Multiple-Choice Questions Answer ALL 20 multiple-choice questions on the Scantron Card in PENCIL

Transcription

1 Multiple-Choice Questions Answer ALL 20 multiple-choice questions on the Scantron Card in PENCIL For Questions 1-10 choose ONE INCORRECT answer. 1. Which ONE of the following statements concerning the amino acid glycine is INCORRECT? a) The side-chain on the alpha carbon of glycine is an excellent hydrogen bond donor. b) Glycine is commonly found in reverse turns at the i+2 position. c) Glycine and alanine have small side-chains and are often found at helix-helix interfaces. d) Glycine is a poor helix former and is found in flexible regions of proteins. 2. Which ONE of the following statements concerning the right-handed alpha-helix is INCORRECT? a) The alpha-helix has hydrogen bonds between C=O of residue n and NH of residue n+4. b) The ideal alpha-helix has phi (φ) and Ψ (psi) dihedral angles of about -57 and -47 respectively, located in the lower left quadrant of Ramchandran plots. c) Helices found on the surface of globular proteins project their hydrophilic face towards the core and their hydrophobic face towards the solvent water. d) The alpha helix has 3.6 residues per turn, a rise of 1.5 A per residue, and a rotation of 100 degrees between each successive residue. 3. Which ONE of the following statements concerning the amino acid leucine is INCORRECT? a) It is the most common amino acid found in both soluble and membrane proteins. b) It is a non-polar amino acid and commonly found facing the lipid bilayer in membrane proteins. c) Leucine and isoleucine are isomers and both are excellent alpha helix formers. d) Leucine and valine both have two terminal methyl groups. 4. Which ONE of the following statements concerning the amino acid histidine is INCORRECT? a) Its side-chain has a very low pka making it both a good hydrogen bond donor and acceptor at neutral ph b) Poly-histidine binds to Ni-affinity columns and is a commonly used tag to purify recombinant proteins expressed in bacteria c) The mutation of histidine to alanine in the active site of the enzyme ribonuclease results in a loss of enzyme activity d) It is classified as a basic, positively-charged amino acid but less polar than arginine and lysine

2 5. You are working on hemoglobin (Hb) S and are interested in studying the effect of other amino acid substitutions at position 6 other that Glu6Val. You find that Glu6Ala Hb does not aggregate but that Glu6lle Hb does. Which ONE of the following interpretations is INCORRECT? a) Alanine is less hydrophobic than valine, so an alanine mutant of Hb is less likely to aggregate. b) Isoleucine is hydrophobic and beta-branched like valine so the isoleucine mutant would have a similar effect on Hb as the valine mutant. c) Isoleucine is a strong beta-strand former so the Glu6Ile mutant would have a similar effect on the properties of Hb as the valine mutant. d) If a Glu6Asp mutant is made, it will not aggregate since Asp is negatively charged like Glu and a strong helix former. 6. You are studying the stability of a ribonuclease containing a single buried tryptophan residue using the protein denaturant urea. You perform fluorescence, circular dichroism (CD) and infrared (IR) spectroscopy to study the effect of urea on the structure of the protein. Which ONE of the following predictions is INCORRECT? a) The CD and IR spectra should show the presence a-helices and beta-strands in the protein, but will decrease in the presence of urea. b) The fluorescence of the tryptophan residue in the protein will increase upon denaturation due to its exposure to water. c) Complete unfolding of ribonuclease in urea requires the presence of the reducing agent betamercaptoethanol to break disulfide bonds in the protein. d) Removal of urea in the presence of a trace amount of beta-mercaptoethanol should allow the protein to regain its secondary and tertiary structure. 7. Which ONE of the following statements concerning fibrous proteins is INCORRECT? a) Silk contains a high content of glycine within a 6-residue repeating unit that forms a betapleated sheet, making its fibers highly flexible. b) Wool (keratin) has a low glycine content and can be stretched via a helix to sheet transition with disulfide crosslinks providing the main restoring force. c) Collagen contains a high content of proline and hydroxy-proline and forms a triple a-helix with 3.6 residues per turn. d) Actin exists as a monomer (G-actin) and in long filaments (F-actin) of multiple subunits that make up the cytoskeleton of cells, giving them their shape. 8. Which ONE the following statements concerning the peptide bond is INCORRECT? a) It is formed during protein biosynthesis in the ribosome b) Jt is a single bond that is free to rotate. c) It can be cleaved by proteolytic enzymes like trypsin. d) It has a planar conformation that is linked by the C a carbon that has defined phi/psi angles to the N-H and C=O groups, respectively.

