Biochem Exam 3

Front 1

Two His residues play important roles in the oxygen binding sites of hemoglobin, and myoglobin. ____________ imidazole nitrogen of proximal histidine is close enough to bond directly to the Fe2+ atom of heme whereas _____________ imidazole nitrogen of distal histidine is important for allowing an appropriate binding of O2 to the Fe2+ atom. The binding of oxygen to myoglobin and hemoglobin has what effect on the heme iron?

Back 1

a) Protonated; unprotonated; It causes the iron to move closer to the plane of the porphyrin ring. b) Protonated; unprotonated; It has no effect because the iron is restricted to being within the plane of the porphyrin ring and cannot move on binding oxygen. c) Unprotonated; protonated; It causes the iron to move closer to the plane of the porphyrin ring. d) Unprotonated; protonated; It has no effect because the iron is restricted to being within the plane of the porphyrin ring and cannot move on binding oxygen.

Hint 1

C

Front 2

Hemoglobin has a binding site for 2,3-bisphosphoglycerate (2,3-BPG) in the interface between two β subunits. This 2,3-BPG binding site of adult hemoglobin contains four positively charged His residues and two ____________ residues. Fetal hemoglobin has two γ polypeptides/subunits rather than two β polypeptides/subunits of adult hemoglobin. The reason why fetal hemoglobin has two γ polypeptides and adult hemoglobin has two β polypeptides is that ______________ .

Back 2

a) Ser; the two γ genes in fetus are transcriptionally active and those are transcriptionally inactive after birth b) Ser; the γ gene in fetus is transcriptionally active and it is transcriptionally inactive after birth c) Lys; the two γ genes in fetus are transcriptionally active and those are transcriptionally inactive after birth d) Lys; the γ gene in fetus is transcriptionally active and it is transcriptionally inactive after birth

Hint 2

D

Front 3

Sickle-cell disease causes severe anemia that is due to a single point mutation of ___________ to ___________ at the position 6 in β polypeptides/subunits of hemoglobin tetramer (α2β2). In the sickle cell disease, this mutation creates an additional hydrophobic interaction between two hemoglobin molecules. In sickle cell disease patients, each hemoglobin molecule has __________the additional hydrophobic interactions in order to the form a polymer of hemoglobin

Back 3

a) glutamate; valine; two b) glutamate; valine; four c) valine; glutamate; two d) valine; glutamate; four

Hint 3

A

Front 4

Back 4

a) enhance; adding more carbonic anhydrase b) enhance; increasing the pH c) inhibit; adding more carbonic anhydrase d) inhibit; increasing the pH

Hint 4

B

Front 5

What is percent O2 delivered to the tissues at sea level in the presence of normal 2,3-BPG level? What is percent O2 delivered to the tissues at 4,500 meter assuming in the presence of normal 2,3-BPG level?

Back 5

a) ~32%; ~32% b) ~32%; ~37% c) ~37%; ~32% d) ~37%; ~37%

Hint 5

C

Front 6

What is percent O2 delivered to the tissues at 4,500 meter at an elevated 2,3-BPG level? Will an elevated 2,3-BPG level at high altitude most likely affect O2 binding and release of myoglobin?

Back 6

a) ~40%; No b) ~40%; Yes c) ~45%; No d) ~45%; Yes

Hint 6

A

Front 7

Enzymes can increase chemical reaction rates generally by 106 – 1014 times in comparison with the non-enzyme catalyzed rate because enzymes _____________ . An enzyme that catalyzes the reaction A ↔ B often increases the _____________ .

Back 7

a) lower free energy of product(s); rate of the forward reactions, but not reverse reaction b) lower free energy of product(s); rate of both the forward and reverse reactions c) lower free energy of transition state(s); rate of the forward reactions, but not reverse reaction d) lower free energy of transition state(s); rate of both the forward and reverse reactions e) lower free energy of transition state(s); rate of the forward reaction and decreases the rate of the reverse reaction

Hint 7

D

Front 8

An abzyme is a protein generated using _____________ as an antigen. _____________ has a higher binding affinity to abzyme than substrate.

Back 8

a) a substrate; A transition state or a transition state analog b) a substrate; The antibody c) a transition state or a transition state analog; A transition state or a transition state analog d) a transition state or a transition state analog; The antibody

Hint 8

C

Front 9

Back 9

a) Staphylococcal protease, trypsin, elastase, and chymotrypsin b) trypsin, chymotrypsin, elastase and Staphylococcal protease c) trypsin, elastase, chymotrypsin and Staphylococcal protease d) trypsin, elastase, Staphylococcal protease and chymotrypsin e) trypsin, Staphylococcal protease, elastase, and chymotrypsin

Hint 9

D

Front 10

Acetylcholine esterases catalyze _____________ .

