BIOL/BIOC Come to the PASS workshop with your mock exam complete. During the workshop you can work with other students to review your work.

Transcription

1 It is most beneficial to you to write this mock midterm UNDER EXAM CONDITIONS. This means: Complete the midterm in 1.5 hour(s). Work on your own. Keep your notes and textbook closed. Attempt every question. After the time limit, go back over your work with a different colour or on a separate piece of paper and try to do the questions you are unsure of. Record your ideas in the margins to remind yourself of what you were thinking when you take it up at PASS. The purpose of this mock exam is to give you practice answering questions in a timed setting and to help you to gauge which aspects of the course content you know well and which are in need of further development and review. Use this mock exam as a learning tool in preparing for the actual exam. Please note: Come to the PASS workshop with your mock exam complete. During the workshop you can work with other students to review your work. Often, there is not enough time to review the entire exam in the PASS workshop. Decide which questions you most want to review the Facilitator may ask students to vote on which questions they want to discuss in detail. Facilitators do not bring copies of the mock exam to the session. Please print out and complete the exam before you attend. Facilitators do not produce or distribute an answer key for mock exams. Facilitators help students to work together to compare and assess the answers they have. If you are not able to attend the PASS workshop, you can work alone or with others in the class. Good Luck writing the Mock Exam!! Dates and locations of mock exam take-up: Thursday, October 11 th (6:00-8:00pm) SA 416 Monday, October 15 th (6:00-8:00pm) SA 417

2 BIOL/BIOC 2200 PASS Mock Midterm Please note that your actual (graded) midterm is on Wednesday, October 17 th at 10:05am in River Building Room Good luck! 1. If 1L of water weighs 1000 grams and 1 mole of water weighs 18 grams, what is the molarity of water? a M b M c M d M 2. What molecule is released during the formation of a peptide bond? a. Hydrogen b. Carbon dioxide c. Water d. Oxygen 3. Which of the following amino acids is not non-superimposable with its mirror image (i.e. is not an enantiomer)? a. Proline b. Asparagine c. Leucine d. Glycine 4. Thermolysin is a protease that cleaves peptides at the N-terminal side chain of branched alkyl residues. Which of the following peptides has the most thermolysin cleavage sites? a. DNKGSTVYQRWC b. HGICSVGPKLNT c. GHPTLDQIWCER d. RTHCQGYNESDK 5. In a neutral solution, most amino acids exist as: a. Positively charged compounds b. Negatively charged compounds c. Zwitterions d. Hydrophobic molecules

3 6. How does the gel for isoelectric focusing differ from the gel for traditional electrophoresis? a. Isoelectric focusing uses a gel with much larger pore sizes to allow for complete migration. b. Isoelectric focusing uses a gel with SDS added to encourage uniform negative charges. c. Isoelectric focusing uses a gel with a ph gradient that encourages a variable change. d. The gel is unchanged in isoelectric focusing; the protein mixture is treated before loading. 7. Consider the biochemical reaction A B, which is catalyzed by A B dehydrogenase. Which of the following statements is true? a. The reaction will proceed until the enzyme concentration decreases. b. The reaction will be most favourable at 0 C. c. A component of the enzyme is transferred from A to B. d. The free energy ( G) of the catalyzed reaction is the same as that of the uncatalyzed reaction. 8. Which term below best defines the quaternary structure of a protein? a. The arrangement of two or more polypeptides subunits into a single functional complex. b. The folding of the polypeptide backbone in three-dimensional space. c. The interaction of amino acid side chains. d. The sequence of amino acids in a polypeptide chain. 9. Which of the following statements is NOT true regarding the comparison of alpha-helix structure to the beta-sheet structure in proteins? a. Each may occur in typical globular proteins. b. Each is stabilized by inter-chain hydrogen bonds. c. All possible hydrogen bonds between peptide carbonyl oxygen (C=O) and the amide hydrogen (N-H) are formed in each. d. Each is an example of secondary structure. e. The peptide bond in each is planar and trans.

4 10. Which of the following best describes a protein domain? a. The α-helical portion of a protein. b. A discrete region of polypeptide chain that has folded into a self-contained three-dimensional structure. c. The β-pleated sheet portion of a protein. d. A feature that rarely occurs in globular protein. 11. Which of the following statements about enzyme kinetics is FALSE? a. Most enzymes in the human body work best at a temperature of 37 C. b. An enzyme-substrate complex can either form a product or dissociate back into the enzyme and substrate. c. An increase in the substrate concentration (at constant enzyme concentration) leads to a proportional increase in the rate of the reaction. d. Maximal activity of many human enzymes occurs around ph Which of the following determines an enzyme s specificity? a. The Michaelis constant b. The three-dimensional shape of its active state c. The type of cofactor required for the enzyme to be active d. The prosthetic group on the enzyme 13. What is the purpose of the sodium dodecyl sulfate (SDS) in SDS-PAGE? a. SDS stabilizes gel matrix, improving resolution during electrophoresis. b. SDS solubilizes proteins to give uniformly negative charges, so the separation is based purely on size. c. SDS raises the ph of the gel, separating multi-unit proteins into individual subunits. d. SDS solubilizes the proteins to give them uniformly positive charges, so separation is based purely on ph. 14. Which of the following is most likely to be preserved when a protein is denatured? a. Primary structure b. Secondary structure c. Tertiary structure d. Quaternary structure

