Do any FIVE problems.
You may use any literature source you like, and discuss the problems with each other or with me. However, your answers must be in your own words and structure drawings. I am looking for complete, well thought out answers.
1. We have said that the conversion of dehydroquinate to dehydroshikimate is a cis- elimination. (a) Explain how this conclusion was obtained for the in vivo reaction; (b) in vitro, for example with POCl3 and pyridine, this would be a trans- elimination. Write a mechanism for the laboratory reaction and explain why trans- is the preferred pathway. Your sophomore organic text will help with part (b).
2. What is the structure of the herbicide Roundup? How does it work? Be specific! Why is it supposedly safe to use around pets (unless you keep bacteria for pets)? Numerous crops (for example, 83% of all soybeans grown in the US) are now engineered to be "Roundup ready", that is, resistant to Roundup. What is the alteration made in these plants? (Places to start: Healy-Fried, et al., J. Biol. Chem., 2007, 282, 32949; Funke, et al., Proc. Natnl. Acad. Sci., 2006, 103, 13010)
3. Lysine is another of the essential amino acids; that is, humans cannot synthesize it and must obtain it from their diets. The biosynthesis of lysine is outlind on p. 866 of Lehninger. Select one of the following questions to answer:
(a) The last step in thepath is the conversion of a symmetrical (meso) diaminopimelate to the chiral lysine. Explain in detail how this is accomplished. Some help: J. Biol. Chem., 2003, 278, 18588; J. Mol. Biol., 2009, 385, 580
OR
(b) Just as development of inhibitors of the shikimate pathway is a mode of generating new anitbiotics, so is the inhibition of lysine biosynthesis. Summarize the recent efforts in this area. Some help: Molec. BioSystems, 2007, 3, 458.
4. The molecules below all are terpenes, formed by condensations involving isopentenyl pyrophosphate. Locate the isoprene units in each.
5. We have described in class feedback inhibition, in which a compound from later in a biosynthetic sequence is an allosteric inhibitor of an earlier enzyme. What is feed-forward activation? Provide a specific example; that is a specific enzyme and a specific activator. Explain how the activation works. Then try to find the structure of the enzyme in the Protein Databank, preferably with the activator bound. Provide a Rasmol picture. (No penalty if you can't find it in the pdb.)
6. We showed the reaction of dimethylallyl pyrophosphate with isopentenyl pyrophosphate as an SN1 reaction. However, allyl substrates readily undergo SN2 reactions, much more rapidly than other 1o substrates. Why? What is the evidence that the enzymatic reaction is actually SN1? See J. Am. Chem. Soc., 1993, 115, 1245 for a start at answering this question.
7. Our mechanism for the formation of enolpyruvyl shikimate included defining the stereochemistry of formation of the tetrahedral intermediate. Describe in detail how this stereochemistry was established. Some help: J. Am. Chem. Soc., 2003, 125, 12759.
8. [This is long, but not very difficult. do either part (a) or part (b)] (a) Mother Nature regulates the biosynthesis of cholesterol at the HMG-CoA reductase stage, by phosphorylation of the enzyme. It now appears that other regulatory modes may be operating as well. Read Parish, Parish, and Li, Crit. Rev. Biochem. Mol. Biol., 1999, 34, 265, and summarize its suggestions about another mode of regulation;
OR
(b) Relatively recently, squalene synthetase has become a target for development of anti-cholesterol drugs by pharmaceutical companies. Identify one such drug and explain in detail how it works. Look for a crystal structure of the enzyme with the inhibitor bound and, if one can be found, provide a picture showing the binding of the inhibitor.
9. Although it has long been assumed that isopentenyl pyrophosphate is synthesized only from mevalonate as we showed in class, another pathway recently has been discovered. The new pathway condenses glyceraldehyde 3-phosphate and pyruvate to 1-deoxyxylulose 5-phosphate. Describe the new pathway and any of the enzymes that have been identified. [A place to start: Hunter, J. Biol. Chem., 2007, 282, 21573].
10. Some effort has been expended on explaining the evolutionary relationship between the two isoprenoid pathways (problem # 9). Describe thoroughly the suggestions. [Mol. Microbiol., 2000, 37, 707; Proc. Nat. Acad. Sci., 2000, 97, 13172]