EXAM 2 practice problems

A substrate, S, can be degraded by two different isozymes (#1 and #2), both displaying Michaelis-Menten kinetics. The KM for isozyme #1 is 0.1 mM and that for isozyme #2 is 10 mM. Both isozymes have the same Vmax. If [S] = 5 mM, which of the following statements is correct? A. Isozyme #1 will degrade S faster than isozyme #2. B. Isozyme #2 will degrade S faster than isozyme #1. C. Isozyme #1 will degrade S at a rate equal to half of its maximal velocity. D. Isozyme #2 will degrade S at a rate equal to half of its maximal velocity

A

A substrate, S, can be degraded by two different isozymes (#1 and #2), both displaying Michaelis-Menten kinetics. The KM for isozyme #1 is 0.1 mM and that for isozyme #2 is 10 mM. Both isozymes have the same Vmax. If [S] = 5 mM, which of the following statements is correct? A. Isozyme #1 will degrade S faster than isozyme #2. B. Isozyme #2 will degrade S faster than isozyme #1. C. Isozyme #1 will degrade S at a rate equal to half of its maximal velocity. D. Isozyme #2 will degrade S at a rate equal to half of its maximal velocity.

A

Aldolase, one of the enzymes involved in glycolysis, requires Zn2+ for catalysis. Under conditions of zinc deficiency, the enzyme without the zinc ion would be referred to as the A. Apoenzyme B. Coenzyme C. Holoenzyme D. Proenzyme

A

Chymotrypsin has a reaction intermediate that is covalently bound to the A. Active site Ser B. Oxyanion hole C. Hydrophobic pocket D. Active site His

A

Consider a reaction catalyzed by an enzyme with a KM value of 5 × 10-6 M and Vmax of 20 mmol/min. What is the rate of reaction when the substrate concentration is 5 × 10-6 M? A. 10 mmol/min B. 20 mmol/min C. 30 mmol/min D. 40 mmol/min

A

Cooking eggs results in the denaturation of its main egg-white protein, ovalbumin. Which of the following is least affected? A. Primary structure B. Secondary structure C. Tertiary structure D. Quaternary structure

A

Hemoglobin contributes to buffering in the blood and the Bohr effect through roughly two dozen histidine residues. One important contributor is His 146, whose side chain is in close proximity to that of Asp 94 in the deoxy form of hemoglobin. Which of the following statements best describes the interactions that occur between the two side chains? (4 Points) A. Under acidic conditions, His 146 will form an ion pair with Asp 94, while the close proximity of Asp 94 increases the pKa value of His 146. B. Under acidic conditions, His 146 will form an ion pair with Asp 94, while the close proximity of Asp 94 decreases the pKa value of His 146. C. Under acidic conditions, His 146 will form a van der Waals interaction with Asp 94, while the close proximity of Asp 94 decreases the pKa value of His 146. D. Under acidic conditions, His 146 will form a van der Waals interaction with Asp 94, while the close proximity of Asp 94 increases the pKa value of His 146

A

Hemoglobin contributes to buffering in the blood and the Bohr effect through roughly two dozen histidine residues. One important contributor is His 146, whose side chain is in close proximity to that of Asp 94 in the deoxy form of hemoglobin. Which of the following statements best describes the interactions that occur between the two side chains? A. Under acidic conditions, His 146 will form an ion pair with Asp 94, while the close proximity of Asp 94 increases the pKa value of His 146. B. Under acidic conditions, His 146 will form an ion pair with Asp 94, while the close proximity of Asp 94 decreases the pKa value of His 146. C. Under acidic conditions, His 146 will form a van der Waals interaction with Asp 94, while the close proximity of Asp 94 decreases the pKa value of His 146. D. Under acidic conditions, His 146 will form a van der Waals interaction with Asp 94, while the close proximity of Asp 94 increases the pKa value of His 146.

A

In the binding of oxygen to myoglobin, the relationship between the concentration of oxygen and the fraction of binding sites occupied can best be described as A. Hyperbolic B. Linear, positive slope C. Sigmoidal D. Linear, negative slope

A

When oxygen binds to a heme-containing protein, the two open coordination bonds of Fe2+ are occupied by: A. One O2 molecule and one amino acid atom B. One O2 molecule and one heme atom C. Two O atoms D. Two O2 molecules

A

Which of the following best illustrates hydrophobic forces that stabilize the conformations of proteins? A. Clustering of nonpolar amino acid side chains B. Heat denaturation of globular proteins. C. The unfolding of proteins at low pH. D. The formation of α-helices. E. The formation of β-sheets.

