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Chapter 3 Amino Acids, Peptides, and Proteins

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Chapter 3 Amino Acids, Peptides, and Proteins

Multiple Choice Questions 1. Amino acids Page: 72 Difficulty: 1 Ans: C The chirality of an amino acid results from the fact that its  carbon: A) B) C) D) E)

has no net charge. is a carboxylic acid. is bonded to four different chemical groups. is in the L absolute configuration in naturally occurring proteins. is symmetric.

2. Amino acids Page: 72 Difficulty: 2 Ans: B Of the 20 standard amino acids, only ___________ is not optically active. The reason is that its side chain ___________. A) B) C) D) E)

alanine; is a simple methyl group glycine; is a hydrogen atom glycine; is unbranched lysine; contains only nitrogen proline; forms a covalent bond with the amino group

3. Amino acids Page: 72 Difficulty: 1 Ans: C Two amino acids of the standard 20 contain sulfur atoms. They are: A) B) C) D) E)

cysteine and serine. cysteine and threonine. methionine and cysteine methionine and serine threonine and serine.

4. Amino acids Page: 75 Difficulty: 1 Ans: A All of the amino acids that are found in proteins, except for proline, contain a(n): A) B) C) D) E)

amino group. carbonyl group. carboxyl group. ester group. thiol group.

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Chapter 3 Amino Acids, Peptides, and Proteins

5. Amino acids Pages: 75–76 Difficulty: 3 Ans: C Which of the following statements about aromatic amino acids is correct? A) B) C) D)

All are strongly hydrophilic. Histidine’s ring structure results in its being categorized as aromatic or basic, depending on pH. On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine. The major contribution to the characteristic absorption of light at 280 nm by proteins is the phenylalanine R group. E) The presence of a ring structure in its R group determines whether or not an amino acid is aromatic. 6. Amino acids Page: 77 Difficulty: 2 Ans: A Which of the following statements about cystine is correct? A) Cystine forms when the —CH2—SH R group is oxidized to form a —CH2—S—S—CH2— disulfide bridge between two cysteines. B) Cystine is an example of a nonstandard amino acid, derived by linking two standard amino acids. C) Cystine is formed by the oxidation of the carboxylic acid group on cysteine. D) Cystine is formed through a peptide linkage between two cysteines. E) Two cystines are released when a —CH2—S—S—CH2— disulfide bridge is reduced to —CH2— SH. 7. Amino acids Page: 77 Difficulty: 2 Ans: A The uncommon amino acid selenocysteine has an R group with the structure —CH2—SeH (pKa  5). In an aqueous solution, pH = 7.0, selenocysteine would: A) B) C) D) E)

be a fully ionized zwitterion with no net charge. be found in proteins as D-selenocysteine. never be found in a protein. be nonionic. not be optically active.

8. Amino acids Pages: 78–79 Difficulty: 1 Ans: A Amino acids are ampholytes because they can function as either a(n): A) B) C) D) E)

acid or a base. neutral molecule or an ion. polar or a nonpolar molecule. standard or a nonstandard monomer in proteins. transparent or a light-absorbing compound.

Chapter 3 Amino Acids, Peptides, and Proteins

9. Amino acids Pages: 79–80 Difficulty: 2 Ans: D Titration of valine by a strong base, for example NaOH, reveals two pK’s. The titration reaction occurring at pK2 (pK2 = 9.62) is: A) B) C) D) E)

—COOH + OH —COOH + —NH2 —COO + —NH2+ —NH3+ + OH —NH2 + OH

    

—COO + H2O. —COO + —NH2+. —COOH + —NH2. —NH2 + H2O. —NH + H2O.

10. Amino acids Pages: 79–80 Difficulty: 1 Ans: C In a highly basic solution, pH = 13, the dominant form of glycine is: A) B) C) D) E)

NH2—CH2—COOH. NH2—CH2—COO. NH2—CH3+—COO. NH3+—CH2—COOH. NH3+—CH2—COO.

11. Amino acids Pages: 80–81 Difficulty: 2 Ans: B For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have: A) B) C) D) E)

a net negative charge. a net positive charge. no charged groups. no net charge. positive and negative charges in equal concentration.

12. Amino acids Pages: 80–81 Difficulty: 2 Ans: A At pH 7.0, converting a glutamic acid to -carboxyglutamate, will have what effect on the overall charge of the protein containing it? A) B) C) D) E)

it will become more negative it will become more positive. it will stay the same. there is not enough information to answer the question. the answer depends on the salt concentration.

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Chapter 3 Amino Acids, Peptides, and Proteins

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13. Amino acids Pages: 80–81 Difficulty: 2 Ans: C At pH 7.0, converting a proline to hydroxyproline, will have what effect on the overall charge of the protein containing it? A) B) C) D) E)

it will become more negative it will become more positive. it will stay the same. there is not enough information to answer the question. the answer depends on the salt concentration.

