Download Biochemistry 3020 1. The consumption of

Department of Chemistry and Biochemistry
University of Lethbridge
Biochemistry 3020
1. The consumption of alcohol (ethanol), especially after periods of
strenuous activity or after not eating for several hours, result in a
deficiency of glucose in the blood, a condition known as hypoglycemia
The first step in the metabolism of ethanol by the liver is oxidation to
acetaldehyde, catalyzed by liver alcohol dehydrogenase:
CH3CH2OH + NAD+ → CH3CHO + NADH + H+
Explain how this reaction inhibits the transformation of lactate to
pyruvate. Why does this lead to hypoglycemia?
Consumption of alcohol forces competition for NAD+ between ethanol
metabolism and gluconeogenesis. The problem is compounded by
strenuous exercise and lack of food, because at these times the level
of blood glucose is already low.
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Lactate Fermentation
Enzyme = Lactate Dehydrogenase
Pyruvate + NADH + H+
L-Lactate + NAD+
Regenerates NAD+ from NADH (reducing equivalents) produced in glycolysis.
Lactate fermentation is important in red blood cells, parts of the retina and
in skeletal muscle cells during extreme high activity.
Also important in plants and microbes growing in absence of O2.
∆G’° = -25.1 kJ/mol
2. 14C-Labeled glyceraldehyde 3-phosphate was added to a yeast extract.
After a short time, fructose 1,6-bisphosphate labeled with 14C at
C-3 and C-4 was isolated. What was the location of the 14C lable
in the starting glyceraldehyde 3-phosphate? Where did the second
14C lable in fructose 1,6-bisphosphate come from?
This experiment demonstrates the reversibility of the aldolase reaction.
The C-1 of glyceraldehyde 3-phosphate is equivalent to C-4 of
fructose 1,6-bisphosphate.
The starting glyceraldehyde 3-phosphate must have been labeled at C-1.
The C-3 of dehydroxyacetone phosphate becomes labeled through the
triose phosphate isomerase reaction thus giving rise to 14[C-3] fructose
1,6-bisphosphate.
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3. The oxidation of glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate,
catalyzed by glyceraldehyde 3-phosphate dehydrogenase, proceeds
with an unfavorable equilibrium constant:
Keq = 0.08; ∆G’0 = 6.3 kJ/mol
But the flow through this point in the glycolytic pathway proceeds
smoothly. How does the cell overcome the unfavorable equilibrium?
It rapidly removes the 1,3-bisphosphoglycerate in a favorable subsequent step,
catalyzed by phosphoglycerate kinase.
4. In the last reaction of the citric acid cycle, malate is hydrogenated to
regenerate the oxaloacetate necessary for the entry of acetyl-CoA
into the cycle:
L-Malate + NAD+ → oxaloacetate + NADH + H+
∆G’0 = 30.0 kJ/mol
(a) Calculate the equilibrium constant for this reaction at 25°C.
(b) The measured concentration of L-malate in rat liver mitos
is about 0.2 mM when [NAD+]/[NADH] is 10.
Calculate the concentration of oxaloacetate at pH 7 in these
mitochondria.
(a) 5.6 x 10-6
(b) 1.1 x 10-8 M
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5. A eukaryotic cell can use glucose (C6H12O6) and hexanoic acid (C6H12O2)
as fuels for cellular respiration. On the basis of their structural
formulas which substance releases more energy per gram on
complete combustion to CO2 and H2O?
Hexanoic acid is more reduced (H/C ratio 11/6) than
glucose (7/6)
6. People with beriberi, a disease caused by thiamine deficiency, have
elevated levels of blood pyruvate and α-ketoglutarate,
especially after consuming a meal rich in glucose. How
are these effects related to a deficiency of thiamine?
Thiamin is required for the synthesis of thiamine pyrophosphate
(TPP), a prosthetic group in the pyruvate DH and α-ketoglutarate
DH complexes. Thiamine deficiency reduces the activity of these
enzyme complexes and causes the observed accumulation
of the precursers.
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Pyruvate is Oxidized to Acetyl-CoA and CO
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Combined dehydrogenation and decarboxylation of pyruvate requires
the sequential action of three different enzymes and five different coenzymes.
Reactions of the Citric Acid Cycle
Step 4 Oxidation of α-ketoglutarate to succinyl-CoA and CO2
The mechanism is identical to the pyruvate dehydrogenase reaction.
α-ketoglutarate dehydrogenase complex is very similar to the
pyruvate dehydrogenase complex (homologs of E1, E2, and E3).
It also contains TPP, E2 bound lipoat, FAD, NAD and CoA.
E3 is identical in both complexes.
What about specificity?
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7. Free palmitate is activated to its coenzyme A derivative (palmitoyl-CoA)
in the cytosol before it can be oxidized in the mitochondrion.
If palmitate and [14C]coenzyme A are added to a liver homogenate,
palmitoyl-CoA isolated from the cytosolic fraction is radioactive,
but that isolated from the mitochondrial fraction is not.
