Question 1

Which of the following structures has the greatest complementarity to enzyme active sites?

Accepted Answer

A) substrate 
B) transition state 
C) product 
D) stable intermediate 
A) substrate 
B) transition state 
C) product 
D) stable intermediate B

Question 2

Which of the following pairs below forms a low-barrier hydrogen bond?

Accepted Answer

A) Asp102 and Ser195 
B) Asp102 and His57 
C) His57 and Ser195 
D) Ser195 and carbonyl oxygen in the peptide bond 
A) Asp102 and Ser195 
B) Asp102 and His57 
C) His57 and Ser195 
D) Ser195 and carbonyl oxygen in the peptide bond B

Question 3

The catalytic triad common to many serine proteases involves shuttling of protons between the amino acids in the catalytic triad.Which of the following amino acid sequences is in the correct order for this process?

Accepted Answer

A) Ser-His-Asp 
B) His-Ser-Asp 
C) Ser-His-His 
D) Asp-His-Ser 
A) Ser-His-Asp 
B) His-Ser-Asp 
C) Ser-His-His 
D) Asp-His-Ser A

Question 4

Which of the following determines the enzymatic reaction rate?

Accepted Answer

A) the difference in energy between ES and S 
B) the difference in energy between ES and P 
C) the difference in energy between ES and EX‡ 
D) the difference in energy between ES and ESI 
A) the difference in energy between ES and S 
B) the difference in energy between ES and P 
C) the difference in energy between ES and EX‡ 
D) the difference in energy between ES and ESI

Question 5

Which of the following attributes does NOT explain why enzymes are flexible proteins and NOT rigid molecules?

Accepted Answer

A) Active sites are able to conform to the shape of the substrate. 
B) Strain is placed upon the substrate while it binds to the enzyme. 
C) Catalytic residues are oriented in such a way that they play a minor role in bond breakage and bond formation. 
D) Near-attack conformations are achieved during formation of the transition state during an enzyme-catalyzed reaction. 
A) Active sites are able to conform to the shape of the substrate. 
B) Strain is placed upon the substrate while it binds to the enzyme. 
C) Catalytic residues are oriented in such a way that they play a minor role in bond breakage and bond formation. 
D) Near-attack conformations are achieved during formation of the transition state during an enzyme-catalyzed reaction.

Question 6

Which of the following amino acid side chains is often involved in general acid-base catalysis because its pKₐ is near 7?

Accepted Answer

A) cysteine 
B) aspartate 
C) histidine 
D) lysine 
A) cysteine 
B) aspartate 
C) histidine 
D) lysine

Question 7

Which of the following types of kinetic mechanisms is used by enzymes carrying out covalent catalysis?

Accepted Answer

A) Ping-Pong 
B) sequential bisubstrate 
C) random bisubstrate 
D) simple unimolecular 
A) Ping-Pong 
B) sequential bisubstrate 
C) random bisubstrate 
D) simple unimolecular

Question 8

Which of the following values is the estimated approximate lifetime of the transition state?

Accepted Answer

A) microseconds (10-6 s) 
B) nanoseconds (10-9 s) 
C) (10-14 to 10-13 s) 
D) (10-20 s) 
A) microseconds (10-6 s) 
B) nanoseconds (10-9 s) 
C) (10-14 to 10-13 s) 
D) (10-20 s)

Question 9

Which of the following is a feature of transition-state analogs?

Accepted Answer

A) They are approximations of the transition state that bind less tightly than the substrate. 
B) They are compounds that compete for the active site and are always very similar to the substrate. 
C) They are stable molecules that are chemically and structurally similar to the transition state. 
D) They are stable molecules that can be expected to resemble the true transition state very closely. 
A) They are approximations of the transition state that bind less tightly than the substrate. 
B) They are compounds that compete for the active site and are always very similar to the substrate. 
C) They are stable molecules that are chemically and structurally similar to the transition state. 
D) They are stable molecules that can be expected to resemble the true transition state very closely.

Question 10

Aspartate proteases display a variety of substrate specificities.Which of the following peptide bonds,however,do they most actively cleave?

Accepted Answer

A) those on the carboxyl side of the basic amino acids 
B) those on the amino side of aromatic amino acids 
C) those between 2 small,neutral residues 
D) those between 2 hydrophobic amino acid residues 
A) those on the carboxyl side of the basic amino acids 
B) those on the amino side of aromatic amino acids 
C) those between 2 small,neutral residues 
D) those between 2 hydrophobic amino acid residues

Question 11

Which of the following types of catalytic mechanisms classifies the reaction below?

