Question 1

Metal ion catalysis include all EXCEPT:

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)  metal binding weakly, perhaps only during the catalytic cycle. 
D)  electrophilic catalysis, stabilizing the increased electron density or negative charge that can develop during a reaction. 
E)  all are true. 
A)  increased acidity of a nucleophile with an ionizable proton. 
B)  metal ion requirement to maintain the stable, native state of the enzyme. 
C)  metal binding weakly, perhaps only during the catalytic cycle. 
D)  electrophilic catalysis, stabilizing the increased electron density or negative charge that can develop during a reaction. 
E)  all are true.

Question 2

The mechanism of aspartate protease catalysis is proposed to be:

Accepted Answer

A)  covalent nucleophilic catalysis. 
B)  covalent electrophilic catalysis. 
C)  specific base catalysis. 
D)  general base-general acid catalysis facilitated by a low barrier hydrogen bond. 
E)  all of the above. 
A)  covalent nucleophilic catalysis. 
B)  covalent electrophilic catalysis. 
C)  specific base catalysis. 
D)  general base-general acid catalysis facilitated by a low barrier hydrogen bond. 
E)  all of the above.

Question 3

All are true for low-barrier hydrogen bonds EXCEPT:

Accepted Answer

A)  The hydrogen is centered between the two heteroatoms. 
B)  The interactions are more covalent. 
C)  The bond order approaches 0.5 for both O−H interactions. 
D)  The barrier that the hydrogen atom must surmount to exchange oxygens becomes lower. 
E)  All are true. 
A)  The hydrogen is centered between the two heteroatoms. 
B)  The interactions are more covalent. 
C)  The bond order approaches 0.5 for both O−H interactions. 
D)  The barrier that the hydrogen atom must surmount to exchange oxygens becomes lower. 
E)  All are true.

Question 4

HIV-1 protease is different from most mammalian aspartic acid proteases in that it has:

Accepted Answer

A)  two subunits each with a two-aspartate active site. 
B)  two subunits each contributing an aspartate to the active site. 
C)  two active sites on one protein. 
D)  two subunits, one with an active site, and the other with a regulatory activity. 
E)  none of the above. 
A)  two subunits each with a two-aspartate active site. 
B)  two subunits each contributing an aspartate to the active site. 
C)  two active sites on one protein. 
D)  two subunits, one with an active site, and the other with a regulatory activity. 
E)  none of the above.

Question 5

Effective HIV-1 protease inhibitors should have all of the following characteristics EXCEPT:

Accepted Answer

A)  effective delivery in sufficient quantities to the desired site(s) of action in the organism. 
B)  relative specificity for the HIV-1 protease. 
C)  a backbone −OH group that forms a weak association with the two active-site carboxyl groups of the protease. 
D)  results in inhibiting the production of new virus particles in cells of infected patients. 
E)  broad spectrum enough to be effective against mutant viral forms. 
A)  effective delivery in sufficient quantities to the desired site(s) of action in the organism. 
B)  relative specificity for the HIV-1 protease. 
C)  a backbone −OH group that forms a weak association with the two active-site carboxyl groups of the protease. 
D)  results in inhibiting the production of new virus particles in cells of infected patients. 
E)  broad spectrum enough to be effective against mutant viral forms.

Question 6

Aspartate proteases display a variety of substrate specificities, but normally they are most active in cleavage of peptide bonds:

Accepted Answer

A)  on the carboxyl side of the basic amino acids. 
B)  on the carboxyl side of aromatic amino acids. 
C)  on the carboxyl side of small, neutral residues. 
D)  between two hydrophobic amino acid residues. 
E)  none of the above. 
A)  on the carboxyl side of the basic amino acids. 
B)  on the carboxyl side of aromatic amino acids. 
C)  on the carboxyl side of small, neutral residues. 
D)  between two hydrophobic amino acid residues. 
E)  none of the above.

Question 7

If the transition state of an enzyme catalyzed reaction contained a positive charge, which of the following amino acids would most likely be present in the active site to aid in transition state formation?

Accepted Answer

A)  Lys 
B)  Val 
C)  Asn 
D)  Glu 
E)  Cys 
A)  Lys 
B)  Val 
C)  Asn 
D)  Glu 
E)  Cys

Question 8

The catalytic mechanism below is an example of:

Accepted Answer

A)  covalent nucleophilic catalysis. 
B)  covalent electrophilic catalysis. 
C)  specific base catalysis. 
D)  general base catalysis. 
E)  low barrier hydrogen bond catalysis. 
A)  covalent nucleophilic catalysis. 
B)  covalent electrophilic catalysis. 
C)  specific base catalysis. 
D)  general base catalysis. 
E)  low barrier hydrogen bond catalysis.

Question 9

An enzyme-catalyzed reaction rate will be increased if the energy level of ES can be increased. Which of the following will not increase the energy level of ES?

