Chapter 2: Protein Composition and Structure

Question 1

Answer 1

1. (A) Proline, Pro, P; (B) tyrosine, Tyr, Y; (C) leucine, Leu, L; (D) lysine, Lys, K

Question 2

Question 2.2

Properties. In reference to the amino acids shown in Problem 1, which are associated with the following characteristics?

Hydrophobic side chain ______________

Basic side chain ______________

Three ionizable groups ______________

pKa of approximately 10 in proteins ______________

Modified form of phenylalanine ______________

Answer 2

2. (a) C, B, A; (b) D; (c) D, B; (d) B, D; (e) B.

Question 3

Question 2.4

Solubility. In each of the following pairs of amino acids, identify which amino acid would be more soluble in water: (a) Ala, Leu; (b) Tyr, Phe; (c) Ser, Ala; (d) Trp, His.

Answer 3

4. (a) Ala; (b) Tyr; (c) Ser; (d) His.

Question 4

Question 2.5

Bonding is good. Which of the following amino acids have R groups that have hydrogen-bonding potential? Ala, Gly, Ser, Phe, Glu, Tyr, Ile, and Thr.

Answer 4

5. Ser, Glu, Tyr, Thr

Question 5

Question 2.7

Who’s charged? Draw the structure of the dipeptide Gly-His. What is the charge on the peptide at pH 5.5? pH 7.5?

Answer 5

Question 6

Question 2.9

Sweet tooth, but calorie conscious. Aspartame (NutraSweet), an artificial sweetener, is a dipeptide composed of Asp-Phe in which the carboxyl terminus is modified by the attachment of a methyl group. Draw the structure of Aspartame at pH 7.

Answer 6

Question 7

Question 2.10

Vertebrate proteins? What is meant by the term polypeptide backbone?

Answer 7

10. The (nitrogen–α carbon–carbonyl carbon) repeating unit.

Question 8

Question 2.11

Not a sidecar. Define the term side chain in the context of amino acid or protein structure.

Answer 8

11. Side chain is the functional group attached to the α-carbon atom of an amino acid.

Question 9

Question 2.12

One from many. Differentiate between amino acid composition and amino acid sequence.

Answer 9

12. Amino acid composition refers simply to the amino acids that make up the protein. The order is not specified. Amino acid sequence is the same as the primary structure—the sequence of amino acids from the amino terminal to the carboxyl terminal of the protein. Different proteins may have the same amino acid composition, but amino acid sequence identifies a unique protein.

Question 10

Question 2.14

Contrasting isomers. Poly-l-leucine in an organic solvent such as dioxane is α helical, whereas poly-l-isoleucine is not. Why do these amino acids with the same number and kinds of atoms have different helix-forming tendencies?

Answer 10

14. The methyl group attached to the β-carbon atom of isoleucine sterically interferes with α-helix formation. In leucine, this methyl group is attached to the γ-carbon atom, which is farther from the main chain and hence does not interfere.

Question 11

Question 2.15

Exceptions to the rule. Ramachandran plots for two amino acids differ significantly from that shown in Figure 2.23. Which two, and why?

Answer 11

15. Proline and glycine. The cyclic side chain of proline linking the nitrogen and α-carbon atoms limits ϕ to a very narrow range (around −60 degrees). The lack of steric hindrance exhibited by the side chain hydrogen atom of glycine enables this amino acid to access a much greater area of the Ramachandran plot.

Question 12

Question 2.16

Active again. A mutation that changes an alanine residue in the interior of a protein to valine is found to lead to a loss of activity. However, activity is regained when a second mutation at a different position changes an isoleucine residue to glycine. How might this second mutation lead to a restoration of activity?

Answer 12

16. The first mutation destroys activity because valine occupies more space than alanine does, and so the protein must take a different shape, assuming that this residue lies in the closely packed interior. The second mutation restores activity because of a compensatory reduction of volume; glycine is smaller than isoleucine.

Question 13

Question 2.17

Exposure issues. Many of the loops on proteins are composed of hydrophilic amino acids. Why might this be the case?

Answer 13

17. Loops invariably are on the surface of proteins, exposed to the environment. Because many proteins exist in aqueous environments, the exposed loops will be hydrophilic to interact with water.

Question 14

Question 2.18

Shuffle test. An enzyme that catalyzes disulfide–sulf-hydryl exchange reactions, called protein disulfide isomerase (PDI), has been isolated. PDI rapidly converts inactive scrambled ribonuclease into enzymatically active ribonuclease. In contrast, insulin is rapidly inactivated by PDI. What does this important observation imply about the relation between the amino acid sequence of insulin and its three-dimensional structure?

Answer 14

18. The native conformation of insulin is not the thermodynamically most stable form, because it contains two separate chains linked by disulfide bonds. Insulin is formed from proinsulin, a single-chain precursor, that is cleaved to form insulin, a 51-residue molecule, after the disulfide bonds have formed.

Question 15

Question 2.19

Stretching a target. A protease is an enzyme that catalyzes the hydrolysis of the peptide bonds of target proteins. How might a protease bind a target protein so that its main chain becomes fully extended in the vicinity of the vulnerable peptide bond?

Answer 15

19. A segment of the main chain of the protease could hydrogen bond to the main chain of the substrate to form an extended parallel or antiparallel pair of β strands.