A

Which of the following factors determine an enzyme's specificity? A. The three-dimensional shape of the active site B. The Michaelis constant C. The type of cofactor required for the enzyme to be active D. The prosthetic group on the enzyme

A

Which of the following lists amino acids in which all of the side chains can act as either acid or base catalysts in an enzyme's active site? A. K, C, D B. D, G, H C. Y, E, G D. F, S, H E. E, Q, Y

A

Which of the following statements best describes a Lineweaver-Burk plot of an enzyme with a tight-binding E·S complex? A. The x-intercept has a relatively more negative value B. The x-intercept has a relatively less negative value C. The y-intercept has a relatively more positive value D. The y-intercept has a relatively less positive value E. Both A and D F. Both B and C

A

Which one of the following statements about the β-sheet is FALSE? A. The β-sheet is a type of secondary structure that fulfills the hydrogen bonding requirements of amino acid side chains. B. The β-sheet is a type of regular secondary structure. C. The β-sheet contains hydrogen bonds between the carbonyl oxygen of one residue and an amide hydrogen of a residue on an adjacent strand. D. The side chains in a β-sheet alternate between the two sides of the sheet. E. β-sheets can be parallel or antiparallel.

A

Which of the following amino acids is least likely to be found in the middle of an -helix? A. Pro B. Lys C. Ala D. Glu

A proline has no amide H (glycine as well will not be found because to conformationally flexible)

What is the difference between a polypeptide and a protein?

A polypeptide chain is a series of amino acids connected together by peptide bonds, essentially a protein's primary structure. A protein is a polypeptide chain that has been folded into a specific three-dimensional, or tertiary, structure.

. Some enzymes require the presence of a non-protein molecule to be catalytically active. An enzyme devoid of this molecule is called a(n) A. Holoenzyme. B. Apoenzyme. C. Coenzyme. D. Proenzyme.

B

A good transition-state analog A. Binds covalently to the enzyme. B. Binds to the enzyme more tightly than the substrate. C. Has a higher KM than the substrate. D. Is too unstable to isolate. E. Must be almost identical to the substrate.

B

ATP is both a substrate and a negative effector of the allosteric, glycolytic enzyme phosphofructokinase (PFK). Which of the following answers best explains this observation? A. ATP has equal affinity for the active site and the regulatory site of PFK B. ATP has a higher KM for the regulatory site than for the active site of PFK C. ATP has a higher KM for the active site than for the regulatory site of PFK D. ATP and ADP (the product of ATP hydrolysis) are both negative effectors of PFK

B

An allosteric interaction between a ligand and a protein is one in which A. Binding of a molecule to one site affects binding of additional molecules to the same site on the protein. B. Binding of a molecule to one site affects binding of additional molecules to a different site on the protein. C. Binding of a molecule to a protein is determined primarily by steric interactions. D. Binding of a molecule to a protein is determined exclusively by steric interactions.

B

An intestinal protease functions at maximal velocity when the pH is 8.0 and the temperature is 37°C. Which procedure would have the least effect on the rate of protein digestion? A. Adding more protease B. Adding more protein substrate C. Decreasing the pH to 6.0 D. Increasing the temperature to 45 °C

B

Chymotrypsin has a reaction intermediate that is covalently bound to the A. Oxyanion hole B. Active site Ser C. Hydrophobic pocket D. Active site His

B

Consider the formation of a salt bridge between the side chains of an Asp residue and a His residue. Assuming that the side chains must be at least 50% ionized for the salt bridge to remain, over what pH range will the salt bridge be most stable? A. 1 and 3 B. 3 and 5 C. 5 and 7 D. 7 and 9 E. 9 and 11

B

Denaturing a protein by heat is called melting. Consider three proteins, one rich in valine residues, another rich in cysteine residues, and the last rich in serine residues. (You may assume that there are no other significant differences in the amino acid compositions of the proteins.) Assuming oxidizing conditions, which protein would you predict to have the highest melting temperature? A. Valine-rich protein B. Cysteine-rich protein C. Serine-rich protein D. Cannot be determined without additional information.

