Chapter 8

The rate constant for a certain reaction is k = 7.20×10−3 s−1 . If the initial reactant concentration was 0.850 M, what will the concentration be after 8.00 minutes? ---------- A zero-order reaction has a constant rate of 4.70×10−4 M/s. If after 70.0 seconds the concentration has dropped to 9.00×10−2 M, what was the initial concentration?

0.0268 M 0.123 M

In some reactions, in which a protein molecule is binding to a specific site on DNA, a rate greater than that predicted by the diffusion limit is observed. Suggest an explanation. [Hint: The protein molecule can also bind weakly and nonspecifically to any DNA site.] Fill in the blanks using: 3-D 1-D enthalipically entropically If the protein can bind to a random location on the DNA and slide along until it finds the specific site, a more efficient _________ search replaces an _________ less favorable __________ search.

1-D entropically 3-D

The enzyme urease catalyzes the hydrolysis of urea to ammonia plus carbon dioxide. At 21 C the uncatalyzed reaction has an activation energy of about 125 kJ/mol , whereas in the presence of urease the activation energy is lowered to about 46 kJ/mol . By what factor does urease increase the velocity of the reaction?

1.1 x 10^14

Consider the enzyme-catalyzed reaction with Vmax = 164 (micro mol/L)min^-1 and Km = 32 micro mol/L. If the total enzyme concentration was 1 nmol/L, how many molecules of substrate can a molecule of enzyme process in each minute? --------- Calculate kcat / Km for the enzyme reaction. --------- Is this a fairly efficient enzyme?

1.64 x 10^5 min^-1 8.50 x 10^7 (M*s)^-1 yes

Estimate Vmax from a direct graph of v versus [S] using the plot you created in part A. --------- Estimate Km from a direct graph of v versus [S] using the plot you created in part A. ---------- What is the equation of the line? ---------- Use the equation from part E to estimate Vmax. --------- Use the equation from part E to estimate Km. --------- Given the two plots in parts A and D and the analysis methods available within each part, which is better to estimate Vmax and Km?

160 (micro mol /L) min^-1 25 micromol/L y = 0.196x + 0.0061 164 (micro mol /L) min^-1 32 micro mol/L Lineweaver-Burk plot

Match each term with its definition. 1) rxn coordinate 2) delta G degree 3) delta G ++ A) the higher point on the energy curve B) the plot of the rxn progress as a fcn of time C) the free energy of the rxn

1B, 2C, 3A

Match each of the following terms from the Michaelis-Menten equation to its correct definition. 1) Vmax 2) kcat 3) kcat / Km 4) Km A) substrate concentration at 0.5 Vmax B) rate of a rxn when enzyme is satruated with substrate c) enzyme efficiency d) number of substrate molecules turned over by enzyme

1B, 2D, 3C, 4A

Please match each cofactor with its function. 1) thiamine pyrophosphate 2) coenzyme a 3) biotin 4) NAD+ A) CO2 B) oxidation/reduction C) activation of aldehydes D) acyl group transfer

1C, 2D, 3A, 4B

Initial rate data for an enzyme that obeys Michaelis-Menten kinetics are shown in the following table. When the enzyme concentration is 3 nmol ml−1, a Lineweaver-Burk plot of this data gives a line with a y-intercept of 0.00426 (μmol−1 ml s). Calculate kcat for the reaction. --------- Calculate Km for the enzyme. --------- When the reactions in part (B) are repeated in the presence of 12 microM of an uncompetitive inhibitor, the y-int of the Lineweaver-Burk plot is 0.352 (micromol^-1 ml s). Calculate K'i for this inhibitor.

7.82 x 10^4 s^-1 124 microM 1.45 x 10^-7 M

Enzymes work by _____. A) decreasing the potential energy difference between reactant and product B) reducing EA C) adding energy to a reaction D) increasing the potential energy difference between reactant and product E) adding a phosphate group to a reactant

B

A second-order reaction: A) has a rate constant with units of (time)-1. B) only occurs in multistep processes. C) is characterized by two molecules coming together to form a product. D) is the rate-limiting step of a reaction. E) occurs when one substrate is converted into one product.

C

Which of the following statements is most likely to be true in the case of the feedback-regulated enzymatic pathway shown? a) P0 binds E4 and activates it. b) P2 binds E2 and activates it. c) P4 binds E1 and deactivates it. d) P3 binds E2 and activates it e) P4 binds E3 and deactivates it.

