Question 1

In trypsin the specificity for one substrate over another comes from

Accepted Answer

A) the negatively charged pocket. 
B) the positively charge pocket. 
C) the hydrophobic pocket. 
D) the amino acid serine. 
E) the amino acid histidine. 
A) the negatively charged pocket. 
B) the positively charge pocket. 
C) the hydrophobic pocket. 
D) the amino acid serine. 
E) the amino acid histidine. A

Question 2

Glu 35 of lysozyme is found in a nonpolar environment.Which of the following is true?

Accepted Answer

A) Its pK is lower than the usual value in this environment. 
B) Its pK is higher than the usual value in this environment. 
C) Its pK would not change in this environment. 
D) Its pK would depend on the sample buffer. 
E) None of the above is correct. 
A) Its pK is lower than the usual value in this environment. 
B) Its pK is higher than the usual value in this environment. 
C) Its pK would not change in this environment. 
D) Its pK would depend on the sample buffer. 
E) None of the above is correct. B

Question 3

Matching

-Metal ion cofactors can coordinate to the substrate or stabilize electrostatic effects by enabling proper ______in the active site.

Accepted Answer

A)  high 
B)  deprotonated 
C)  protonated 
D)  catalytic mechanism 
E)  covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid 
J) low
K) coenzymes 
L) concerted acid-base
M) orientation
N) oxidation 
A)  high 
B)  deprotonated 
C)  protonated 
D)  catalytic mechanism 
E)  covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid 
J) low
K) coenzymes 
L) concerted acid-base
M) orientation
N) oxidation M

Question 4

A pH versus rate curve with an inflection point at pH~4 suggests the involvement of a(n)________ in the catalytic step.

Accepted Answer

A) proton abstraction that requires a metal ion in close proximity 
B) proton transfer with a pK close to 4 
C) proton donation that is mediated by a coenzyme 
D) free proton surrounded by a hydrophobic environment 
E) redox cofactor 
A) proton abstraction that requires a metal ion in close proximity 
B) proton transfer with a pK close to 4 
C) proton donation that is mediated by a coenzyme 
D) free proton surrounded by a hydrophobic environment 
E) redox cofactor

Question 5

Matching

-Large rate enhancement in enzyme catalysis may occur when binding the substrate via _________ attachment.

Accepted Answer

A)  high 
B)  deprotonated 
C)  protonated 
D)  catalytic mechanism 
E)  covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid 
J) low
K) coenzymes 
L) concerted acid-base
M) orientation
N) oxidation 
A)  high 
B)  deprotonated 
C)  protonated 
D)  catalytic mechanism 
E)  covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid 
J) low
K) coenzymes 
L) concerted acid-base
M) orientation
N) oxidation

Question 6

The transition state of an enzyme and substrate reaction

Accepted Answer

A) must always bind the enzyme active site with lower energy than the products. 
B) is stabilized by enhancing the reverse reaction of E + S→ES. 
C) is composed of true covalent bonds which decrease its energy. 
D) is stabilized due to the specificity of the active site for the substrate. 
E) is stabilized by decreasing the effective concentration. 
A) must always bind the enzyme active site with lower energy than the products. 
B) is stabilized by enhancing the reverse reaction of E + S→ES. 
C) is composed of true covalent bonds which decrease its energy. 
D) is stabilized due to the specificity of the active site for the substrate. 
E) is stabilized by decreasing the effective concentration.

Question 7

Matching

-Since proteins are limited in their abilities to catalyze oxidation-reduction reactions,enzymes often employ ______ to assist with catalysis.

Accepted Answer

A)  high 
B)  deprotonated 
C)  protonated 
D)  catalytic mechanism 
E)  covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid 
J) low
K) coenzymes 
L) concerted acid-base
M) orientation
N) oxidation 
A)  high 
B)  deprotonated 
C)  protonated 
D)  catalytic mechanism 
E)  covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid 
J) low
K) coenzymes 
L) concerted acid-base
M) orientation
N) oxidation

Question 8

Which of these amino acid groups would not make a good nucleophilic catalyst?

Accepted Answer

A) amino 
B) sulfhydryl 
C) imidazole 
D) methyl 
E) hydroxyl 
A) amino 
B) sulfhydryl 
C) imidazole 
D) methyl 
E) hydroxyl

Question 9

Carbohydrate metabolic enzymes bind D-glucose specifically.D-glucose has an estimated caloric value of 1 kcal per 4 grams of carbohydrate.Based on the methods used to convert the energy of D-glucose into a useable form,what would you estimate the caloric value of L-glucose to be using the same method?