Accepted Answer

A) covalent nucleophilic 
B) covalent electrophilic 
C) specific base catalysis 
D) general base catalysis 
A) covalent nucleophilic 
B) covalent electrophilic 
C) specific base catalysis 
D) general base catalysis

Question 12

Which of the following is NOT a characteristic of an effective HIV-1 protease inhibitor?

Accepted Answer

A) effective delivery in sufficient quantities to the desired site(s)of action in the organism 
B) broad spectrum enough to be effective against mutant viral forms 
C) a backbone -OH group that forms a weak association with the 2 active-site carboxyl groups of the protease 
D) results in inhibiting the production of new virus particles in cells of infected patients 
A) effective delivery in sufficient quantities to the desired site(s)of action in the organism 
B) broad spectrum enough to be effective against mutant viral forms 
C) a backbone -OH group that forms a weak association with the 2 active-site carboxyl groups of the protease 
D) results in inhibiting the production of new virus particles in cells of infected patients

Question 13

Which of the following is NOT a characteristic of metal ion catalysis?

Accepted Answer

A) increased acidity of a nucleophile with an ionizable proton 
B) metal ion requirement to maintain the stable,native state of the enzyme 
C) strongly metal binding,perhaps not only during the catalytic cycle 
D) electrophilic catalysis,stabilizing the increased electron density or negative charge that can develop during a reaction 
A) increased acidity of a nucleophile with an ionizable proton 
B) metal ion requirement to maintain the stable,native state of the enzyme 
C) strongly metal binding,perhaps not only during the catalytic cycle 
D) electrophilic catalysis,stabilizing the increased electron density or negative charge that can develop during a reaction

Question 14

Which of the following amino acid side chains are NOT found in nucleophilic centres used for covalent catalysis?

Accepted Answer

A) methyl 
B) amines 
C) carboxylate 
D) aryl and alkyl hydroxyls 
A) methyl 
B) amines 
C) carboxylate 
D) aryl and alkyl hydroxyls

Question 15

Where is the initial bond formation located in the covalent intermediate in the chymotrypsin-catalyzed reaction?

Accepted Answer

A) between serine and the carbonyl carbon in the peptide backbone 
B) between nitrogen and the carbonyl carbon in the peptide backbone 
C) between histidine and the carbonyl carbon in the peptide backbone 
D) between aspartate and the carbonyl carbon in the peptide backbone 
A) between serine and the carbonyl carbon in the peptide backbone 
B) between nitrogen and the carbonyl carbon in the peptide backbone 
C) between histidine and the carbonyl carbon in the peptide backbone 
D) between aspartate and the carbonyl carbon in the peptide backbone

Question 16

Which of the following is NOT a catalytic mechanism or factor that contributes to the performance of enzymes?

Accepted Answer

A) entropy gain in ES formation 
B) covalent catalysis 
C) general acid or base catalysis 
D) proximity and orientation 
A) entropy gain in ES formation 
B) covalent catalysis 
C) general acid or base catalysis 
D) proximity and orientation

Question 17

Which of the following regarding for low-barrier hydrogen bonds is correct?

Accepted Answer

A) The barrier that the hydrogen atom must surmount to exchange oxygens becomes higher. 
B) The interactions are not like covalent bonds. 
C) The bond order approaches 2 for both O-H interactions. 
D) The hydrogen is centred between the 2 heteroatoms. 
A) The barrier that the hydrogen atom must surmount to exchange oxygens becomes higher. 
B) The interactions are not like covalent bonds. 
C) The bond order approaches 2 for both O-H interactions. 
D) The hydrogen is centred between the 2 heteroatoms.

Question 18

Which of the following is the proposed mechanism of aspartate protease catalysis?

Accepted Answer

A) covalent nucleophilic 
B) covalent electrophilic facilitated by a low-barrier hydrogen bond 
C) specific base catalysis 
D) general base-general acid facilitated by a low-barrier hydrogen bond 
A) covalent nucleophilic 
B) covalent electrophilic facilitated by a low-barrier hydrogen bond 
C) specific base catalysis 
D) general base-general acid facilitated by a low-barrier hydrogen bond

Question 19

Which of the following statements regarding enzymes and transition states is correct?

