INTRODUCTORY BIOCHEMISTRY

BI 28 Second Midterm Examination April 3, 2007

Name 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. Exams will be photocopied before being returned on Thursday.
Please note: All regrade requests for this exam are due by Thursday April 12th at 5pm.
Regrades can lead to an overall lower score on the exam.

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Extra Credit__________/4

Exam total __________/100

1. [2] Which combination of cofactors is involved in the conversion of pyruvate to acetyl-CoA?

A) Biotin, FAD, and TPP

B) Biotin, NAD+, and FAD
C) NAD+, biotin, and TPP
D) Pyridoxal phosphate, FAD, and lipoic acid
E) TPP, lipoic acid, and NAD+
Circle the correct answer

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) Citrate
B) Fumarate
C) Isocitrate
D) Pyruvate
E) Succinate
Circle the correct answer

3. [2] Briefly describe the relationship of the pyruvate dehydrogenase complex reaction to
glycolysis and 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
Circle the correct answer

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.

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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 for each question.

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
Circle the correct answer

8. [2] In the respiratory electron transport chain electrons are passed from ___________.

A) NADH and QH2 to O2 B) O2 to NAD+ and Q

C) O2 to NADH D) NADH to ATP
Circle the correct answer

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 B) cytochrome c
C) FADH2 D) heme
Circle the correct answer

10. [4] Explain why there are only 6 protons translocated for each FADH2 that is reduced by the
succinate dehydrogenase complex.

11. [2] During oxidative phosphorylation, NADH equivalents are transferred into the mitochondrial
matrix via the ____________-_____________ shuttle in liver cells and the ___________________
shuttle in muscle cells.
Enter the correct answer in the missing spaces provided

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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
Circle the correct answer

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
Circle the correct answer

14. [2] Per carbon atom fixed, operation of the complete Calvin cycle requires the reducing
equivalents derived from oxidation of ____ molecules of NADPH to NADP+ and the energy derived
from hydrolysis of ____ molecules of ATP to ADP.
Enter the correct number in the missing spaces provided

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 ____ molecules of ATP to ADP, and an additional amount of reducing equivalents
equivalent to the amount derived from oxidation of ____ molecules of NADPH to NADP+.
Enter the correct number in the missing spaces provided

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 _______

Ferredoxin _________

Chlorophyll b ______

Oxygen-evolving complex ________

Cyclic photophosphorylation _________

Noncyclic photophosphorylation ______

Plastoquinone ________

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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
|
CH2OPO3H2-
18. [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.
Circle the correct answer

19. [4] Considering the function of fructose 2,6 bisphosphate (F2,6BP) in the regulation of
glycolysis and gluconeogenesis, enter in the spaces provided below its function, which enzyme(s)
determine the cellular levels of this molecule, which enzyme(s) are regulated by this molecule, and
what effect high concentrations of F2,6BP will have on glycolysis and gluconeogenesis.

Function of F2,6BP:

Enzyme(s) determining cellular levels: _________________________

F2,6BP regulates: ________________________________

High [F2,6BP]: __________________________________

20. [2] The glycogen-branching enzyme catalyzes:

A) degradation of (a1 → 4) linkages in glycogen

B) formation of (a1 → 4) linkages in glycogen.
C) formation of (a1 → 6) linkages during glycogen synthesis.
D) glycogen degradation in tree branches.
E) removal of unneeded glucose residues at the ends of branches.
Circle the correct answer

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21. [4] Explain the function of glycogenin

22. [2] During polysaccharide breakdown, glycogen and starch are converted to ________________
by the enzyme _____________________.
Enter the correct answer in the missing spaces provided

23. [4] Indicate whether the following statements about fatty acid catabolism are true of false by
circling T or F for each question.

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 ____________. Ketone bodies are synthesized
from ________________.
Enter the correct answer in the missing spaces provided

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: ________________________________

Synthesized by: _____________________________________

Enzyme that synthesizes fatty acids: _________________________________

Acyl carrier for synthesis: _________________________________

Electron donor cofactor: __________________________________

Fatty acid released: ______________________________________

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26. [2] A 30-carbon precursor of the steroid nucleus (during cholesterol synthesis) is:

A) farnesyl pyrophosphate.
B) geranyl pyrophosphate.
C) isopentenyl pyrophosphate.
D) lysolecithin.
E) squalene.
Circle the correct answer

27. [2] Transamination from alanine to α-ketoglutarate requires the coenzyme:

A) biotin.
B) NADH.
C) No coenzyme is involved.
D) pyridoxal phosphate (PLP).
E) thiamine pyrophosphate (TPP).
Circle the correct answer

28. [2] Serine or cysteine may enter the citric acid cycle as acetyl-CoA after conversion to:

A) oxaloacetate.
B) propionate.
C) pyruvate.
D) succinate.
E) succinyl-CoA
Circle the correct answer

29. [6] Amino acid biosynthesis: In the empty boxes in the

figure to the right, mark the correct box 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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30. [2] During starvation, more urea production occurs. Explain this observation (in 50 words or
less).

31. [2] Which of the following enzymes is not involved in the assimilation of inorganic nitrogen
into an organic molecule?

A) Arginase
B) Glutamate dehydrogenase
C) Glutamate synthase
D) Glutamine synthetase
E) Nitrogenase
Circle the correct answer

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):

____ urea synthesis

____ glycolysis
____ fatty acid synthesis
____ β-oxidation
Enter the correct letter in the missing spaces provided

33. [2] Insulin is an example of a(n) ____________ hormone.

A) catecholamine
B) eicosanoid
C) paracrine
D) peptide
E) steroid
Circle the correct answer

34. [2] The largest energy store in a well-nourished human is:

A) ATP in all tissues.

B) blood glucose.
C) liver glycogen.
D) muscle glycogen.
E) triacylglycerols in adipose tissue.
Circle the correct answer

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35. [2] When blood glucose is abnormally high, the pancreas releases:

A) epinephrine.
B) glucagon.
C) glucose.
D) insulin.
E) trypsin.
Circle the correct answer

36. [4] Which class of hormones acts via nuclear receptors? Briefly describe the mode of action of
these hormones.

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.