chapter 6 questions.pdf

Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 X? b. What type of separation technique can be used to separate protein NPBP-1 from protein Y? c. What type of separation technique can be used to separate protein NPBP-1 from protein Z? Ans:...

Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 X? b. What type of separation technique can be used to separate protein NPBP-1 from protein Y? c. What type of separation technique can be used to separate protein NPBP-1 from protein Z? Ans: a. On a size (mass) basis: gel permeation chromatography, SDS-PAGE, or ultracentrifugation. b. On a charge basis: ion exchange chromatography or isoelectric focusing c. On a binding behavior basis: phosphotyrosine affinity chromatography Level of Difficulty: Moderate Section: 5.2C Learning objective: Protein Purification and Analysis 183 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 69. You have purified the receptor for a hormone by affinity chromatography. During gel filtration chromatography under native conditions the receptor elutes between pyruvate decarboxylase (250 kDa) and glutamine synthetase (620 kDa). During SDS-PAGE, in the absence of reducing agents, the receptor migrates as a single band of approximately 230 kDa. When SDS-PAGE is carried out in the presence of 2-mercaptoethanol the receptor migrates as two bands of approximately 95 and 135 kDa. Explain this result. Ans: The receptor is a heterotetramer composed of two subunits of 95 kDa and two subunits of 135 kDa. Heterodimers of one subunit and one subunit are stabilized by disulfide bonds. Two heterodimers are held together by hydrophobic interactions. In the absence of detergents during gel filtration all subunits stay together and we observe a 460 kDa protein. During SDS-PAGE (in the absence of reducing agents) SDS interferes with the hydrophobic interactions that hold the two dimers together and we observe a 230 kDa protein. Finally, when we add 2-mercaptoethanol during SDS-PAGE the disulfide bonds are broken and we observe 2 polypeptides of 135 and 95 kDa. Level of Difficulty: Moderate Section: 5.2D Learning objective: Protein Purification and Analysis Chapter 6: Proteins: Three-Dimensional Structure Matching 184 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 For questions 1-10: A) tertiary structure B) keratin C) molecular chaperones D) hydropathy E) cis F) trans G) sterically forbidden conformation H) regular secondary structure I) collagen J) peptide bond K) ribonuclease A (RNase A) L) alpha 1. Repeating values of and make up predictable orientations of amino acid with a chain, this predictable orientation forms. Ans: H Level of Difficulty: Easy Section 6.1.B Learning objective: Secondary Structure 2. The strength of comes from close packing of glycine residues and the characteristics of hydroxyproline allowing formation of a left- handed helical conformation which combines with two other left handed structures to form a right-handed triplet helix. Ans: I 185 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 Level of Difficulty: Easy Section 6.1.C Learning Objective: Secondary Structure 3. The overall arrangement of the regular structural elements such as the helix and the sheet in the protein are considered the protein's. Ans: A Level of Difficulty: Easy Section 6.2.C Learning Objective: Tertiary Structure 4. - mercaptoethanol reduction of disulfide b - mercaptoethanol was carried out using the protein. This experiment demonstrated the importance of disulfide bonds and amino acid sequence in folding of proteins. Ans: K Level of Difficulty: Easy Section 6.4.B Learning Objective: Protein Stability 5. A rigid, planar structure between at least two amino acids consisting of about 40% double bond character is characteristic of a. Ans: J Section 6.1.A Level of Difficulty: Easy 186 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 Learning Objective: Primary Structure 6. The of an amino acid can be used to predict whether an amino acid side chain folds towards the inside or outside of a globular protein. Ans: D Level of Difficulty: Easy Section 6.2.B Learning Objective: Tertiary Structure 7. is a fibrous protein that contains a hydrophobic amino acid approximately every 4 residues which helix with one hydrophobic side. Ans: B Level of Difficulty: Easy Section 6.1.C Learning Objective: Secondary Structure 8. In most peptide groups the conformation is not sterically favored. Ans: EF Level of Difficulty: Easy Section 6.1.A Learning Objective: Secondary Structure 187 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 9. In vivo protein folding is often is assisted by. Ans: C Level of Difficulty: Easy Section 6.5.B Learning Objective: Protein Folding 10. In a , the and angles of the peptide backbone would orient atoms closer than their van der Waals distance. Ans: G Level of Difficulty: Moderate Section 6.1.A Learning