Back 10

a) A; Acetylcholine + H2O → Choline + Acetate b) A; Choline + Acetate → Acetylcholine + H2O c) B; Acetylcholine + H2O → Choline + Acetate d) B; Choline + Acetate → Acetylcholine + H2O

Hint 10

A

Front 11

P-loop domains of NMP kinases are commonly found in many enzymes. They are able to undergo conformational changes upon the binding of the substrate. A P-loop domain of NMP kinases typically contains a motif of __________________ that can interact with phosphates of ___________ .

Back 11

a) Gly-X-X-X-X-Gly-Lys; ATP b) Gly-X-X-X-X-Gly-Lys; NMP c) Pro-X-X-X-X-Pro-Lys; ATP d) Pro-X-X-X-X-Pro-Lys; NMP

Hint 11

A

Front 12

Carbonic anhydrase catalyzes a bisubstrate and bidirectional reaction: CO2 + H2O ↔ HCO3 - + H+ . The kinetics parameters, KM and Vmax are calculated by varying substrate concentrations and keeping constant enzyme concentration. Its acting on bicarbonate, HCO3 - , has KM = 0.027 M and its acting on carbon dioxide, CO2, has KM = 0.012 M. ______________ binds with higher affinity to carbonic anhydrase. If we double enzyme concentration, Vmax for acting either HCO3 - or CO2 will ______________ .

Back 12

a) CO2; double as well b) CO2; keep the same c) HCO3 - ; double as well d) HCO3 - ; keep the same

Hint 12

A

Front 13

Back 13

a) a general acid in catalysis; a general acidic residue in substrate binding site b) a general acid in catalysis; a general basic residue in substrate binding site c) a general base in catalysis; a general acidic residue in substrate binding site d) a general base in catalysis; a general basic residue in substrate binding site e) neither a general base nor a general acid in catalysis; neither a basic nor an acidic residue

Hint 13

A

Front 14

Type II restriction enzymes cut double-stranded DNA (ds DNA) known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses. Inside a bacterial host, the restriction enzymes selectively cut up foreign DNA in a process called restriction. Methylation at EcoR V sites of host genomic DNA blocks a hydrogen bond to _____________ . The restriction enzymes, EcoR V, EcoR I and BamH I have similar active sites, and their activity is pH-dependent. Their active sites often contain two amino acids, ______________

Back 14

a) EcoR V; one Asn and one Gln, or two Asn, or two Gln b) EcoR V; one Asp and one Glu, or two Asp, or two Glu c) EcoR V methylase; one Asn and one Gln, or two Asn, or two Gln d) EcoR V methylase; one Asp and one Glu, or two Asp, or two Glu

Hint 14

B

Front 15

Back 15

a) A; X b) A; Y c) B; Z d) B; X e) C; Y

Hint 15

A

Front 16

Back 16

a) A > B > C > D; X > Y > X b) A > B > C > D; Y > X > Y c) A > B > D > C; X > Y > X d) A > B > D > C; Y > X > Y

Hint 16

D

Front 17

Back 17

a) 0.75 mM; double as well; double as well b) 0.75 mM; double as well; keeps the same c) 2.10 mM; double as well; double as well d) 2.10 mM; double as well; keeps the same e) 2.10 mM; keeps the same; keeps the same

Hint 17

D

Front 18

Penicillin is an example of irreversible inhibitors through a covalent interaction with an essential serine residue in the active site of glycopeptide transpeptidase, an enzyme that acts to crosslink the peptidoglycan chains during synthesis of bacterial cell walls. What are the types of biomolecules used to build bacterial cell walls? If a bacterial cell contains a plasmid that has a penicillin resistant gene, what is the substrate of PenR?

Back 18

a) carbohydrates and lipids; glycopeptide transpeptidase b) carbohydrates and lipids; penicillin c) carbohydrates and amino acids; glycopeptide transpeptidase d) carbohydrates and amino acids; penicillin

Hint 18

D

Front 19

Which of the following is the effect of fluconazole on the lanosterol 14-DM? Which of the following amino acid changes shown in Figure 2 is most likely to alter sensitivity to fluconazole?

Back 19

a) Competitive inhibition; His → Thr b) Competitive inhibition; Lys → Arg c) Noncompetitive; His → Thr d) Noncompetitive; Lys → Arg

Hint 19

C

Front 20

The mutation alters which of the following kinetic or thermodynamic properties of the reaction catalyzed by 14-DM?