Explain.
Fatty acyl groups condensed with CoA in the cytosol are first
transferred to carnitine, releasing CoA, then transported into
the mitochondrion, where they are again condensed with CoA
Cytosolic and mitochondrial pools of CoA are kept separate,
and no radioactive CoA from the cytosolic pool enters the
mitochondrion.
8. How many turns of fatty acid oxidation cycle are required for
complete oxidation of arachidic acid ( CH3(CH2)18COOH)
to acetyl-CoA?
9 turns. Arachidic acid is a 20-C saturated fatty acid and yields
10 molecules of acetyl-CoA. The last two from in the ninth turn.
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9. Isocitrate dehydrogenase is found only in the mitochondrion, but malate
dehydrogenase is found in both the cytosol and mitochondrion.
What is the role of cytosolic malate dehydrogenase?
Cytosolic malate dehydrogenase plays a key role in the transport of
reducing equivalents across the inner mitochondrial membrane via
the malate-aspertate shuttle.
The Path of NADH Into the Mitochondrium
NADH generated by dehydrogenases in the cytosol (Glycolysis) has to
be transported into the mito matrix.→ The malate-aspartate shuttle
Most active in liver, kidney & hart.
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10. In electron transfer, only the quinone portion of ubiquinone undergoes
oxidation-reduction; the isoprenoid side chain remains unchanged.
What is the function of the chain?
The side chain makes ubiquinone soluble in lipids and allows it to diffuse
in thesemifluid membrane.
11. The rate of photosynthesis, measured by O2 production, is higher when
a green plant is illuminated with light of wavelength 680 nm than
with light of 700 nm. However, illumination by a combination of
light of 680 nm and 700 nm gives a higher rate of photosynthesis
than light either wavelength alone.
For the maximum photosynthesis rate, PSI (abs at 700) and PSII (abs 680)
must be operating simultaneously.
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12. In a laboratory experiment spinach chloroplasts are illuminated in the
absence of ADP and Pi, then the light is turned off and ADP
and Pi are added. ATP is synthesized for a short time in the
dark. Explain the finding.
During illumination a proton gardient is established. When ADP and Pi
are added, ATP synthesis is driven by the gradient, which becomes
achausted in the absence of light.
13. Iodacetate reacts irreversibly with free –SH groups of Cys residues in
proteins. Predict which Calvin cycle enzyme(s) would be inhibited
and explain why.
Ribulose 5-phosphate kinase, fructose 1,6-bisphosphatase,
seduheptulose 1,7-biphosphatase, and glyceraldehyde 3-phosphate
dehydrogenase. All are activated by reduction of a critical disulfide
to a pair of sulfhydryls; iodoacetate reacts irreversibly with
free sulfhydryls.
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14. The reductive pentose phosphate pathway generates a number of intermediates identical to those of the oxidative pentose phosphate
pathway. What role does each pathway play in cells where it is
active?
Reductive pentose phosphate pathway regenerates ribulose 1,5-bisphosphate
from triose phosphates produced during photosynthesis.
Oxidative pentose phosphate pathway provides NADHPH for reductive
biosynthesis and pentose phosphates for nucleotide synthesis.
15. Double-stranded regions of RNA:
A) are less stable than double-stranded regions of DNA.
B) can be observed in the laboratory, but probably have no
biological relevance.
C) can form between two self-complementary regions of the
same single strand of RNA.
D) do not occur.
E) have the two strands arranged in parallel (unlike those of DNA,
which are antiparallel).
C
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16. Why does lowering the ionic strength of a solution of double-stranded
DNA permit the DNA to denature more readily (for example,
to denature at a lower temperature than at a higher
ionic strength)?
Lower ionic strength reduces the screening of the negative charges
on the phosphate groups by positive ions in the medium. The result
is stronger charge-charge repulsion between the phosphate, which
favors strand separation.
17. Circle the fatty acid in each pair that has the higher melting temperature.
(a) 18:1∆9
18:2∆9,12
(b) 18:0
18:1∆9
(c) 18:0
16:0
(a) 18:1∆9 (b) 18:0 (c) 18:0
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18. Show the basic structure of all glycerophospholipids.
All glycerophospholipids have two fatty acids in ester linkage with C-1
and C-2 of glycerol; often the fatty acid at C-1 is saturated, and that
at C-2 is unsaturated. C-3 of glycerol is joined to an alcohol-containing
head group through a phosphodiester linkage, which is negatively
charged at neutral pH.
19. The fluidity of a lipid bilayer will be increased by:
A) decreasing the number of unsaturated fatty acids.
B) decreasing the temperature.
C) increasing the length of the alkyl chains.
D) increasing the temperature.
E) substituting 18:0 (stearic acid) in place
of 18:2 (linoleic acid).
D
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20. The structure of NAD+ does not include:
A) a flavin nucleotide.
B) a pyrophosphate bond.
C) an adenine nucleotide.
D) nicotinamide.
E) two ribose residues
A
21. The standard reduction potentials (E'°) for the following half
reactions are given.