Objective: Secondary Structure Multiple Choice 11. In a Ramachandran diagram, a larger area represents sterically allowed torsion angles of and that are allowed in rather than in because there is greater opportunity for separation of amino acid side chains. A) secondary structure B) C) helix D) tertiary struc structure 188 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 E) none of the above Ans: C Level of Difficulty: Difficult Section 6.1.A and B Learning Objective: Secondary Structure 12. In a protein, the most conformationally restricted amino acid is ; the least conformationally restricted is. A) Trp, Gly B) Met, Cys C) Pro, Gly D) Ile, Ala E) Ala, Pro Ans: C Level of Difficulty: Moderate Section 6.1.A Learning Objective: Secondary Structure 13. Which of the following has (have) both a favorable hydrogen bonding pattern and and values that fall within the allowed Ramachandran conformational regions? A) helix B) collagen helix C) sheet D) all of the above 189 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 E) none of the above Ans: D Level of Difficulty: Moderate Section 6.1.A, B, and C Learning Objective: Secondary Structure 14. Which one of these characteristics is not true for the helix? A) There are 3.6 amino acids per turn. B) There is a requirement for glycine every third amino acid residue. C) A hydrogen bond forms between the carbonyl oxygen of the nth amino acid residue and the - NH group of the (n + 4)th amino acid residue. D) Proline is typically not found in the helix. E) It is right-handed. Ans: B Level of Difficulty: Easy Section 6.1.B Learning Objective: Secondary Structure 15. Which of these characteristics does not describe the sheet? A) Amino acid side chains are located both above and below the sheet. B) sheets have a pleated edge-on appearance. C) They can exist in either parallel or antiparallel configurations. D) The sheets contain as few as two and as many as 22 polypeptide chains. 190 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 E) Parallel sheets containing fewer than five chains are the most common. Ans: E Level of Difficulty: Moderate Section 6.1.B Learning Objective: Secondary Structure 16. Which statement below does not describe fibrous proteins? A) Domains have a globular fold. B) These proteins usually contain only one type of secondary structure. C) These proteins usually exhibit structural or protective characteristics. D) These proteins have usually elongated hydrophilic surfaces. E) These proteins are usually insoluble in water. Ans: A Level of Difficulty: Moderate Section 6.1.C Learning Objective: Secondary Structure 17. Which of the following changes would not keratin? 191 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 A) Increasing the number of residues per turn to 4.1 while maintaining the same amino acid sequence. B) Substitution of a hydrophilic amino acid for a hydrophobic amino acid at position a and d of the 7-residue pseudorepeat. C) Decreasing the number of cysteine amino acids within each protofilament. D) Changing the environment surrounding the protein to one that is more reductive. E) All of the above would alter the functional characteristics of keratin. Ans: E Level of Difficulty: Difficult Section 6.1.C Learning Objective: Secondary Structure 18. Which of the following statements is true regarding collagen? A) The inability to hydroxylate proline results in the inability to synthesize collagen. B) The helical structure is ideal for intertwining 3 filaments. C) Hydrogen bonds between groups of Hyp residues stabilize the helix. D) The requirement for glycine every 3rd amino acid is essential for the triplet helix formation. E) On average, there is one proline for every hydroxyproline. Ans: D Level of Difficulty: Difficult Section 6.1.C Learning Objective: Secondary Structure 192 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 19. Which of the following gives the best example of a nonrepetitive structure in a protein? A) a random sequence of 12 amino acids with high P values forming an helix B) an amino acid sequence with the following pattern -b-c-d-e-a-b-c-d-a-b-c- C) position n+10 D) All of the above statements describe nonrepetitive protein structures. E) None of the above describe nonrepetitive protein structures. Ans: C Level of Difficulty: Difficult Section 6.1.D Learning Objective: Secondary Structure 20. Which of the following is true regarding crystalline proteins? A) Many crystallized enzyme proteins remain catalytically active. B) The diffractive pattern observed during X-ray exposure to the crystal can be used to calculate the electron density map of the crystalline protein. C) The larger region indicating electron density with in the electron density map, the more accurate the structure determination. D) A and B are true. E) A, B, and C are true. 193 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 Ans: D Level of Difficulty: Moderate Section 6.2.A Learning Objective: Tertiary Structure 21. In the absence of ascorbic acid, prolyl oxidase is unable to oxidize proline residues in collagen to hydroxyproline, resulting in: A) lathyrism B) prion diseases C) amyloid formation D) scurvy E) allysine Ans: D Level of Difficulty: Easy Section 6.5.C Learning Objective: Protein Folding 22. Of the following, which keratin? A) Phe B) Ala 194 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 C) Lys D) Trp E) Pro Ans: B Level of Difficulty: Moderate Section 6.2.B and 6.1.C Learning Objective: Tertiary Structure and Secondary Structure 23. Which of the following amino acids combinations have side chains with groups that have the greatest ability to stabilize the tertiary structure of a protein? A) Lys and Arg B) Cys and Glu C) Glu and Lys D) Gln and Glu E) Pro and Asp Ans: C Level of Difficulty: Difficult Section 6.4.A Learning Objective: Protein Stability 24. The low pH found in the gut can enhance the digestibility of dietary protein by causing. A) amide hydrolysis B) protein denaturation 195 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 C) disulfide reduction D) prion formation E) cysteine oxidation Ans: B Level of Difficulty: Moderate Section 6.4.B Learning Objective: Protein Stability 25. Which of the following occurs first when folding a disordered polypeptide chain into a stable protein formation? A) formation of a low energy state B) association of ordered subunits C) aggregation of hydrophobic regions in the protein D) tertiary structure refinement E) formation of a low entropy state Ans: C Level of Difficulty: Moderate Section 6.5.A 196 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 Learning Objective: Protein Folding 26. Imagine that a researcher treated a protein with a high concentration of a chaotropic agent. Which of the following is the most likely result of the treatment? I. Nonpolar portions of the protein become more soluble. II. The protein begins to denature , III. The protein stability increases due to hydrophobic collapse, A) I, II, III B) I, II C) II, III D) I, III E) II Ans: B Level of Difficulty: Difficult Section 6.4.B and 6.5.A Learning Objective: Protein Folding 27. For -sheets, the terms and refer to. A) the of the associated peptide strands B) the orientation of the amide cross-links C) the quaternary structure of the protein D) the orientation of the hydrogen bonding D) the topology of the reverse turns 197 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 Ans: A Level of Difficulty: Easy Section 6.1.B Learning Objective: Secondary Structure 28. In general molecular chaperone proteins function by A) mediating disulfide bond formation B) synthesizing new proteins when one is misfolded. C) preventing premature folding by binding hydrophobic regions of the protein. D) enhancing salt bridge formation. E) none of the above Ans: C Level of Difficulty: Moderate Section 6.5.B Learning Objective: Protein Folding 29. Conventional one dimensional NMR spectroscopy is not generally an effective tool for determination of protein I. Proteins (including small proteins) have a high number of hydrogen atoms. II. NMR requires a high quality protein crystal. III. The NMR spectra exhibit high peak overlap. A) I and II 198 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 B) II and III C) I and III D) I, II, and III E) III only Ans: C Level of Difficulty: Moderate Section 6.2.A Learning Objective: Tertiary Structure 30. When comparing similarities among multiple protein structures, which of the following is false? A) Proteins with the same function from a different species are likely to have similar motifs. B) Proteins with the same function from different species are likely to be more similar in sequence than in structure. C) An effective protein motif isl likely be observed in multiple proteins. D) Proteins with the same motifs are likely to perform similar functions. E) None of the above statements are false. Ans: B Level of Difficulty: Difficult Section 6.2.C Learning Objective: Tertiary Structure 31. The structure and sequence of a protein of unknown function was examined. Which of the following provides the best prediction of the protein's function? 