C

Subtilisin is used in some laundry detergents to help remove protein-type stains. What unusual kind of stability does this suggest for subtilisin? a) The enzyme must be stable to very high pressures. b) The enzyme must be stable to the presence of hydrogen. c) The enzyme must be stable both to the presence of detergents and to high pressures. d) The enzyme must be stable both to the presence of detergents and to moderately high temperatures.

D

Which of the following statement is FALSE? A) An enzyme can increase a reaction rate by lowering the activation energy. B) The free energy barrier in a chemical reaction must be overcome in order for products to form. C) An increase in temperature can result in an increased reaction rate. D) Lowering the free energy of the transition state can increase a reaction rate. E) At a given temperature and time all molecules in a solution or a sample will have the same energy.

E

What is the role of Glu 270 and Arg 145 in catalysis? Fill in the blanks: GBC (general base catalyst) dipole-dipole carbamate ion-ion dipole-induced dipole GAC (general acid catalyst) carboxylate E270 acts as a _________ in step one and as a ___________ in step two. R145 provides specific ______ interactions with the C-terminal ______ of the substrate. This confers specificity for cleavage of the C-terminal residue from the peptide substrate.

GBC GAC ion-ion carboxylate

The enzyme urease catalyzes the breakdown of urea in the body. Urease breaks urea down to 2NH3+CO2. This is an example of a hydrolysis reaction (urea plus water). For each equivalent of carbon dioxide (CO2), two equivalents of ammonia (NH3) are produced. Label the enzyme, substrate, enzyme-substrate complex, enzyme-product complex, and product in the enzymatic reaction for the breakdown of urea by urease using the induced-fit model. Starting with top blue + orange and around the circle. Use: Urea Urease-Urea 2NH3 + CO2 Urease Urea - 2NH3 + CO2 Urease- 2NH3 +CO2

Urease Urea Urease-Urea Urease-2NH3+CO2 2NH3+CO2

Which of the following is NOT a feature of substrate-level enzyme regulation? a) It is sufficient for regulation of most enzyme-catalyzed reactions. b) A high substrate concentration will speed up the rate of reaction. c) A high product concentration will slow the rate of reaction. d) The product can be a competitor. e) Sometimes products can be competitive or uncompetitive.

a

Which of the following is a feature of allosteric regulation of enzyme activity? a) Cooperativity in substrate binding. B) Allosteric enzymes often have multiple active sites. c) There is often a range of different effectors for a single enzyme. d) Ligand binding causes a conformation change in the enzyme. e) All of the above

all of the above

Considering both of the mechanisms proposed for catalysis by lysozyme, which of the following rate-enhancing features does lysozyme use to increase the rate of the hydrolysis reaction it catalyzes? 1) general acid-base catalysis 2) electrostatic catalysis 3) distortion of substrate 4) covalent catalysis

all of the listed choices are correct

As a result of its involvement in a reaction, an enzyme _____. a) loses energy b) is unchanged c) permanently alters its shape. d) is used up e) loses a phosphate group

b

The cofactor NAD+ is: a) oxidized to NADH/H+ in dehydrogenase reactions. b) an oxidant. c) able to accept 2 electrons and 2 protons. d) covalently linked to enzymes in whose catalytic activity it assists. e) a reductant.

b

Which of the following amino acid residues are often involved in proton transfers in enzyme-catalyzed reactions? a) Histidine, aspartate, lysine, and serine b) Histidine, aspartate, glutamate, arginine, and lysine c) Glutamine, asparagine, lysine, and tyrosine d) Serine, tyrosine, arginine, and cysteine e) Histidine, aspartate, serine, and cysteine

b

The enzyme is studied in the presence of a different inhibitor (inhibitor B). In this case, two different concentrations of inhibitor are used. Data are as follows: **CHART** What kind of inhibitor is inhibitor B? competitive uncompetitive mixed ----------- Determine the apparent Vmax at each inhibitor concentration. ----------- Determine the apparent Km at each inhibitor concentration. ------------ Estimate Ki from these data.