B

Enzymes form a complex with their substrates in the process of conversion to product. What feature of this complex would facilitate catalysis? A. Stabilization of the transition state by lowering the ΔG° of the reaction B. Holding substrates close together, increasing their effective concentration C. Increasing the energy of activation by inducing bond stress or strain D. Binding substrates in a stable, low energy conformation

B

Enzymes form a complex with their substrates in the process of conversion to product. What feature of this complex would facilitate catalysis? A. Stabilization of the transition state by lowering the ΔG° of the reaction B. Holding substrates close together, increasing their effective concentration C. Increasing the energy of activation by inducing bond stress or strain D. Binding substrates in a stable, low energy conformation

B

Enzymes form a complex with their substrates in the process of conversion to product. What feature of this complex would facilitate catalysis? A. Stabilizing the transition state by lowering the G° of the reaction B. Holding substrates close together, effectively increasing their concentration C. Increasing the activation energy by inducing bond stress or strain D. Binding substrates in stable, low-energy conformations

B

How does the ideal temperature for a reaction change with and without an enzyme catalyst? A. The ideal temperature is generally higher with a catalyst than without. B. The ideal temperature is generally lower with a catalyst than without. C. The ideal temperature is characteristic of the reaction, not the enzyme. D. No conclusion can be made without knowing the enzyme type.

B

Select the sentence that is false. A. The rate of a chemical reaction changes with temperature B. The rate of a chemical reaction changes with the G° of the reaction C. The rate of a chemical reaction changes with reactant concentration(s) D. The rate of a chemical reaction changes with the addition of catalysts

B

The active ingredient in most meat tenderizing powders is either papain (found in papayas) or bromelain (found in pineapples). Papain and bromelain are enzymes that break down collagen. If you coated a piece of meat with meat tenderizing powder placed it in the refrigerator, what would it do to the enzyme's activity? A. It would decrease the activity because it would denature the enzyme B. It would decrease the activity because it would slow down the probability of collision between enzyme and substrate C. It would increase the activity because it would enhance the proximity and orientations effects D. It would increase the activity because it would allow the enzyme to better stabilize the transition state. E. Both A and B F. Both C and D

B

What secondary structure feature is most commonly associated with protein aggregation? A. -helix B. -sheet C. Supersecondary D. Random coil E. Loop regions

B

Which of the following amino acids is most likely to be found on the outer surface of a protein? A. Phe B. Asp C. Ile D. Met

B

Which of the following is most critical for maintaining the tertiary structure of a protein? A. Hydrogen bonds B. Hydrophobic interactions C. Disulfide bonds D. Salt bridges

B

Which of the following statements about a plot of reaction velocity versus substrate concentration for an enzyme that follows Michaelis-Menten kinetics is false? A. At low substrate concentration, reaction velocity increases linearly with [S] . B. At very high [S], the velocity curve becomes a nearly horizontal and intersects the y-axis at KM. C. KM is the substrate concentration at half-maximal velocity. D. The shape of the curve is a hyperbola

B

Asp189 lies at the base of the specificity pocket of trypsin. If this residue was mutated to Lys, what would be the substrate specificity of the mutant enzyme? A. Large hydrophobic residues B. Acidic residues C. Basic residues D. Small hydrophobic residues

B base of pocket mutated from acidic (neg) to basic(pos), want to bind opposite charges to bind acidic residues

9. Kinetics studies on an enzyme with mutations of some of the amino acid residues in its active site showed a decrease in the enzyme's catalytic activity but not its KM. The best interpretation of these results is that the A. KM for the substrate does not depend on any of the amino acids of the active site. B. kcat for the substrate does not depend on any of the amino acids of the active site. C. The amino acids which stabilize the transition state are different from those that stabilize the substrate. D. An enzyme with these characteristics cannot be described by the MichaelisMenten model since it violates the assumptions.