Accepted Answer

A) 1 kcal per 4 grams 
B) 1 kcal per 2 grams 
C) 1 kcal per 8 grams 
D) 0 kcal per 4 grams 
E) 2 kcal per 8 grams 
A) 1 kcal per 4 grams 
B) 1 kcal per 2 grams 
C) 1 kcal per 8 grams 
D) 0 kcal per 4 grams 
E) 2 kcal per 8 grams

Question 10

In the lysozome reaction the D ring in NAM is in the ________ conformation providing a contribution of catalytic energy via the ____ distortion.

Accepted Answer

A) half-chair;electrostatic 
B) chair;strain 
C) boat;strain 
D) boat;electrostatic 
E) half-chair;strain 
A) half-chair;electrostatic 
B) chair;strain 
C) boat;strain 
D) boat;electrostatic 
E) half-chair;strain

Question 11

If you add enzyme to a solution containing only the product(s)of a reaction,would you expect any substrate to form?

Accepted Answer

A) It depends on the time interval and temperature of reaction. 
B) It depends on the concentration of products added. 
C) It depends on the energy difference between E + P and the transition state. 
D) All of the above may determine if product forms. 
E) None of the above determines if product forms. 
A) It depends on the time interval and temperature of reaction. 
B) It depends on the concentration of products added. 
C) It depends on the energy difference between E + P and the transition state. 
D) All of the above may determine if product forms. 
E) None of the above determines if product forms.

Question 12

Which of the following amino acid residues would not provide a side chain for acid-base catalysis at physiological pH? (Assume pK values of each amino acid are equal to the pK value for the free amino acid in solution. )
(I)leucine
(II)lysine
(III)aspartic acid
(IV)histidine

Accepted Answer

A) I,II,III 
B) I,II 
C) I 
D) II 
E) I,III 
A) I,II,III 
B) I,II 
C) I 
D) II 
E) I,III

Question 13

Serine proteases use _________ to catalyze the cleavage of a peptide bond.
(I)covalent catalysis
(II)proximity and orientation effects
(III)general base catalysis
(IV)electrostatic catalysis

Accepted Answer

A) I,II 
B) II 
C) III 
D) I,II,III 
E) I,II,III,IV 
A) I,II 
B) II 
C) III 
D) I,II,III 
E) I,II,III,IV

Question 14

Enzymes that bind reaction transition states with greater affinity than substrates or products

Accepted Answer

A) have a lower free energy ES complex than E + S. 
B) increase reaction rates by decreasing the concentration of the transition state . 
C) progress slowly due to the stability of the transition state complex. 
D) compensate for small differences in the energy of the free substrate and free product. 
E) All of the above are correct. 
A) have a lower free energy ES complex than E + S. 
B) increase reaction rates by decreasing the concentration of the transition state . 
C) progress slowly due to the stability of the transition state complex. 
D) compensate for small differences in the energy of the free substrate and free product. 
E) All of the above are correct.

Question 15

The imidazole side chain of histidine can function as either a general acid catalyst or a general base catalyst because
(I)the imidazole group has a pKa in the physiological pH range.
(II)in the physiological pH range,the nitrogen in the ring can be easily protonated/deprotonated.
(III)one guanidino group is protonated,and the other is deprotonated at physiological pH.
(IV)the imidazole group is a strong reducing agent at physiological pH.

Accepted Answer

A) I,II 
B) I 
C) II,IV 
D) II,III 
E) IV 
A) I,II 
B) I 
C) II,IV 
D) II,III 
E) IV

Question 16

Matching

-For efficient nucleophilic catalysis,a group such as the sulfhydryl on a cysteine residue must be able to form a good ______,in addition to being a good nucleophile.

Accepted Answer

A)  high 
B)  deprotonated 
C)  protonated 
D)  catalytic mechanism 
E)  covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid 
J) low
K) coenzymes 
L) concerted acid-base
M) orientation
N) oxidation 
A)  high 
B)  deprotonated 
C)  protonated 
D)  catalytic mechanism 
E)  covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid 
J) low
K) coenzymes 
L) concerted acid-base
M) orientation
N) oxidation

Question 17

Which of the following would result in the greatest decrease in function of the catalytic triad found in serine proteases?