5 BIOL/BIOC Which of the following statements is most likely to be true of nonpolar R groups in aqueous solution? a. They are hydrophilic and found buried within proteins. b. They are hydrophilic and found on protein surfaces. c. They are hydrophobic and found buried within proteins. d. They are hydrophobic and found on protein surfaces. 16. Proline differs from the other standard amino acids in that only the former: a. Has a negative charge in its side chain. b. Forms peptide bonds that are planar. c. Contain a secondary amine in its backbone. d. Is commonly found in flexible loop regions of folded proteins. 17. Which event could alter a protein s primary structure? a. Site-directed mutagenesis of the gene that encodes the protein. b. A conformational change in the protein induced by ligand binding. c. Protein denaturation by guanidinium chloride. d. Reduction of disulfide bonds by β-mercaptoethanol. 18. Collagen consists of 3 helices with carbon backbones that are tightly wrapped around one another in a triple helix (a super secondary structure). Which one of these amino acids is most likely to be found in the highest concentration in collagen? a. Proline b. Cysteine c. Threonine d. Glycine 19. Which of the amino acids has one chiral carbon in its side chain? I. Serine II. Threonine III. Isoleucine a. I only b. II only c. II and III only d. I, II and III e. None of the above

6 20. In lysine, the pka of the side chain is about Assuming the pka of the carboxyl and amino groups are 2 and 9, respectively, the pi of lysine is closest to: a. 5.5 b. 6.2 c. 9.8 d Which property of a substance is proportional to the number of ways in which the available energy can be distributed over the atoms or molecules of the system? a. Temperature b. Entropy c. Standard free energy d. Enthalpy 22. A closed system is one that: a. Does not exchange energy or matter with the universe b. Exchanges energy but not matter with the universe c. Exchanges matter but not energy with the universe d. Exchanges both energy and matter with the universe 23. The type of chromatography that uses a negatively charged resin and allows for protein purification based on the overall charge of the protein. a. Cation exchange chromatography b. Anion exchange chromatography c. Ion exclusion chromatography d. Affinity chromatography 24. Scientists could confirm that an allosteric effector increase the catalytic efficiency of an enzyme if it has what effect on kcat and Km? a. kcat decreases, Km increases b. kcat decreases, Km remains unchanged c. kcat increases, Km decreases d. kcat remains unchanged, Km increases

7 25. Which bond stabilizes primary structure? a. Peptide bond b. Covalent bond c. Hydrogen bond d. Disulfide bond 26. Which of the following is a true statement about the role of catalysts in a reaction? I. Catalysts more effectively lowers the activation energy in the forward direction. II. Catalysts generally react with one or more reactants to form intermediates that subsequently give the final reaction product. III. If a catalyst affects the equilibrium of the reaction, it must be consumed as the reaction proceeds. IV. Catalysts may increase the reaction rate or selectivity or enable the reaction at a lower temperature. a. II and IV b. I and III c. II and III d. II, III, and IV 27. According to Le Chatelier s Principle, addition of which of the following compounds will cause the equilibrium of the following endothermic reaction NOT shift to the right? CaCO3(s) + CO2(g) + H2O(l) Ca 2+ (aq) + 2HCO3-3(aq) a. CO2 b. LiOH c. Na3PO4 d. CaCO3 28. Which of the following is NOT an essential amino acid? a. Phenylalanine b. Tryptophan c. Cysteine d. Valine

8 29. What is the most significant and (theoretically) correct model for enzyme activity? a. Induced-fit model b. Lock & key c. Jigsaw puzzle d. Transition state 30. Consider the following reaction: C(s, graphite) + H2(g) + O2(g) CH3OH(l) ; H = kJ Which of the following would increase the value of Keq? a. Increase pressure b. Increase [H2] c. Decrease temperature d. Decrease [C] 31. Which of the following statements concerning peptide bonds is FALSE? a. The formation of the reaction involves a reaction between an amino group and a carboxyl group. b. The formation involves hydration reactions. c. They are the primary bonds that hold amino acids together. d. They have partial (40%) double bond character. 32. The major protein component of human hair is α-keratin. Hair straighteners are commonly used tools which use heat to iron hair into temporarily lying flat and straight. What is the biological explanation for this phenomenon? a. Hair straighteners denature proteins by disrupting the ph. b. Hair straighteners disrupt ionic bonds between α-keratin molecules. c. Hair straighteners disrupt hydrogen bonds in α-keratin. d. Hair straighteners disrupt disulfide bridges in α-keratin. 33. A molecule that has both hydrophobic and hydrophilic properties is known as: a. Ampholytic b. Amphipathic c. Aliphatic d. Amphoteric