14. Amino acids Pages: 80–81 Difficulty: 3 Ans: B What is the approximate charge difference between glutamic acid and -ketoglutarate at pH 9.5? A) B) C) D) E)

0 ½ 1 1½ 2

15. Peptides and proteins Page: 82 Difficulty: 1 Ans: B The formation of a peptide bond between two amino acids is an example of a(n) ______________ reaction. A) B) C) D) E)

cleavage condensation group transfer isomerization oxidation reduction

16. Peptides and proteins Page: 82 Difficulty: 1 Ans: C The peptide alanylglutamylglycylalanylleucine has: A) B) C) D) E)

a disulfide bridge. five peptide bonds. four peptide bonds. no free carboxyl group. two free amino groups.

17. Peptides and proteins Pages: 82–83 Difficulty: 1 Ans: C An octapeptide composed of four repeating glycylalanyl units has: A) B) C) D) E)

one free amino group on an alanyl residue. one free amino group on an alanyl residue and one free carboxyl group on a glycyl residue. one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue. two free amino and two free carboxyl groups. two free carboxyl groups, both on glycyl residues.

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18. Peptides and proteins Page: 82–83 Difficulty: 1 Ans: C At the isoelectric pH of a tetrapeptide: A) B) C) D) E)

only the amino and carboxyl termini contribute charge. the amino and carboxyl termini are not charged. the total net charge is zero. there are four ionic charges. two internal amino acids of the tetrapeptide cannot have ionizable R groups.

19. Peptides and proteins Pages: 83–84 Difficulty: 2 Ans: C Which of the following is correct with respect to the amino acid composition of proteins? A) B) C) D) E)

Larger proteins have a more uniform distribution of amino acids than smaller proteins. Proteins contain at least one each of the 20 different standard amino acids. Proteins with different functions usually differ significantly in their amino acid composition. Proteins with the same molecular weight have the same amino acid composition. The average molecular weight of an amino acid in a protein increases with the size of the protein.

20. Peptides and proteins Page: 83 Difficulty: 2 Ans: B The average molecular weight of the 20 standard amino acids is 138, but biochemists use 110 when estimating the number of amino acids in a protein of known molecular weight. Why? A) The number 110 is based on the fact that the average molecular weight of a protein is 110,000 with an average of 1,000 amino acids. B) The number 110 reflects the higher proportion of small amino acids in proteins, as well as the loss of water when the peptide bond forms. C) The number 110 reflects the number of amino acids found in the typical small protein, and only small proteins have their molecular weight estimated this way. D) The number 110 takes into account the relatively small size of nonstandard amino acids. E) The number 138 represents the molecular weight of conjugated amino acids. 21. Peptides and proteins Page: 84 Difficulty: 1 Ans: C In a conjugated protein, a prosthetic group is: A) B) C) D) E)

a fibrous region of a globular protein. a nonidentical subunit of a protein with many identical subunits. a part of the protein that is not composed of amino acids. a subunit of an oligomeric protein. synonymous with “protomer.”

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Chapter 3 Amino Acids, Peptides, and Proteins

22. Peptides and proteins Pages: 84–85 Difficulty: 1 Ans: A Prosthetic groups in the class of proteins known as glycoproteins are composed of: A) B) C) D) E)

carbohydrates. flavin nucleotides. lipids. metals . phosphates.

23. Working with proteins Page: 85 Difficulty: 1 Ans: E For the study of a protein in detail, an effort is usually made to first: A) B) C) D) E)

conjugate the protein to a known molecule. determine its amino acid composition. determine its amino acid sequence. determine its molecular weight. purify the protein.

24. Working with proteins Page: 87 Difficulty: 2 Ans: B In a mixture of the five proteins listed below, which should elute second in size-exclusion (gelfiltration) chromatography? A) B) C) D) E)

cytochrome c immunoglobulin G ribonuclease A RNA polymerase serum albumin

Mr = 13,000 Mr = 145,000 Mr = 13,700 Mr = 450,000 Mr = 68,500

25. Working with proteins Page: 89 Difficulty: 2 Ans: E By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to: A) B) C) D) E)

determine a protein’s isoelectric point. determine an enzyme’s specific activity. determine the amino acid composition of the protein. preserve a protein’s native structure and biological activity. separate proteins exclusively on the basis of molecular weight.

26. Working with proteins Page: 90 Difficulty: 2 Ans: B To determine the isoelectric point of a protein, first establish that a gel: A) B) C) D) E)

contains a denaturing detergent that can distribute uniform negative charges over the protein’s surface. exhibits a stable pH gradient when ampholytes become distributed in an electric field. is washed with an antibody specific to the protein of interest. neutralizes all ionic groups on a protein by titrating them with strong bases. relates the unknown protein to a series of protein markers with known molecular weights, Mr.

