BCH2333 - Final Exam Practice Exam

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University of Ottawa *

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2333

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Chemistry

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Dec 6, 2023

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50

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BCH2333 - FINAL EXAM PRACTICE QUESTIONS Quiz 1 1. Given the image below, indicate the covalent bond a. None of the above b. Bond 1 and Bond 2 c. Unable to determine d. Bond 1 e. Bond 2 2. Given the image below, indicate the intermolecular bond a. None of the above b. Bond 1 and Bond 2 c. Unable to determine d. Bond 1 e. Bond 2
3. If the pH of a voledronic acid solution is 4.3, and the voledronate concentration is 4mM, what is the concentration of voledronic acid? (pKa = 5.0) a. 1.4 b. 379.5 c. 185.2 d. 20 e. 0.5 4. Which of the following statements about compartmentation is FALSE? a. High concentrations of biomolecules can be maintained locally as a result of compartmentation b. By decreasing environmental variability in microdomain, compartmentation promotes a life c. Microdomains form through self-assembly processes, partitioning the cell into compartments d. Compartmentation is necessary to promote the mixing of cellular components with the bulk environment e. Chemical evolution would not possible without compartmentation 5. The original bond energy of a dipole-induced dipole interaction is 3 kJ/mole. If the bonding partners change their bond radius by 3.2, what is the new bond energy? a. 20.31 b. 0.24 c. 0.61 d. 0.01 e. 6.37 6. Match the chemical structure to the functional group name provided. 5 3 1
4 6 2 a. Ester → 1 b. Amide → 2 c. Thiol → 3 d. Disulfide → 4 e. Phosphodiester → 5 f. Amine → 6 7. Which of the following indicates an equivalence point of the titration given in the image below? a. Point 1 b. Region 1 c. Point 2 d. Region 2 e. None of the features indicated
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8. Which of the following indicates a midpoint of the titration given in the image? a. Region 2 b. Point 1 c. Point 2 d. Region 1 e. None of the features indicated 9. The optimal bond distance in charge-charge interactions is determined by the sum of the kinetic energies of attraction and repulsion. a. True b. False 10. Propionic acid is provided (pKa = 2.0) to make a 0.1 M buffer at pH = 2.0. What is the ratio of proprionate:proprionic acid (round to the nearest whole number): ___1___ What volume of a 1M solution of proprionic acid is required to make 1 L of buffer (answer in mL, rounded to the nearest whole number): ___10___ 11. The Miller-Urey experiment was conducted in order to … a. … simulate gas exchange from plants that promote life on Earth b. … simulate the surface of a meteorite c. … show that the elevated temperature of primordial Earth initiated life d. … demonstrate that life began with the help of lightning as a source of energy e. … demonstrate that buildings block of the life needed oxygen to form 12. Which of the following statements regarding hydrogen bonding is FALSE?
a. H-bonding is one of the most important non-covalent bonds in biochemistry b. H-bonds occur in assemblies of proteins where individual supramolecular structure undergo intermolecular interactions c. The linear overlap of the anti-bonding orbital of the acceptor lone pair electrons and the bonding orbital of the donor H is critical to an H-bond d. In a H-bond, the donor is a weak acid and the acceptor is a weak base e. While an individual H-bond is moderately strong, the presence of groups of H-bonds contributes to the stability of large biomolecular structures 13. Which of the following statements about the Hydrophobic effect is FALSE? a. The formation of a bilayer vesicle from amphiphiles in water results in polar headgroups facing towards the aqueous phase b. Clathrate result in ice-like water, resulting in Δ S>0 c. Reducing the surface area of a clathrate results in an increase in entropy d. The hydrophobic effect is a driving force for biochemical self-assembly e. The hydrophobic effect is driven by the solvent and is considered a non-covalent intermolecular interaction 14. What non-covalent interaction(s) is/are most likely to occur between water and water? a. Hydrogen bonding and dipole-dipole b. Dipole-dipole c. Hydrogen bonding d. Charge-charge e. Charge-dipole 15. Given that the concentration of the hydroxy anion is 10 -2 M, what is the pH of the resulting solution? a. 12 b. 2 c. 6 d. 9 e. 4 16. According to the deprotonation reaction shown below, which of the carboxylic acid species (1 to 4) would you expect to be the least acidic?
a. 2 b. 3 c. The pKa is equivalent for all carboxylic acids shown d. 1 e. 4 17. According to the deprotonation reaction shown below, which of the carboxylic acid species (1 to 4) would you expect to have the highest pKa?
