point for UDP-glucose, 1 point for direct glycosylation of
tyrosine (covalent attachment of glucose to protein is acceptable) on glycogenin
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25. [2 points] Which of the following reactions are direct sources of glycerol 3-phosphate that is used in
triacylglycerol and glycerophospholipid synthesis?
A) Reduction of dihydroxyacetone phosphate
B) Oxidation of glyceraldehyde 3-phosphate
C) Phosphorylation of glycerol
D) Dephosphorylation of 1,3-bisphosphoglycerate
E) Reductive phosphorylation of pyruvate
Circle all correct answer(s) More than one answer may be correct. 2 points for all correct, 1 point
off for each incorrect or missing answer
26. [2 points] Which statement is incorrect about cholesterol biosynthesis?
A) It involves the reduction of β-Hydroxy-β-methylglutaryl-CoA by NADPH to form mevalonate
B) The rate of synthesis is regulated by the cellular activity of HMGCoA reductase
C) It involves 2 head to tail and one head to head condensations
D) It involves the cyclization of squalene to lanosterol by cyclase enzyme
Circle the correct answer.
27. [4 points] Which four of the following compounds provide the carbon skeletons for biosynthesis of
amino acids?
A) 2-Deoxyribose
E) Ribose 5-phosphate
B) Oxaloacetate
F) Glucose 6-phosphate
C) α-Ketoglutarate
G) 3-Phosphoglycerate
D) Succinate
H) α-Ketobutyrate
Circle all four correct answer(s). 1 points for each correct, 1 point off for each incorrect or
missing answer
28. [2 points] Considering all forms of life, which of the following are major excretory forms of the aamino groups of amino acids?
A) Guanine
B) Uracil
C) Ammonia
D) Uric acid
E) Adenine
Circle all correct answer(s) More than one answer may be correct. 1 points for each correct, 1
point off for each incorrect or missing answer
29. [2 points] Which of the following statements about the reaction catalyzed by carbamoyl phosphate
synthetase I is incorrect
A) it takes place in the mitochondrial matrix
B) it involves the hydrolysis of 2 ATP per urea molecule
C) it consumes two molecules of ammonia per urea molecule
D) the enzyme that catalyzes it is regulated by N-acetylglutamate
E) it involves the phosphorylation of bicarbonate
Circle the correct answer.
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30. [2 points] Glycerophospholipids are synthesized by activation with a nucleotide either of the
____Phosphatidic acid___ or the _____head group____. The activated molecules then condense
in a single step to the final glycerophospholipid product.
31. [4 points] Match the functions from the right column with the appropriate coenzymes, listed in the
left column, that are involved in amino acid catabolism.
Pyridoxal phosphate ______A_______
NAD+ _______________D_________
Tetrahydrofolate _______C_________
A) Transamination reactions
B) One carbon transfer (CH3 only)
C) One carbon transfer (intermediate oxidation
states)
D) Transfer of electrons
AdoMet ______________B_________
1 points for each correct
32. [2 points] Catabolism of which of the following amino acids requires the direct involvement of O2?
A) Tyrosine
B) Isoleucine
C) Serine
D) Alanine
E) Threonine
Circle the correct answer.
33. [2 points] For use during bursts of heavy activity, muscle cells store "high-energy" phosphate as:
A) glyceraldehyde 3-phosphate
B) 1,3-bisphosphoglycerate
C) phosphoenolpyruvate
D) phosphocreatine
E) pyrophosphate
Circle the correct answer.
34. [2 points] Liver cells have the necessary enzymes to perform the following conversions except
A) alanine into palmitic acid
B) palmitic acid into cholesterol
C) glucose into stearic acid
D) palmitic acid into glucose
E) glucose into serine
Circle the correct answer.
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35. [4 points] Select the statements from the right column that best describe the metabolism of each
organ, tissue, or cell in the left column. Please indicate all correct answers.
Brain _________B__________________
Muscle ____D,E______________________
Adipose Tissue ____A________________
Liver _________C, F_______________
A) releases glycerol and fatty acids into the
blood during periods of fasting
B) in a normal nutritional state, utilizes glucose
as the exclusive fuel
C) synthesizes ketone bodies when the supply of
acetyl CoA is high
D) can release lactate into the blood
E) can store glycogen but cannot release glucose
into the blood
F) can synthesize fatty acids, triacylglycerols,
and VLDL when fuels are abundant
1 point for indicating all the correct answers for each pathway, -0.5 for each missing answer, -0.5
for each incorrect answer
36. [2 points] Fill in the blank in the following statement:
During prolonged fasting, fatty acids in the liver are converted to _____A__________ which is/are
transported to the _______B__________ to be used as fuel.
A=ketone bodies, or Acetone or Acetoacetate or b-hydroxybutyrate. no credit for acetoacetylCoA since this molecule is not directly transported.
B=brain. no credit for muscle since this is not true during prolonged fasting
37. [4 points] Glycogen synthase is activated with the addition of insulin. Describe the signaling
pathway, clearly identifying at least four of the kinases, proteins, or lipids that participate AND how
each is activated.
1) Insulin binds insulin receptor, turning on the receptor's tyrosine kinase activity which 2)
phsophorylates IRS1, 3) recruting and actvating PI3K by binding to its SH2 domain. 4) PI3K
phosphorylates PIP2 to PIP3, 5) activating PKB by phosphorylation by PDK1. 6) PKB
phosphorylates GSK3, inactivating it. 7) Glycogen synthase remains active in the absence of
phosphorylation by GSK3. 1 point for each protein and how it is activated, only 4 being
required for full credit. 0.5 points for identification of each and 0.5 points for a description of
how it is activated.