199 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 A) the observation of several disordered helical domains. B) the observation of multiple protein subunits. C) the observation of motif known as the Rossmann fold. D) the observation of a large number of random coil regions. E) All of the above offer excellent prediction of the protein's function. Ans: C Level of Difficulty: Difficult Section 6.2.C Learning Objective: Tertiary Structure 32. The Protein Data Bank (PDB) is a database provides structural information about proteins that may be useful for which of the following? I. A researcher studying the changes in protein fold associated with prions. II. A researcher classifying structural elements by function. III A researcher designing a compound to bind tightly to a particular region in the protein. A) I only B) II only C) III only D) I, II E) I, II, II Ans: E Level of Difficulty: Moderate Section 6.2.E 200 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 Learning Objective: Tertiary Structure 33. Noncovalent forces that stabilize protein structure include all of the following except. A) the hydrophobic effect B) salt bridges C) electrostatic interactions with metal ions D) hydrogen bonding E) disulfide bridges Ans: E Level of Difficulty: Easy Section 6.4.A Learning Objective: Protein Stability 34. The classic experiment demonstrating that reduced and denatured RNase A could refold into the native form demonstrates that. A) 1° structure can determine 3° structure B) denaturation does not disrupt protein 2° structure C) disulfide bonds do not stabilize folded proteins D) All of the above. E) None of the above Ans: A Level of Difficulty: Moderate Section 6.4.B 201 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 Learning Objective: Protein Stability 35. The first step in the folding of disordered polypeptides into ordered functional protein is the formation of _. A) 1o structure B) 2° structure C) 3° structure D) 4° structure E) hydrogen bonds Ans: B Level of Difficulty: Easy Section 6.5.A Learning Objective: Protein Folding 36. Evolutionary processes have A) increased the stability of 4° structures. B) decreased the number of subunits. C) increased similarity amount 1° structures. D) enhanced efficient folding pathways. E) all of the above Ans: D Level of Difficulty: Moderate Section 6.5.A Learning Objective: Protein Folding 202 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 37. Chaperonins such as the GroEL/ES system A) function with thermophilic proteins only. B) are required at low pH. C) require ATP hydrolysis. D) in vitro only. E) function in a nonaqueous environment. Ans: C Level of Difficulty: Moderate Section 6.5.B Learning Objective: Protein Folding 38. Protein diseases can be caused by which of the following A) mutations affecting the 1° structure. B) mutations affecting the 3° structure. C) changes in the post-synthetic processing of proteins. D) All of the above are potential causes. E) None of the above are potential causes. 203 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 Ans: D Level of Difficulty: Difficult Section 6.5.C Learning Objective: Protein Folding 39. Which of the following would be most stable based on the information you have learned about protein structure? A) a loop region with 8 amino acids B) a region made up of amino acids Val, Ile, Phe C) an helix made up of Cys, Pro, and Phe D) a with 12 amino acids E) All have equal stability. Ans: B Level of Difficulty: Difficult Section 6.1.D Learning Objective: Secondary Structure 40. The structure of hen egg white protein has been solved and the torsion angles and 204 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 are shown for each residue in the table below. What structure motif most likely forms as a result of this protein sequence? Residue Number 31 -61 -44 32 -72 -29 33 -66 -65 34 -67 -23 35 -81 -51 Break Break Break 42 -30 142 43 -142 150 44 -154 121 45 -91 136 46 -110 174 A) strand connected to another with a break (or loop/turn) in between B) Helix connect to another Helix with a break (or loop/turn) in between C) connected to another with a alpha helix in between D) Helix connected to with a break (or loop/turn) in between E) None of the above are correct. Ans: D Level of Difficulty: Moderate Section 6.1.A Learning Objective: Secondary Structure 205 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 41. Hydrogen bonds and maximum separation of amino acid side chains make the very stable and energetically. A) helix and sheet, favorable B) helix, unfavorable C) sheet, unfavorable D) helix, favorable E) sheet, favorable Ans: A Level of Difficulty: Moderate Section 6.1.B Learning Objective: Secondary Structure 42. A chaperonin A) helps fold some proteins in their lowest energy state. B) is required for all proteins to fold properly. C) mediates the unfolding of proteins. D) is required for protein denaturation. E) counteracts the laws of thermodynamics. Ans: A Level of Difficulty: Moderate 206 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 Section 6.5.B Learning Objective: Protein Folding 43. amino group of residue which of the following is TRUE? A) It has 3.6 residues per turn. B) It is a random coil, not a helix. C) It is an helix. D) It has more residues per turn than an helix. E) It has fewer residues per turn than helix. Ans: D Level of Difficulty: Difficult Section 6.1.B Learning Objective: Secondary Structure 44. Which of the following contribute to the minimization of energy that occurs with protein folding? A) orientating amino acid groups to maximize