Back 20

a) neither KM nor Vmaxb) KM only c) Vmax only d) both KM and Vmax

Hint 20

D

Front 21

The bisubstrate reaction catalyzed by carbonic anhydrase is an example of __________ . The correct order of four complexes: A, B, C and D, from the first to last steps is __________ .

Back 21

a) ordered sequential mechanism; A → B → D → C b) ordered sequential mechanism; B → A → D → C c) ping pong mechanism; A → B → D → C d) ping pong mechanism; B → A → D → C

Hint 21

D

Front 22

The hydrogen of His64 imidazole nitrogen of carbonic anhydrase during the conversion of X → Y is from _____________ . The correct order of His64 of carbonic anhydrase from the first to last steps is _____________ .

Back 22

a) H2O; X → Y → X b) H2O; Y → X → Y c) enzyme surface; X → Y → X d) enzyme surface; Y → X → Y

Hint 22

A

Front 23

Cys184 of sortase A is involved in _____________ .

Back 23

a) Acid-base catalysis b) Covalent catalysis c) Electrstatic catalysis d) Hydrogen bond catalysis e) Radical catalysis

Hint 23

B

Front 24

His120 of sortase A is involved in _______

Back 24

a) Acid-base catalysis b) Covalent catalysis c) Electrstatic catalysis d) Hydrogen bond catalysis e) Radical catalysis

Hint 24

A

Front 25

Consider the amino acid R-groups in Figure 2. What percent of sortase A enzyme molecules are catalytically active at physiologic pH=7.0 condition? pKa of Cysteine R chain is 8.37. pKa of Histidine R chain is 6.25.

Back 25

a) ~5% b) ~20% c) ~35% d) ~55% e) ~75%

Hint 25

A

Front 26

Two His residues play important roles in the oxygen binding site of hemoglobin, _____________. ____________ imidazole nitrogen of proximal histidine is close enough to bond directly to the Fe2+ atom of heme whereas _____________ imidazole nitrogen of distal histidine is important for allowing an appropriate binding of O2 to the Fe2+ atom

Back 26

a) and myoglobin; protonated; unprotonated b) and myoglobin; unprotonated; protonated c) but not myoglobin; protonated; unprotonated d) but not myoglobin; unprotonated; protonated e) but not myoglobin; either protonated or unprotonated; either protonated or unprotonated

Hint 26

B

Front 27

Hemoglobin, _____________, has/have a binding site for 2,3-BPG. Fetal hemoglobin has lower binding affinity to 2,3-BPG than adult hemoglobin because of specific _____________ regulation.

Back 27

a) and myoglobin; transcriptional b) and myoglobin; post-translational c) and myoglobin; transcriptional and post-translational d) but not myoglobin; transcriptional e) but not myoglobin; post-translational

Hint 27

D

Front 28

Back 28

a) A b) B c) C d) D e) E

Hint 28

B

Front 29

Sickle-cell disease causes severe anemia that is due to a single point mutation of glutamate to valine at the position 6 in β polypeptides/subunits of hemoglobin tetramer (α2β2). In the sickle cell disease, this mutation creates an additional hydrophobic interaction. Each hemoglobin molecule of sickle cell disease patients has two additional hydrophobic interactions. Each such additional hydrophobic interaction is mediated by valine of one hemoglobin β subunit and phenylalanine and ___________ of ____________

Back 29

a) leucine; another β subunit of the same hemoglobin b) leucine; a β subunit of another hemoglobin c) isoleucine; another β subunit of the same hemoglobin d) isoleucine; a β subunit of another hemoglobin e) isoleucine; β subunits of the same and another hemoglobins

Hint 29

B

Front 30

Oxygen binding of hemoglobin is more sensitive to the changes of oxygen pressure than myoglobin. What is the reason for this high sensitivity of hemoglobin, not myoglobin, in response to changes in oxygen pressure? What percent O2 is released for hemoglobin to transport O2 from lung to peripheral tissues based on the graph above (last page)?

Back 30

a) Binding of oxygen to a subunit of hemoglobin will influence oxygen binding of other subunits through covalent interactions; ~66% b) Binding of oxygen to a subunit of hemoglobin will influence oxygen binding of other subunits through covalent interactions; ~73% c) Binding of oxygen to a subunit of hemoglobin will influence oxygen binding of other subunits through noncovalent interactions; ~66% d) Binding of oxygen to a subunit of hemoglobin will influence oxygen binding of other subunits through noncovalent interactions; ~73% e) Binding of oxygen to a subunit of hemoglobin will influence oxygen binding of other subunits through both covalent and noncovalent interactions; between ~66% and ~73%

Hint 30

D

Front 31

What percent O2 is released for myoglobin from resting muscle to working muscle during muscle contraction based on the graph above? If assuming that function of myoglobin is to transport oxygen from lung to peripheral tissues. What percent O2 is released for myoglobin to transport O2 from lung to peripheral tissues based on the graph above (last page)?