Fumarate + 2H+ + 2e– → succinate
FAD + 2H+ + 2e– → FADH2
E'° = +0.031 V
E'° = –0.219 V
If you mixed succinate, fumarate, FAD, and FADH2 together, all at
l M concentrations and in the presence of succinate dehydrogenase,
which of the following would happen initially?
A) Fumarate and succinate would become oxidized;
FAD and FADH2 would become reduced.
B) Fumarate would become reduced, FADH2 would
become oxidized.
C) No reaction would occur because all reactants and
products are already at their standard concentrations.
D) Succinate would become oxidized, FAD would become
reduced.
E) Succinate would become oxidized, FADH2 would be
unchanged because it is a cofactor.
B
Why only initially?
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22. Explain in quantitative terms the circumstances under which the
following reaction can proceed.
Citrate → isocitrate
DG'° = +13.3 kJ/mol
A reaction for which ∆G'° is positive can proceed under conditions in
which ∆G is negative. From the relationship
∆G = ∆G'° + RT ln [product]
[reactant]
it is clear that if the concentration of product is kept very low (by its
subsequent metabolic removal, for instance), the logarithmic term
becomes negative and ∆G can then have a negative value.
23. Inorganic fluoride inhibits enolase. In an anaerobic system that is
metabolizing glucose as a substrate, which of the following
compounds would you expect to increase in concentration
following the addition of fluoride?
A) 2-phosphoglycerate
B) Glucose
C) Glyoxylate
D) Phosphoenolpyruvate
E) Pyruvate
A
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24. Which of the following is a cofactor in the reaction catalyzed
by glyceraldehyde 3-phosphate dehydrogenase?
A) ATP
B) Cu2+
C) heme
D) NAD+
E) NADP+
D
25. CO2 is produced in two reactions in the citric acid cycle.
For each of these reactions, name and show the structures of
reactant and product, name the enzyme, and show how any
cofactors participate.
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26. The role of hormone-sensitive triacylglycerol lipase is to:
A) hydrolyze lipids stored in the liver.
B) hydrolyze membrane phospholipids in hormone-producing cells.
C) hydrolyze triacylglycerols stored in adipose tissue.
D) synthesize lipids in adipose tissue.
E) synthesize triacylglycerols in the liver.
C
27. What is the correct order of function of the following enzymes
of β oxidation?
1. β-Hydroxyacyl-CoA dehydrogenase
2. Thiolase
3. Enoyl-CoA hydratase
4. Acyl-CoA dehydrogenase
A) 1, 2, 3, 4
B) 3, 1, 4, 2
C) 4, 3, 1, 2
D) 1, 4, 3, 2
E) 4, 2, 3, 1
C
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28. In the citric acid cycle, a double bond is introduced into a four-carbon
compound containing the —CH2—CH2— group, producing
fumarate. Show a similar reaction that occurs in the β-oxidation
pathway.
29.
Cyclic electron flow in chloroplasts produces:
A) ATP and O2, but not NADPH.
B) ATP, but not NADPH or O2 .
C) NADPH, and ATP, but not O2 .
D) NADPH, but not ATP or O2 .
E) O2, but not ATP or NADPH.
B
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30. What is an action spectrum, and what do peaks in an action spectrum
signify? Show a typical action spectrum plot for photosynthesis.
An action spectrum is a plot of the effectiveness of a process
(such as photosynthesis) versus wavelength of incident light.
Its peaks signify the presence of a chromophore that absorbs
light at that wavelength.
31. Describe what happens at photosystem I from the point where an antenna
chlorophyll molecule absorbs a photon of light to the passage of an
electron to NADP+.
The antenna chlorophyll molecule passes the energy of the photon, via
exciton transfer, to neighboring chlorophyll molecules and ultimately to
reaction center chlorophyll molecules. This excites P700 to P700*,
which donates an electron to A0. From A0, electrons pass to
phylloquinone (A1), through an Fe-S protein, to ferredoxin, then through
a flavoprotein to NADP+.
P700* → A0 → A1 → Fe-S → NADP+
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32. Transketolase requires the coenzyme:
A) cobalamin (vitamin B12).
B) lipoic acid
C) pyridoxal phosphate.
D) tetrahydrofolic acid.
E) thiamine pyrophosphate.
E
33. How does glyceraldehyde 3-phosphate formed in the chloroplast
stroma by the Calvin cycle reactions enter the cytosol?
It is converted to dihydroxyacetone phosphate or to 3-phosphoglycerate
and carried into the cytosol by the Pi-triose phosphate antiporter, a
specific transporter in the inner chloroplast membrane.
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What About ATP and NADPH?
ATP and NADPH can not cross the chloroplast membrane.
But the Pi-triose phosphate antiport
system has the indirect effect of
moving ATP and reducing
equivalents across the membrane.
Dihydroxyaceton is
transported to the cytosol
where it is converted to
3-phosphoglycerate (ATP/NADH)
→ glycolytic enzymes
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