Chapter 7: The Behavior of Proteins- Enzymes, Mechanisms, and Control / Biochemistry / Johnson

What is the advantage of the sequential model over the concerted model for allosteric enzymes?

The concerted model is simple and describes the behavior of enzyme systems very well. However, the sequential model, though less simple, gives a more realistic picture of the structure and behavior of proteins. It also deals very well with the behavior of some enzyme systems

Explain how an active site affects the specificity of enzymes.

The nature of the active site plays an important role in the specificity of enzymes. An enzyme that displays absolute specificity, catalyzing the reaction of one, and only one, substrate to a particular product, is likely to have a rigid active site that is best described by the lock-and-key model of substrate binding. The enzymes that display relative specificity, catalyzing the reactions of structurally related substrates to related products, apparently have more flexibility in their active sites and are better characterized by the induced-fit model of enzyme-substrate binding. Also, there are stereospecific enzymes with specificity in which optical activity plays a role. The binding site itself must be asymmetric in this situation.

How do K systems and V systems of enzymes differ from each other?

There are two types of enzyme systems, called K systems and V systems. K systems include combinations of allosteric enzymes and inhibitors or activators in which the presence of the inhibitor/activator changes the substrate concentration that yields one-half Vmax. On the other hand, V systems include combinations of allosteric enzymes and inhibitors or activators in which the presence of the inhibitor/activator changes the maximal velocity of the enzyme but not the substrate level that yields one-half Vmax.

. Many metabolic pathways involve multistep reactions. Consider the following pathway. E1 E2 E3 E4 A → B → C → D → F (final product) Which of the following would be an example of feedback inhibition? a. the product of the final reaction, F, interacting with E1. b. F interacting with an allosteric site in E4. c. B interacting with an allosteric site in E1. d. all of the intermediates or products in the reaction interacting with the active site in E1.

a

A transition-state analog is likely to bind to an enzyme a. more tightly than the substrate. b. less tightly than the substrate. c. about as tightly as the substrate. d. at a site other than the catalytic site

a

ATP is a negative allosteric effector for glycogen phosphorylase. This is an example of a. feedback inhibition. b. positive cooperativity. c. negative cooperativity. d. competitive inhibition.

a

Cofactors are a. non-protein in chemical nature. b. always small proteins. c. modified amino acids. d. never required for enzymatic activity.

a

Enzyme kinetics falls into two general categories, simple saturation and cooperative kinetics. a. True b. False

a

Homotropic effects for allosteric enzymes involve a. the same molecule binding to different sites in the enzyme. b. different molecules binding to the same site in an enzyme. c. different molecules binding to different sites in the same enzyme. d. All of these are homotropic effects.

a

In the concerted model for allosteric enzymes a. the relative affinities of substrate for the T and R conformations plays an important role in the cooperativity of the reaction. b. the equilibrium between the T and R conformations plays a minor role. c. the enzymatic activity of the T conformation is considerably higher than that of the R form. d. it is possible to describe the reactions of all allosteric enzymes accurately

a

In the concerted model the most active enzyme form will be when a. all subunits are in the R state. b. all subunits are in the T state. c. there is a 50:50 mix of R & T states. d. none of these

a

In the concerted model, which state binds the substrate more tightly? a. the relaxed (R) state b. the taut (T) state c. Both states bind equally well.

a

Inhibitors which bind covalently to specific amino acids are useful in determining which amino acids are in the active site of an enzyme. a. True b. False

a

Kinase reactions describe enzymes which a. add phosphate groups to another molecule. b. oxidize alcohols to aldehydes. c. use NAD+ /NADH in their reactions. d. transfer groups from one part of a molecule to another. e. add or remove double bonds in molecules.

a

Kinases usually transfer phosphates from a. ATP. b. inorganic phosphate. c. NADP+ /NADPH. d. amino acids

a

Labeling the amino acid residues in the active site of an enzyme requires a. a reagent structurally similar to the substrate. b. a highly polar reagent. c. a reagent that contains an aromatic group. d. a reagent that contains a halogen atom.