hydrogen bonding B) folding hydrophobic groups towards the exterior of the protein C) burying polar groups towards the interior of the protein D) extensive cavity formation E) all of the above Ans: A Level of Difficulty: Moderate 207 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 Section 6.5.A Learning Objective: Protein Folding 45. Which of the following best describes the cause of Creutzfeld-Jakob Disease (a disease which human can develop with symptoms similar to those of mad cow disease)? A) aggregation of a misfolded protein. B) aggregation of random coil regions on a protein. C) ingestion of ammonium salts. D) the serious side effects of experimental treatment with Quinacrine E) All are potential causes Creutzfeld-Jakob disease. Ans: A Level of Difficulty: Difficult Section 6.5.C Learning Objective: Protein Folding 46. Which of the following lines in the figure at right indicates a hairpin structure? A) A, C, D 208 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 B) B and C C) A only D) A, B, and D E) C only Ans: D Level of Difficulty: Easy Section 6.1.C Learning Objective: Secondary Structure 47. Proteins can denature due to a change in A) pH. B) temperature. C) ionic strength. D) all of the above E) none of the above Ans: D Level of Difficulty: Easy Section 6.4.A-C Learning Objective: Protein Stability 209 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 48. Examine the three sequences below for collagen-like proteins. If hydrogen bonding were the most important feature in determining strength in fibrous proteins, which of the following sequences likely has the highest melting temperature and why? (Note: Flp = fluoroproline; Hyp = hydroxyproline) I. Pro-Hyp-Gly-Pro-Hyp-Gly-Pro-Hyp-Gly II. Pro-Flp-Gly-Pro-Flp-Gly-Pro-Flp-Gly III. Gly-Pro-Thr-Gly-Pro-Thr-Gly-Pro-Thr A) because Hyp has OH groups B) because the electronegativity of oxygen is greater C) because the electronegativity of proline is greater D) because the electronegativity of the OH group increases hydrogen bond strength E) because Thr is a small amino acid which allows close packing Ans: A Level of Difficulty: Difficult Section 6.1.C and 6.4.A-C Learning Objective: Protein Stability and Secondary Structure 49. Based on what you know about fibrous protein structure and sequence, what type of fibrous protein is this sequence most likely to from (You can assume that the protein is longer than what is shown and is repeating as shown, also note the polarity of each amino acid.)? Val Cys Lys Val - Cys Ala Cys - Val Cys Lys Val - Cys Ala Cys A) keratin 210 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 B) C) collagen D) pleated collagen E) This sequence cannot be from any of the structural proteins. Ans: A Level of Difficulty: Difficult Section 6.1.C Learning Objective: Secondary Structure 50. Which of the following structural proteins has the greatest elasticity? A) keratin B) ketatin C) collagen D) pleated collagen E) A and B are equal 211 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 Ans: D Level of Difficulty: Difficult Section 6.1.C Learning Objective: Secondary Structure 51. Noncovalent interactions account for the strength of which of the following structural proteins? A) keratin B) collagen C) pleated collagen D) A and B E) B and C Ans: B Level of Difficulty: Moderate Section 6.1.C Learning Objective: Secondary Structure 52. Examine the three sequences below for collagen-like proteins and their melting temperatures (Tm). (Note: Flp = fluoroproline; Hyp = hydroxyproline) Based on this data, what is the most important feature in determining the strength of the collagen protein? 1) -Pro-Hyp-Gly-Pro-Hyp-Gly-Pro-Hyp-Gly- Tm=60oC 2) -Pro-Flp-Gly-Pro-Flp-Gly-Pro-Flp-Gly- Tm=78oC 3) -Gly-Pro-Thr-Gly-Pro-Thr-Gly-Pro-Thr- Tm=30oC A) hydrogen bonding 212 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 B) inductive effect C) electrostatic effect D) electrostatic and Inductive effect are equal E) hydrogen bonding and inductive effect are equal Ans: B Level of Difficulty: Difficult Section 6.1.C, Chapter Supplement: Case 6 (Note to instructor: the text does not use the term inductive, the case does if you have not assigned the case, you may want to consider whether your students should be expected to know the term inductive.) Learning Objective: Secondary Structure; Chapter Supplement: Case 6 53. When considering fibrous proteins, which of the following statements is TRUE? A) Noncovalent interactions contribute to the strength of all of these proteins. B) All of them consist of helix structure. C) All of them require vitamin C. D) Decrease in amounts of any of them cause scurvy. E) All of these are true of fibrous proteins. Ans: A Level of Difficulty: Easy Section 6.1.C Learning Objective: Secondary Structure 54. In a Ramachandran diagram the region representing the angles of and that correspond to those commonly made by an amino