Name:				Total test points:			Course grade:

Exam score is on the exam. 20 = A, 15 = B, 10 = C, 5 = D. (ignoring +/-) 

In figuring your course grade, I look at several things. First, I average your four test letter grades. For most people, this will give a proper course grade. But I do look to see if one of your early tests was unusually low (and I may consider that, discounting the early low score a little). After that, I generally look over the whole picture, trying to make sure everything looks fair and consistent. 

For test point total, the nominal cutoffs (ignoring +/-) are: A = 69, B = 52, C = 34, D = 17 (possible = 87). Your test total is shown above; check for accuracy of my records.

If there are any questions that might reasonably affect your course grade, please contact me ASAP. I’ll mail in the official grades Tuesday morning 5/30. (Of course, legitimate problems can be fixed later, but it is easier before submission.) Beyond that, feel free to call/e-mail anytime to discuss other issues, or to chat. If you want to do further work from Ouellette, I am happy to discuss it with you, or to read any written work. 

Additional feedback/suggestions always welcomed; e-mail is fine. Comments/suggestions on the web pages are particularly welcomed. If you haven’t already done so, look at the Supplemental Information page at the web site for some things you might comment on. (You can also send me anonymous messages by using the message form at the web site.)

A brief answer key follows. Alternative answers are reasonable in some cases. I have avoided drawing structures here as much as possible. 

1. Charge difference is 2; the avian virus enzyme is -2 relative to the human virus enzyme. Glu has a negatively charged side chain, whereas lysine has a positively charged side chain.

R M Krug, Virology: Clues to the virulence of H5N1 viruses in humans. Science 311:1562, 3/17/06. News. The feature discussed in the question is just one part of the story of why the bird and human viruses behave differently. This article discusses this difference, and others.

2. a.
	18        13  11  9               1
C-C-C-C-C-C-C=C-C=C-C-C-C-C-C-C-C-COOH
          
          OH	

b. A double bond has moved! In linoleic acid, the double bonds are 9,12. More obviously upon visual inspection, the double bonds are not conjugated in the linoleic acid, but are in the product.

It’s actually worse than that. The “new” double bond is trans. The reason behind this is complex, and I have not sorted it out. But it seems that the initial oxidation at 13 leads to a rearrangement; if it is “spontaneous”, making the more stable trans isomer is not surprising.

c. Linoleic acid is more suitable for use in ordinary membranes. Lipids are supposed to have a non-polar tail; in the oxidation product that non-polar tail has been severely disrupted.

3. a. citrate. -OH on a C that has three C attached to it.

b. Any of reactions 3, 4, 6, 8, all shown coupled to NAD+ or FAD gaining H.

c. There are none. One reaction does produce GTP, but that is not the question.

d. Simplest is #7, but also #1, and the addition of water to cis-aconitate, which is not shown on this chart. Each involves adding A-B across a double bond.

e. Reactions 3 or 4. Each shows loss of CO2 from a carboxylic acid.

4. It will form a lactam (cyclic amide). The given chemical contains three functional groups. From the left: acyl chloride, C=C, and amino group. Acyl chloride + amine is a good way to make an amide. (The spacing is actually optimal here. It will make a 5-ring; 5- and 6-rings are generally the most favorable. Smaller ones are strained, and larger ones have entropic costs.)

The structure shown at the right shows this, using one type of shorthand: the big complicated line from the C at the left to the N at the right is to show the ring (the amide link). HCl is a byproduct.	   
              
   C-CH=CH-CH2-NH 
   
   O	

5. a. DAP is very similar to lysine. It contains an extra carboxyl group. In fact, one pathway for making lysine is the decarboxylation of DAP. Note that the question specified that you should be able to see how DAP is converted to your chosen aa.

How do you approach this? What is distinctive about DAP? Perhaps that it has amino and carboxyl groups at both ends. A quick perusal of the aa chart should lead you to look at Glu and Lys more carefully. The C chain is consistent with Lys but not Glu, and Lys also better fits the given info that you should see how to make your chosen aa from DAP.

This question is very similar to the one about GABA on the Ch 15 practice quiz.

b. Cysteine, where the H of the -SH has been replaced by “alanine”. (Some tried Met here, but the C-chain is inconsistent with that.)

