12.12: Additional Problems

Amino Acid Structures and Chirality

PROBLEM 12-29 Except for cysteine, only S amino acids occur in proteins. Several R amino acids are also found in nature, however. (R)-Serine is found in earthworms, and (R)-alanine is found in insect larvae. Draw Fischer projections of (R)-serine and (R)-alanine. Are these D or L amino acids?

PROBLEM 12-30 Cysteine is the only amino acid that has L stereochemistry but an R configuration. Make up a structure for another L amino acid of your own creation that also has an R configuration.

PROBLEM 12-31 Draw a Fischer projection of (S)-proline.

PROBLEM 12-32 Show the structures of the following amino acids in their zwitterionic forms:

(a) Trp (b) Ile (c) Cys (d) His

PROBLEM 12-53 Evidence for restricted rotation around amide ¹H NMR spectrum of N,N-dimethylformamide shows three peaks: 2.9 δ (singlet, 3 H), 3.0 δ (singlet, 3 H), and 8.0 δ (singlet, 1 H). As the temperature is raised, however, the two singlets at 2.9 δ and 3.0 δ slowly merge. At 180 °C, the ¹H NMR spectrum shows only two peaks: 2.95 δ (singlet, 6 H) and 8.0 δ (singlet, 1 H). Explain this temperature-dependent behavior.

PROBLEM 12-33 Proline has pK_a1 = 1.99 and pK_a2 = 10.60. Use the Henderson–Hasselbalch equation to calculate the ratio of protonated and neutral forms at pH = 2.50. Calculate the ratio of neutral and deprotonated forms at pH = 9.70.

PROBLEM 12-34 Using both three- and one-letter codes for amino acids, write the structures of all possible peptides that contain the following amino acids:

(a) Val, Ser, Leu. (b) Ser, Leu₂, Pro

PROBLEM 12-35 Look at the side chains of the 20 amino acids in Table 12.1, and then think about what is not present. None of the 20 contains either an aldehyde or a ketone carbonyl group, for instance. Is this just one of nature’s oversights, or is there a likely chemical reason? What complications might an aldehyde or ketone carbonyl group cause?

PROBLEM 12-51 Arginine, the most basic of the 20 common amino acids, contains a guanidino functional group in its side chain. Explain, using resonance structures to show how the protonated guanidino group is stabilized.

Amino Acid Reactions

PROBLEM 12-41 Predict the product of the reaction of valine with the following reagents:

(a) CH₃CH₂OH, acid    (b) KOH, H₂O    (c) CH₃COCl, pyridine; then H₂O

Peptides and Enzymes

PROBLEM 12-42 Write full structures for the following peptides:

(a) C-H-E-M.      (b) P-E-P-T-I-D-E

PROBLEM 12-48 Which of the following amino acids are more likely to be found on the exterior of a globular protein, and which on the interior? Explain.

(a) Valine (b) Aspartic acid (c) Phenylalanine (d) Lysine

PROBLEM 12-49 Leuprolide is a synthetic nonapeptide used to treat both endometriosis in women and prostate cancer in men.

1. Both C-terminal and N-terminal amino acids in leuprolide have been structurally modified. Identify the modifications.
2. One of the nine amino acids in leuprolide has D stereochemistry rather than the usual L. Which one?
3. Write the structure of leuprolide using both one- and three-letter abbreviations.
4. What charge would you expect leuprolide to have at neutral pH?

PROBLEM 12-58 Aspartame, a non-nutritive sweetener marketed under such trade names as Equal, NutraSweet, and Canderel, is the methyl ester of a simple dipeptide, Asp-Phe-OCH₃.

1. Draw the structure of aspartame.
2. The isoelectric point of aspartame is 5.9. Draw the principal structure present in aqueous solution at this pH.
3. Draw the principal form of aspartame present at physiological pH = 7.3.

PROBLEM 12-54 Propose a structure for an octapeptide that shows the composition Asp, Gly₂, Leu, Phe, Pro₂, Val on amino acid analysis. Edman analysis shows a glycine N-terminal group, and leucine is the C-terminal group. Acidic hydrolysis gives the following fragments:

Val-Pro-Leu, Gly, Gly-Asp-Phe-Pro, Phe-Pro-Val

PROBLEM 12-57 Oxytocin, a nonapeptide hormone secreted by the pituitary gland, functions by stimulating uterine contraction and lactation during childbirth. Its sequence was determined from the following evidence:

1.  Oxytocin is a cyclic compound containing a disulfide bridge between two cysteine residues.
2.  When the disulfide bridge is reduced, oxytocin has the constitution Asn, Cys₂, Gln, Gly, Ile, Leu, Pro, Tyr.
3.  Partial hydrolysis of reduced oxytocin yields seven fragments: Asp-Cys, Ile-Glu, Cys-Tyr, Leu-Gly, Tyr-Ile-Glu, Glu-Asp-Cys, and Cys-Pro-Leu.
4.  Gly is the C-terminal group.

What is the primary structure of oxytocin?

Mechanism Problems (not required for our class)

PROBLEM 12-24 The reaction of ninhydrin with an α-amino acid occurs in several steps.

(a) The first step is the formation of an imine by the reaction of the amino acid with ninhydrin. Show its structure and the mechanism of its formation.

(b) The second step is a decarboxylation. Show the structure of the product and the mechanism of the decarboxylation reaction.