a

M-N-O-P-Q-R 1 2 3 4 5 The final product, R, will most likely inhibit which reaction? a. 1 b. 2 c. 3 d. 4 e. 5

a

M-N-O-P-Q-R 1 2 3 4 5 Which two enzymes would be the most likely ones to regulate if this pathway is dedicated to the formation of only one product? a. 1&2 b. 1&3 c. 1&5 d. 2&4 e. 4&5

a

Redox reactions often use this cofactor: a. Riboflavin b. Lipoic acid c. Pyridoxal d. Thiamine e. Biotin

a

The critical serine residue in the active site of chymotrypsin functions as a. a nucleophile. b. an electrophile. c. a base. d. a methyl donor. e. none of these

a

The initial bond formation in the covalent intermediate in the reaction catalyzed by chymotrypsin is between a. serine and the carbonyl carbon in the peptide backbone b. serine and the nitrogen in the peptide backbone c. histidine and the carbonyl carbon in the peptide backbone d. histidine and the nitrogen in the peptide backbone

a

The main distinguishing feature of the concerted model for the behavior of allosteric enzymes is that a. the conformation of all subunits changes simultaneously. b. it applies only to dimeric enzymes. c. it involves three possible conformations for all subunits. d. the T and R conformations exist in roughly equal amounts.

a

The sequential model for allosteric enzymes was proposed by: a. Koshland b. Pauling c. Pasteur d. Monod, Wyman and Changeux e. All of these

a

The term K0.5 is analogous to the KM a. True b. False

a

The vitamin biotin is involved in this type of reaction: a. Carboxylation reactions b. Decarboxylation reactions c. Redox reactions d. Acyl transfer reactions e. Transamination reactions

a

The vitamin pantothenic acid is involved in this type of reaction: a. Carboxylation reactions b. Decarboxylation reactions c. Redox reactions d. Acyl transfer reactions e. Transamination reactions

a

What happens when a K-acting inhibitor is added to an allosteric enzyme system? a. The apparent KM for the substrate increases. b. The apparent KM for the substrate decreases. c. The apparent Vmax for the substrate increases. d. The apparent Vmax for the substrate decreases

a

Where do allosteric inhibitors bind on an enzyme? a. They always bind at a site different from the active site. b. They always bind at the active site. c. They can bind at either active site or another site. d. They always bind directly to the substrate e. none of these

a

Which of the following is not true about B vitamins? a. They are usually fully active in the form we eat them b. They are usually water soluble c. Niacin and riboflavin are examples d. They are important in many metabolic reactions

a

A velocity curve (V vs. [S]) for a typical allosteric enzyme will be a. a rectangular hyperbola. b. a sigmoid curve. c. a straight line. d. a parabola. e. none of these

b

Zymogens are a. inactive precursors of enzymes which can be activated by the irreversible cleavage of covalent bonds. b. inactive forms of enzymes which require phosphorylation by a kinase to become active. c. allosteric enzymes that are always in the R state. d. allosteric enzymes that are always in the T state.

a

Abzymes a. invariably bind to pyridoxal phosphate. b. are antibodies with catalytic activity. c. differ markedly from transition states in enzymatic reactions. d. have proline as part of their structure.

b

According to the concerted model of allosteric behavior, an allosteric activator a. favors the taut (tight) form of the enzyme. b. favors the relaxed form of the enzyme. c. can only bind to the enzyme if the substrate is already bound. d. can only bind to the enzyme if the substrate has not already bound.a

b

Acyl transfer reactions often use this cofactor: a. Riboflavin b. Lipoic acid c. Pyridoxal d. Thiamine e. Biotin

b

B vitamins are often stored in the body. a. True b. False

b

CTP is a known inhibitor of ATCase, the enzyme that catalyzes the first reaction in the pathway for the synthesis of this compound. This is an example of a. irreversible inhibition b. feedback inhibition c. zymogenic inhibition d. negative cooperativity