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a. 4 b. 2 c. The pKa is equivalent for all carboxylic acids shown d. 1 e. 3 18. The formation of large polymers from individual units contributes to molecular complexity in biochemistry. a. True b. False ______________________________________________________________________________ Quiz 2 1. Processes that result in Δ S universe > 0 will yield a Δ G > 0 a. True b. False 2. Processes where Δ H = T Δ S result in Δ G > 0 a. True
b. False 3. Which of the following statements regarding the peptide bond is FALSE? a. Peptide bond formation is enabled by coupling the dehydration reaction with high - energy phosphate bond hydrolysis b. Side -chain atoms contribute to the coplanarity of the nth and the n+1th residues of the peptide bond c. The rigidity of the peptide bonds comes from electron delocalization between the carbonyl and amine that make up the amide bond d. The trans-conformation of the peptide bond is favored over the cis conformation e. Both the nth and n+1th residue contribute to the 6 co-planar atoms surrounding the peptide bond 4. Name the product of the galactose transformation shown below. a. Galacitol b. Galacturonic acid c. Galactonolactone d. methyl-D-galactose 5. Name the reaction that results in the chemical transformation of galactose shown below. a. C6 oxidation b. Anomeric anhydration c. Reduction
d. C1 oxidation e. Amination 6. Identify the stereochemical relationship of the two carbohydrate structures presented: a. Anomer b. Carbomer c. Epimer d. Enantiomer e. Diastereomer 7. Identify the stereochemical relationship of the two carbohydrate structures presented: a. Anomer b. Diastereomer c. Carbomer d. Epimer e. Enantiomer 8. Identify the stereochemical relationship of the two carbohydrate structures presented :
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a. Epimer b. Enantiomer c. Diastereomer d. Anomer e. Carbomer 9. Given the structure of glycogen below, what is the correct name for the glycosidic linkage indicated by arrow #2? a. 𝛽 - D - glu cos ep(1 → 4) 𝛽 - D - glu cos ep b. 𝛽 - D - glu cos ep(1 → 6) 𝛽 - D - glu cos ep c. Ɑ - D - glu cos ep(1 → 6) Ɑ - D - glu cos ep d. Ɑ - D - glu cos ep(1 → 4) 𝛽 - D - glu cos ep e. Ɑ - D - glu cos ep(1 → 4) Ɑ - D - glu cos ep 10. At pH = 2, what is the net charge of the peptide DAMASK? a. -1.0
b. -0.5 c. 0 d. +1.5 e. +1.0 11. At pH = 4, what is the net charge of the peptide PLAID? a. -1.0 b. -0.5 c. 0 d. +1.5 e. +1.0 12. At pH = 6.5, what is the net charge of the peptide PAISLEY? a. -1.0 b. -0.5 c. 0 d. +1.5 e. +1.0 13. Given the following titration curve for Aspartic Acid and indicated pKa values, the pI for Aspartic acid is: a. 3.0 b. 4.0 c. 10.0 d. 5.0 e. 7.0
14. For a given reaction proceeding from reactants to products, the value of Q = 12.5 and the equilibrium constant is 12.5. Which of the following is true: a. The reverse reaction will be faster than the forward reaction b. The reaction will proceed the forward direction to form product c. The forward reaction will be faster than the reverse reaction d. The reaction is at equilibrium and will not proceed e. The reaction will proceed in the reverse direction to form reactants 15. Which of the following statements regarding cellular lipid membranes is FALSE? a. Cholesterol is necessary for proper cell membrane function, promoting membrane rigidification b. The distribution of lipids in the cell membrane is asymmetrical between inner and outer leaflets c. The lipid composition of cell membranes impacts glycosylation patterns, transmembrane protein distribution, and membrane transport d. The cell membrane lipids can readily flip between leaflets, but require energy to diffuse within leaflets e. Glycerophospholipids are the major lipid component of cell membranes 16. The amino acid depicted below is: a. L-Tryptophan b. L-Tyrosine c. D-Tyrosine d. D-Tryptophan e. L-Phenylalanine f. D–Phenylalanine
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17. The amino acid depicted below is: a. L - Arginine b. D - Arginine c. D - Glutamine d. L - Glutamine e. D - Glutamic Acid f. L - Glutamic Acid 18. The amino acid depicted below is: a. L - tyrosine b. D - Tyrosine c. D - Phenylalanine d. D - Tryptophan e. L - Phenylalanine f. L - Tryptophan 19. The beta-branched amino acid depicted below is:
a. L-L Threonine b. L-D Isoleucine c. L-L Isoleucine d. None of the answers are correct e. L-D Theonine 20. For a given reaction with enthalpy of 50 kJ/mol and free energy of 20 kJ/mol, the value of T Δ S is ___-30___ kJ/mol (round to whole numbers). 21. Match the base indicated on the biopolymer below with its name. a. Adenine → 1 b. Thymine → 2 c. Cytidine → 3 d. Guanine → 4 e. Uracil → 5 ___ 5 ___ 7 ___ 4 ___ 6
22. Given the biopolymer below, match the numbered component with the moiety description provided. a. Glycosidic bond → 1 b. Anomeric carbon → 2 c. Phosphodiester group → 3 d. C2’ hydroxyl → 4 ___ 3 ___ 1 ___ 2 23. The biopolymer given below is DNA. a. True b. False
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24. The biopolymer given below is DNA. a. True b. False ______________________________________________________________________________ Quiz 3 1. Which of the following statements regarding the Rossmann Fold is FALSE? a. The Rossmann fold is comprised of two beta-alpha-beta motifs linked by an alpha helix b. The relatively disordered structural components of the Rossmann fold comprising the beta-turns are critical for cofactor recognition and positioning c. One of the cofactors bound by the Rossmann fold is nicotinamide adenine dinucleotide d. The dipole-nature of the alpha helix is utilized by the Rossmann fold to properly position the dinucleotide cofactor for its catalytic function, aligning the alpha-helix C-terminus with the diphosphate of the cofactor e. The Rossmann fold would fall in the "alpha + beta" domain class 2. The quaternary structure cartoon below possesses which type of symmetry?
a. C3 b. C2 c. D4 d. C4 e. D2 3. The quaternary structure cartoon below possesses which type of symmetry? a. C4 b. C2 c. D4 d. D2 e. C3 4. The peptide segment shown below is part of a right-handed alpha helix. Please indicate the hydrogen-bonding partner of the residue contained in the dashed box. a. K b. L c. E d. S e. A
5. Given the cruciform structure shown below, which of the following sequences would correctly fill the segment indicated by the blue box? a. 5'-ACCGTCGA-3' b. 5'-AGCTGCCA-3' c. 5'-ACAGTCGC-3 d. 5'-TCGACGGT-3' e. 5'-TGGCAGCT-3’ 6. Which of the following statements about protein quaternary structure is FALSE? a. Quaternary structures are held together exclusively by the same covalent interactions that stabilize secondary and tertiary structure. b. Quaternary structure provides the benefit that defects in the final structure can be repaired by replacing a small unit instead of one huge polypeptide chain c. Quaternary structure allows cells to produce the protein components in relatively distant sites or compartments from where the fully assembled protein needs to be active d. Quaternary structure provides a mechanism to control protein activity e. Overall, for the formation of the quaternary structure of a protein, Δ G < 0 7. Consider the following amino acid sequence, which makes up a beta sheet: YEFSLAID APLI NLRFQITW
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The residues in bold are part of a turn. If the side chain of residue Y points to the top face of the sheet, and the side chain of residue N points to the bottom face of the sheet, which of the following statements is FALSE? a. The top face is hydrophobic b. The intrastrand hydrogen bond angle approaches 180° within this beta sheet c. This beta-sheet is of the more predominant form found in folded proteins d. This beta-sheet contains a Type 2 beta-turn e. This represents an antiparallel beta-sheet 8. Which of the peptide sequences below best matches the hydropathy plot shown? a. ILYYAGSREDHSGYLIL b. LHGDQNRERDGHSQERD c. EQSDTERNQHGALIYLI d. LIFLAIFPAGSTSEDRR e. RAFLILFMTYFLILFLI 9. Which of the peptide sequences below best matches the hydropathy plot shown? a. EQSDTERNQHGALIYLI b. RAFLILFMTYFLILFLI c. LIFLAIFPAGSTSEDRR d. LHGDQNRERDGHSQERD e. ILYYAGSREDHSGYLIL