Question 16

Question 2.20

Often irreplaceable. Glycine is a highly conserved amino acid residue in the evolution of proteins. Why?

Answer 16

20. Glycine has the smallest side chain of any amino acid. Its size is often critical in allowing polypeptide chains to make tight turns or to approach one another closely.

Question 17

Question 2.21

Potential partners. Identify the groups in a protein that can form hydrogen bonds or electrostatic bonds with an arginine side chain at pH 7.

Answer 17

21. Glutamate, aspartate, and the terminal carboxylate can form salt bridges with the guanidinium group of arginine. In addition, this group can be a hydrogen-bond donor to the side chains of glutamine, asparagine, serine, threonine, aspartate, tyrosine, and glutamate and to the main-chain carbonyl group. Histidine can form hydrogen bonds with arginine at pH 7.

Question 18

Question 2.22

Permanent waves. The shape of hair is determined in part by the pattern of disulfide bonds in keratin, its major protein. How can curls be induced?

Answer 18

22. Disulfide bonds in hair are broken by adding a thiol-containing reagent and applying gentle heat. The hair is curled, and an oxidizing agent is added to re-form disulfide bonds to stabilize the desired shape.

Question 19

Question 2.23

Location is everything 1. Most proteins have hydrophilic exteriors and hydrophobic interiors. Would you expect this structure to apply to proteins embedded in the hydrophobic interior of a membrane? Explain.

Answer 19

23. Some proteins that span biological membranes are “the exceptions that prove the rule” because they have the reverse distribution of hydrophobic and hydrophilic amino acids. For example, consider porins, proteins found in the outer membranes of many bacteria. Membranes are built largely of hydrophobic chains. Thus, porins are covered on the outside largely with hydrophobic residues that interact with the neighboring hydrophobic chains. In contrast, the center of the protein contains many charged and polar amino acids that surround a water-filled channel running through the middle of the protein. Thus, because porins function in hydrophobic environments, they are “inside out” relative to proteins that function in aqueous solution.

Question 20

Question 2.24

Location is everything 2. Proteins that span biological membranes often contain α helices. Given that the insides of membranes are highly hydrophobic (Section 12.2), predict what type of amino acids would be in such an α helix. Why is an α helix particularly suited to existence in the hydrophobic environment of the interior of a membrane?

Answer 20

24. The amino acids would be hydrophobic in nature. An α helix is especially suited to crossing a membrane because all of the amide hydrogen atoms and carbonyl oxygen atoms of the peptide backbone take part in intrachain hydrogen bonds, thus stabilizing these polar atoms in a hydrophobic environment.

Question 21

Question 2.26

Greasy patches. The α and β subunits of hemoglobin bear a remarkable structural similarity to myoglobin. However, in the subunits of hemoglobin, certain residues that are hydrophilic in myoglobin are hydrophobic. Why might this be the case?

Answer 21

26. Recall that hemoglobin exists as a tetramer while myoglobin is a monomer. Consequently, the hydrophobic residues on the surface of hemoglobin subunits are probably involved in van der Waals interactions with similar regions on the other subunits, and will be shielded from the aqueous environment by this interaction.

Question 22

Question 2.28

Issues of stability. Proteins are quite stable. The lifetime of a peptide bond in aqueous solution is nearly 1000 years. However, the free energy of hydrolysis of proteins is negative and quite large. How can you account for the stability of the peptide bond in light of the fact that hydrolysis releases much energy?

Answer 22

28. The energy barrier that must be crossed to go from the polymerized state to the hydrolyzed state is large even though the reaction is thermodynamically favorable.

Question 23

Question 2.30

A matter of convention. All l amino acids have an S absolute configuration except l-cysteine, which has the R configuration. Explain why l-cysteine is designated as having the R absolute configuration.

Answer 23

30. The assignment of absolute configuration requires the assignment of priorities to the four groups connected to a tetrahedral carbon atom. For all amino acids except cysteine, the priorities are: (1) amino group; (2) carbonyl group; (3) side chain; (4) hydrogen. For cysteine, because of the sulfur atom in its side chain, the side chain has a greater priority than does the carbonyl group, leading to the assignment of an R rather than S configuration.

Question 24

Question 2.32

Who goes first? Would you expect Pro—X peptide bonds to tend to have cis conformations like those of X—Pro bonds? Why or why not?

Answer 24

32. No, Pro–X would have the characteristics of any other peptide bond. The steric hindrance in X–Pro arises because the R group of Pro is bonded to the amino group. Hence, in X–Pro, the proline R group is near the R group of X, which would not be the case in Pro–X.

Question 25

Question 2.34

Scrambled ribonuclease. When performing his experiments on protein refolding, Christian Anfinsen obtained a quite different result when reduced ribonuclease was reoxidized while it was still in 8 M urea and the preparation was then dialyzed to remove the urea. Ribonuclease reoxidized in this way had only 1% of the enzymatic activity of the native protein. Why were the outcomes so different when reduced ribonuclease was reoxidized in the presence and absence of urea?

Answer 25

34. The reason is that the wrong disulfides formed pairs in urea. There are 105 different ways of pairing eight cysteine molecules to form four disulfides; only one of these combinations is enzymatically active. The 104 wrong pairings have been picturesquely termed “scrambled” ribonuclease.