9 34. The reversible reaction Hb + 4O2 Hb(O2)4 exists in blood between hemoglobin (Hb) and oxyhemoglobin Hb(O2)4. According to the law of mass action, doubling the O2 concentration would: a. decrease the reaction quotient by a factor of ½ b. decrease the reaction quotient by a factor of 1/16 c. increase the reaction quotient by a factor of 2 d. increase the reaction quotient by a factor of Identify the amino acid residues in the following pentapeptide: a. Aspartic acid, Proline, Proline, Arginine, Cysteine. b. Glutamic acid, Histidine, Histidine, Lysine, Cysteine. c. Glutamine, Phenylalanine, Phenylalanine, Methionine. d. Glutamic acid, Tyrosine, Tyrosine, Lysine, Methionine. 36. For the 3 rd amino acid in the pentapeptide chain from #35, which of the following is its defining characteristic? a. It forms disulfide linkages. b. It causes kinks in the polypeptide chain. c. It works as a physiological buffer and facilitates enzyme-catalyzed reactions at the active site. d. None of the above.

10 37. Which amino acid substitution would result in the greatest change in the net charge of a polypeptide at ph 7? a. Asp to Ala b. Lys to Arg c. Thr to Ser d. Glu to Lys 38. Which of the following is the most important factor in protein folding? a. The molten globule b. Hydrophobic effect c. The R groups of amino acids d. Tertiary & Quaternary protein structure 39. Household cleaners commonly contain either ammonia (NH3) or bleach (NaOCl) as the principal acting ingredient. Mixing ammonia-based and bleach-based cleaners can be hazardous, as the resulting reactions can form several toxic products, such as the irritant dichloramine (NHCl2) in the reaction: 2 NaOCl(aq) + NH3 (aq) NHCl2 (aq) + 2NaOH(aq) Note that for the overall reaction: H = -55kJ/mol and S = -150 J/mol K. During the formation of dichloramine and NaOH, the order (organization) of the system: a. decreases because entropy is always increasing b. stays the same because the number of moles stays the same c. increases because the change in entropy is negative d. does not change because the system is at equilibrium 40. During the formation of a disulfide bridge between two cysteine residues, a type of reaction occurs. If the enzyme thioredoxin cleaves these protein disulfide bonds, which statement correctly describes its activity? a. A protease breaks the bond by catalyzing the addition of water across it. b. An isomerase catalyzes the rearrangement of functional groups to break the bond. c. A phosphorylase breaks the bond by catalyzing the addition of a phosphate group. d. An oxidoreductase catalyzes the transfer of electrons to break the bond.

11 41. Which of the following is the Henderson-Hasselbalch equation? a. ph = pka log ( A HA ) b. ph = pka + log ( A HA ) c. ph = pka + log ( HA A ) d. ph = pka log ( HA A ) 42. Which type of bond will typically NOT be attracted to water? a. Ionic b. Polar covalent c. Pure covalent d. Amphipathic 43. Polyglutaraldehyde (PGA) can form linkages with amines. PGA could potentially cross-link with which residue in the active site of signal peptidase, shown below? a. T 101 b. K 90 c. M 75 d. S 175

12 44. Assuming all other reaction conditions remain constant and that the reaction can proceed to equilibrium, how would the reaction S P be affected by the addition of an enzyme catalyst? a. Neither increased reaction rate or increased formation of production b. Increased reaction rate c. Increased total product formed d. Both increased reaction and increased formation of product 45. The initial rate of decrease in the concentration of a reactant, or the increase in concentration of a product is also known as the: a. Instantaneous rate of reaction b. Average rate of reaction c. Immediate rate of reaction d. Reaction rate of reaction 46. Given that G for the reaction S P is negative in the direction of S P, reaction equilibrium favours the formation of which substrate? a. The reaction proceeds equally in both directions b. P c. S d. The reaction does not proceed in either direction 47. Breaking of bonds to turn a macromolecule into its basic building blocks is best known as: a. Catabolism b. Anabolism c. Metabolism d. Enzyme catalysis 48. Which of the following is NOT a crucial property of water? a. Cohesion / adhesion b. Weak electrophile c. Hydrogen bonding d. Auto-ionization

13 49. What is the native state of a protein? a. The shape in which it exists naturally in a living organism b. The most thermodynamically stable state c. Another word for the tertiary structure of a protein d. Its state at ph 7 and temperature 37 C 50. Albumin is a large protein which circulates freely in human plasma. Another type of protein, called aquaporins, act as a channel for water to enter and exit a cell, and are located within the lipid bilayer of a cell s plasma membrane. Based on their physiological locations, how would the tertiary structure of the two proteins most likely compare? a. Albumin has a more nonpolar core with a nonpolar outer layer, while aquaporins have a more polar core with a polar outer layer. b. Albumin has a more nonpolar core with a polar outer layer, while aquaporins have a more polar core with a nonpolar outer layer. c. Albumin has a more polar core with a nonpolar outer layer, while aquaporins have a more nonpolar core with a polar outer layer. d. Albumin has a more polar core with a polar outer layer, while aquaporins have a more nonpolar core with a nonpolar outer layer.