29. Amino Acids

For the enzyme isopentenyl pyrophosphate isomerase, IPP binds tightly as a result of interactions between the active site amino acid residues and the diphosphate of IPP. Without concerning yourself with the structure of amino acids, what charges might you expect to be present in the active site to hold IPP in place so that the enzymatic reactions can occur?

Give equations for the formation and hydrogenolysis

of N-benzyloxycarbonyl methionine.

Three peptides were obtained from a trypsin digestion of two different polypeptides. In each case, indicate the possible sequences from the given data and tell what further experiment should be carried out in order to determine the primary structure of the polypeptide.

a. polypeptide I:

1. Val-Gly-Asp-Lys

2. Leu-Glu-Pro-Ala-Arg

3. Ala-Leu-Gly-Asp

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

Show how valine can be prepared by

d. a N-phthalimidomalonic ester synthesis. 

Provide a synthesis of the following amino acids using a combination of the HVZ and amination reactions.

b. Leu

(•••) Show how you would synthesize the following amino acids using the Strecker amino acid synthesis.

a. Ala

Show how you would use a Strecker synthesis to make

(c) aspartic acid.

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

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?

(a) Show how you would use a Strecker synthesis to

make phenylalanine.

(b) Propose a mechanism for each step in the synthesis in part (a).

(b) Propose a mechanism for each step in the synthesis

in part (a).

Predict the products of the following reactions.

(g) 4-methylpentanoic acid + Br2/PBr3 →

Predict the products of the following reactions.

(h) product from part (g) + excess NH3 →