Mueller Cume. Five Carbon Metabolism. February 8 th, Name: 1. (10) 2. (15) 3. (12) 4. (9) 5. (4) TOTAL (50)

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1 Mueller Cume Five Carbon Metabolism February 8 th, 2003 Name: 1. (10) 2. (15) 3. (12) 4. (9) 5. (4) TOTAL (50)

2 1. The Calvin Cycle utilizes critical 5-carbon intermediates, and a diagram of the cycle appears below. Answer the questions on the following pages about the Calvin Cycle and the enzymes in it that handle 5- carbon substrates. 2

3 a. What is the name of the Calvin Cycle enzyme that is estimated to be the most abundant enzyme on Earth? You can write either the full name or its commonly used acronym. [2 pts] b. The enzyme phosphopentose epimerase uses no cofactors. Propose a mechanism for this enzyme assuming that there are two critical acid/base groups in the active site to catalyze proton transfer. Denote general acids as AH and general bases as B. Denote stereochemistry of key enzymic groups and at all chiral centers in the substrate and product using bold and dashed wedges. Note that the pathway given on the previous page has Fisher projections of the Calvin Cycle intermediates. [8 pts] 3

4 2. The pentose phosphate pathway (a.k.a., the pentose cycle, the hexose monophosphate shunt, the phosphogluconate pathway) is used by cells in part to generate ribose 5-phosphate. Answer the following questions concerning the pathway. a. What is the main need of an E. coli cell for ribose 5-phosphate? Circle your answer. [2 pts] allowing the Calvin Cycle to proceed by providing a source of ribulose 5-phosphate after the action of phosphopentose epimerase generating the building blocks for nucleic acids allosterically relaxing the negative regulation of glycolysis providing the starting material for threonine biosynthesis providing the primary energy source for the flagellar motor, which allows E. coli to swim b. Fill in the missing names of the enzymes in the Hal White drawing of the pentose phosphate pathway below. Write the letter corresponding to your answer in each box. [1 pt each] A triosephosphate isomerase B phosphopentose isomerase C phosphogluconate dehydrogenase D glucose-6-phosphate dehydrogenase E phosphopentose epimerase F fructose bisphosphatase 4

5 c. Transketolase is an enzyme that requires the cofactor thiamin pyrophosphate (TPP), which is shown below. Transketolase carries out both reactions on the previous page with the arrows labeled TPP. Propose a mechanism for the conversion of xylulose 5-phosphate and erythrose 4-phosphate into glyceraldehyde 3- phosphate and fructose 6-phosphate. You only need to show the business end of TPP. Invoke general acids ( AH) and general bases ( B ) as you see fit. Use Fisher projections to denote stereochemistry. [8 pts] TPP 5

6 3. Mammals use isoprenoid metabolism to generate several classes of critical compounds starting with isopentenyl pyrophosphate and dimethylallyl pyrophosphate. One class of molecules resulting from isoprenoid metabolism are used to covalently modify certain proteins so that they are anchored in the membrane (a phenomenon known as prenylation). a. Name two of the molecules generated by isoprenoid metabolism that are used to prenylate proteins to anchor them to the membrane. Write the name of the substrate of the enzymes that add the membrane anchors to the proteins, not the just the name of the group that is covalently attached to the protein. [2 pts] b. Give an example of a protein that is anchored to the membrane by an attached isoprenoid group, and state the protein s physiological role. Be brief and fairly general in stating the physiological role. [4 pts] Another class of molecules derived from isoprenoid metabolism have this skeleton: c. What is the name of this class of compounds? [2 pts] d. Name one particular member of this class of compounds, and state its phsyiological role. Be brief and fairly general in stating the physiological role. [4 pts] 6

7 4. The urea cycle gets its name from the production of urea and the five-carbon amino acid L-ornithine from the hydrolysis of L-arginine. This reaction is catalyzed by the enzyme arginase, which has a di-manganese center in its active site. a. Propose a mechanism for this reaction that includes a catalytic role for at least one Mn 2+. Invoke general acids ( AH) and general bases ( B ) as you see fit. Denote stereochemistry at all chiral carbons (and only at chiral carbons) with bold and dashed wedges. You should know the structures of arginine and urea, which will allow you to deduce the structure of ornithine. If you are in doubt, you may buy the structure of urea for 2 pts ask me (or Prof. Thorpe) to draw it for you. [7 pts] b. In mammals (like you), the urea cycle is the main route of disposal (in the urine) of what potentially toxic catabolic by-product? Write the name, not the structure, of the compound. [2 pts] 7

8 5. Pyrimidine biosynthesis proceeds by the generation of the five-carbon compound orotate, which is then added to a ribose to make orotodine monophosphate, which is decarboxylated to give uridine monophosphate. Consider one step in that pathway, the reaction catalyzed by dihydroorotase: Every time I look at this reaction, I am surprised to see that it occurs so readily and that it is easily reversible (at ph 7.5, K eq ~ 10 in favor of carbamoyl aspartate). a. Briefly explain why a basic knowledge of organic chemistry suggests (at least to me) that thermodynamics would favor carbamoyl aspartate more strongly. [2 pts] b. Briefly explain why a basic knowledge of organic chemistry makes it appear (at least to me) that the reaction would be difficult to achieve in a kinetic sense as well as a thermodynamic sense. In other words, what is/are the chemical process(es) that must occur and what are the relative propensities of the reactive groups to undergo such transformations. [2 pts] 8