Chem3303 Chapter 3 Amino Acids, Peptides, and Proteins, Exams of Bioorganic Chemistry

Download Chem3303 Chapter 3 Amino Acids, Peptides, and Proteins and more Exams Bioorganic Chemistry in PDF only on Docsity! 1 Chem3303 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) has no net charge. B) is a carboxylic acid. C) is bonded to four different chemical groups. D) is in the L absolute configuration in naturally occurring proteins. E) 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) alanine; is a simple methyl group B) glycine; is a hydrogen atom C) glycine; is unbranched D) lysine; contains only nitrogen E) 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) cysteine and serine. B) cysteine and threonine. C) methionine and cysteine D) methionine and serine E) 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) amino group. B) carbonyl group. C) carboxyl group. D) ester group. E) thiol group. 2 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) All are strongly hydrophilic. B) Histidine’s ring structure results in its being categorized as aromatic or basic, depending on pH. C) On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine. D) 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) be a fully ionized zwitterion with no net charge. B) be found in proteins as D-selenocysteine. C) never be found in a protein. D) be nonionic. E) 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) acid or a base. B) neutral molecule or an ion. C) polar or a nonpolar molecule. D) standard or a nonstandard monomer in proteins. E) transparent or a light-absorbing compound. 5 18. Peptides and proteins Pages: 82–83 Difficulty: 1 Ans: C At the isoelectric pH of a tetrapeptide: A) only the amino and carboxyl termini contribute charge. B) the amino and carboxyl termini are not charged. C) the total net charge is zero. D) there are four ionic charges. E) 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) Larger proteins have a more uniform distribution of amino acids than smaller proteins. B) Proteins contain at least one each of the 20 different standard amino acids. C) Proteins with different functions usually differ significantly in their amino acid composition. D) Proteins with the same molecular weight have the same amino acid composition. E) 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) a fibrous region of a globular protein. B) a nonidentical subunit of a protein with many identical subunits. C) a part of the protein that is not composed of amino acids. D) a subunit of an oligomeric protein. E) synonymous with “protomer.” 6 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) carbohydrates. B) flavin nucleotides. C) lipids. D) metals . E) 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) conjugate the protein to a known molecule. B) determine its amino acid composition. C) determine its amino acid sequence. D) determine its molecular weight. E) 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 (gel- filtration) chromatography? A) cytochrome c Mr = 13,000 B) immunoglobulin G Mr = 145,000 C) ribonuclease A Mr = 13,700 D) RNA polymerase Mr = 450,000 E) serum albumin 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) determine a protein’s isoelectric point. B) determine an enzyme’s specific activity. C) determine the amino acid composition of the protein. D) preserve a protein’s native structure and biological activity. E) 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) contains a denaturing detergent that can distribute uniform negative charges over the protein’s surface. B) exhibits a stable pH gradient when ampholytes become distributed in an electric field. C) is washed with an antibody specific to the protein of interest. D) neutralizes all ionic groups on a protein by titrating them with strong bases. E) relates the unknown protein to a series of protein markers with known molecular weights, Mr. 7 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) is measured only under optimal conditions. B) is the activity (enzyme units) in a milligram of protein. C) is the activity (enzyme units) of a specific protein. D) refers only to a purified protein. E) 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) Primary structure B) Secondary structure C) Tertiary structure D) Quaternary structure E) 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) Primary structure B) Secondary structure C) Tertiary structure D) Quaternary structure E) None of the above 10 Chapter 3 Amino Acids, Peptides, and Proteins 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. 75). 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. 