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1. a & b. Sarcosine is N-methylglycine. c. Yes. It is a secondary amine. Only tertiary amines (with no H on the amino N) cannot form amides. d. No. The resulting amide would not have an H on the N, thus could not donate to a H-bond.
2. a. HSCH2CH2CH(NH2)COOH b. It is like cysteine, but has one more -CH2- group. [It is called homocysteine. The "homo" here means homolog.] c. A lactone is a cyclic ester, so a thiolactone is ... ? Make the thiolactone by attack of the thiol S on the carboxyl group. Water is also made. d. The thiolactone of part c has a five-membered ring. The thiolactone of the amino acid in part b would have a four-membered ring, which is quite strained.
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3. glutamic acid --> GABA + CO2. That is, decarboxylate the 1-carboxyl group of glutamic acid.
| 4. a. Hydrolyze the amide groups. |
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| At pH = 7, all the amino groups and all the carboxyl groups are in the ionized form. | |
b. In these products, the amino group is on the #3 (or β) C atom; in the protein amino acids, the amino group is on the #2 (or α) C atom. Thus the original peptide given in the question is a β-peptide.
c. From the left: valine, alanine, leucine. That is, the first amino acid is the like valine, except that it has an extra -CH2- between the amino-bearing C and the carboxyl C; this is sometimes written β-hVal, where the hVal means homovaline, valine with an extra -CH2-. (Recall homocysteine, in another question, above.)
d. Enzymatic. The other common methods of hydrolysis use one or another extreme of pH.
e. They are amide N; amides are neutral functional groups.
This question is based on the article: B Geueke et al, A Novel beta-Peptidyl Aminopeptidase (BapA) from Strain 3-2W4 Cleaves Peptide Bonds of Synthetic beta-Tri- and beta-Dipeptides. J Bacteriol 187:5910-5917, 9/05. http://jb.asm.org/cgi/content/abstract/187/17/5910. The structures shown are cut from their Fig 4.
5. Be sure to use the amino and carboxyl groups from the common part, not the side chains.
6. Label the H of the water as "δ+" and the O as "δ-". The polar group of the amino acid side chain should also be labeled to show its polarity. Then, show a weak interaction (dotted line, fairly long) between the Hδ+ of one molecule and the Oδ- or Nδ- of the other.
For #5 and 6, I encourage you to show me your answers. They involve fairly complex drawings, and for #6, many answers are possible. I can give you much better feedback by looking at your work than by offering answers here.
7. a. S
b. cysteine. In doing part a, you found that the amino group is top priority and the H is low priority. That leaves the carboxyl group and the side chain competing for priorities 2 & 3. For serine, in part a, the carboxyl group is higher priority than the side chain (OOO vs OHH on the first C). How could a side chain "beat" a C with OOO? By having an element above O on its first C. The only such example among the standard amino acids is cysteine. Thus, L-cysteine has an R stereocenter.
The discussion above makes a statement that is not entirely correct. It asks "How could a side chain "beat" a C with OOO?". And the given answer is "By having an element above O on its first C." Now, in the context of this particular question, that answer is fine. However, there is another way to beat the OOO of a carboxylic acid group. In fact, it uses a common group, which should be familiar to you from course material. What is it?
That cysteine is "odd" in its R/S designation is also noted on my page of Further reading: Old articles, in the discussion of the article by Leung (2000).
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Last update: August 15, 2011