b

Generally speaking, enzymes involved in pathways which generate ATP will be activated by addition of phosphate groups to the enzyme. a. True b. False

b

How do each of these compounds affect the function of ATCase? a. ATP inhibits and CTP activates b. ATP activates and CTP inhibits c. Both ATP and CTP inhibit d. Both ATP and CTP activate e. none of these is true

b

In a comparison of allosteric and non-allosteric enzymes a. it is always possible to define a KM b. it is always possible to define a Vmax c. competitive inhibition is always a possibility d. much of the terminology is completely unchanged

b

Metal ions play an important role in reaction mechanisms because a. they block the active site of enzymes so that inhibitors cannot bind. b. they can act as Lewis acids. c. water is excluded from the active site when metal ions are bound. d. they prevent protein aggregation.

b

Pyridoxal phosphate is required for transfer of a. one-carbon groups b. amino groups c. acyl groups d. aldehyde groups

b

The active site of chymotrypsin contains all of the following, except: a. Histidine residue. b. A magnesium ion. c. Hydrophobic pocket to bind the substrate. d. Serine residue. e. All of these are in the active site of chymotrypsin

b

The amino acids in the active site can be involved in all of these processes, except: a. Binding of the substrate. b. Becoming part of the product of the reaction. c. The actual chemical mechanism for the reaction. d. Binding of some necessary cofactor for the reaction. e. All of these can be functions of the amino acids in the active site

b

The process by which the final product of a series of reactions inhibits the first reaction in the series is called _____. a. competitive inhibition b. feedback inhibition c. mixed inhibition d. slow-tight inhibition

b

The saturation curve for aspartyl transcarbamylase has a similar shape to the curve for: a. Myoglobin b. Hemoglobin c. Chymotrypsin d. Both hemoglobin and chymotrypsin. e. All of these.

b

The sequential model for allosteric behavior a. cannot account for reactions that display negative cooperativity. b. postulates binding of substrates and inhibitors by the induced-fit model. c. requires that the conformation of all subunits change simultaneously. d. is mathematically simpler than the concerted model.

b

Which of the following best describes negative cooperativity? a. Binding of one substrate molecule prevents the enzyme from working at all. b. Binding of one substrate molecule inhibits the binding of a second substrate. c. Binding of one substrate molecule enhances the binding of a second substrate. d. Binding of one substrate molecule inhibits the binding of other effectors.

b

Which of the following is NOT required in order for an enzyme to display cooperative kinetics? a. Multiple subunits. b. A value for the Michaelis constant, KM. c. Allosteric sites which affect the binding of substrate to the active site. d. Ability to display a Vmax. e. All of these are characteristic of cooperative enzymes.

b

An important step in elucidating the behavior of an enzyme is a. obtaining a crystalline sample of the enzyme. b. insuring that metal ions are always excluded from the enzyme sample. c. determining the active site residues. d. none of these

c

How are cofactors bound to their enzymes? a. always covalently b. always non-covalently c. either covalently or non-covalently d. via linking with a metal ion e. none of these

c

How do each of these compounds affect the function of ATCase? a. ATP is a K effector and CTP is a V effector. b. ATP is a V effector and CTP is a K effector. c. Both ATP and CTP are K effectors. d. Both ATP and CTP are V effectors. e. none of these

c

In reactions catalyzed by allosteric enzymes a. substrate, activators, and inhibitors all compete for the same binding site on the enzyme. b. there is no distinction between catalytic and regulatory subunits. c. the presence of an activator makes the plot of reaction rate against substrate concentration less cooperative. d. the presence of an inhibitor makes the plot of reaction rate against substrate concentration less cooperative.

c

In the concerted model for allosteric enzymes, if the taut form of the enzyme cannot bind substrate then a. KT < KR b. L = R/T c. c = 0 d. an inhibitor must be present e. none of these

c

In the concerted model the binding of the first substrate molecule will achieve all except a. facilitation of the binding of other substrate molecules. b. facilitation of the conversion of other subunits to the active state. c. facilitation of the binding of inhibitors to the enzyme. d. All of these are facilitated by the binding of the first substrate molecule. e. None of these answers is correct.

