Download INTRODUCTORY BIOCHEMISTRY BI 28 Second Midterm

INTRODUCTORY BIOCHEMISTRY
BI 28
Name
Second Midterm Examination
KEY
April 3, 2007
SIS #
Make sure that your name or SIS # is on every page. This is the only way we have of
matching you with 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. Points are indicated by the question
within brackets [ ]. There are no calculators or other electronic devices needed or
allowed on this exam.
Page 2 total ____10______/
Page 3 total ____15______/
Page 4 total __________/
Page 5 total __________/
Page 6 total __________/
Page 7 total __________/
Page 8 total __________/
Page 9 total __________/
Extra Credit__________/
Exam total __________/100
1. [2] Which combination of cofactors is involved in the conversion of pyruvate to acetyl-CoA?
A)
B)
C)
D)
E)
Biotin, FAD, and TPP
Biotin, NAD+, and FAD
NAD+, biotin, and TPP
Pyridoxal phosphate, FAD, and lipoic acid
TPP, lipoic acid, and NAD+
2. [2] Malonate is a competitive inhibitor of succinate dehydrogenase. If malonate is added to a
mitochondrial preparation that is oxidizing pyruvate as a substrate, which of the following
compounds would you expect to decrease in concentration?
A)
B)
C)
D)
E)
Citrate
Fumarate
Isocitrate
Pyruvate
Succinate
3. [2] Briefly describe the relationship of the pyruvate dehydrogenase complex reaction to
glycolysis and the citric acid cycle.
Ans: The pyruvate dehydrogenase complex converts pyruvate, the product of glycolysis, into
acetyl-CoA, the starting material for the citric acid cycle.
4. [2] Most of the energy released in the citric acid cycle reactions is conserved in _________.
A) GTP
B) ATP
C) NADH
D) ADP
5. [2] The formation of oxaloacetate by malate dehydrogenase is endergonic (ΔG’0 = 29.7 kJ/mol),
so the concentration of oxaloacetate would be much lower than that of the substrate L-malate at
equilibrium. Explain why the reaction moves forward in the citric acid cycle.
A: Oxaloacetate is effectively removed in step 1 of the cycle, which has a high affinity for
axaloacetate and is highly exergonic ((ΔG’0 = -32.2kJ/mol). Alternative answer: exergonic step 1
drives the reaction forward. Points for removed, exergonic, step 1
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6. [3] Indicate whether the following statements about the citric acid cycle are true or false by
circling T or F.
T / F The carbon atoms that enter the citric acid cycle via acetyl-CoA are the same ones released
as carbon dioxide during one round of the citric acid cycle.
T / F The overall goal of the citric acid cycle is to oxidize pyruvate, form reduced coenzymes, and
produce ATP.
T / F A racemic mixture of the enantiomeric forms of isocitrate is produced during the citric acid
cycle reactions.
7. [2] Circle the enzyme(s) that are unique to the glyoxylate cycle
A) malate synthase
B) malate dehydrogenase
C) isocitrate lyase
D) citrate synthase
E) isocitrate dehydrogenase
8. [2] In the respiratory electron transport chain electrons are passed from ___________.
A) NADH and QH2 to O2
C) O2 to NADH
B) O2 to NAD+ and Q
D) NADH to ATP
9. [2] A lipid soluble cofactor that can diffuse freely in the membrane of the electron transport chain
and carry electrons across the membrane is __________.
A) ubiquinone
C) FADH2
B) cytochrome c
D) heme
10. [4] Explain why there are only 6 protons translocated for each FADH2 that is reduced by the
succinate dehydrogenase complex.
A: Electrons that enter the electron transport chain from succinate dehydrogenase bypass complex I
(which transports 4 protons)
11. [2] During oxidative phosphorylation, NADH equivalents are transferred into the mitochondrial
matrix via the __malate___-___aspartate_____ shuttle in liver cells and the __glycerol 3phosphate_
shuttle in muscle cells.
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12. [2] Rotation of the ______ subunit of ATP synthase causes conformational changes in the
catalytic sites that produce ATP.
A) α
B) β
C) δ
D) ε
E) γ
13. [2] Heat can be generated in the brown fat tissue of hibernating mammals due to _______.