Back 31

a) ~11%; ~10% b) ~11%; ~25% c) ~50%; ~10% d) ~50%; ~25%

Hint 31

A

Front 32

The diagram in above (last page) show the salt bridges in the _____________. What are the functional groups of A, B and C in the following diagram?

Back 32

a) lung; A: amino group; B: carboxylic group; C: carboxylic group b) lung; A: carboxylic group; B: amino group; C: carboxylic group c) tissues; A: amino group; B: carboxylic group; C: carboxylic group d) tissues; A: carboxylic group; B: amino group; C: carboxylic group e) either lung or tissues; not enough information is available;

Hint 32

C

Front 33

What percentage of His 146 R chain of β subunit is protonated in the tissues? pKa of His R group is 6.00.

Back 33

a) ~6% b) ~18% c) ~50% d) ~75% e) ~95%

Hint 33

A

Front 34

Enzymes speed up thousands of biochemical reactions that sustain life. Enzymes lower free energy of _____________ . For some enzymes, the catalytic active complex of ____________ group is called the _____________

Back 34

a) transition state, but not substrate; holoenzyme and cofactor; apoenzyme b) transition state, but not substrate; apoenzyme and cofactor; holoenzyme c) transition state and substrate; holoenzyme and cofactor; apoenzyme d) transition state and substrate; apoenzyme and cofactor; holoenzyme e) substrate and product; apoenzyme and cofactor; holoenzyme

Hint 34

B

Front 35

Back 35

a) competitive; uncompetitive b) noncompetitive; uncompetitive c) noncompetitive; competitive d) uncompetitive; competitive e) uncompetitive; noncompetitive

Hint 35

E

Front 36

An abzyme is an antibody produced by an animal through injection of an antigen. When a substrate binds its abzyme, the abzyme will convert the substrate to its _____________ . Ribozymes are RNAs that have catalytic activities. An example of ribozymes is ____________ .

Back 36

a) antibody; RNase P b) antibody; RNA polymerase c) antigen; RNase P d) antigen; RNA polymerase e) product; transition state analog

Hint 36

C

Front 37

Penicillin covalently binds an essential _________ residue in the active site of transpeptidase, an enzyme that acts to crosslink the peptidoglycan chains during synthesis of bacterial cell walls. Another example of irreversible inhibitors is DIPF that covalently links to acetylcholine esterase. DIPF covalently linked acetylcholine esterase will _______ neurotransmission.

Back 37

a) antibody; RNase P b) antibody; RNA polymerase c) antigen; RNase P d) antigen; RNA polymerase e) product; transition state analog

Hint 37

C

Front 38

Penicillin covalently binds an essential _________ residue in the active site of transpeptidase, an enzyme that acts to crosslink the peptidoglycan chains during synthesis of bacterial cell walls. Another example of irreversible inhibitors is DIPF that covalently links to acetylcholine esterase. DIPF covalently linked acetylcholine esterase will _______ neurotransmission.

Back 38

a) Asn; enhance b) Asn; inhibit c) Ser; enhance d) Ser; inhibit e) no enough information is available; no enough information is available

Hint 38

C

Front 39

Back 39

a) A; C b) A; D c) B; C d) B; D e) Either A or B; Either C or D

Hint 39

A

Front 40

Back 40

a) A; C b) A; D c) B; C d) B; D e) Not enough information is available; Not enough information is available

Hint 40

C

Front 41

Back 41

a) Arginine b) Glutamate c) Leucine d) Serine e) Tyrosine

Hint 41

E

Front 42

P-loop domains of NMP kinases are commonly found in many enzymes. They are able to undergo conformational changes upon the binding of ATP. A P-loop domain of NMP kinases typically contains a motif of _____________ that can interact with _____________ phosphates of ATP

Back 42

a) Gly-X-X-X-X-Gly-Lys; α and β b) Gly-X-X-X-X-Gly-Lys; β and γ c) Pro-X-X-X-X-Pro-Lys; α and β d) Pro-X-X-X-X-Pro-Lys; α and γ e) Pro-X-X-X-X-Pro-Lys; β and γ

Hint 42

B

Front 43

Carbonic anhydrase catalyzes a bisubstrate and bidirectional reaction: CO2 + H2O ↔ HCO3 - + H+. The kinetics parameters, KM and Vmax are calculated by varying substrate concentration and keeping constant enzyme concentration. Its acting on bicarbonate, HCO3 - , has KM = 0.027 M and its acting on carbon dioxide, CO2, has KM = 0.012 M. ______________ binds with higher affinity to carbonic anhydrase. If we double enzyme concentration, KM for acting either HCO3 - or CO2 will ______

Back 43

a) CO2; double as well b) CO2; keep the same c) HCO3 - ; double as well d) HCO3 - ; keep the same e) No enough information is available; no enough information is available

Hint 43

B

Front 44

1.0 mg of an enzyme has a Vmax of 75 μmol product formed per minute and a KM of 5 μM for substrate. When a reaction mixture contains the enzyme and 10 μM substrate, which of the following percentages of the maximum velocity will be closest to the initial reaction velocity?