Accepted Answer

A) Stabilization of the transition state must be less than stabilization of ES for catalysis to occur. 
B) Binding of substrate to an enzyme often causes strain,thus promoting transition-state formation. 
C) The transition-state conformation of an enzyme-catalyzed reaction is identical to the conformation seen in the uncatalyzed transition state. 
D) Formation of the transition state always assures that the reaction will proceed to product. 
A) Stabilization of the transition state must be less than stabilization of ES for catalysis to occur. 
B) Binding of substrate to an enzyme often causes strain,thus promoting transition-state formation. 
C) The transition-state conformation of an enzyme-catalyzed reaction is identical to the conformation seen in the uncatalyzed transition state. 
D) Formation of the transition state always assures that the reaction will proceed to product.

Question 20

Which of the following regarding the enzyme-transition state complex is correct?

Accepted Answer

A) The enzyme is designed to bind the transition-state structure less tightly than the substrate or product. 
B) It is designated as EX‡. 
C) The enzyme stabilizes the transition-state complex less than it stabilizes the substrate complex. 
D) The energy barrier between ES and EX‡ is more than the energy barrier between S and X‡. 
A) The enzyme is designed to bind the transition-state structure less tightly than the substrate or product. 
B) It is designated as EX‡. 
C) The enzyme stabilizes the transition-state complex less than it stabilizes the substrate complex. 
D) The energy barrier between ES and EX‡ is more than the energy barrier between S and X‡.

Exam 13: Mechanisms of Enzyme Action

Which of the following structures has the greatest complementarity to enzyme active sites?

Which of the following pairs below forms a low-barrier hydrogen bond?

The catalytic triad common to many serine proteases involves shuttling of protons between the amino acids in the catalytic triad.Which of the following amino acid sequences is in the correct order for this process?

Which of the following determines the enzymatic reaction rate?

Which of the following attributes does NOT explain why enzymes are flexible proteins and NOT rigid molecules?

Which of the following amino acid side chains is often involved in general acid-base catalysis because its pKₐ is near 7?

Which of the following types of kinetic mechanisms is used by enzymes carrying out covalent catalysis?

Which of the following values is the estimated approximate lifetime of the transition state?

Which of the following is a feature of transition-state analogs?

Aspartate proteases display a variety of substrate specificities.Which of the following peptide bonds,however,do they most actively cleave?

Which of the following types of catalytic mechanisms classifies the reaction below?

Which of the following is NOT a characteristic of an effective HIV-1 protease inhibitor?

Which of the following is NOT a characteristic of metal ion catalysis?

Which of the following amino acid side chains are NOT found in nucleophilic centres used for covalent catalysis?

Where is the initial bond formation located in the covalent intermediate in the chymotrypsin-catalyzed reaction?

Which of the following is NOT a catalytic mechanism or factor that contributes to the performance of enzymes?

Which of the following regarding for low-barrier hydrogen bonds is correct?

Which of the following is the proposed mechanism of aspartate protease catalysis?

Which of the following statements regarding enzymes and transition states is correct?

Which of the following regarding the enzyme-transition state complex is correct?

The Facts of Life: Chemistry Is the Logic of Biological Phenomena

Water: the Medium of Life

Thermodynamics of Biological Systems

Amino Acids

Proteins: Their Primary Structure and Biological Functions

Proteins: Secondary, tertiary, and Quaternary Structure

Carbohydrates and the Glycoconjugates of Cell Surfaces

Lipids

Lipid Biosynthesis

Membranes and Membrane Transport

The Reception and Transmission of Extracellular Information

Enzymes Kinetics and Specificity

Enzyme Regulation

Molecular Motors

Nutrition and the Organization of Metabolism

Glycolysis

The Tricarboxylic Acid Cycle

Electron Transport and Oxidative Phosphorylation

Photosynthesis

Gluconeogenesis, glycogen Metabolism, and the Pentose Phosphate Pathway

Fatty Acid Catabolism

Nitrogen Acquisition and Amino Acid Metabolism

Nucleotides and Nucleic Acids

Structure of Nucleic Acids

Synthesis and Degradation of Nucleotides

Recombinant Dna: Cloning and Creation of Chimeric Genes

DNA Metabolism: Replication, recombination, and Repair

Transcription and the Regulation of Gene Expression

Protein Synthesis

Post-Transcriptional Regulation of Gene Expression

Completing the Protein Life Cycle: Folding, processing, and Degradation

Metabolic Integration and Organ Specialization

Filters