3 9. Which ONE of the following methods concerning protein separation methods is INCORRECT? a) SDS gel electrophoresis separates proteins based on their net charge b) Gel filtration chromatography separates proteins based on their molecular size. c) Affinity chromatography separates proteins based on their ability to bind specifically to a ligand bound to a resin. d) HPLC reverse-phase chromatography separates proteins and peptides based on their hydrophobicity. 10. Which ONE of the following statements concerning spectroscopic methods IS INCORRECT? a) CD spectroscopy can be used to determine the loss of protein secondary structure in a denaturation experiment. b) Fluorescence spectioscopy can be used to follow conformational changes in a protein. C) IR spectroscopy can be used to distinguish a-helix and beta-sheet content in proteins d) NMR spectroscopy can be used to determine the molecular structure of large protein complexes. For Questions choose the BEST answer. 11. Single amino acid changes in proteins can affect their stability and ability to function properly. Sickle cell hemoglobin is an example that was discussed in class. Which ONE of the following statements BEST describes the effect of the (Glu6Val mutation on hemoglobin? a) It causes the hemoglobin tetramer to dissociate into individual subunits. b) It prevents hemoglobin from binding oxygen leading to impaired function. c) It causes destabilization of a helix and the exposure of a hydrophobic patch. d) It causes hemoglobin to unfold resulting in a complete loss of helical structure. 12. We developed our own BCH210 hydrophobicity scale in class that orders amino acid from most hydrophobic to most hydrophilic. Which ONE of the following scales BEST represents the one we developed in class going from hydrophobic on the left to hydrophilic on the right? a) FLIVWYMPGACSTNQDEHKR b) FLIVWYSTNQMPGACDEHKR c) FLIVWYMPGACSTDENQHKR d) FLIVGACWYMPSTNQDEHKR

4 13. The Ramachandran plot represents the phi/psi dihedral angles al each backbone peptide bond in a protein. Which ONE of the following statements BEST represents the changes observed in dihedral angles in the transition of a prion protein from a-helical to beta-sheet? a) The Ramachandran plot would be identical since the amino acid sequence remains the same. b) The phi/psi angles would change from about -60 and -50to -140 and +135 o respectively. c) The omega angle around the C-N peptide bond of proline would change from trans to cis. d) The chi angles describing side chain rotations would not change. 14. Like many serine proteases Subtilisin has three residues (Asp32, His64, Ser221) that make up a charge relay network at the active site of the enzyme. Which ONE of the following statements BEST describes the expected results of site-directed mutagenesis experiments that were carried out on Subtilisin? a) Replacement of the active site His64 with lysine would result in a fully active enzyme. b) Replacement of Met222 that is sensitive to oxidation with Ala would result in a partially active enzyme. c) Replacement of Met222 with Cys222 would result in the formation of a disulfide bond within the protein. d) Replacement of Asn155, which provides a carboxyamide side chain, with Gln155 would result in a completely inactive enzyme. 15. The conformation of a peptide often depends on its environment. Which ONE of the following statements BEST describes the influence of the environment on synthetic polymers of amino acids? a) A 20 amino acid polymer of span of leucine would not be soluble in water but would be able to span a 30A thick lipid bilayer as an a-helix b) A 20 amino acid polymer of proline would form a helix-turn-helix structure in water c) A 20 amino acid polymer of glutamic acid would form a helix in water at ph 7.0 d) A 20 amino acid polymer of alternating leucine and glutamic acid would form a beta-sheet structure with an acidic surface and a hydrophobic surface 16. You have discovered a drug that binds specifically to the hydrophobic patch in sickle hemoglobin (HbS). Which ONE of the following mechanisms BEST describes the molecular action of this drug? a) It causes HbS to misfold thereby preventing aggregation. b) It blocks the binding site preventing surface hydrophobic interactions. c) It dissociates HbS into its subunits preventing aggregation. d) It keeps HbS totally in the oxygenated state preventing aggregation.

5 17. You are studying a-helix/beta-strand transitions in a model peptide with the sequence Val-His-Leu-Thr-Pro-Glu that has equal propensity to form an a-helix or a beta-strand, and indeed forms an equal mixture of the two conformations in aqueous solution. Which of ONE of the following peptides containing a single amino acid change would be MORE likely to form a helix? a) Val-His-Leu-Thr-Pro-Val b) Val-His-Ile-Thr-Pro-Glu c) Val-His-Leu-Thr-Ala-Glu d) Ile-His-Leu-Thr-Pro-Glu 18. Imagine that there is a 19-amino acid world rather than the 20 naturally occurring amino acids used in protein biosynthesis. Students were asked which amino acid they would eliminate and why. Pick the ONE BEST response. a) I would eliminate Leu because Ile or Val could substitute. b) I would eliminate Met because it only has one codon and Cys, a sulfur-containing amino acid, could substitute. c) I would eliminate Pro because it bends proteins out of shape. d) I would eliminate Thr because Ser also contains a hydroxyl group and Ser is often needed in active sites of enzymes. 19. beta-barrel proteins found in the outer membrane of E. coli form water-filled channels that allow polar molecules like sugar to cross the membrane. Which ONE statement BEST describes the properties of these membrane beta-barrel proteins. a) They contain a hydrophobic interior and a hydrophilic exterior. b) They consist of an anti-parallel beta-sheet where the first strand in the sequence is hydrogen-bonded to the last strand forming a closed structure. c) They consist of transmembrane segments with non-polar residues found every 3.6 residues on average. d) They contain small glycine residues facing the channel that allows for the passage of molecules. 20. Which ONE of the following statements BEST describes the take home message from Dr. Reithmeier s lectures? a) Proteins take very long time to fold into their native structures because they must sample all possible conformational states. b) Since the prion protein can assume two very different conformations, the Anfinsen principle that the amino acid sequence defines the final folded state must be incorrect. c) Proteins are simple polymers of amino acids joined in a linear fashion through peptide bonds and can be understood by polymer chemistry. d) Mutations in genes can cause amino acid changes in proteins that affect their function, resulting in inherited diseases.

6 Suggested Answers 1b 2c 3c 4a 5d 6b 7c 8b 9a 10d 11c 12a 13b 14b 15a 16b 17c 18d 19b 20d