(c) The third step is hydrolysis of an imine to yield an amine and an aldehyde. Show the structures of both products and the mechanism of the hydrolysis reaction.

(d) The final step is the formation of the purple anion. Show the mechanism of the reaction.

PROBLEM 12-25 The chloromethylated polystyrene resin originally used for Merrifield solid-phase peptide synthesis was prepared by treatment of polystyrene with chloromethyl methyl ether and a Lewis acid catalyst. Propose a mechanism for the reaction.

PROBLEM 12-26 An Fmoc protecting group can be removed from an amino acid by treatment with the amine base piperidine. Propose a mechanism.

PROBLEM 12-27 Proteins can be cleaved specifically at the amide bond on the carboxyl side of methionine residues by reaction with cyanogen bromide, BrC≡N.

The reaction occurs in several steps:

(a) The first step is a nucleophilic substitution reaction of the sulfur on the methionine side chain with BrCN to give a cyanosulfonium ion, [R₂SCN]⁺. Show the structure of the product, and propose a mechanism for the reaction.

(b) The second step is an internal S_N2 reaction, with the carbonyl oxygen of the methionine residue displacing the positively charged sulfur leaving group and forming a five-membered ring product. Show the structure of the product and the mechanism of its formation.

(c) The third step is a hydrolysis reaction to split the peptide chain. The carboxyl group of the former methionine residue is now part of a lactone (cyclic ester) ring. Show the structure of the lactone product and the mechanism of its formation.

(d) The final step is a hydrolysis of the lactone to give the product shown. Show the mechanism of the reaction.

PROBLEM 12-28 A clever recent method of peptide synthesis involves the formation of an amide bond by the reaction of an α-keto acid with an N-alkylhydroxylamine:

The reaction is thought to occur via nucleophilic addition of the N-alkylhydroxylamine to the keto acid, forming an oxime (Section 5.8), followed by decarboxylation and elimination of water. Show the mechanism.

Amino Acid Synthesis (not required for our class)

PROBLEM 12-36 Show how you could use the acetamidomalonate method to prepare the following amino acids:

(a) Leucine.   (b) Tryptophan

PROBLEM 12-37 Show how you could prepare the following amino acids using a reductive amination:

(a) Methionine    (b) Isoleucine

PROBLEM 12-38 Show how you could prepare the following amino acids enantioselectively:

(a) Pro.     (b) Val

PROBLEM 12-39 Serine can be synthesized by a simple variation of the amidomalonate method using formaldehyde rather than an alkyl halide. How might this be done?

PROBLEM 12-42 Draw resonance forms for the purple anion obtained by reaction of ninhydrin with an α-amino acid (see Problem 12-24).

Peptides Synthesis and Reactions (not required for our class)

PROBLEM 12-43 Propose two structures for a tripeptide that gives Leu, Ala, and Phe on hydrolysis but does not react with phenyl isothiocyanate.

PROBLEM 12-44 Show the steps involved in a synthesis of Phe-Ala-Val using the Merrifield procedure.

PROBLEM 12-45 Draw the structure of the PTH derivative product you would obtain by Edman degradation of the following peptides:

(a) I-L-P-F.    (b) D-T-S-G-A

PROBLEM 12-46 Which amide bonds in the following polypeptide are cleaved by trypsin? By chymotrypsin?

Phe-Leu-Met-Lys-Tyr-Asp-Gly-Gly-Arg-Val-Ile-Pro-Tyr

PROBLEM 12-47 What kinds of reactions do the following classes of enzymes catalyze?

(a) Hydrolases (b) Lyases (c) Transferases

General Problems (not required for our class)

PROBLEM 12-50 The α-helical parts of myoglobin and other proteins stop whenever a proline residue is encountered in the chain. Why is proline never present in a protein α helix?

PROBLEM 12-52 Cytochrome c is an enzyme found in the cells of all aerobic organisms. Elemental analysis of cytochrome c shows that it contains 0.43% iron. What is the minimum molecular weight of this enzyme?

PROBLEM 12-55 Look at the structure of human insulin, and indicate where in each chain the molecule is cleaved by trypsin and chymotrypsin.

PROBLEM 12-56 What is the structure of a nonapeptide that gives the following fragments when cleaved?

Trypsin cleavage: Val-Val-Pro-Tyr-Leu-Arg, Ser-Ile-Arg

Chymotrypsin cleavage: Leu-Arg, Ser-Ile-Arg-Val-Val-Pro-Tyr

PROBLEM 12-59 Refer to Figure 12.5 and propose a mechanism for the final step in Edman degradation—the acid-catalyzed rearrangement of the ATZ derivative to the PTH derivative.

PROBLEM 12-60 Amino acids are metabolized by a transamination reaction in which the −NH₂ group of the amino acid changes places with the keto group of an α-keto acid. The products are a new amino acid and a new α-keto acid. Show the product from transamination of isoleucine.

PROBLEM 12-61 The first step in the biological degradation of histidine is the formation of a 4-methylidene-5-imidazolone (MIO) by cyclization of a segment of the peptide chain in the histidine ammonia lyase enzyme. Propose a mechanism.

PROBLEM 12-62 The first step in the biological degradation of lysine is reductive amination with α-ketoglutarate to give saccharopine. Nicotinamide adenine dinucleotide phosphate (NADPH), a relative of NADH, is the reducing agent. Show the mechanism.