competitive 5.08, 5.13, 5.38 (mmol/L)min^-1 2.48, 3.83, 5.41 mmol/L 4.87 mM

Fill in the blanks: irreversible noncompetitive competitive active site substrate enzyme 1. A (n) __________ inhibitor has a structure that is so similar to the substrate that it can bond to the enzyme just like the substrate. 2. A (n) ___________inhibitor binds to a site on the enzyme that is not the active site. 3. Usually, a(n) ____________ inhibitor forms a covalent bond with an amino acid side group within the active site, which prevents the substrate from entering the active site or prevents catalytic activity. 4. The competitive inhibitor competes with the substrate for the ___________ on the enzyme. 5. When the noncompetitive inhibitor is bonded to the enzyme, the shape of the __________ is distorted. 6. Enzyme inhibitors disrupt normal interactions between an enzyme and its __________.

competitive noncompetitive irreversible active site enzyme substrate

The Haber process is typically carried out at a temperature of approximately 500∘C. What would happen to the rate of the forward reaction if the temperature were lowered to 100∘C? The rxn rate would ________. -------- What would happen to the rate of the forward reaction if the concentration of nitrogen were decreased? The rxn rate would ________. --------- Which of the following would increase the rate of the reverse reaction? A) increasing the concentration of ammonia B) decreasing the temperature C) increasing the concentration of nitrogen ---------- What will happen to the rates of the forward and reverse reactions when a catalyst is added? A) Forward rate increases; reverse rate decreases. B) Both forward and reverse rates increase. C) Both forward and reverse rates decrease. D) Forward rate decreases; reverse rate increases.

decrease decrease A B

Fill in the blanks. specific cofactor denatured active site catalyst substrate complex 1. An enzyme is ________ when it loses its native conformation and its biological activity. 2. An enzyme is considered a _________ because it speeds up chemical reactions without being used up. 3. An enzyme is considered _________ because of its ability to recognize the shape of a particular molecule. 4. A __________, such as a vitamin, binds to an enzyme and plays a role in catalysis. 5. When properly aligned, the enzyme and substrate form an enzyme-substrate (ES) __________. 6. A substrate binds to an enzyme at the __________, where the reaction occurs. 7. In a catalyzed reaction a reactant is often called a _____________.

denatured catalyst specific cofactor complex active site substrate

The lock and key model of substrate binding and enzymatic catalysis explains: a) structural changes that occur on substrate binding. b) the release of product. c) formation of a transition state. d) the catalytic mechanism. e) substrate specificity.

e

Which of the following statements about inhibitors of enzyme-catalyzed reactions is TRUE? a) A competitive inhibitor binds irreversibly to the enzyme at the active site. b) An uncompetitive inhibitor will always bind at the active site. c) An uncompetitive inhibitor typically affects KM but not kcat. d) Reversible inhibitors bind to either free enzyme or the enzyme-substrate complex but not both. e) A competitive inhibitor does not affect Vmax.

e

Which of the following statements applies to metalloenzymes? a) Some metal ions assist in ATP binding. b) Amino acid residues in the enzyme are never covalently linked to the metal ion. c) The metal does not bind at the catalytic site. d) Many are oxido-reductases. e) A and D

e

What is the correct label for "A"? **GRAPH** substrate energy ATP enzyme energy uphill energy of activation

energy of activation

A mutation causing an amino acid change in an enzyme that affects the turnover number kcat will always affect the KM as well. True False

false

A stopped-flow apparatus is used to measure rates of pre-steady state slow enzymatic reactions. True False

false

Almost all irreversible enzyme inhibitors bind noncovalently to the enzyme. True False

false

Catalysts affect the thermodynamic f of a chemical reaction. True False

false

Coenzymes or cofactors are irreversibly changed during catalysis. True False

false

Elastase is closely related to chymotrypsin. Suggest two kinds of amino acid residues you might expect to find in or near the active site. Check all that apply. histidine valine alanine proline serine

his ser

Subtilisin does have a problem in that it becomes inactivated by oxidation of a methionine close to the active site. Suggest a way to make a better subtilisin. Fill in the blanks: Val hydrophobic hydrophilic Ser His Replace the methionine, by site-directed mutagenesis, with another residue. Because methionine is quite ___________, a ___________ replacement would seem appropriate. A single base change in the Met codon could yield Phe, Leu, Ile, or _______.

hydrophobic hydrophobic Val

Fill in the blanks: stronger weaker higher lower The dielectric constant, , is ________ in the enzyme active site than it is in water; thus, Coulomb,s law predicts a __________ interaction between the H-bond donor and acceptor.

