Ch 4 - Problems 2s1643

Problems

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1. Identify the amino acids that differ from each other by a single methyl or methylene group. Answer: Gly and Ala; Ser and Thr; Val, Leu, and Ile; Asn and Gln; Asp and Glu. 2. The 20 standard amino acids are called α-amino acids. Certain β-amino acids are found in nature. Draw the structure of β-alanine (3-amino-n-propionate). Answer: +

H3N—CH2—CH2—COO–

3. Identify the hydrogen bond donor and acceptor groups in asparagine. Answer: Hydrogen bond donors: α-amino group, amide nitrogen. Hydrogen bond acceptors: α-carboxylate group, amide carbonyl. 4. Draw the dipeptide Asp-His at pH 7.0. Answer:

5. Calculate the number of possible pentapeptides that contain one residue each of Ala, Gly, His, Lys, and Val. Answer: The first residue can be one of five residues, the second one of the remaining four, etc. 6. Determine the net charge of the predominant form of Asp at (a) pH 1.0, (b) pH 3.0, (c) pH 6.0, and (d) pH 11.0. Answer: (a) (b) (c) (d)

+1; 0; –1; –2.

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Problems

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7. Calculate the pI of (a) Ala, (b) His, and (c) Glu. Answer: (a) pI = (2.35 + 9.87)/2 = 6.11 (b) pI = (6.04 + 9.33)/2 = 7.68 (c) pI = (2.10 + 4.07)/2 = 3.08 8. A sample of the amino acid tyrosine is barely soluble in water. Would a polypeptide containing only Tyr residues, poly(Tyr), be more or less soluble, assuming the total number of Tyr groups remains constant? Answer: The polypeptide would be even less soluble than free Tyr, because most of the amino and carboxylate groups that interact with water and make Tyr at least slightly soluble are lost in forming the peptide bonds in poly(Tyr). 9. Circle the chiral carbons in the following compounds:

Answer:

10. Draw the four stereoisomers of threonine. Answer:

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Problems

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11. The two CαH atoms of Gly are said to be prochiral, because when one of them is replaced by another group, Cα becomes chiral. Draw a Fischer projection of Gly and indicate which H must be replaced with CH3 to yield D-Ala. Answer:

12. The bacterially produced antibiotic gramicidin A forms channels in cell membranes that allow the free diffusion of Na+ and K+ ions, thereby killing the cell. This peptide consists of a sequence of D- and L-amino acids. The sequence of a segment of five amino acids in gramicidin A is R–Gly–L-Ala–D-Leu– L-Ala–D-Val–R′. Complete the Fischer projection below by adding the correct group to each vertical bond.

Answer:

13. Describe isoleucine (as shown in Table 4-1) using the RS system. Answer: (2S,3S)-Isoleucine 14. Some amino acids are synthesized by replacing the keto group (C α-keto acid with an amino group

O) of an organic acid known as an

. Identify the amino acids that can be produced this way

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Problems

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from the following α-keto acids:

Answer: (a) Glutamate; (b) aspartate 15. Identify the amino acid residue from which the following groups are synthesized: (a)

(b)

Answer: (a) Serine (N-acetylserine); (b) lysine (5-hydroxylysine); (c) methionine (N-formylmethionine). 16. Draw the peptide ATLDAK. (a) Calculate its approximate pI. (b) What is its net charge at pH 7.0? Answer:

(a) The pK''s of the ionizable side chains (Table 4-1) are 3.90 (Asp) and 10.54 (Lys); assume that the terminal Lys carboxyl group has a pK of 3.5 and the terminal Ala amino group has a pK of 8.0 (Section 4-1D). The pI is approximately midway between the pK''s of the two ionizations involving the neutral species (the pK of Asp and the N-terminal pK):

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Problems

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(b) The net charge at pH 7.0 is 0 (as drawn above). 17. The protein insulin consists of two polypeptides termed the A and B chains. Insulins from different organisms have been isolated and sequenced. Human and duck insulins have the same amino acid sequence with the exception of six amino acid residues, as shown below. Is the pI of human insulin lower than or higher than that of duck insulin? Amino acid residue A8

A9

A10 B1

Human

Thr Ser

Ile

Duck

Glu Asn Pro

B2

B27

Phe Val

Thr

Ala

Ala Ser

Answer: At position A8, duck insulin has a Glu residue, whereas human insulin has a Thr residue. Since Glu is negatively charged at physiological pH and Thr is neutral, human insulin has a higher pI than duck insulin. (The other amino acids that differ between the proteins do not affect the pI because they are uncharged.)

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