Accepted Answer

A) Mutation to Ser,Cys,Asp 
B) Mutation to Ser,His,Asp 
C) Mutation to Cys,His,Asp 
D) Mutation to Ser,His,Glu 
E) Mutation to Cys,His,Glu 
A) Mutation to Ser,Cys,Asp 
B) Mutation to Ser,His,Asp 
C) Mutation to Cys,His,Asp 
D) Mutation to Ser,His,Glu 
E) Mutation to Cys,His,Glu

Question 18

Research scientists are trying to clone a gene.In order to accomplish this task they join two pieces of DNA.Which class of the enzymes below might accomplish this task?

Accepted Answer

A) oxidoreductase 
B) ligase 
C) hydrolase 
D) isomerase 
E) lyase 
A) oxidoreductase 
B) ligase 
C) hydrolase 
D) isomerase 
E) lyase

Question 19

Matching

-Some serine proteases are believed to have developed by convergent evolution,because the ______ sequences of some serine proteases show no resemblance to those of others.

Accepted Answer

A)  high 
B)  deprotonated 
C)  protonated 
D)  catalytic mechanism 
E)  covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid 
J) low
K) coenzymes 
L) concerted acid-base
M) orientation
N) oxidation 
A)  high 
B)  deprotonated 
C)  protonated 
D)  catalytic mechanism 
E)  covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid 
J) low
K) coenzymes 
L) concerted acid-base
M) orientation
N) oxidation

Question 20

Which of the following amino acid residues would provide a side chain capable of increasing the hydrophobicity of a binding site?

Accepted Answer

A) histidine 
B) lysine 
C) isoleucine 
D) arginine 
E) serine 
A) histidine 
B) lysine 
C) isoleucine 
D) arginine 
E) serine

Exam 11: Enzyme Catalysis

In trypsin the specificity for one substrate over another comes from

Glu 35 of lysozyme is found in a nonpolar environment.Which of the following is true?

Matching -Metal ion cofactors can coordinate to the substrate or stabilize electrostatic effects by enabling proper ______in the active site.

A pH versus rate curve with an inflection point at pH~4 suggests the involvement of a(n)________ in the catalytic step.

Matching -Large rate enhancement in enzyme catalysis may occur when binding the substrate via _________ attachment.

The transition state of an enzyme and substrate reaction

Matching -Since proteins are limited in their abilities to catalyze oxidation-reduction reactions,enzymes often employ ______ to assist with catalysis.

Which of these amino acid groups would not make a good nucleophilic catalyst?

In the lysozome reaction the D ring in NAM is in the ________ conformation providing a contribution of catalytic energy via the ____ distortion.

If you add enzyme to a solution containing only the product(s)of a reaction,would you expect any substrate to form?

Which of the following amino acid residues would not provide a side chain for acid-base catalysis at physiological pH? (Assume pK values of each amino acid are equal to the pK value for the free amino acid in solution. ) (I)leucine (II)lysine (III)aspartic acid (IV)histidine

Serine proteases use _________ to catalyze the cleavage of a peptide bond. (I)covalent catalysis (II)proximity and orientation effects (III)general base catalysis (IV)electrostatic catalysis

Enzymes that bind reaction transition states with greater affinity than substrates or products

Matching -For efficient nucleophilic catalysis,a group such as the sulfhydryl on a cysteine residue must be able to form a good ______,in addition to being a good nucleophile.

Which of the following would result in the greatest decrease in function of the catalytic triad found in serine proteases?

Research scientists are trying to clone a gene.In order to accomplish this task they join two pieces of DNA.Which class of the enzymes below might accomplish this task?

Matching -Some serine proteases are believed to have developed by convergent evolution,because the ______ sequences of some serine proteases show no resemblance to those of others.

Which of the following amino acid residues would provide a side chain capable of increasing the hydrophobicity of a binding site?

Introduction to the Chemistry of Life

Water

Nucleotides, nucleic Acids, and Genetic Information

Amino Acids

Proteins: Primary Structure

Proteins: Three-Dimensional Structure

Protein Function Part I: Myoglobin and Hemoglobin

Carbohydrates

Lipids and Biological Membranes

Membrane Transport

Enzyme Kinetics, inhibition and Control

Biochemical Signaling

Introduction to Metabolism

Glucose Catabolism

Glycogen Metabolism and Gluconeogenesis

Citric Acid Cycle

Electron Transport and Oxidative Phosphorylation

Photosynthesis

Lipid Metabolism

Amino Acid Metabolism

Mammalian Fuel Metabolism: Integration and Regulation

Nucleotide Metabolism

Nucleic Acid Structure

DNA Replication, repair and Recombination

Transcription and Rna Processing

Protein Synthesis

Regulation of Gene Expression

Filters

In the lysozome reaction the D ring in NAM is in the ____ conformation providing a contribution of catalytic energy via the distortion.