Total points: 25

General
•	Some Figures are provided. You may use your (one) page of notes. Otherwise, “closed book”: no models, books, other notes, or periodic table.
•	If a question isn’t clear, please ask me about it.
•	In a multi-part question, if a difficulty with one part is keeping you from continuing, please check with me. If later parts depend on a structure you drew, you might have me look over the structure.
•	Some questions request a simple answer and an explanation. It’s the explanation that is important. No credit for answer without a requested explanation. 
•	When you are asked to mark something, please do so clearly, and label it clearly.
•	In naming compounds, IUPAC names are preferred, but valid common names will be accepted. (A name will be graded based on the compound you show.)
•	Unless specifically noted, chemical equations need not be balanced. Equations should show which chemicals are involved, both as reactants and major products. If no reaction is expected, say so.

•	Electronegativies: H 2.1; C 2.5; O 3.5; S 2.5.

1. (1 pt.) One of the enzymes coded for by influenza virus is an RNA-dependent RNA polymerase, used for replicating the genome. PB2 is one of the polymerase subunits. Amino acid #627 of PB2 is glutamic acid in avian flu viruses, but lysine in flu viruses that can replicate well in mammals. Describe this amino acid variation in terms of its effect on the charge of the protein. (Be specific.)

2. (3 pts.) Linoleic acid is the major polyunsaturated acid in the fat we consume. In the body, some of it gets oxidized to 13-hydroxy-9,11-octadecadienoic acid. The parts below refer to this oxidation product.

a. (1 1/2 pts.) Draw the structure of this oxidation product.

b. (1/2 pt.) What is rather odd about this oxidation product? (Accept that the 13-hydroxy is ok.)

c. (1 pt.; no credit without explanation) Consider this oxidation product and the original compound. Which one is, in general, more suitable for use in membranes? Explain, using general considerations about how biological membranes are organized. 

3. (5 pts.; 1 pt. per part) For each feature listed
–	briefly describe what it means, and 
–	give one example of it in the citric acid cycle. If the requested feature does not occur in the citric acid cycle, say so. 

For description just a few words, at most; maybe draw a key structural feature, if relevant. The point is simply to show that you know what the feature means.

For the example You can give just the name of the compound or the number of the reaction (from the handout with the test), as appropriate.

a. a tertiary alcohol

b. a reaction that is coupled to a hydrogen (or electron) carrier

c. a reaction that is directly coupled to formation of ATP

d. an addition reaction

e. a decarboxylation reaction 

4. (1 pt.) The following chemical was mentioned in a discussion: 

Cl-C-CH=CH-CH2-NH2 
   
   O
	Then, someone noted that this chemical probably does not exist as such, because you would expect it to  ? To do what -- based on X402-level chemistry? Show the product. (Hint Step 1: What are the functional groups in this molecule?)	

5. (3 pts.; 1 pt. per part) The two structures below show two non-protein amino acids that show up sometimes.

DAP (diaminopimelic acid)	lanthionine	

Parts a and b ask you to relate these two amino acids to the standard amino acids. Sometimes that is done fairly easily simply by comparing the structures as given. But sometimes it is helpful to think about how you might make the new amino acid from one of the old ones -- or vice versa -- in a very small number of steps. (You need not explain or even know how to do it.)

•	Note. They are not related to each other, in how they are made.

a. What standard amino acid is DAP most closely related to? How does it differ from that standard amino acid? (In this case, the standard amino acid could be -- and actually is -- made from the “unusual” amino acid shown here. And it is made by a step that we have seen as normal biochemistry.)

b. What standard amino acid is lanthionine most closely related to? How is it related to that standard amino acid?

c. This pair of amino acids was discussed in a recent paper, with the idea that these two amino acids might be interchangeable in a structure. Does that seem reasonable? Explain.

6. (2 pts.; 1 pt. per part) The Fig is a sketch of the structure of a protein that crosses the cell membrane. 

[The “periplasm” is the space just outside the cell membrane, between the membrane and the wall, in gram negative bacteria. That subtlety is not important here.]

a. (1 pt.) Give one example of an amino acid likely to be found in the stretched out part (right by where it says “20 aa”). Explain your choice. Choose one that is an excellent choice, so we don’t quibble over borderlines.

b. (1 pt.) The region of the protein just “above” the membrane in the Fig is shown coiled, to indicate an -helix. 

–	That helical structure is largely due to [hydrogen OR ionic] bonds. Choose correct term from the brackets. 
	
–	What chemical groups (functional groups) are involved in that bonding?

7. (2 pts.) Consider an amine that cannot serve as a hydrogen bond donor.

a. (1 pt.) Show the structure of such a compound (that is, a specific example).

b. (1/2 pt.) Even though this compound cannot serve as an H-bond donor, it can serve as an H‑bond acceptor. Include in your structure for part a the feature that makes it possible for the compound to accept an H-bond. Point out that feature (not just an atom, but a feature).

c. (1/2 pt.) What is the “degree” (e.g., primary, etc.) of the amine that you drew in part a?

8. (3 pts.) The Fig shows part of the structure of the cell wall polymer in bacteria. The antibiotic penicillin works by inhibiting the enzyme that cross links these subunits into a larger structure. This polymer is more complex than those we have seen. However, its parts should be recognizable. To start, you might look at the two ring structures at the top, which are part of a long chain of such structures; the left hand ring has a long side chain.

a. (1/2 pt.) The top structure (chain of rings) is most closely related to which common class of biopolymers?

b. (1/2 pt.) What functional group best describes the linkage between the rings?

c. (1 pt.) The subunits in the side chain (lower left) are not entirely the ones you normally expect. Why? How do they (or, rather, some of them) differ from “normal”?

d. (1 pt.) The structure shown contains two amide linkages (which for our purposes here are equivalent). (This refers to amide linkages that are shown explicitly. There are also other amide linkages implied, but not shown explicitly; ignore those.) What acid would be obtained by hydrolysis of the amide linkages?

9. (1 pt.) The characteristic odor of fish (especially if not fresh) is due to low molecular weight amines. People often squirt a little lemon juice on fish, in part to reduce the fish odor. In terms of (general nature of) amine chemistry, why does this work? (You should be able to offer a good suggestion even if you do not know what the active ingredient is in the lemon juice.) (Ignore any possible odor of the lemon juice.)

10. (2 pts.) A company recently announced a new product, useful for lab work because it binds to the cannabinoid receptor. The compound is the amide from 2-fluoroethylamine and 2-methylarachidonic acid. Draw this compound; show all the hydrogens.

11. (2 pts.; 1 pt. per part) Methylglyoxal (2-oxopropanal) is sometimes made by cells, but is toxic. There are a number of ways cells can get rid of it. This question deals with two of them; the two parts are independent, except for starting with the same compound. (If you are not sure you have the correct initial structure, please check with me.) You can ignore stereochemistry.

a. One way to get rid of methylglyoxal is to convert it to 1,2-propanediol. What common biochemical cofactor(s) is/are needed to do this? How much of them is needed? Show the cofactor(s) as they enter into the reaction and show what they are converted to.

b. Another way to get rid of methylglyoxal is to reduce one of its functional groups and oxidize another. This is all done within the guidelines of the basic organic chem that we have discussed. What is the product? Explain how you can tell.

cq\bq4	(Sp 06)
5/14/06