acid that favors a left-handed helix are different from those angles commonly made by an amino acid that favors right-handed helix formation. Which of the following statements provides a plausible explanation for 213 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 this difference? A) Groups which would normally undergo high steric hindrance in the right-handed arrangement are separated maximally in the left-handed arrangement. B) Left-handed helices have smaller pitch than right-handed helices. C) The peptide backbone can coil tighter in the left-handed helices than in the right- handed helices. D) Left-handed helices exhibit cyclic symmetry, while righthanded helices are asymmetric. E) All of the above are plausible explanations. Ans: A Level of Difficulty: Difficult Section 6.1.A Learning Objective: Secondary Structure 55. Which of the characteristics of collagen structure listed below contrubute to the tensi le strength of collagen? I. Collagen is made up of a triplet helix where 3 left-handed helices twist together in a right handed sense. II. Collagen includes at repeating sequence of amino acids with glycine every 3 amino acids in a helix with about 3 amino acids per turn. III. The three left-handed helices are staggered to allow close packing between glycine residues and rigidity from the bulky and inflexible proline/hydroxyproline. A) I B) I and II C) I, II, and III 214 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 D) II and III E) I and III Ans: C Level of Difficulty: Difficult Section 6.1.C Learning Objective: Secondary Structure 56. Native protein purifications often require multiple reaction steps in order to purify the protein of interest from other proteins. One method used for protein separation in purification procedures is a change from water to an organic solvent. Which of the following would be accomplished by this solvent change? A) Proteins with hydrophobic groups on the interior would maintain their native state. B) Proteins with hydrophilic groups on the exterior would denature and likely precipitate. C) Proteins with exposed hydrophobic groups would maintain their structure and remain in solution. D) Both A and B would occur. E) Both B and C would occur. Ans: E Level of Difficulty: Difficult Section 6.4.A Learning Objective: Protein Stability 57. When solving a protein structure using X-ray crystallography, the crystallographer generates a 3-D grid called an electron density map based on the observed diffraction 215 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 pattern. The higher the resolution, the more detailed the electron density map and therefore the easier it is to identify what atoms (and therefore what amino acids) are in a given position. Based on the three choices below, in which of the following groups could the two of amino acids be the easiest to differentiate regardless of resolution? I. Leucine vs. Isoleucine II. Phenylalanine vs. Alanine III. Glutamate vs. Glutamic acid A) Those in both groups I and II could be differentiated B) Those in both groups I and III could be differentiated C) Only those in group II could be differentiated D) Only those in group III could be differentiated E) Only those in groupI could be differentiated Ans: C Level of Difficulty: Difficult Section 6.2.A Learning Objective: Tertiary Structure 58. Protein dynamics is a field of study that examines the movements with in a protein. Which type of protein structure determination would be most useful to study this type of change? A) X-ray crystallography B) Nuclear Magnetic Resonance (NMR) C) X-ray absorption spectroscopy D) A and B E) B and C 216 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?  Stuvia.com - The Marketplace to Buy and Sell your Study Material 2016 Ans: B Level of Difficulty: Difficult Section 6.2.A Learning Objective: Tertiary Structure 59. What observation about protein refolding or renaturation helped to solidify the connection between primary amino acid sequence and 3-D structure? A) Spontaneous refolding of proteins into their native state under physiologic conditions. B) Assisted refolding of proteins into their native state under laboratory conditions. C) Identification of thermostable proteins than maintain their native state in adverse temperatures. D) A and B E) B and C Ans: A Level of Difficulty: Moderate Section 6.2.A Learning Objective: Protein Structure 60. Molecular chaperones bind to unfolded or partially folded polypeptide chains in order to accomplish which of the following? A) ensure that improper aggregation of hydrophobic segments does not occur B) engulf the protein in order to ensure that the protein is not damaged by heat denaturation C) facilitate native folding by exposing hydrophobic segments of the protein as it is 217 Downloaded by: carolinescott | [email protected] Want to earn $1.236 Distribution of this document is illegal extra per year?