Biochemistry

Mary K. Campbell, Shawn O. Farrell

Chapter 3

Amino Acids and Peptides - all with Video Answers

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Chapter Questions

Problem 1

RECALL How do D-amino acids differ from L-amino acids? What
biological roles are played by peptides that contain n-amino acids?

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Problem 2

RECALL Which amino acid is technically not an amino acid? Which amino acid contains no chiral carbon atoms?

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Problem 3

RECALL For each of the following, name an amino acid in which the $\mathrm{R}$ group contains it: a hydroxyl group, a sulfur atom, a second chiral carbon atom, an amino group, an amide group, an acid group, an aromatic ring, and a branched side chain.

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Problem 4

RECALL Identify the polar amino acids, the aromatic amino acids, and the sulfur-containing amino acids, given a peptide with the following amino acid sequence:
Val-Met-Ser-Ile-Phe-Arg-Cys-Tyr-Leu

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Problem 5

RECALL Identify the nonpolar amino acids and the acidic amino acids in the following peptide:
Glu-Thr-Val-Asp-Ile-Ser-Ala

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Problem 6

RECALL Are amino acids other than the usual 20 amino acids found in proteins? If so, how are such amino acids incorporated into proteins? Give an example of such an amino acid and a protein in which it occurs.

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Problem 7

MATHEMATICAL Predict the predominant ionized forms of the following amino acids at pH 7: glutamic acid, leucine, threonine, histidine, and arginine.

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Problem 8

MATHEMATICAL Draw structures of the following amino acids, indicating the charged form that exists at pH 4: histidine, asparagine, tryptophan, proline, and tyrosine.

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Problem 9

MATHEMATICAL Predict the predominant forms of the amino acids from Question 8 at $\mathrm{pH} 10$

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Problem 10

MATHEMATICAL Calculate the isoelectric point of each of the following amino acids: glutamic acid, serine, histidine, lysine, tyrosine, and arginine.

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Problem 11

MATHEMATICAL Sketch a titration curve for the amino acidd cysteine, and indicate the $\mathrm{p} K_{\mathrm{a}}$ values for all titratable groups. Also indicate the $\mathrm{pH}$ at which this amino acid has no net charge.

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Problem 12

MATHEMATICAL Sketch a titration curve for the amino acid lysine, and indicate the $\mathrm{p} K_{\mathrm{a}}$ values for all titratable groups. Also indicate the $\mathrm{pH}$ at which the amino acid has no net charge.

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Problem 13

MATHEMATICAL An organic chemist is generally happy with $95 \%$ yields. If you synthesized a polypeptide and realized a $95 \%$ yield with each amino acid residue added, what would be your overall yield after adding 10 residues (to the first amino acid)? After adding 50 residues? After 100 residues? Would these low yields be biochemically "satisfactory"? How are low yields avoided, biochemically?

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Problem 14

MATHEMATICAL Sketch a titration curve for aspartic acid, and indicate the $\mathrm{p} K_{\mathrm{a}}$ values of all titratable groups. Also indicate the pH range in which the conjugate acid-base pair +1 Asp and 0 Asp will act as a buffer.

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Problem 15

REFLECT AND APPLY Suggest a reason why amino acids are usually more soluble at $\mathrm{pH}$ extremes than they are at neutral pH. (Note that this does not mean that they are insoluble at neutral pH.)

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Problem 16

REFLECT AND APPLY Write equations to show the ionic dissociation reactions of the following amino acids: aspartic acid, valine, histidine, serine, and lysine.

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Problem 17

REFLECT AND APPLY Based on the information in Table $3.2,$ is there any amino acid that could serve as a buffer at pH 8 ? If so, which one?

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Problem 18

REFLECT AND APPLY If you were to have a mythical amino acid based on glutamic acid, but one in which the hydrogen that is attached to the $\gamma$ -carbon were replaced by another amino group, what would be the predominant form of this amino acid at $\mathrm{pH} 4$ $7,$ and $10,$ if the $p K_{a}$ value were 10 for the unique amino group?

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Problem 19

REFLECT AND APPLY What would be the pI for the mythical amino acid described in Question 18 ?

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Problem 20

REFLECT AND APPLY Identify the charged groups in the peptide shown in Question 4 at $\mathrm{pH} 1$ and at $\mathrm{pH} 7 .$ What is the net charge of this peptide at these two pH values?

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Problem 21

REFLECT AND APPLY Consider the following peptides: Phe- GluSer-Met and Val-Trp-Cys-Leu. Do these peptides have different net charges at $\mathrm{pH} 1$ ? At $\mathrm{pH} 7$ ? Indicate the charges at both $\mathrm{pH}$ values.