Approach? Distinctive feature is the S. Only Met and Cys contain S. The C-chain is consistent with Cys, but not with Met. That leaves you with Cys as the only reasonable choice. That choice certainly leaves open how one gets to lanthionine from Cys, but that is not for you to worry about here.

c. Yeah, probably. The only difference is the middle -S- vs -CH2-. The geometry will be similar, and the electronegativities of S and C are similar, so the polarity of the amino acids is similar. 

S A Consaul et al, An unusual mutation results in the replacement of diaminopimelate with lanthionine in the peptidoglycan of a mutant strain of Mycobacterium smegmatis. J Bacteriol 187:1612-1620, 3/05. M. smegmatis is often studied as a model for the pathogenic (but poor-growing) mycobacteria that cause tuberculosis and leprosy.

6. a. an amino acid with a large hydrophobic side chain, such as leucine or phenylalanine. The interior of the membrane is hydrophobic, with fatty acids tails.

b. hydrogen bonds; amide groups. (The H-bonds, in both -helix and -sheet, are between two parts of amide groups: the N-H of one amide group and the C=O of another amide group.)

L-M Guzman et al, FtsL, an essential cytoplasmic membrane protein involved in cell division in Escherichia coli. J Bacteriol 174:7717, 12/92. Fig 4B,

7. a. The simplest would be (CH3)3N: = trimethylamine. (The colon on the N indicates a lone pair.)

b. lone pair on the N (a highly electronegative atom)

c. tertiary

8. a. polysaccharides (carbohydrates)

b. acetal

c. Some of the amino acids here are D-; the standard amino acids found in proteins are L-.

d. ethanoic (acetic) acid

N S Ringan & L Grayson, Molecular modelling in the undergraduate chemistry curriculum: The use of -lactams as a case study. J Chem Educ 71:856, 10/94. Fig 1.

Questions 5 and 8 both refer to the bacterial peptidoglycan, the major cell wall polymer. Note how the term peptidoglycan reflects the two major parts: peptide-like and polysaccharide (glycan)-like. The amino acid side chains vary a lot, and contain unusual amino acids, as these two questions show. Numerous antibiotics, most famously the penicillins (-lactams), work by interfering with cell call synthesis.

9. Amines are basic, lemon juice is acidic. The acidic lemon juice converts the amine (neutral and volatile) to an ammonium salt (ionic, not volatile). (Simple mixing of an amine and an acid does not produce an amide, because of this proton transfer, which leaves the much less reactive carboxylate ion.)

10. 
								    amide linkage
								    
CH3(CH2)4CH=CHCH2CH=CHCH2CH=CHCH2CH=CHCH2CH2CHC-NH-CH2CH2F
								   
							     H3C O
 
11. Given compound:
	    O
    
CH3-C-C=O
      
      H	

a. Make

   HO H
       
CH3-C-C-OH
     
    H H

That is, both carbonyl groups are reduced to alcohols. Thus you need a reducing agent, or hydrogen carrier: NADH+H+ (or FADH2). Two reductions; need two moles of reducing agent. The reducing cofactors would be converted to their oxidized forms: NAD+ or FAD.

b. The key issue is that the keto group is not easily oxidized, so it makes more sense to reduce it, while oxidizing the aldehyde. The result is 2-hydroxypropanoic acid (lactic acid).

J Ko et al, Conversion of methylglyoxal to acetol by Escherichia coli aldo-keto reductases. J Bacteriol 187:5782-5789, 8/05. “Acetol” is 2-oxo-1-propanol, the product of the first reduction step for part a. This step uses NADPH (a common phosphorylated variation of NADH), the 2nd step uses NADH.

--
 
I encourage you to check my book list -- and to contribute to it. Also, have a look at the bird flu page and other “BITN” (Biotechnology in the News) pages. Comments/questions/suggestions welcomed. 

Have you seen the happy-face spider??? (Live link on X402 Updates page.)
http://www.starbulletin.com/96/09/17/features/story1.html

Best wishes to all,

Bob Bruner
<contact info>

cq\bq4a	(Spring 2006)
5/21/06