Back 44

a) 5% b) 15% c) 33% d) 50% e) 67%

Hint 44

E

Front 45

The specificity of trypsin is determined by _________ on the enzyme. The specificity of elastase is determined by _________ on the enzyme. Three amino acids: Asp, His and Ser, of ________ form a triad to cleave peptide bonds of a substrate.

Back 45

a) an Asp in the deep pocket; a shallow binding pocket for an amino acid with a small neutral side; trypsin, but not elastase b) an Asp in the deep pocket; a shallow binding pocket for an amino acid with a small neutral side; trypsin or elastase c) a shallow binding pocket for an amino acid with a small neutral side; an Asp in the deep pocket; trypsin, but not elastase d) a shallow binding pocket for an amino acid with a small neutral side; an Asp in the deep pocket; trypsin or elastase e) size of the pocket; charge of the pocket; elastase, but not trypsin

Hint 45

B

Front 46

Type II restriction enzymes cut double-stranded DNA known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses. Inside a bacterial host, the restriction enzymes selectively cut up foreign DNA in a process called restriction because foreign DNA is _____________ and host DNA is ____________ . The restriction enzymes, EcoR V, EcoR I and BamH I have little primary sequence homolgy at the amino acid level, but they all have similar active sites. Their active sites often contain two amino acids, and they are ______

Back 46

a) methylated at specific sites; unmethylated; Asn and Gln b) methylated at specific sites; unmethylated; Asp and Glu c) unmethylated; methylated at specific sites; Asn and Gln d) unmethylated; methylated at specific sites; Asn and Glu e) unmethylated; methylated at specific sites; Asp and Glu

Hint 46

E

Front 47

The correct order of four complexes: A, B, C and D, from the first to last steps is __________ . The side chains (R) of three His covalently bound to Zn2+ are __________

Back 47

a) A → B → D → C; protonated b) A → B → D → C; deprotonated c) B → A → D → C; protonated d) B → A → D → C; deprotonated e) C → A → D → B; either protonated ot deprotonated

Hint 47

D

Front 48

The correct order of His64 of carbonic anhydrase from the first to last steps is _____________ . The proton of His64 is transferred to _______

Back 48

a) X → Y → X; H2O b) X → Y → X; the surface of the eznyme c) Y → X → Y; H2O d) Y → X → Y; the surface of the eznyme e) Y → X → Y; the reaction center of the enzyme

Hint 48

B

Front 49

In the cell culture experiment, the incorporation of 35S into newly synthesized proteins continued for several hours in the presence of the inhibitor. In these experiments, continuation of protein synthesis occurred mostly because of the time it takes for ____

Back 49

a) preexisting mRNAs to decay b) diassembly of ribosome c) the inhibitor to enter the nuclus d) newly synthesized RNAs to exit the nuclus e) RNA polymerase to finish transcription once started

Hint 49

A

Front 50

As determined by the labeling experiments in Figure 1, the percent of the total RNA synthesis that is sensitive to the inhibitor is closest to ______

Back 50

a) 95% b) 90% c) 85% d) 80% e) 75%

Hint 50

D

Front 51

Based on the information from Figures 1, 2 and 3, which of the following statements is(are) true? Please select all correct statements.

Back 51

a) The RNA polymerase inhibited by this inhibitor is responsible for synthesis of mRNAs but not for tRNAs and rRNAs. b) The RNA polymerase inhibited by this inhibitor is responsible for synthesis of mRNAs, rRNAs and tRNAs. c) There are different RNA polymerases in HeLa cells. d) The order of relative charge of RNA polymerase(s) from negative to positive: fraction 2 → fraction 5 → fraction 8. e) The order of size of RNA polymerase(s) from small to large: fraction 2 → fraction 5 → fraction 8.

Hint 51

C

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A. 3

B. 4

C. 5

D. 6

E. 7

Hint 52

B

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B

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D

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B

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B

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D

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B

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B

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B

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E

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B

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D

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C

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A