c

In zymogen activation a. only digestive enzymes are involved. b. a conformational change takes place with no alteration of primary structure. c. an inactive protein is converted to an active one by bond cleavage. d. there is aggregation of several enzyme molecules when the substrate binds.

c

M-N-O-P-Q-R 1 2 3 4 5 Which two enzymes would be the most likely ones to regulate if this pathway is freely reversible and can go both ways? a. 1&2 b. 1&3 c. 1&5 d. 2&4 e. 4&5

c

Phosphorylation of enzymes a. has no effect on their catalytic activity. b. does not require ATP. c. usually takes place on serine, threonine, and tyrosine residues. d. always increases the activity of the enzyme

c

The binding of aspartate to different subunits of ATCase is an example of a. enzyme inhibition b. a heterotropic effect c. a homotropic effect d. negative cooperativity e. none of these

c

The concerted and sequential models for the behavior of allosteric enzymes differ in a. the conformational change in the enzyme in one model and not in the other. b. the number of predicted binding sites on the enzyme. c. the manner in which changes in quaternary structure take place. d. the response of the enzyme to changes in temperature

c

The pH profile of an enzyme can help identify specific amino acids in the active site because: a. all enzymes have a pH optimum b. only the active site amino acids can detect changes in pH c. acidic and basic amino acids are often involved in the active site and pH changes can change their ability to catalyze a reaction d. the pH optimum is always the pI of the most critical amino acid in the active site

c

Which of the following amino acid side chains would best serve as a general acid, assuming the protein functions at a pH of 7? a. alanine b. aspartic acid c. lysine d. asparagine

c

Which of the following can function as coenzymes? a. lead ion, biotin, and lipoic acid. b. copper ion, p-hydroxymercuribenzoate, diisopropylphophofluoridate. c. zinc ion, pyridoxal phosphate, and nicotinamide adenine nucleotides. d. lead ion, p-hydroxymercuribenzoate, diisopropylphophofluoridate.

c

Which of the following does not apply to the concerted model for subunit behavior: a. Each subunit can exist in a relaxed (R) and taut (T) conformation. b. All subunits will be in either the R or the T conformation at the same time. c. Some subunits can be in the R state while others are in the T state. d. The presence of inhibitors will lead to more of the enzyme being in the T form e. the presence of activators will lead to more of the enzyme being in the R form

c

Which of the following is not a difference between the concerted model and the sequential model of allosteric enzymes? a. The sequential model allows for different subunits to be in different conformations while the concerted model does not b. Negative cooperativity can be explained by the sequential model but not by the concerted model c. Positive cooperativity can be explained by the sequential model but not by the concerted model d. The sequential model is explained better by considering the induced-fit model of substrate binding, whereas the concerted model focuses on perturbing the equilibrium between the T and R forms.

c

Which of the following is true about cocaine addiction a. it is easy to treat by using a drug that blocks a neurotransmitter receptor b. it is based on release of the neurotransmitter GABA c. it can be treated with catalytic antibodies d. catalytic antibodies against cocaine are designed to mimic the cocaine molecule itself e. none of these

c

Which of the following is true? a. Phosphorylation always increases enzyme activity b. Kinases often use AMP as a co-substrate in their phosphorylation reactions c. Some enzymes are activated by phosphorylation while others are inhibited d. ADP is the most common substrate for a kinase reaction

c

Which of the following is unlikely to occur in binding of a substrate to an enzyme? a. stereospecific interactions. b. hydrogen bonding. c. adsorption to surfaces of metallic catalysts. d. interactions with metal-ions.

