C485 Exam I Fall ‘15
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. (12 pts) (a)There are three organic molecules (proteins or small molecules) that
directly (or indirectly) regulate the Calvin cycle. What are they? How do they do this,
and explain the logic of their function given the makeup of the cycle. (b) What inorganic
factors regulate the function of the cycle? How do they do this, and explain the logic of
their function given the makeup of the cycle.
1a
Ferredoxin (reduced), thioredoxin (reduced), NADPH. Ferredoxin regulates indirectly by
determining the reduction state of thioredoxin. Thioredoxin activates CC enzymes by reducing
disulfide bonds that hold these proteins in inactive conformations. NADPH is an allosteric
regulator that displaces regulatory inhibitory proteins that keep enzymes inactive. These
regulatory mechanisms make sense because you don’t want the CC operating unless the light
reactions have been generating sufficient redox equivalents to be able to carry out biosynthesis.
These regulatory agents act as redox sensors for the chloroplast.
1b- CO2, high pH, magnesium. These all regulate the function of rubisco. In the absence of
sufficient CO2, you cannot form the active site carbamate and rubisco is inactive. This precludes
the wasteful oxygenation reaction from taking place in preference to CO2 fixation when CO2
concentrations are relatively low. Mg organizes the active site and rubisco is inactive without it.
Mg is released to the stroma when light reactions are taking place. This helps coordinate the
activity of rubisco with the light reactions, so that rubisco will only be active when ATP and
NADPH are made. High pH occurs as protons are removed from the stroma by light reactions.
High pH is necessary for carbamate formation and rubisco is inactive in its absence. This also
coordinates rubisco activity with light reactions.
Mechanisms 2-5!!!!!
2. (8 pts) Draw an example of an transaldolase reaction from the pentose phosphate
pathway. Draw its mechanism. (YOU MUST USE STRUCTURES AND ARROWS).
You may assume active site general acids and bases as necessary.
Figure 20.21 additionally, you must show formation of the active site imine from the
lysine residue + substrate, and then show hydrolysis of the product imine. You must
define all R groups.
1
3. (10 pts) A basic carbon-carbon bond forming reaction in the Calvin cycle 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.
Figure 20.20. You must specify what R is.
4. (10 pts) Give an example of a carbon-carbon bond forming reaction in the Calvin
cycle that transfers a one carbon unit. Draw the mechanism of this reaction, showing the
active site structure and any special enzyme features that are at play here. Please use the
back of the exam if necessary.
See end of exam for rubisco mechanism. Necessary active site features: Mg ligated to
substrates and active site carbamate
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? Use the back of the exam if necessary.
See end of exam for oxygenation reaction. This takes place preferentially under drought
conditions because carbon dioxide is sparingly soluble in water and cannot be replenished
during the day, as the plant closes its pores to minimize water loss. Since water levels are
low in the plant, the amount of available carbon dioxide is limiting. Oxygen is generated
in the light reactions and is more soluble than cabon dioxide in any event, so its supply is
not exhausted during turnover.
6. (8 pts) What is structure of glutathione? Explain its role in red blood cells. How does
an important enzymopathy affects this function?
see book for structure; gsh performs three functions in red blood cells- (they only need the first
two). It keeps proteins in the correct disulfide redox state, and protects against ROS,
particularly peroxides. It also detoxifies electrophiles. GSH is kept in its correct redox state by
glutathione reductase, which reqires NADPH. If G6PDH is inactive, the oxidative portion of the
PPP will not operate. Therefore, red blood cells will have insufficient NADPH because they lack
mitochondria. As a result, GSH will largely be oxidized (GSSG) and unable to monitor protein
oxidation state. This can lead to polymerization of Hb and erythrocyte death known as
hemolytic anemia.
7. (8 pts) Diagram the Q cycle and explain how this accounts for the stoichiometry of
proton pumping and uptake in the relevant complex. See class handout, or chemistry
course lecture notes on C485 site.
8. (8 pts)Assign each function or product in the right column to the appropriate structure
or pathway in the left colum. (there may be more than one function assigned and they
2
may be used more than once). or pathway in the left colum. (there may be more than one
function assigned and they may be used more than once). See student companion ch
19 self test question 2
(a) chlorophyll _________
(b) light-harvesting complex _________
(c) photosystem1_________
(d) photosystem II_________
(1) O2 generation
(2) ATP synthesis
(3) light collection
(4) NADPH synthesis
(5) separation of charge
(6)light absorption
(7) transmembrane proton gradient
8. (8 pts) Assume that a cell only needs to synthesize ribose, but not NADPH. Please
diagram how this can be done. (structures please). You may assume that the cell has
adequate access to hexoses.
Run the nonoxidative portion of the PPP backwards. (Table 20.3 in structures)
9. (12 pts) What is the overall stoichiometry of photosynthesis in chloroplasts? If eight
photons are absorbed, the net yield is __1_____O2, _2_______NADPH___3______ATP
The amount of water oxidized is __2_____H2O, the number of protons released to the
lumen is ____12____H+, and the number taken up from the stroma is ___10______H+
10. (12 pts) Consider the regeneration portion of the Calvin cycle and the nonoxidative
portion of the pentose phosphate pathway. From a fundamental thermodynamic
perspective, what are the major differences in these two pathways? Explain how these
differences fit into the differing goals of the two pathways.
The CC regeneration portion contains two phosphatases (F1,6-Bisphosphatase and S1,7Bisphosphatase) and a kinase (phosphoribulose kinase). These three enzymes catalyze
thermodynamically very favorable reactions that are way downhill in energy. This makes the CC
irreversible, which is good because you want the cycle to operate in only one direction. In
contrast, the nonoxidation portion of the PPP must be reversible, because the cell sometimes
needs to convert hexoses to pentoses without doing an oxidation. All of the reactions in the
nonoxidative pathway operate in a freely reversible manner. These reactions are similar to those
of the CC regeneration phase, except for the substitution of transaldolase for aldolase (and the
downhill reactions mentioned above). However both of these enzymes operate under fairly
similar thermodynamic constraints, so from a theormodynamic perspective, this difference isn’t
very important.
11. (10 pts) For each reaction, say whether it is an oxidation, reduction, or neither. State
the number of electrons associated with the process.
3
Electrons and process ________________
4e oxidation
Electrons and process _________________
6e oxidation
Rubisco mechanisms
4