C

All of the interactions that contribute to the tertiary and/or quaternary structure of a protein are noncovalent except for A. Hydrogen Bonds B. Salt Bridges C. Disulfide Bonds D. Hydrophobic Interactions

C

Consider a reaction catalyzed by an enzyme with a KM value of 5 × 10-6 M and Vmax of 20 mmol/min. What is the rate of reaction when the substrate concentration is 5 × 10-4 M? A. 10 mmol/min B. 15 mmol/min C. 20 mmol/min D. 40 mmol/min

C

Consider the reaction of Substrate Product. An enzyme would lower the activation energy, Ea, of the A. Forward reaction only B. Reverse reaction only C. Both forward and reverse reactions D. Neither forward nor reverse reactions

C

Denaturing a protein by heat is called melting. Consider three proteins, one rich in valine residues, another rich in cysteine residues, and the last rich in serine residues. (You may assume that there are no other significant differences in the amino acid compositions of the proteins.) Assuming reducing conditions, which protein would you predict to have the highest melting temperature? A. Valine-rich protein B. Cysteine-rich protein C. Serine-rich protein D. Cannot be determined without additional information.

C

Digestive enzymes are often produced in inactive forms called A. Apoenzymes B. Prosthetic Groups C. Proenzymes D. Allosteric Effectors E. Inhibitors

C

For enzymes in which the slowest, or rate-determining, step is the reaction of ES P, KM is equivalent to the A. turnover number B. [S] at Vmax C. Kd for the ES complex D. enzyme efficiency

C

In hemoglobin, the transition from the low affinity T state to high affinity R state is triggered by: A. Fe2+ binding B. Heme binding C. Oxygen binding D. Subunit association E. Subunit dissociation

C

In sickle-cell anemia a mutation of a Glu residue of Hemoglobin to Val results in aggregation of the protein because of ________ interactions between molecules. A. Disulfide B. Hydrogen bonding C. Hydrophobic D. Ionic

C

Some patients with erythrocytosis (excess red blood cells) have a mutation that converts a lysine to alanine at residue 82 in the β-subunit of hemoglobin. This particular lysine normally participates in binding 2,3-bisphosphoglycerate (DPG). Which of the following effects would you predict this mutation (Lys82Ala) will have on the affinity of hemoglobin for BPG and for O2, respectively, in patients with erythrocytosis? (Below, the terms "increase" and "decrease" are relative to hemoglobin without mutations.) Affinity for BPG ,Affinity for O2 A. increase ,decrease B. increase, increase C. decrease ,increase D. decrease, decrease

C

The affinity of hemoglobin for oxygen increases when A. Proton concentration increases B. Concentration of 2,3-BPG increases C. Blood pH increases D. CO2 pressure increases

C

The diagram below shows the energy pathway of an uncatalyzed reaction. How would the energy diagram change if an enzyme was used in this reaction? A. The energy of the product would decrease B. The energy of the intermediate would increase C. The energy of the transition state would decrease D. The energy of the reactant would increase

C

The substrate specificity of chymotrypsin is determined largely by its A. Oxyanion hole B. Catalytic triad C. Hydrophobic pocket D. Heme cofactor

C

Under which of the following conditions would hemoglobin have the highest affinity for molecular oxygen? A. High [BPG] and higher pH, i.e. > 7.40 B. High [BPG] and lower pH, i.e. < 7.40 C. Low [BPG] and higher pH, i.e. > 7.40 D. Low [BPG] and lower pH, i.e. < 7.40

C

What effect does hyperventilation have on the oxygen binding affinity of hemoglobin? A. P50 and oxygen affinity decrease. B. P50 and oxygen affinity increase. C. P50 decreases and oxygen affinity increases. D. P50 increases and oxygen affinity decreases. E. P50 and oxygen affinity remain the same.

C

Which of the following amino acids can donate hydrogen bonds through its side chains? A. Val B. Leu C. Gln D. Pro

C

Patients develop pancreatitis when digestive enzymes are activated in the pancreas instead of the small intestine. Which of the following would be the most effective in its treatment? A. Pepsin inhibitor B. Chymotrypsin inhibitor C. Trypsin inhibitor D. Elastase inhibitor

C because enzyme that cleaves the most zymogens

Describe how chaotropes and reducing agents can denature proteins.