75.) 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 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. 75 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. 3 3 3 3 a 11 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 —NH + group. 45. Amino acids Page: 79 Difficulty: 1 As more OH– equivalents (base) are added to an amino acid solution, what titration reaction will occur around pH = 9.5? Ans: Around pH = 9.5, the —NH + group will be titrated according to the reaction: —NH + + OH–  —NH2 + H2O. 46. Amino acids Page: 80 Difficulty: 3 In the amino acid glycine, what effect does the positively charged —NH + group have on the pK of an amino acid’s —COOH group? Ans: The positively charged amino group stabilizes the negatively charged ionized form of the carboxyl group, —COO–, and repels the departing H+ thereby promoting deprotonation. The effect is to lower the pKa of the carboxyl group (see Fig. 3-11, p. 80). 47. Amino acids Page: 79 Difficulty: 3 How does the shape of a titration curve confirm the fact that the pH region of greatest buffering power for an amino acid solution is around its pK’s? Ans: In a certain range around the pKa’s of an amino acid, the titration curve levels off. This indicates that for a solution with pH  pK, any given addition of base or acid equivalents will result in the smallest change in pH—which is the definition of a buffer. 48. Amino acids Page: 79 Difficulty: 2 Leucine has two dissociable protons, one with a pKa of 2.3, the other with a pKa of 9.7. Sketch a properly labeled titration curve for leucine titrated with NaOH; indicate where the pH = pK and the region(s) in which buffering occurs. Ans: See the titration curve for glycine in Fig. 3-10, p. 79. 49. Amino acids Page: 80 Difficulty: 2 What is the pI, and how is it determined for amino acids that have nonionizable R groups? Ans: The pI is the isoelectric point. It occurs at a characteristic pH when a molecule has an equal number of positive and negative charges, or no net charge. For amino acids with nonionizable R 12 Chapter 3 Amino Acids, Peptides, and Proteins groups, pI is the arithmetic mean of a molecule’s two pKa values: pI = 1/2 (pK1 + pK2) 50. Amino acids Page: 80 Difficulty: 2 The amino acid histidine has a side chain for which the pKa is 6.0. Calculate what fraction of the histidine side chains will carry a positive charge at pH 5.4. Be sure to show your work. [conjugate base] Ans: pH = pKa + log [acid] pKa – pH = log [acid] [conjugate base] [acid] antilog (pKa – pH) = [conjugate base] [acid] antilog (6.0 – 5.4) = [conjugate base] 4 = [acid]/[conjugate base], or 4[conjugate base] = [acid] Therefore, at pH 5.4, 4/5 (80%) of the histidine will be in the protonated form. 51. Amino acids Page: 80 Difficulty: 2 The amino acid histidine has three ionizable groups, with pKa values of 1.8, 6.0, and 9.2. (a) Which pKa corresponds to the histidine side chain? (b) In a solution at pH 5.4, what percentage of the histidine side chains will carry a positive charge? Ans: (a) 6.0; (b) 80%. (See the previous problem for expanded solution to this problem.) 52. Amino acids Page: 81 Difficulty: 2 What is the uniquely important acid-base characteristic of the histidine R group? Ans: Only the imidazole ring of the histidine R group has a pKa near physiological pH (pKa = 6.0), which suggests that histidine may provide buffering power in intercellular and intracellular fluids. 53. Peptides and proteins Page: 82 Difficulty: 1 How can a polypeptide have only one free amino group and one free carboxyl group? Ans: This is possible only if the peptide has no side chains with carboxyl or amino groups. Then, with the exception of the single amino-terminal amino acid and the single carboxyl-terminal amino acid, all the other -amino and carboxyl groups are covalently condensed into peptide bonds. 15 63. Working with proteins Pages: 90-91 Difficulty: 2 How can isoelectric focusing be used in conjunction with SDS gel electrophoresis? Ans: Isoelectric focusing can separate proteins of the same molecular weight on the basis of differing isoelectric points. SDS gel electrophoresis can then separate proteins with the same isoelectric points on the basis of differing molecular weights. When combined in two-dimensional electrophoresis, a great resolution of large numbers of proteins can be achieved. 