c

Which of the following substances can modify the quaternary structure and the behavior of a protein such as aspartate transcarbamoylase (ATCase) by binding to it? a. Apoplastic effectors b. Bacterial effectors c. Allosteric effectors d. Cytoplasmic effectors

c

Allosteric enzymes must exhibit which of the following? a. feedback inhibition b. a phosphorylation site c. general acid-base catalysis d. a quaternary structure e. none of these must be exhibited

d

Enzymes that catalyze similar functions will invariably have a. similar overall structures b. serine in their active sites. c. histidine in their active sites. d. active sites that can catalyze the reactions in question.

d

Important mechanisms of enzymatic catalysis include a. nucleophilic reactions b. general acid-base catalysis c. Lewis acid-base catalysis d. all of these

d

Nicotinamide adenine dinucleotide is a. an enzyme inhibitor used in smoking cessation programs. b. an inhibitor of ATP production. c. a coenzyme in reactions that transfer acyl groups. d. a coenzyme in oxidation-reduction reactions

d

Phosphorylation and allosteric control of enzymes. a. are not involved in reactions of carbohydrates. b. play an insignificant role in generating energy. c. are important processes in prokaryotes, but not in eukaryotes. d. can be combined to afford a high degree of control over enzymatic reactions. e. none of these

d

The behavior of allosteric enzymes a. does not play any role in feedback inhibition in metabolic pathways b. is strongly dependent on the presence of metal ions c. is related to their ability to hydrolyze themselves d. depends on changes in their quaternary structure on binding of substrates or inhibitors

d

The concerted model for allosteric behavior was proposed by: a. Koshland b. Pauling c. Pasteur d. Monod, Wyman and Changeux e. All of these

d

The serine in the active site of chymotrypsin functions as a. a Lewis acid. b. a metal ion. c. an electrophile. d. a nucleophile

d

Which groups of amino acids are most likely to be found in the active site of an enzyme? a. leucine, lysine, alanine. b. cysteine, isoleucine, phenylalanine. c. tyrosine, threonine, leucine. d. serine, histidine, aspartate.

d

Which of the following enzymes is not a serine protease? a. trypsin b. chymotrypsin c. thrombin d. aspartyl transcarbamylase (ATCase)

d

Which of the following is an advantage of an allosteric drug compared to an orthosteric one? a. they can modulate their effect in a more subtle way b. an allosteric drug may be more specific for a specific reaction than one that binds to the receptor itself c. they may be safer as they have no effect at all unless the natural substrate is present d. all of these are advantages e. none of these is an advantage

d

Which of the following is true? a. Allosteric enzymes are rarely important in the regulation of metabolic pathways. b. Michaelis-Menten kinetics describe the reactions of allosteric enzymes c. Allosteric enzymes have a hyperbolic plot of reaction rate vs. substrate concentration d. none of these is true

d

Which of the following types of amino acids in an active site is least likely to be involved in enzyme catalysis? a. Those with hydrophilic, neutral side-chains. b. Those with negatively charged side-chains. c. Those with positively charge side-chains. d. Those with hydrocarbon side-chains.

d

Which of the following is a mechanism of regulating enzyme activity? a. Feedback inhibition by product. b. Addition or removal of phosphate groups from of the enzyme. c. Presence of activators. d. Activation of zymogens. e. All of these regulate enzyme activity.

e

Which of the following is true about caspases? a. they are a class of proteases b. they are involved in apoptosis c. they are initially produced as inactive procaspases d. once activated, they attach specific targets leading to cell death e. all of these

e

Which of the following is true about salicylate? a. it is a natural compound from the bark of a tree b. it is structurally similar to aspirin c. it stimulates the protein kinase, AMPK d. it has therapeutic effects in lowering the risk of heart disease e. all of these

e

Which of the following statements about coenzymes is true? a. They are commonly derived from vitamins. b. They bind to the active site region on specific types of enzymes. c. They can be metal ions, such as Zn(II). d. NAD+ , FAD and biotin are all examples of coenzymes. e. All of these statements are true.

e

Is the Michaelis-Menten equation useful when studying allosteric enzymes? a. Yes b. No c. Only if the enzyme displays positive cooperativity. d. Only if the enzyme displays negative cooperativity.

no