Chaotropes disrupt hydrogen bonds and reducing agents break disulfide bonds

A protein's tertiary structure is dependent upon its A. total charge B. isoelectric point C. amino acid composition D. amino acid sequence

D

A β-pleated sheet structure A. can occur in both right and left handed forms B. has neighboring residues that are hydrogen bonded to each other C. has neighboring chains that are connected by α-helices D. has neighboring chains that are hydrogen bonded to each other

D

As applied to enzyme kinetics, the steady-state assumption proposes that A. KM = Kd B. KM = [S] at ½ Vmax C. Enzymes reach maximal velocity when they are saturated D. The ES complex is formed and broken down at equivalent rates

D

Consider a biochemical reaction A → B, which is catalyzed by A-B dehydrogenase. Which of the following statements is true? A. The reaction will proceed until the enzyme concentration decreases. B. The reaction will be most favorable at 0°C. C. A component of the enzyme is transferred from A to B. D. G° of the catalyzed reaction is the same as that for the uncatalyzed reaction.

D

Dr. Christian Anfinsen's experiments in which a protein was denatured and, subsequently, renatured demonstrated that A. Proteins need heat to be properly folded B. Proteins can have multiple tertiary structures C. Unfolded proteins can retain their biological activity D. Primary sequence determines folded structure

D

Enzymes catalyze the rapid formation of product by A. shifting the position of the equilibrium in favor of the product. B. lowering G° of the reaction. C. shifting the position of the equilibrium in favor of the reactant. D. lowering G° ‡ - i.e. Ea - of the reaction.

D

How does CO2 affect hemoglobin-oxygen binding? A. CO2 binds directly to the oxygen binding site, displacing oxygen and thus promoting the deoxy state B. CO2 displaces BPG, thus promoting the oxy state C. CO2 is converted to bicarbonate and H+ which promotes the oxy state D. CO2 is converted to bicarbonate and H+ which promotes the deoxy state E. None of the above

D

Myoglobin, the oxygen-storing protein in muscle, lacks A. Primary structure B. Secondary structure C. Tertiary structure D. Quaternary structure E. None of the above; myoglobin exhibits all four levels of protein structure

D

The number of substrate molecules converted to product in a given unit of time by a single enzyme molecule at saturation is referred to as the A. Dissociation constant. B. Maximum velocity. C. Michaelis constant. D. Turnover number.

D

Which of the following statements best describes exergonic reactions? A. They require more activation energy than endergonic reactions. B. They require less activation energy than endergonic reactions. C. The products have more free energy, higher G°, than the reactants. D. The products have less free energy, lower G°, than the reactants. E. Both A and C are correct. F. Both B and D are correct.

D

Which one of the following statements is true of enzyme catalysts? A. They bind to substrates, but can never become covalently attached to substrate or product. B. They favor product formation by increasing the equilibrium constant of the reaction. C. They increase the stability of the product of the desired reaction. D. They lower the activation energy for the conversion of substrate to product.

D

The three-dimensional structure of an enzyme in complex with its substrate, as determined by X-ray crystallography, revealed that a methionine residue in the active site of the enzyme interacts with an isoleucine residue on the substrate. Which of the following would best characterize the interaction between these two amino acids? A. Covalent bond B. Disulfide bond C. Salt bridge D. Hydrophobic interaction

D (non polar=hydrophobic)

Which of the following most accurately describes how secondary structures in proteins are stabilized? A. Through ionic bonds between oppositely charged amino acid side chains. B. Through peptide bonds joining different parts of the peptide backbone. C. Through hydrogen bonds between different amino acid side chains. D. Through disulfide bonds between cysteine residues E. Through hydrogen bonds joining different parts of the peptide backbone.

E

Which of the following statements about allosteric control of enzymatic activity is incorrect? A. Allosteric effectors give rise to sigmoidal velocity versus substrate concentration kinetic plots. B. Allosteric proteins are generally, but not always, composed of multiple subunits. C. Allosteric effectors may either inhibit or activate enzymes. D. Allosteric effectors change the conformation of enzymes upon binding. E. Allosteric effectors compete with substrates for binding to enzymes.

E

Which of the following statements about protein structure is correct? A. The α-helix is stabilized primarily by ionic interactions between the side chains of amino acids. B. The formation of the disulfide bond in a protein requires that the two participating cysteine residues be adjacent to each other. C. The stability of quaternary structure in proteins is mainly due to covalent bonds among the subunits. D. The denaturation of proteins always leads to irreversible loss of secondary and tertiary structure. E. The information for the correct folding of a protein is contained in the specific sequence of amino acids along the polypeptide chain.