10. The hydrophobic effect is only a consideration for predicting the thermodynamics of protein folding, and is irrelevant in kinetic considerations. a. True b. False 11. Given the Ramachandran Plot below, identify the protein components that could adopt the phi-psi angle combination indicated by the number 4 a. Glycine residues b. Right-handed alpha helix c. Beta sheet & Glycine residues d. Beta sheet e. Right-handed alpha helix & Glycine residues 12. Which of the following answers most accurately describes who contributed to the discovery the structure of DNA? a. Watson b. Watson-Crick-Franklin c. Watson-Crick d. Crick
e. Franklin 13. If a particular 180 amino acid polypeptide is known to sample 3 preferred states as it folds into its native protein conformation, and if 10 14 conformations can be sampled per second, then how many hours would it take for this protein to fold according to Leventhal? a. 4 x 10 23 b. 2 x 10 68 c. 6 x 10 17 d. 6 x 10 71 e. 8 x 10 107 14. According to the Newman Projection provided below, the correct dihedral angle is: a. phi = +45° b. psi = +60° c. psi = -60° d. phi = -90° e. phi = -45° 15. Which of the characteristics of a polypeptide listed below does not meet the principles of peptide structure laid out by Linus Pauling? a. The energy-minimized folded state maximizes hydrogen bonding. b. Bond lengths and bond angles in a polypeptide can vary substantially from those found in individual amino acids. c. Non-covalent bonding is the predominant interaction stabilizing secondary structure. d. The angle ω = 180°
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e. The conformation of single residues will prevent steric clashing 16. The Leucine Zipper is an alpha-alpha motif important for the ability of some proteins to interact with DNA. Which of the following statements about the Leucine Zipper is FALSE? a. The helix regions of the Leucine Zipper contain Lys and Arg residues that can form charge-charge interactions with the phosphodiester backbone b. Repetitive L residues help to stabilize the loop region of the zipper motif c. The Leucine Zipper is an example of a helix-loop-helix structure d. The loop region has a repeating residue heptad that allow hydrophobic interactions exclusively to hold the loop conformation together e. The helical wheel would clump hydrophobic residues towards the inside of the Leucine Zipper loop region 17. A plasmid comprised of B-DNA changed its linking number from 420 to 457, resulting in a superhelix density of 0.031. What is the length of the plasmid in base pairs? a. 8765 b. 15050 c. 11200 d. 12532 e. 3500 18. Considering the protein denaturation curves provided below, which of the following is correct? a. For Protein A, Tm=65°C; For Protein B, Tm>100°C
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b. For Protein A, Tm=55°C; For Protein B, Tm=75°C. c. For Protein A, Tm>100°C; For Protein B, Tm=65°C. d. Protein B is more stable than Protein A e. For Protein A, Tm=75°C; For Protein B, Tm=55°C. 19. Below is a nucleotide base pair from B-DNA with three different regions indicated by A, B, and C. Which of the following descriptions of regions A, B, and C are INCORRECT? a. B = major groove, Hoogsteen edge b. A = minor groove, sugar edge c. C = Watson-Crick-Franklin edge d. A = minor groove, water spine, sugar edge e. All choices presented are corre ct 20. Which of the following bonding interactions DOES NOT contribute to correct protein folding? a. Hydrogen bonding b. Disulfide bonds c. Hydrophobic interactions d. Charge-charge interactions e. All of these contribute to correct protein folding. ______________________________________________________________________________ Quiz 4 1. The Michaelis constant, or Km is:
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a. a measure of affinity when the enzyme is a very poor catalyst b. All answers are correct c. the substrate concentration required to attain effective catalysis d. (K -1 + K cat )/K 1 e. calculated at time points corresponding to nearly constant [ES] 2. From the Hill Plot below, the K D of the first binding event for the receptor-ligand system under study is: a. 6nM b. -4nM c. 0.0001nM d. 3nM e. 1nM 3. Given the binding curve below, what is the K D for Ligand A?