64. Working with proteins Pages: 91-92 Difficulty: 3 You are given a solution containing an enzyme that converts B into A. Describe what you would do to determine the specific activity of this enzyme solution. Ans: First, add a known volume of the enzyme solution (say, 0.01 mL) to a solution of its substrate B and measure the initial rate at which product A is formed, expressed as mol/mL of enzyme solution/min. Then measure the total protein concentration, expressed as mg/mL. Finally, divide the enzyme activity (mol/min/mL) by the protein concentration (mg/mL); the quotient is the specific activity. 65. Working with proteins Pages: 91-92 Difficulty: 2 As a protein is purified, both the amount of total protein and the activity of the purified protein decrease. Why, then, does the specific activity of the purified protein increase? Ans: Specific activity is the units of enzyme activity (mol of product/min) divided by the amount of protein (mg). As the protein is purified, some of it is lost in each step, resulting in a drop in activity. However, other contaminating proteins are lost to a much greater extent. Therefore, with each purification step, the purified protein constitutes a greater proportion of the total, resulting in an increase in specific activity. (See also Table 3-5, p. 88.) 66. Peptides and proteins Page: 84 Difficulty: 1 Define the primary structure of a protein. Ans: The primary structure of a protein is its unique sequence of amino acids and any disulfide bridges present in the native structure, that is, its covalent bond structure. 67. The covalent structure of proteins Pages: 94-100 Difficulty: 2 In one or two sentences, describe the usefulness of each of the following reagents or reactions in the analysis of protein structure: (a) Edman reagent (phenylisothiocyanate) (b) Sanger reagent (1-fluoro-2,4-dinitrobenzene, FDNB) (c) trypsin Ans: (a) used in determination of the amino acid sequence of a peptide, starting at its amino terminus; (b) used in determination of amino-terminal amino acid of a polypeptide; (c) used to produce specific peptide fragments from a polypeptide. 16 Chapter 3 Amino Acids, Peptides, and Proteins 68. The covalent structure of proteins Pages: 96-97 Difficulty: 2 A polypeptide is hydrolyzed, and it is determined that there are 3 Lys residues and 2 Arg residues (as well as other residues). How many peptide fragments can be expected when the native polypeptide is incubated with the proteolytic enzyme trypsin? Ans: Six fragments would be expected, unless the carboxyl-terminal residue is Lys or Arg, in which case there would be five. 69. The covalent structure of proteins Pages: 94-95 Difficulty: 2 The following reagents are often used in protein chemistry. Match the reagent with the purpose for which it is best suited. Some answers may be used more than once or not at all; more than one reagent may be suitable for a given purpose. (a) CNBr (cyanogen bromide) (e) performic acid (b) Edman reagent (phenylisothiocyanate) (f) chymotrypsin (c) FDNB (g) trypsin (d) dithiothreitol hydrolysis of peptide bonds on the carboxyl side of Lys and Arg cleavage of peptide bonds on the carboxyl side of Met breakage of disulfide (—S—S—) bonds determination of the amino acid sequence of a peptide determining the amino-terminal amino acid in a polypeptide Ans: g; a; d and e; b; c 70. The covalent structure of proteins Pages: 94-97 Difficulty: 2 A biochemist wishes to determine the sequence of a protein that contains 123 amino acid residues. After breaking all of the disulfide bonds, the protein is treated with cyanogen bromide (CNBr), and it is determined that that this treatment breaks up the protein into seven conveniently sized peptides, which are separated from each other. It is your turn to take over. Outline the steps you would take to determine, unambiguously, the sequence of amino acid residues in the original protein. Ans: (1) Use Edman degradation to determine the sequence of each peptide. (2) Create a second set of peptides by treatment of the protein with a specific protease (for example, trypsin), and determine the sequence of each of these. (3) Place the peptides in order by their overlaps. (4) Finally, by a similar analysis of the original protein without first breaking disulfide bonds, determine the number and location of —S—S— bridges. 71. The covalent structure of proteins Pages: 94-97 Difficulty: 3 You are trying to determine the sequence of a protein that you know is pure. Give the most likely explanation for each of the following experimental observations. You may use a simple diagram for your answer. (a) The Sanger reagent (FDNB, fluorodinitrobenzene) identifies Ala and Leu as amino- terminal residues, in roughly equal amounts. (b) Your protein has an apparent Mr of 80,000, as determined by SDS-polyacrylamide gel electrophoresis. After treatment of the protein with performic acid, the same 17 technique