A) increased ATP production by ATP synthase
B) uncoupling by thermogenin
C) a greater pH gradient across the inner mitochondrial membrane by complex IV
D) insufficient NADH production during the citric acid cycle due to less active pyruvate
dehydrogenase
14. [2] Per carbon atom fixed, operation of the complete Calvin cycle requires the reducing
equivalents derived from oxidation of _2__ molecules of NADPH to NADP+ and the energy derived
from hydrolysis of _3__ molecules of ATP to ADP.
15. [2] Plants that use the C4 mechanism to acquire CO2, compared to plants that do not use this
mechanism (C3 plants), need an additional amount of energy equivalent to that derived from
hydrolysis of _2__ molecules of ATP to ADP, and an additional amount of reducing equivalents
equivalent to the amount derived from oxidation of _0__ molecules of NADPH to NADP+.
16. [9] For each process or component listed below, indicate in the space provided whether it is
associated with Photosystem I, Photosystem II, or both Photosystems.
Pheophytin ___II____
Ferredoxin ____I_____
Chlorophyll b __I,II____
Oxygen-evolving complex ____II____
Cyclic photophosphorylation ___I______
Noncyclic photophosphorylation __I,II____
Plastoquinone ___II_____
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17. [2] Indicate with an asterisk (*) which atom or atoms of the compound shown below would be
radioactively labeled when 14CO2 is fixed during one turn of the Calvin cycle.
*CH2OH
|
H-C-OH
|
CH2OPO3H218. [2] Gluconeogenesis shares some, but not all, enzymes with the glycolytic pathway. It would
appear to be more efficient if both pathways used all of the same enzymes since the pathways are
essentially the reverse of each other. Why don’t both pathways use all of the same enzymes?
A) The reactions where enzymes differ occur in different parts of the cell for glycolysis versus
gluconeogenesis
B) Enzymes can catalyze a reaction only in one direction, so naturally the two pathways have
some enzymes that differ.
C) In tissues where gluconeogenesis occurs, the glycolytic enzymes are present at extremely
low concentrations.
D) Three of the reaction steps in gluconeogenesis would have prohibitively large, positive free
energies if they used glycolytic enzymes for their catalysis.
19. [4] Function of fructose 2,6 bisphosphate in the regulation of glycolysis and gluconeogenesis.
Mention which enzymes determine the cellular levels of this molecule, which enzymes are
regulated by this molecule and which effect high concentrations of F2,6BP will have on glycolysis
and gluconeogenesis.
Function of F2,6BP: allosteric regulator of PFK1 and FBPase1, or reciprocally regulates
glycolysis and gluconeogenesis
Enzyme(s) determining cellular levels: PFK2/FBPase2
F2,6BP regulates: PFK1 and FBPase1
High [F2,6BP]: increase (activate, upregulate) glycolysis and decrease (inhibit, downregulate)
gluconeogenesis
20. [2] The glycogen-branching enzyme catalyzes:
A)
B)
C)
D)
E)
degradation of (a1 → 4) linkages in glycogen
formation of (a1 → 4) linkages in glycogen.
formation of (a1 → 6) linkages during glycogen synthesis.
glycogen degradation in tree branches.
removal of unneeded glucose residues at the ends of branches.
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21. [4] Explain the function of glycogenin
A: Glycogenin is a protein that acts as a primer for the initiation of new glycogen molecules. It
catalyzes the transfer of a glucose residue from UDP-glucose to a tyrosine residue of itself. It then
adds seven more glucose residues and forms a complex with glycogen synthase, which further
extends the growing glycogen chain.
22. [2] During polysaccharide breakdown, glycogen and starch are converted to _glucose 1phosphate_ by the enzyme ___glycogen phosphorylase_______.
23. [4] Indicate whether the following statements about fatty acid catabolism are true of false by
circling T or F.
T / F hydrolysis of glycerolipids releases glycerol 3-phosphate and fatty acids
T / F The rate limiting step in fatty acid oxidation is the activation of free fatty acids with ATP
T / F fatty acids are transported into mitochondria as acyl carnitine
T / F β-oxidation of odd numbered fatty acids yields propionyl-CoA that is then further converted
to succinyl-CoA
24. [2] In the human body, ketogenesis occurs in the ___liver____. Ketone bodies are synthesized
from ____acetyl-CoA_____.