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a. 0.005M b. 0.03M c. 0.015M d. None of the answers are correct e. 0.045M 4. You are evaluating the kinetics of an enzyme catalyzed reaction containing 4uM total enzyme and 30.3uM substrate. At this substrate concentration, you determine that the v o = 46.0 umol mL-1 s-1. If the v max = 235.0mM S-1 the K M is: a. 30.9 uM b. 10.4 uM c. 234 uM d. 124.6 uM e. 94.5 uM 5. Calculate the Hill Coefficient from the receptor-ligand binding data below:
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a. 2 b. 1000 c. 3 d. 100 e. 4 6. Match the irreversible inhibitor shown to its associated mechanism of irreversible inhibition. 1. 2. 3.
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_3__ traditions state analog _2__ mechanism based inhibitor _1__ affinity label 7. Which of the following statements surrounding Hemoglobin function is INCORRECT? a. Myoglobin shows a hyperbolic binding curve since there is only one heme subunit, preventing the subunit-to-subunit communication afforded by the heterodimeric quaternary structure of hemoglobin b. 2,3-bisphosphoglycerate is a negative allosteric regulator of Hemoglobin, perventing the T-to-R transition required to switch conformations and alter ligand affinity. c. The sigmoidal binding curve of oxygen exhibited by Hemoglobin disobeys the Law of Mass Action, since ligand binding alters the receptor and its affinity for subsequent ligand binding events d. In conditions of acidosis, a critical His at the ɑ 1 - 𝛃 2 interface is protonated, favouring salt bridge formation and maximizing oxygen offloading. e. The ability of hemoglobin to switch between the R and T states allows the protein to maximize loading in tissues with low PO2 offloading in tissues with high PO2 and maintenance of an oxygen reserve during periods of exertion. 8. The following is a hypothetical reaction: A --> B Which of the following parameters describing this reaction is/are changed by an enzyme? a. The free energy of the reactants and products b. The free energy of the products c. The overall free energy change of the reaction d. The standard free energy of activation e. The free energy of the reactants 9. On the Lineweaver-Burke plot shown below, the grey line represents the kinetics of an enzyme-catalyzed reaction. On the same plot, the orange line represents the kinetics of the same enzyme-catalyzed reaction in the presence of an inhibitor. What is the mechanism of inhibition?
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a. Mixed b. Uncompetitive c. Competitive d. Non-Competitive 10. On the Lineweaver-Burke plot shown below, the grey line represents the kinetics of an enzyme-catalyzed reaction. On the same plot, the orange line represents the kinetics of the same enzyme-catalyzed reaction in the presence of an inhibitor. What is the mechanism of inhibition? a. Mixed b. Uncompetitive c. Competitive d. Non-Competitive
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11. From the Lineweaver-Burke plot of an enzyme-catalyzed reaction containing 4um total enzyme, you find the y-intercept to be 4.26 X 10^-3 s mM^-1. The kcat for this reaction is: a. 14537.5 s^-1 b. 14.5 s^-1 c. 58750 s^-1 d. 58.8 s^-1 e. 151509.1 s^-1 12. Which of the following represents a Ping-Pong bisubstrate reaction? 13. You are trying to confirm that an enzyme you are studying has the following amino acid in its active site, and that this amino is critical for catalysis:
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Which of the following inhibitors could you use to provide evidence of the importance of this amino acid for enzyme function? a. Nevirapine b. Diethylpyrocarbonate c. Iodoacetate d. Tetranitromethane e. 2,3-Butanedione 14. Which of the following statements regarding the allosteric mechanism of hemoglobin is INCORRECT? a. The coordination of oxygen by the heme iron and reduction of steric clashing through F-helix movement are more enthalpically favourable than the presence of salt bridges at the dimer-dimer interface, favouring the R-state at high oxygen concentrations. b. The T-to-R state transition occurs due to the loss of critical ionic bonds at the dimer-dimer interface. c. The KNF (or Sequential) model better describes Hemoglobin allostery than the MWC (or Symmetry) mode d. In the T state, the deoxygenated heme unit assumes a domed conformation; The R state occurs upon oxygen binding, which flattens the heme and forces an 8° rotation of the proximal His e. While the presence of the D helix differentiates the 𝛃 from the ɑ subunits, both subunit types have helices E and F involved in the heme binding pocket. 15. What is the standard free energy of the transition state for a first order reaction proceeding at 37°C at a rate of 12S^-1. Gas constant = 8.31J mol^-1 K^-1; Bond vibrational frequency = 6.2X10^12 s^-1 a. 8.3kJ/mol b. 62.0kJ/mol c. 58.5 kJ/mol d. 69.5 kJ/mol e. 6.5 kJ/mol
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16. Which of the following statements surrounding enzyme catalysis is INCORRECT? 17. A receptor, R, binds to its ligand, L, according to the binding curve shown below. If [R]= 17.5mM at the K D what is the concentration of the receptor-ligand complex at the K D ?