Chapter 3 Amino Acids, Peptides, and Proteins

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27. Working with proteins Pages: 90–91 Difficulty: 3 Ans: A The first step in two-dimensional gel electrophoresis generates a series of protein bands by isoelectric focusing. In a second step, a strip of this gel is turned 90 degrees, placed on another gel containing SDS, and electric current is again applied. In this second step: A) proteins with similar isoelectric points become further separated according to their molecular weights. B) the individual bands become stained so that the isoelectric focus pattern can be visualized. C) the individual bands become visualized by interacting with protein-specific antibodies in the second gel. D) the individual bands undergo a second, more intense isoelectric focusing. E) the proteins in the bands separate more completely because the second electric current is in the opposite polarity to the first current. 28. Working with proteins Page: 91 Difficulty: 1 Ans: B The term specific activity differs from the term activity in that specific activity: A) B) C) D) E)

is measured only under optimal conditions. is the activity (enzyme units) in a milligram of protein. is the activity (enzyme units) of a specific protein. refers only to a purified protein. refers to proteins other than enzymes.

29. Peptides and proteins Page: 92 Difficulty: 1 Ans: B Which of the following refers to particularly stable arrangements of amino acid residues in a protein that give rise to recurring patterns? A) B) C) D) E)

Primary structure Secondary structure Tertiary structure Quaternary structure None of the above

30. Peptides and proteins Page: 92 Difficulty: 1 Ans: D Which of the following describes the overall three-dimensional folding of a polypeptide? A) B) C) D) E)

Primary structure Secondary structure Tertiary structure Quaternary structure None of the above

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31. The covalent structure of proteins Page: 93 Difficulty: 1 Ans: B The functional differences, as well as differences in three-dimensional structures, between two different enzymes from E. coli result directly from their different: A) B) C) D) E)

affinities for ATP. amino acid sequences. roles in DNA metabolism. roles in the metabolism of E. coli. secondary structures.

32. The covalent structure of proteins Page: 95 Difficulty: 2 Ans: C One method used to prevent disulfide bond interference with protein sequencing procedures is: A) cleaving proteins with proteases that specifically recognize disulfide bonds. B) protecting the disulfide bridge against spontaneous reduction to cysteinyl sulfhydryl groups. C) reducing disulfide bridges and preventing their re-formation by further modifying the —SH groups. D) removing cystines from protein sequences by proteolytic cleavage. E) sequencing proteins that do not contain cysteinyl residues. 33. The covalent structure of proteins Pages: 96–97 Difficulty: 3 Ans: C A nonapeptide was determined to have the following amino acid composition: (Lys) 2, (Gly) 2, (Phe) 2, His, Leu, Met. The native peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB) and then hydrolyzed; 2,4-dinitrophenylhistidine was identified by HPLC. When the native peptide was exposed to cyanogen bromide (CNBr), an octapeptide and free glycine were recovered. Incubation of the native peptide with trypsin gave a pentapeptide, a tripeptide, and free Lys. 2,4-Dinitrophenylhistidine was recovered from the pentapeptide, and 2,4-dinitrophenylphenylalanine was recovered from the tripeptide. Digestion with the enzyme pepsin produced a dipeptide, a tripeptide, and a tetrapeptide. The tetrapeptide was composed of (Lys) 2, Phe, and Gly. The native sequence was determined to be: A) B) C) D) E)

Gly–Phe–Lys–Lys–Gly–Leu–Met–Phe–His. His–Leu–Gly–Lys–Lys–Phe–Phe–Gly–Met. His–Leu–Phe–Gly–Lys–Lys–Phe–Met–Gly. His–Phe–Leu–Gly–Lys–Lys–Phe–Met–Gly. Met–Leu–Phe–Lys–Phe–Gly–Gly–Lys–His.

34. The covalent structure of proteins Pages: 96–97 Difficulty: 1 Ans: C Even when a gene is available and its sequence of nucleotides is known, chemical studies of the protein are still required to determine: A) B) C) D) E)

molecular weight of the protein. the amino-terminal amino acid. the location of disulfide bonds. the number of amino acids in the protein. whether the protein has the amino acid methionine in its sequence.

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35. The covalent structure of proteins Page: 100 Difficulty: 1 Ans: C The term “proteome” has been used to describe: A) B) C) D) E)

regions (domains) within proteins. regularities in protein structures. the complement of proteins encoded by an organism’s DNA. the structure of a protein-synthesizing ribosome. the tertiary structure of a protein.

