29. Amino Acids

How many amino acids does each $\mathrm{codon}$ code for in the genetic code?

Show the peptides that would result from cleavage by the indicated reagent: 

a. Val-Arg-Gly-Met-Arg-Ala-Ser by carboxypeptidase A

b. Ser-Phe-Lys-Met-Pro-Ser-Ala-Asp by cyanogen bromide

c. Arg-Ser-Pro-Lys-Lys-Ser-Glu-Gly by trypsin

Which of the following molecules is responsible for coding the sequence of amino acids in a protein?

In which way do the structures of amino acids differ from each other?

How would a protein that resides in the nonpolar interior of a membrane fold compared with the water-soluble protein just discussed?

Which bonds in the backbone of a peptide can rotate freely?

Show how you would use bromination followed by amination to synthesize the following amino acids.

(b) leucine

What dipeptides would be formed by heating a mixture of valine and N-protected leucine?

Show how the following amino acids might be formed in the laboratory by reductive amination of the appropriate α-ketoacid.

(a) alanine

Proof that an imine was formed between aldolase and its substrate was obtained by using D-fructose-1,6-bisphosphate labeled at the C-2 position with ¹⁴C as the substrate. NaBH₄ was added to the reaction mixture. A radioactive product was isolated from the reaction mixture and hydrolyzed in an acidic solution. Draw the structure of the radioactive product obtained from the acidic solution. (Hint: NaBH₄ reduces an imine linkage.)

Show how you would synthesize any of the standard amino acids from each starting material. You may use any necessary reagents.

(b)

Erwin Chargaff’s discovery that DNA contains equimolar amounts of guanine and cytosine and also equimolar amounts of adenine and thymine has come to be known as Chargaff’s rule:

G = C and A = T

(a) Does Chargaff’s rule imply that equal amounts of guanine and adenine are present in DNA? That is, does G = A?

(b) Does Chargaff’s rule imply that the sum of the purine residues equals the sum of the pyrimidine residues? That is, does A + G = C + T?

(c) Does Chargaff’s rule apply only to double-stranded DNA, or would it also apply to each individual strand if the double helical strand were separated into its two complementary strands?

Reaction of a polypeptide with carboxypeptidase A releases Met. The polypeptide undergoes partial hydrolysis to give the following peptides. What is the sequence of the polypeptide?

1. Ser, Lys, Trp

2. Gly, His, Ala

3. Glu, Val, Ser

4. Leu, Glu, Ser

5. Met, Ala, Gly

6. Ser, Lys, Val

7. Glu, His

8. Leu, Lys, Trp

9. Lys, Ser

10. Glu, His, Val

11. Trp, Leu, Glu

12. Ala, Met

A decapeptide undergoes partial hydrolysis to give peptides whose amino acid compositions are shown. Reaction of the intact decapeptide with Edman's reagent releases PTH-Gly. What is the sequence of the decapeptide?

1. Ala, Trp

2. Val, Pro, Asp

3. Pro, Val

4. Ala, Glu

5. Trp, Ala, Arg

6. Arg, Gly

7. Glu, Ala, Leu

8. Met, Pro, Leu, Glu

Show how you would use the Strecker synthesis to make tryptophan. What stereochemistry would you expect in your synthetic product?