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18. The following is a Hill Plot for a receptor-ligand interaction:
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What fold-difference exists between the K D of the first and the K D of the second binding event? a. 10 b. 6 c. 1000000 d. 100000000002 ______________________________________________________________________________ Quiz 5 1. Given the active site diagram below, identify the numbered region corresponding to a basic catalytic residue.
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a. 2 b. 3 c. 1 d. 4 e. There is no basic catalytic residue present 2. Given the active site diagram below, which best described the mechanism(s) of catalysis? a. Acid-Base & Covalent Catalysis b. Acid-Base c. Covalent Catalysis d. Metal Ion e. Acid-Base & Metal Ion
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3. Given the active site diagram below, which best described the mechanism(s) of catalysis? a. Acid-Base & Covalent Catalysis b. Acid-Base c. Covalent Catalysis d. Metal Ion e. Acid-Base & Metal Ion 4. Given the active site diagram below, identify the numbered region corresponding to a basic catalytic residue.
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a. 4 b. 1 c. 3 d. 5 e. 2 5. Which of the following thermodynamic changes promotes catalysis for an enzyme whose primary mechanism of action is induced fit? 6. Which of the following statements regarding ATCase activity is INCORRECT?
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7. In the fatty acid synthase enzyme called HMGCS2, a critical lysine residue can be acetylated by an acyl transferase enzyme, which alters the catalytic site and promotes catalysis. However, removal of the acetylation by deactylases can restore the inactive form of HMGCS2. What is the mechanism of regulation of HMGCS2? a. Proteolytic activation b. Reversible covalent modification c. Allostery d. Multiple forms of enzymes e. Transcriptional control 8. Ornithine, a non-proteinogenic amino acid, is produced enzymatically from arginine by an enzyme called arginase. In the fetus there is almost no need for ornithine, but this need is greatly increased after birth. This differential need for ornithine depending on stage of life is accommodated for by having a fetal and adult version of arginase, where the fetal Km is much higher than the adult Km. This mechanism of enzyme regulation is called: a. Proteolytic activation b. Reversible covalent modification c. Allostery d. Multiple forms of enzymes e. Transcriptional control 9. The following is the chemical structure of nicotinamide adenine dinucleotides, a coenzyme commonly used in enzymatic reactions. Which of the indicate regions is the site of the redox activity of this coenzyme? a. 3 b. 1 c. 4 d. 2 e. 5 10. Given the active site diagram below, identify the numbered region corresponding to a acidic catalytic residue.
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a. 2 b. 1 c. 3 d. 5 e. 4 11. Given the active site diagram below, identify the numbered region corresponding to an acidic catalytic residue.
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a. 4 b. 3 c. 2 d. 1 e. There is no acidic, catalytic residue present 12. Given the active site diagram below, identify the numbered region corresponding to a acidic catalytic residue.
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a. 3 b. 4 c. 5 d. 2 e. 1 13. Which of the following statements regarding the regulation of hexokinase activity is INCORRECT? 14. Given the active site diagram below, identify the numbered region corresponding to catalytic nucleophile.
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a. 1 b. 4 c. 2 d. 3 e. 5 15. Which of the following statements regarding the mechanism of serine protease catalysis is INCORRECT? 16. Below is an enzyme activity plot, where the blue curve 'B' is the activity of the enzyme in the absence of allosteric effectors. In the presence of an allosteric effector that increases the T-state fraction of enzyme, which curve most likely represent the enzyme activity?