36. The covalent structure of proteins Pages: 98–100 Difficulty: 2 Ans: C A major advance in the application of mass spectrometry to macromolecules came with the development of techniques to overcome which of the following problems? A) B) C) D)

Macromolecules were insoluble in the solvents used in mass spectrometry. Mass spectrometric analyses of macromolecules were too complex to interpret. Mass spectrometric analysis involved molecules in the gas phase. Most macromolecules could not be purified to the degree required for mass spectrometric analysis. E) The specialized instruments required were prohibitively expensive.

37. Protein sequences and evolution Pages: 102–106 Difficulty: 3 Ans: A Compare the following sequences taken from four different proteins, and select the answer that best characterizes their relationships. A B C 1 DVEKGKKIDIMKCS HTVEKGGKHKTGPNLH GLFGRKTGQAPGYSYT 2 DVQRALKIDNNLGQ HTVEKGAKHKTAPNVH GLADRIAYQAKATNEE 3 LVTRPLYIFPNEGQ HTLEKAAKHKTGPNLH ALKSSKDLMFTVINDD 4 FFMNEDALVARSSN HQFAASSIHKNAPQFH NLKDSKTYLKPVISET

A) Based only on sequences in column B, protein 4 reveals the greatest evolutionary divergence. B) Comparing proteins 1 and 2 in column A reveals that these two proteins have diverged the most throughout evolution. C) Protein 4 is the protein that shows the greatest overall homology to protein 1. D) Proteins 2 and 3 show a greater evolutionary distance than proteins 1 and 4. E) The portions of amino acid sequence shown suggest that these proteins are completely unrelated.

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Chapter 3 Amino Acids, Peptides, and Proteins

Short Answer Questions 38. Amino acids Page: 72 Difficulty: 1 What are the structural characteristics common to all amino acids found in naturally occurring proteins? Ans: All amino acids found in naturally occurring proteins have an  carbon to which are attached a carboxylic acid, an amine, a hydrogen, and a variable side chain. All the amino acids are also in the L configuration. 39. Amino acids Page: 75 Difficulty: 1 Only one of the common amino acids has no free -amino group. Name this amino acid and draw its structure. Ans: The amino acid L-proline has no free -amino group, but rather has an imino group formed by cyclization of the R-group aliphatic chain with the amino group (see Fig. 3-5, p. 79). 40. Amino acids Pages: 74–77 Difficulty: 2 Briefly describe the five major groupings of amino acids. Ans: Amino acids may be categorized by the chemistry of their R groups: (1) nonpolar aliphatics; (2) polar, uncharged; (3) aromatic; (4) positively charged; (5) negatively charged. (See Fig. 3-5, p. 79.) 41. Amino acids Pages: 73–75

Difficulty: 2

A B C D E __________________________________________________________________ Tyr-Lys-Met Gly-Pro-Arg Asp-Trp-Tyr Asp-His-Glu Leu-Val-Phe Which one of the above tripeptides: ____(a) is most negatively charged at pH 7? ____(b) will yield DNP-tyrosine when reacted with l-fluoro-2,4-dinitrobenzene and hydrolyzed in acid? ____(c) contains the largest number of nonpolar R groups? ____(d) contains sulfur? ____(e) will have the greatest light absorbance at 280 nm? Ans: (a) D; (b) A; (c) E; (d) A; (e) C

Chapter 3 Amino Acids, Peptides, and Proteins

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42. Amino acids Pages: 73–75 Difficulty: 2 Draw the structures of the amino acids phenylalanine and aspartate in the ionization state you would expect at pH 7.0. Why is aspartate very soluble in water, whereas phenylalanine is much less soluble? Ans: Aspartate has a polar (hydrophilic) side chain, which forms hydrogen bonds with water. In contrast, phenylalanine has a nonpolar (hydrophobic) side chain. (See Fig. 3-5, p. 79 for structures.) 43. Amino acids Pages: 77–78 Difficulty: 3 Name two uncommon amino acids that occur in proteins. By what route do they get into proteins? Ans: Some examples are 4-hydroxyproline, 5-hydroxylysine, -carboxyglutamate, N-methyllysine, desmosine, and selenocysteine. Uncommon amino acids in proteins (other than selenocysteine) usually result from chemical modifications of standard amino acid R groups after a protein has been synthesized. 44. Amino acids Pages: 78–79 Difficulty: 1 Why do amino acids, when dissolved in water, become zwitterions? Ans: Near pH = 7, the carboxylic acid group (—COOH) will dissociate to become a negatively charged —COO– group, and the —NH2 amino group will attract a proton to become a positively charged —NH3+ group. 45. Amino acids Page: 79 Difficulty: 1 As more OH– equivalents (base) are added to an amino acid solution, what...