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Problem 22

REFLECT AND APPLY In each of the following two groups of amino acids, which amino acid would be the easiest to distinguish from the other two amino acids in the group, based on a titration?
(a) gly, leu, lys
(b) $\mathrm{glu},$ asp, ser

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Problem 23

REFLECT AND APPLY Could the amino acid glycine serve as the basis of a buffer system? If so, in what pH range would it be useful?

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Problem 24

Sketch resonance structures for the peptide group.

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Problem 25

RECALL How do the resonance structures of the peptide group contribute to the planar arrangement of this group of atoms?

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Problem 26

REFLECT AND APPLY Would the peptide group be planar if the amino group of amino acids was bonded to the $\beta$ carbon of the amino acid, rather than to the $\alpha$ carbon?

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Problem 27

Can a peptide act as a buffer? If so, why?

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Problem 28

REFLECT AND APPLY Consider the peptides Ser - Glu-GlyHis-Ala and Gly-His-Ala-Glu-Ser. How do these two peptides differ?

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Problem 29

REFLECT AND APPLY Would you expect the titration curves of the two peptides in Question 28 to differ? Why or why not?

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Problem 30

REFLECT AND APPLY What are the sequences of all the possible tripeptides that contain the amino acids aspartic acid, leucine, and phenylalanine? Use the three-letter abbreviations to express your answer.

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Problem 31

REFLECT AND APPLY Answer Question 30 using one-letter designations for the amino acids.

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Problem 32

REFLECT AND APPLY Most proteins contain more than 100 amino acid residues. If you decided to synthesize a " 100 -mer," with 20 different amino acids available for each position, how many different molecules could you make?

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Problem 33

REFLECT AND APPLY If the amino acids alanine and glycine react to form a peptide bond, is there more than one reaction product? If so, what products?

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Problem 34

REFLECT AND APPLY Why do we not indicate the side chains of the amino acids that form the peptide bond (see Figure 3.10 )?

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Problem 35

REFLECT AND APPLY Would the presence of a chiral center in an amino acid side chain affect the formation of a peptide bond?

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Problem 36

REFLECT AND APPLY What might you infer (or know) about the stability of amino acids, when compared with that of other buildingblock units of biopolymers (sugars, nucleotides, fatty acids, etc.)?

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Problem 37

REFLECT AND APPLY If you knew everything about the properties of the 20 common (proteinous) amino acids, would you be able to predict the properties of a protein (or large peptide) made from them?

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Problem 38

REFLECT AND APPLY Suggest a reason why the amino acids thyroxine and hydroxyproline are produced by posttranslational modification of the amino acids tyrosine and proline, respectively.

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Problem 39

REFLECT AND APPLY Consider the peptides Gly-Pro-Ser -GluThr (open chain) and Gly-Pro-Ser-Glu-Thr with a peptide bond linking the threonine and the glycine. Are these peptides chemically the same?

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Problem 40

REFLECT AND APPLY Can you expect to separate the peptides in Question 39 by electrophoresis?

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Problem 41

REFLECT AND APPLY Suggest a reason why biosynthesis of amino acids and of proteins would eventually cease in an organism with carbohydrates as its only food source.

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Problem 42

REFLECT AND APPLY You are studying with a friend who draws the structure of alanine at $\mathrm{pH} 7 .$ It has a carboxyl group ( $-\mathrm{COOH}$ ) and an amino group $\left(-\mathrm{NH}_{2}\right) .$ What suggestions would you make?

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Problem 43

REFLECT AND APPLY Suggest a reason (or reasons) why amino acids polymerize to form proteins that have comparatively few covalent crosslinks in the polypeptide chain.

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Problem 44

REFLECT AND APPLY Suggest the effect on the structure of peptides if the peptide group were not planar.

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Problem 45

REFLECT AND APPLY Speculate on the properties of proteins and peptides if none of the common amino acids contained sulfur.

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Problem 46

REFLECT AND APPLY Speculate on the properties of proteins that would be formed if amino acids were not chiral.

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Problem 47

RECALL What are the structural differences between the peptide hormones oxytocin and vasopressin?

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Problem 48

RECALL How do the peptide hormones oxytocin and vasopressin differ in function?

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Problem 49

RECALL What is the role of the disulfide bond in oxytocin and vasopressin?

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Problem 50

RECALL Is it possible to form cyclic peptides without bonds between side chains of the component amino acids?

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