25. [6] Fatty acid biosynthesis: In the space provided below, enter which molecule is the carbon
donor for synthesis, which enzyme synthesizes this carbon donor, which enzyme then synthesizes
fatty acids, what functions as the acyl carrier during synthesis, which cofactor serves as the electron
donor and which fatty acid is released from the synthesizing enzyme.
Carbon donor for fatty acid synthesis: malonyl-CoA
Synthesized by: ACC, acetyl-CoA carboxylase
Enzyme that synthesizes fatty acids: fatty acid synthase
Acyl carrier for synthesis: ACP, acyl carrier protein
Electron donor cofactor: NADPH
Fatty acid released: palmitate
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26. [2] A 30-carbon precursor of the steroid nucleus (during cholesterol synthesis) is:
A)
B)
C)
D)
E)
farnesyl pyrophosphate.
geranyl pyrophosphate.
isopentenyl pyrophosphate.
lysolecithin.
squalene.
27. [2] Transamination from alanine to α-ketoglutarate requires the coenzyme:
A)
B)
C)
D)
E)
biotin.
NADH.
No coenzyme is involved.
pyridoxal phosphate (PLP).
thiamine pyrophosphate (TPP).
28. [2] Serine or cysteine may enter the citric acid cycle as acetyl-CoA after conversion to:
oxaloacetate.
propionate.
pyruvate.
succinate.
E) succinyl-CoA
A)
B)
C)
D)
30. [6] Amino acid biosynthesis: In the empty boxes in the
figure to the right, mark the correct position for the following
molecules with the corresponding letter.
A) oxaloacetate
B) histidine
C) pyruvate
D) α-ketoglutarate
E) ribose 5-phosphate
F) serine
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29. [2] During starvation, more urea production occurs. Explain this observation (in 50 words or
less).
Ans: During starvation, cellular proteins are degraded and their carbon skeletons are oxidized for
energy. The first step in amino acid catabolism is removal of the amino groups, which are
ultimately excreted as urea.
31. [2] Which of the following enzymes is not involved in the assimilation of inorganic nitrogen
into an organic molecule?
A)
B)
C)
D)
E)
Arginase
Glutamate dehydrogenase
Glutamate synthase
Glutamine synthetase
Nitrogenase
32. [4] Indicate with a letter the cellular compartment where each of the following metabolic
pathways takes place (indicate with “C”ytosol, “M”atrix, “B”oth compartments):
_B__ urea synthesis
_C__ glycolysis
_C__ fatty acid synthesis
_M__ β-oxidation
33. [2] Insulin is an example of a(n) ____________ hormone.
A)
B)
C)
D)
E)
catecholamine
eicosanoid
paracrine
peptide
steroid
34. [2] The largest energy store in a well-nourished human is:
A)
B)
C)
D)
E)
ATP in all tissues.
blood glucose.
liver glycogen.
muscle glycogen.
triacylglycerols in adipose tissue.
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35. [2] When blood glucose is abnormally high, the pancreas releases:
A)
B)
C)
D)
E)
epinephrine.
glucagon.
glucose.
insulin.
trypsin.
36. [4] Which class of hormones acts via nuclear receptors? Briefly describe the mode of action of
these hormones.
Ans: Steroid hormones. Examples are the sex hormones testosterone and estradiol. They pass
through the plasma membrane and interact with receptor proteins in the nucleus. The hormonereceptor complex interacts with DNA and alters the expression of specific genes.
Challenge Question [4 extra credit]
Preparation of an extract of muscle results in a dramatic decrease in the concentration of citric acid
cycle intermediates compared to their concentrations in the tissue. However, in 1935, Szent-Gyorgi
showed that the production of CO2 by the extract increased when succinate was added. In fact, for
every mole of succinate added, many extra moles of CO2 were produced. Explain this effect in
terms of the known catabolic pathways.
Ans: Succinate is an intermediate in the citric acid cycle that is not consumed but is regenerated
by the operation of the cycle. Its addition to an extract depleted in citric acid cycle
intermediates allows the cycle to resume operating, oxidizing acetyl-CoA to CO2.
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