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Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure Multiple Choice Questions 1) Which of the following is true regarding the -carbon of an amino acid? A) there are always four different functional groups attached B) the most commonly occurring form of amino acids are the D-amino acids C) when assigning the R-S stereochemistry, the carboxylic acid is always the highest priority functional group D) for all amino acids except glycine, the -carbon is a stereocenter E) none of the above Answer: D Difficulty: 1 Topic: Amino Acids 2) At physiological pH, most amino acids are _______, meaning that they contain both a positive and negative charge. A) zwitterions B) amphoteric C) chiral D) amphipathic E) none of the above Answer: A Difficulty: 1 Topic: Amino Acids 3) Which of the following pairs of amino acids contains both an aliphatic and an aromatic amino acid? A) Thr and Tyr B) Val and Gln C) Phe and Ile D) Ser and Cys E) none of the above Answer: C Difficulty: 1 Topic: Amino Acids 1 Copyright © 2013 Pearson Canada, Inc. Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure 4) At a pH of 5, all amino acids have at least ____ charged group(s) and at most, _____ charged group(s). A) 0; B) 1; C) 1; D) 2; E) 2; 1 1 2 2 3 Answer: E Difficulty: 1 Topic: Amino Acids 5) Which of the following pairs of amino acids could form a hydrogen bond through their Rgroups? A) serine and phenylalanine B) aspartic acid and methionine C) histidine and tyrosine D) alanine and glutamine E) leucine and cysteine Answer: C Difficulty: 2 Topic: Amino Acids 6) Which of the following pairs of amino acids could form a charge-charge interaction through their R-groups? A) methionine and histidine B) glutamine and lysine C) serine and glutamic acid D) aspartic acid and arginine E) threonine and asparagine Answer: D Difficulty: 2 Topic: Amino Acids 2 Copyright © 2013 Pearson Canada, Inc. Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure 7) Of the following amino acids, which will have a pI closest to 3? A) Cys B) His C) Gly D) Asp E) Lys Answer: D Difficulty: 2 Topic: Amino Acids 8) Which of the following undergoes an oxidation reaction to form a disulfide bond? A) serine B) cysteine C) methionine D) threonine E) tyrosine Answer: B Difficulty: 1 Topic: Amino Acids 9) Which of the following amino acids is derived from another amino acid by the addition of an amine group? A) lysine B) asparagine C) arginine D) histidine E) none of the above Answer: B Difficulty: 1 Topic: Amino Acids 3 Copyright © 2013 Pearson Canada, Inc. Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure 10) Which of the following amino acids is incorporated into proteins during ribosomal protein synthesis? A) sarcosine B) ornithine C) 4-hydroxyproline D) phosphoserine E) selenocysteine Answer: E Difficulty: 1 Topic: Amino Acids 11) Hydrolysis of a peptide bond produces: A) an alcohol and an amine B) an amine and a carboxylic acid C) a carboxylic acid and an anhydride D) an amide and a carboxylic acid E) an alcohol and an amide Answer: B Difficulty: 1 Topic: Peptides and the Peptide Bond 12) Which of the following bonds has partial double bond character? A) 1 B) 2 C) 3 D) 4 E) 5 Answer: C Difficulty: 1 Topic: Peptides and the Peptide Bond 4 Copyright © 2013 Pearson Canada, Inc. Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure 13) Given the following peptide, what pair of protease enzymes would be able to produce three smaller peptides? Gly-Ser-Ala-His-Phe-Pro-Asn-Ala-Val-Glu-Cys-Ala-Ser A) chymotrypsin and thrombin B) trypsin and chymotrypsin C) thermolysin and chymotrypsin D) trypsin and thermolysin E) none of the above Answer: C Difficulty: 2 Topic: Peptides and the Peptide Bond 14) What is the sequence of the following peptide? A) Ile-Ala-Glu B) Val-Ala-Asp C) Leu-Gly-Glu D) Val-Ala-Asn E) Val-Gly-Gln Answer: B Difficulty: 1 Topic: Peptides and the Peptide Bond 15) If a cis peptide bond is found in a protein, the most likely amino acid to contribute the amine to the amide bond is ______. A) phenylalanine B) leucine C) proline D) glycine E) arginine Answer: C Difficulty: 1 Topic: Peptides and the Peptide Bond 5 Copyright © 2013 Pearson Canada, Inc. Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure 16) Given the following peptide, what would be the overall charge at pH 5? Met-Glu-Ser-Arg-His-Phe-Pro-Asn-Ala-Glu-Cys-Ala-Ser A) +2 B) +1 C) 0 D) -1 E) -2 Answer: C Difficulty: 2 Topic: Peptides and the Peptide Bond 17) The prevalence of the trans orientation in peptide bonds results in the R-groups of adjacent amino acids being oriented approximately ______ degrees with respect to each other. A) 30 B) 60 C) 90 D) 120 E) 180 Answer: E Difficulty: 1 Topic: Peptides and the Peptide Bond 18) The conversion of ________ represents a conservative change while the conversion of ________ represents a nonconservative change. A) Asp to Arg; Ile to Ser B) Tyr to Phe; Lys to Arg C) Gln to Asn; Ser to Thr D) Ile to Leu; Asn to Ala E) Cys to His; Lys to Glu Answer: D Difficulty: 2 Topic: Proteins: Polypeptides of Defined Sequence 6 Copyright © 2013 Pearson Canada, Inc. Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure 19) The peptide hormone insulin is composed of two peptide held together primarily by what mechanism? A) disulfide bonds between cysteine residues B) charge-charge interactions between acidic and basic amino acids C) extensive hydrogen bonding due to the relatively high serine and glutamine content D) hydrophobic interactions E) an amide bond formed from the R-groups of a glutamic acid residue and a lysine residue Answer: A Difficulty: 1 Topic: Proteins: Polypeptides of Defined Sequence 20) Which of the following events occurs after the formation of disulfide bonds during the conversion of preproinsulin to mature insulin? A) folding of proinsulin into a stable conformation B) transport of the molecule through the membranes C) cleavage of the peptide sequence that joins the A and B chains D) cleavage of the leader sequence E) posttranslational modification of specific proline residues Answer: C Difficulty: 1 Topic: From Gene to Protein 21) Which of the following pairs of amino acids represents a conservation of the type of amino acid when considering the sequence of a protein from different species? A) Asp and Asn B) Lys and His C) Leu and Val D) Gly and Ile E) Phe and Trp Answer: C Difficulty: 2 Topic: Protein Sequence Homology 7 Copyright © 2013 Pearson Canada, Inc. Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure 22) In the sequence of cytochrome c, the presence of cysteine at position 17 in hundreds of different species indicates that this particular amino acid is _________. A) conserved B) mutated C) homologous D) variable E) none of the above Answer: A Difficulty: 1 Topic: Protein Sequence Homology 8 Copyright © 2013 Pearson Canada, Inc. Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure Short Answer Questions 1) What is the pI for the following peptide: Ala-Glu-Val-Asp-Lys-Leu Answer: Use R-groups of Glu and Asp: (4.2 + 3.9)/2 = 4.05 (4.1 using correct SF) Difficulty: 1 Topic: Amino Acids 2) Draw each of the structures of aspartic acid that predominate at pH 1, 3, 7, and 11. Answer: 1 Difficulty: 2 3 7 Topic: Amino Acids 9 Copyright © 2013 Pearson Canada, Inc. 11 Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure 3) A peptide was treated with protease enzymes and cyanogen bromide followed by complete hydrolysis of the resulting products. Based upon the following data, determine the sequence of the original peptide. Chymotrypsin gave two peptides containing the following amino acids: Leu, Pro Asp, Gln, Arg, Met, Tyr, Val Cyanogen bromide gave two peptides containing the following amino acids: Asp, Met Gln, Leu, Arg, Tyr, Pro, Val Trypsin gave two peptides containing the following amino acids: Gln, Leu, Tyr, Pro Asp, Arg, Met, Val Answer: Chymotrypsin treatment shows the C-term 3 amino acids to be Tyr-Pro-Leu Cyanogen bromide treatment shows that the N-term is Asp-Met Trypsin places Arg giving the overall peptide as Asp-Met-Val-Arg-Gln-Tyr-Pro-Leu Difficulty: 3 Topic: Peptides and the Peptide Bond 10 Copyright © 2013 Pearson Canada, Inc.