Accepted Answer

A)  destabilization of ES by strain caused by non-covalent interactions between E and S. 
B)  loss of entropy due to binding of E and S. 
C)  destabilization of ES by distortion. 
D)  destabilization of ES by solvation. 
E)  destabilization of ES by electrostatic effects. 
A)  destabilization of ES by strain caused by non-covalent interactions between E and S. 
B)  loss of entropy due to binding of E and S. 
C)  destabilization of ES by distortion. 
D)  destabilization of ES by solvation. 
E)  destabilization of ES by electrostatic effects.

Question 10

Since enzymes are not rigid molecules but rather flexible proteins, which of the following may be attributed to this fact?

Accepted Answer

A)  active sites are able to conform to the shape of the substrate 
B)  catalytic residues are oriented in such as way to aid in bond breakage and bond formation 
C)  strain is placed upon the substrate while it binds to the enzyme 
D)  near-attack conformations are achieved during formation of the transition state during an enzyme catalyzed reaction 
E)  all of the above are correct 
A)  active sites are able to conform to the shape of the substrate 
B)  catalytic residues are oriented in such as way to aid in bond breakage and bond formation 
C)  strain is placed upon the substrate while it binds to the enzyme 
D)  near-attack conformations are achieved during formation of the transition state during an enzyme catalyzed reaction 
E)  all of the above are correct

Question 11

In the chymotrypsin reaction mechanism there is a low-barrier hydrogen bond (LBHB) formed between:

Accepted Answer

A)  Asp102 and Ser195. 
B)  Asp102 and His57. 
C)  His57 and Ser195. 
D)  Ser195 and carbonyl oxygen in the peptide bond. 
E)  None of the above. 
A)  Asp102 and Ser195. 
B)  Asp102 and His57. 
C)  His57 and Ser195. 
D)  Ser195 and carbonyl oxygen in the peptide bond. 
E)  None of the above.

Question 12

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

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 
E)  none of the above are true 
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 
E)  none of the above are true

Question 13

All are catalytic mechanisms or factors that contribute to the performance of enzymes EXCEPT:

Accepted Answer

A)  entropy gain in ES formation. 
B)  covalent catalysis. 
C)  general acid or base catalysis. 
D)  proximity and orientation. 
E)  all are true. 
A)  entropy gain in ES formation. 
B)  covalent catalysis. 
C)  general acid or base catalysis. 
D)  proximity and orientation. 
E)  all are true.

Question 14

Enzymes have active sites which have the greatest complementarity to the:

Accepted Answer

A)  substrate. 
B)  transition state. 
C)  product. 
D)  both substrate and product. 
E)  none of the above. 
A)  substrate. 
B)  transition state. 
C)  product. 
D)  both substrate and product. 
E)  none of the above.

Exam 14: Mechanisms of Enzyme Action

Metal ion catalysis include all EXCEPT:

The mechanism of aspartate protease catalysis is proposed to be:

All are true for low-barrier hydrogen bonds EXCEPT:

HIV-1 protease is different from most mammalian aspartic acid proteases in that it has:

Effective HIV-1 protease inhibitors should have all of the following characteristics EXCEPT:

Aspartate proteases display a variety of substrate specificities, but normally they are most active in cleavage of peptide bonds:

If the transition state of an enzyme catalyzed reaction contained a positive charge, which of the following amino acids would most likely be present in the active site to aid in transition state formation?

The catalytic mechanism below is an example of:

An enzyme-catalyzed reaction rate will be increased if the energy level of ES can be increased. Which of the following will not increase the energy level of ES?

Since enzymes are not rigid molecules but rather flexible proteins, which of the following may be attributed to this fact?

In the chymotrypsin reaction mechanism there is a low-barrier hydrogen bond (LBHB) formed between:

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

All are catalytic mechanisms or factors that contribute to the performance of enzymes EXCEPT:

Enzymes have active sites which have the greatest complementarity to the:

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

Water: the Medium of Life

Thermodynamics of Biological Systems

Amino Acids and the Peptide Bond

Proteins: Their Primary Structure and Biological Functions

Proteins: Secondary, Tertiary, and Quaternary Structure

Carbohydrates and the Glycoconjugates of Cell Surfaces

Lipids

Membranes and Membrane Transport

Nucleotides and Nucleic Acids

Structure of Nucleic Acids

Recombinant Dna, Cloning, Chimeric Genes, and Synthetic Biology

Enzymeskinetics and Specificity

Enzyme Regulation

Molecular Motors

Metabolism: an Overview

Glycolysis

The Tricarboxylic Acid Cycle

Electron Transport and Oxidative Phosphorylation

Photosynthesis

Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

Fatty Acid Catabolism

Lipid Biosynthesis

Nitrogen Acquisition and Amino Acid Metabolism

Synthesis and Degradation of Nucleotides

Metabolic Integration and Organ Specialization

Dna Metabolism: Replication, Recombination, and Repair

Transcription and the Regulation of Gene Expression

Protein Synthesis

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

The Reception and Transmission of Extracellular Information

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