C485 Exam I Fall ’14 answer key
Name___________________
Legible please!
Do not use acronyms unless instructed to do so. Use structures whenever they are asked
for, or appropriate. Your explanations should be brief. Overly lengthy answers with
irrelevant or erroneous material will receive deductions. Use the back of the page if you
need room. GOOD LUCK
1. (6 pts) Match the enzymes that degrade glycogen in the left column with the
appropriate properties in the right column. (More than one property may match. You
need to get each answer completely correct for credit.)
(a) Phosphorylase _1,3_____
(1) cleaves -1,4 glucosidic bonds
(b) -1,6-Glucosidase _2______
(2) releases glucose
(c) Transferase __1,4_____
(3) releases glucose 1-phosphate
(4) moves three sugar residues from
one chain to another
(5) requires ATP
2. (12 Pts) Show the overall reaction for a complete photosynthetic process, showing both
ATP production and NADPH production (start with two water molecules and absorb as
many photons as necessary). Show the specific reactions for photosystem II and the
cytochrome bf complex.
Mechanisms 3-5!!!!!
3. (10 Pts) A basic carbon-carbon bond forming reaction in the pentose phosphate
pathway transfers two carbon fragments. Give an example of this reaction and draw its
mechanism. You may assume active site general acids and bases as necessary. Please
show the necessary parts of any cofactors. (YOU MUST USE STRUCTURES AND
ARROWS). Please use the back of the exam if necessary.
Transketolase: Show either xyl5-P + Rib5-P, or xyl5-P + E4P for full credit. You must
have shown the full structure of reactants and products at least once for full credit.
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Mech: see handout on class website.
4. (14 pts) There are three basic types of carbon-carbon bond forming reactions in the
Calvin cycle. You have drawn the mechanism of one of these in problem 3. What are
the other carbon-carbon bond forming reactions in the Calvin cycle- give an example of
each (structures please). Draw the mechanism of these reactions. Please use the back of
the exam if necessary.
Rubisco and aldolase. (NB- there is NO transaldolase reaction in the Calvin cycle. This
is why there are bisphosphate intermediates. The substrate is DHAP.)
See last page
5. (10 pts) An unwanted side reaction occurs during the dark reactions of photosynthesis.
What is this reaction? Draw its mechanism. Under conditions of drought, this reaction
becomes much more prevalent. Why is this? Please use the back of the exam if
necessary.
Rubisco oxygenase reaction. (mech: see last page). Under drought conditions the
amount of water in the chloroplast diminishes. Since carbon dioxide is not very soluble,
the amount of carbon dioxide becomes limiting and oxygen, which is far more soluble is
the more available reactant.
6. (8 pts) What is structure of glutathione? Explain its role in red blood cells. How does
an important enzymopathy affects this function?
Glutathione maintains sulfhydryl proteins in their proper redox state, keeping them from
polymerizing by disulfide bond formation. This is particularly true for hemoglobin,
which can easily polymerize by disulfide formation, resulting in the formation of Heinz
bodies. Glutathione also protects against reactive oxygen species (ROS), particularly
peroxides, by reducing them to alcohols plus water. This is catalyzed by glutathione
peroxidase. Oxidized glutathione, GSSG, is reduced back to glutathione by the action of
an NADPH-dependent reductase. In the absence of NADPH, glutathione cannot be
recycled back to the reduced state, and the cell is vulnerable to ROS damage and
unwanted disulfide bond formation. This is particularly problematic for people with an
enzymopathy that results in a deficiency in G6-P dehydrogenase, the first step of the
pentose phosphate pathway. Red blood cells lack mitochondria, and so are completely
dependent on this pathway for NADPH formation.
See book for Gluthathione structure.
7. (8 Pts) Diagram the Q cycle and explain how this accounts for the stoichiometry of
proton pumping and uptake.
Use a diagram such as this, to show the bifurcated nature of the pathway. This results in
4 protons pumped into the lumen and two taken up from the stroma/quinol. Since two
quinols are required for a full cycle, that is 8 protons pumped and four taken up.
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7. (8 pts) How is the Calvin cycle regulated? Explain the logic of this regulation.
The CC is regulated by environmental conditions and the presence of specific allosteric
regulators. These are listed below:
Mg ion, high pH, high carbon dioxide concentration, reduced ferridoxin, reduced
thioredoxin, and NADPH.
The first three components are required for the formation of the active site carbamate in
rubisco. Absent this, rubisco will not be active. This ensures that rubisco will only be
active when there is sufficient carbon dioxide for it to compete with oxygen in the
rubisco reaction. High pH in the stroma and Mg ion also mean that the light reactions of
photosynthesis are taking place, since these result in Mg flux into the stroma and proton
flux into the lumen.
The CC requires reducing equivalents, and this is ensured by making the pathway
dependent on the last three items. Fd reduced provides reducing power to reduce
thioredoxin, which activates a number of proteins in the Calvin cycle (as well as other
pathways). NADPH is also necessary for activation (allosteric) of an enzyme in the CC,
as well as other pathways, and is also a necessary reactant in the pathway.
8. (8 pts) Assume that a cell only needs to synthesize NADPH and not ribose. How can
this be done? (Brief explanation) Show the stoichiometry of this process showing the
maximum amount of NADPH that may be synthesized via the pentose phosphate
pathway.
Run the oxidative portion of the pathway and then use the nonoxidative portion to
regenerate glucose. Six turns of the cycle will completely convert glucose into carbon
dioxide.
The overall stoichiometry involves 6 G6-P, 12 NADP , 6H2O going to 5 G6-P, 6CO2, 12
NADPH, 12H+, Pi (you can simplify by reducing the numbers of G6P).
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So overall, one glucose nets 12 NADPH.
9. (14 Pts) Your textbook describes the regeneration phase of the Calvin cycle as the
mirror image of the pentose phosphate pathway. Is this true? Where do these pathways
differ? What is the functional reason for why these pathways must differ, and how is this
accomplished.
Yes and no. From a carbon skeleton perspective, the regeneration phase of the CC and
the nonoxidative part of the PPP are the opposites of each other. However, the pathways
differ in function and so there are specific reactions that MUST be different. This is done
by incorporating two phosphatases into the CC, as well as a kinase in the last step. This
means that many of the intermediates in the CC are bisphosphates, whereas NONE of the
PPP intermediates are. The use of these enzymes renders the CC unidirectional, whereas
the PPP must be reversible, to satisfy the different needs of the cell, for either ribose, or
glucose. The presence of bisphosphates in the CC means it has to use the enzyme
aldolase, whereas the PPP uses the enzyme transaldolase. These have somewhat similar
mechanisms, but different substrates.
10. (8 pts) Draw the mechanism for how the mobile electron carrier between PSII and
Cytochrome bf undergoes oxidation (use chemical structures).
See last page
11. Extra Credit (12 Pts) Energy yielding steps are often thermodynamically
unfavorable, so the cell links these to functionally irreversible steps, or steps that are well
downhill in energy. Give two examples of such steps from the pentose phosphate
pathway, and comment on whether they are similar to, or different from strategies used in
the Krebs Cycle.
The first four steps of the PPP illustrate this point (draw them). There are two oxidations
that aren’t particularly favorable, linked to reactions that are very favorable. The first of
these favorable reactions is the hydrolysis of a lactone, which is driven by the high
concentration of water, the release of ring strain, and the deprotonation of the acid
product. The second oxidation is driven by coupling to a beta decarboxylation.
The first strategy does not appear in the Krebs cycle, since there are no lactones in this
pathway. The second strategy is the exact analogue of the isocitrate to alphaketoglutarate reaction in the Krebs cycle (draw it).
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