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17. Below is an enzyme activity plot, where the blue curve 'B' is the activity of the enzyme in the absence of allosteric effectors. In the presence of an allosteric effector that decreases the R-state fraction of enzyme, which curve most likely represent the enzyme activity?
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B C A 18. Given the active site and reaction mechanism below, what is the mechanism of irreversible inhibition of the inhibitor provided? a. Mechanism-based b. Uncompetitive c. Non-specific d. Transition state analog e. Affinity-based
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19. Given the active site and reaction mechanism below, what is the mechanism of irreversible inhibition of the inhibitor provided? a. Non-specific b. Transition state analog c. Affinity-based d. Uncompetitive e. Mechanism-based 20. The zymogen form of an enzyme is its inactive form. a. True b. False ___________________________________________________________________________ Quiz 6 1. Which of the following protease classes does the HIV protease fall under? a. Cysteine protease b. Aspartyl protease c. Metalloprotease d. Dismutyl protease e. Serine protease 2. At the end of the exon splicing cascade, the G cofactor becomes covalently linked to the 3' end of the spliced intron. a. True b. False 3. The correct protonation states of ribozyme catalytic residues is maintained through which of the following mechanisms?
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a. The stable coordination of metal cations in the active site. b. Organization of the ribozyme active site residues to result in the lowest energy transition state energies when the correct protonation states are present in the catalytic residue c. The close approximation of charged nucleotide groups to catalytic residues to stabilize the protonation state necessary for catalysis d. A and B e. A, B, and C 4. Which of the base pairs shown below represent a non-standard or wobble base pairing? a. 4 b. 2 c. 1 d. 2 and 3 e. 3 5. Which of the following statements is NOT a reason that the folding process of non-coding RNA and proteins are different? a. The folding process of RNA is templated by previously folded RNA structures, but the folding of proteins is not templated b. The polyphosphate backbone of RNA presents a barrier to folding, where the backbone of proteins provide a driving force to folding c. The free energy minima that arise along of the non-coding RNA folding pathway are deeper than those along the protein folding pathway d. RNA has fewer building blocks than proteins e. The hydrophobic collapse only makes a big contribution to protein folding 6. Which of the following bases is only found in RNA? A B C
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D E 7. Match the molecule size to the specific form of miRNA. __3__ primary miRNA __1__ precursor miRNA __3__ mature mRNA a. >500 nucleotides → 1 b. 60-120 nucleotides → 2 c. 20-22 nucleotides → 3 d. 300-400 nucleotides → 4 e. 200-300 nucleotides → 8. In the RNA folding process, counterions help neutralize the backbone charges, promoting RNA strand compaction, and ultimately help drive proper folding of non-coding RNA. a. True b. False 9. In the discovery of miRNA, which of the following statements are INCORRECT? a. lin-4 was found in a gene that had a start codon, but no traditional stop codons. b. lin-4 regulates Lin-14 protein levels by binding the 3'-UTR of the lin-14 transcript. c. lin-4 was found to post-transcriptionally regulate Lin-14 protein expression.
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d. When the open reading frame of lin-4 was mutated, Lin-14 suppression was maintained suggesting it did not require protein. e. lin-4 loss leads to developmental defects in C. elegans. 10. pre-mRNA maturation to mRNA involves a guanosine nucleotide that is not part of the RNA polymer undergoing splicing a. True b. False 11. Which of the following statements regarding the GNRA-motif is INCORRECT? a. The motif is composed of a guanosine-any base-purine-adenosine in the loop region b. The GNRA-motif forms the anti-codon of tRNA to allow for specific recognition of protein structure encoded by mRNA c. The G and A nucleotides undergo a sugar edge-sugar edge non-standard base pair interaction to stabilize the tetraloop d. The GNRA-motif is a specialized hairpin loop stabilized by base pairing and pi-pi stacking e. The GNRA-motif is formed from a single strand of RNA that has folded back on itself. 12. Identify the structure for dihydrouridine from the nucleosides below.
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13. Identify the structure for pseudouridine from the nucleosides below 14. Noncoding RNA includes:
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1. Long non-coding RNA 2. Short non-coding RNA 3. Protein coding RNA a. 3 only b. 2 and 3 c. 1 and 3 d. 1,2 and 3 e. 1 and 2
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