E

Christian Bohr, after whom the Bohr Effect is named, is the _____ of the Nobel Laureate physicist Niels Bohr. (2 Points) A. Brother B. Father C. Son D. Uncle E. Grandfather

Father

Consider a group of enzymes that catalyze the hydrolysis of esters. Which of the statements below best describes how a biochemist might evaluate data when trying to select the enzymes most appropriate for her research?

For experiments with low substrate concentrations it is best to use the enzyme with the lowest KM; but for experiments with high substrate concentrations it is best to use the enzyme with the highest Vmax.

hyperbola curve represents

MM kinetics

Ser->Thr

Minimal; since both contain side chains with alcohol side groups and nearly the same number of carbons

Leu->Val

Minimal; since both have branched, hydrocarbon side chains with a similar number of carbon atoms

Lys->Arg

Minimal; since both have positively-charged side chains with similar chain lengths.

Ser->Asp

Significant; since Asp is capable of forming salt bridges but Ser is not.

Cys->Met

Significant; since Cys contains a polar side chain and Met has a nonpolar one.

Asn->Glu

Significant; since Glu is capable of forming salt bridges and Asn is not.

Consider the diagram below in which the oxygen binding site in myoglobin resides in a heme pocket in which a valine residue provides one of the pocket boundaries. How is oxygen binding affected when the Val residue is mutated to serine?

Substitution of valine with serine would decrease the affinity of oxygen binding because the side chain of Ser increases the polarity of the binding site for oxygen, which is a nonpolar molecule.

Explain why the oxygen binding curve of myoglobin makes it function well as an oxygen-storage protein whereas the oxygen binding curve of hemoglobin makes it function well as an oxygen-transport protein.

The hyperbolic binding of oxygen to the single binding site of myoglobin results in a high affinity even at the relatively low partial pressures of O2 that occur in tissues. In contrast, the cooperative (sigmoidal) binding of O2 to the multiple binding sites of hemoglobin results in high affinity at high partial pressure such as ones that occur in the lungs. but lower affinity in the tissues. This permits hemoglobin to bind to O2 in the lungs and release it in the tissues.

Free heme binds CO 25,000 times tighter than O2, but myoglobin binds CO only 200 times more tightly than O2. Explain why this is the case

The preferred binding geometry of CO to Fe2+ is linear, which is possible in free heme. In myoglobin or, for that matter, in hemoglobin the side chain of the "distal" histidine forces CO into adopting a bent geometry, which is the reason CO binds far more weakly to the heme iron.

Explain why if you measured the rate of an enzyme catalyzed reaction at different temperatures and plotted your results, you would get a bell shaped curve where the rate increases with temperature up to a point then rapidly falls off.

The rate will initially increase with temperature because the frequency with which substrate molecules collide with enzyme molecules will increase. However, at some point the temperature will get high enough to denature the enzyme which is why the reaction velocity slows down.

The plot below shows the saturation curve for an enzyme with its substrate. How would the curve change if a positive allosteric effector were added? Please sketch a curve and include a brief explanation of how Vmax and KM may (or may not) be affected.

There need to be three key features represented in the curve: - It should be sigmoidal -KM should be lower than that of the unactivated enzyme - Vmax should be greater than or equal to that of the unactivated enzyme

Which amino acids of serine proteases comprise the catalytic triad of the active site? A. His, Ser, Asp B. Arg, Ser, Glu C. His, Ser, Glu D. Lys, Ser, Asp

a

sigmodial curve represents

allosteric effector

Which of the following best describes a protein domain? A. The total α-helical and β-sheet content of a protein. B. The total parallel and anti-parallel β-sheet content of a protein C. A region of polypeptide chain folded into a self-contained tertiary structure D. Super-secondary structure

c

Under which of the following conditions will hemoglobin bind less oxygen? A. An increase in pH from 7.4 to 7.6 B. An increase in oxygen pressure increases from 740 torr to 765 torr C. Removal of BPG D. Increase in the carbon dioxide concentration

d

F

hydrogen bond

HO

hydrogen bond

amide (NH=O) or (N=O)

hydrogen bond

Aromatic ring

hydrophobic interaction

S

hydrophobic interaction

What in the interior of a protein

hydrophobic residues(nonpolar)

Carboxyl group

salt bridge, hydrogen bond

NH2 or HN (amine)

salt bridge, hydrogen bond