Review Problems #3(Calvin Cycle, Pentose phosphate pathway)

(Any problems not covered last week are also fair game)

1) Rubisco contains an essential active site magnesium. Draw the relevant substrate contacts, as well as any special groups from the enzyme that make direct contact.

1a) Describe the chemical role of magnesium in promoting catalysis.

2) Draw the reaction and a notional mechanism for the transformation catalyzed by rubisco.

3) Draw the unwanted competing side reaction (and a mechanism) catalyzed by rubisco.

3a) What is the ultimate fate of the molecules produced in this unwanted process?

3b) Why is this process referred to as photorespiration?

4) What are the three stages of the Calvin cycle?

5) Draw the molecules that start and end the first stage of the cycle.

6) Draw the molecules that start and end the second stage of the cycle.

7) What are the three enzymes of the Calvin cycle that are responsible for forming carbon-carbon bonds?

8) Name the essential cofactor and draw the chemically active portion this molecule used in two carbon transfer processes in the Calvin cycle and pentose phosphate pathway.

8a) Draw the mechanism of the reaction catalyzed in question eight

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9) The Calvin cycle contains two transformations that generate five carbon sugars. Draw these two reactions. Draw the reaction that generates a seven carbon sugar.

10) Draw the mechanism for the enzyme that catalyzes addition of DHAP to an aldose. Make sure to show the structure and role of the covalent enzyme-substrate adduct.

11) What are the energetic requirements of a full turn through the cycle? (Don’t forget reductants)

12) What two major storage forms of sugar are found in plants?

13) What molecules regulate the Calvin cycle? Explain the logic of how these molecules relate to photosynthesis.

14) What are two phases of the pentose phosphate pathway? Which of these phases is most similar to the Calvin cycle?

15) What are the two most important roles of the pentose phosphate pathway?

16) How does the pentose phosphate pathway provide a link between five carbon sugars and glycolysis?

17) What is the most common enzymopathy occurring in humans?

18) What normal cell function is limited by this enzymopathy. Why are red blood cells particularly affected? (Hint, they have no mitochondria)

19) Why might this enzymopathy confer a selective advantage in some areas of the world?

20) In what way is the Calvin cycle and the pentose phosphate pathway related?

21) How does the pentose phosphate pathway respond to differing needs of the cell?

22) Explain the function and general structure of accessory pigments.

24) Write the general mechanisms for the two decarboxylation reactions that utilize TPP.