lower stronger

The steady-state kinetics of an enzyme are studied in the absence and presence of an inhibitor (inhibitor A). The initial rate is given as a function of substrate concentration in the following table: **CHART** What kind of inhibition (competitive, uncompetitive, or mixed) is involved? competitive uncompetitive mixed ---------- Determine the Vmax in the absence of inhibitor. ---------- Determine Vmax in the presence of inhibitor. ---------- Determine Km in the absence of inhibitor. ----------- Determine Km in the presence of inhibitor.

mixed 5.13 (mmol/L)min^-1 2.97 (mmol/L)min^-1 2.48 mmol/L 2.55 mmol/L

Would you expect an "enzyme" designed to bind to its target substrate as tightly as it binds the reaction transition state to show a rate enhancement over the uncatalyzed reaction? yes no --------- In other words, would such a protein actually be a catalyst? yes no --------- Explain why not. A) because the activation energy would be identical for both the catalyzed and uncatalyzed reactions B) because the protein is a very strong inhibitor and it slows the reaction C) because the temperature would be identical for both the catalyzed and uncatalyzed reactions D) because the entropy would be identical for both the catalyzed and uncatalyzed reactions

no no A

Consider the following reaction: A → B Which of the following statements about this reaction are correct? 1) If you double the concentration of reagent A, you will double the rate. 2) The reaction rate (or velocity) is dependent only on the concentration of A. 3) The units for the first-order rate constant are M s- 1. 4) A plot of the log[A] versus time yields an inverse hyperbola.

only statements 1 and 2 are correct

In general, enzymes are what kinds of molecules? carbohydrates lipids proteins nucleic acids minerals

proteins

The equilibrium constant for a first-order ________ reaction is equivalent to the ratio of the rate constant for the forward and reverse reactions.

reversible

A Lineweaver-Burk plot can be used to determine KM using initial-rate data for an enzyme-catalyzed reaction. True False

true

Covalent modification can either activate or inhibit enzymes. True False

true

Feedback regulation of a metabolic pathway can either be activation or inhibition. True False

true

In an enzyme-catalyzed reaction, the lifetime of the transition state is similar to the vibrational frequencies of covalent bonds. True False

true

Metal ions are often required for catalytic efficiency but they may not remain permanently bound to the protein or take part in the catalytic process. True False

true

Pyruvate carboxylase is an example of the ligase class of enzymes. True False

true

Serine proteases make use of covalent catalysis as well as electrostatic stability of the transition state to achieve rate enhancement. True False

true

Match each function with the name of a major enzyme class. 1) transfer functional groups between molecules 2) catalyze intramolecular rearrangements 3) catalyze redox chemistry 4) catalyze the joining of two molecules together A) oxidoreductases B) transferases c) hydrolases D) lyases E) isomerases F) ligases

1B, 2E, 3A, 4F

Activation energy is the energy that a reaction must overcome to convert a substrate to the product. Enzymes lower the activation energy of a chemical reaction just as all catalysts lower activation energy. This means that less energy is required to convert reactant molecules to products. Enzymes also increase the rate of a biological reaction compared to the rate of the uncatalyzed reaction. Label the energy reaction graph for the following reaction showing the energy profile for a catalyzed and an uncatalyzed reaction. From top to bottom. 1) Rxn not catalyzed by an enzyme 2) Activation energy 3) Rxn catalyzed by an enzyme 4) Energy released by the rxn

2 1 3 4

Briefly explain the shape of your curve. Check all that apply. 1) At pH = pKa expect 100% of maximal activity because the Asp will be 100% protonated. 2) The Asp must be protonated to act as a general acid catalyst; thus, activity will be higher when pH < pKa and lower when pH > pKa. 3) At pH = pKa expect 50% of maximal activity because the Asp will be 50% protonated. 4) At pH = pKa expect 100% of maximal activity because the Asp will be 100% deprotonated. 5) The Asp must be fully deprotonated to act as a general acid catalyst; thus, activity will be higher when pH < pKa and lower when pH > pKa.

2, 3

Assuming that the side chain cannot -bond to the oxyanion intermediate, by how much (in ) does appear to stabilize the transition state at 37 ?

20 kJ/mol

The inhibitory effect of an uncompetitive inhibitor is greater at high [S] than at low [S]. Explain this observation. Check all that apply. 1) At [S] > KM the effect of the inhibitor on reducing Vmax is apparent because as [S] decreases, V approaches Vmax[S]/α′. 2) At [S] < KM the effect of the inhibitor is minimal because as [S] increases, V approaches Vmax/[S]KM. 3) At [S] < KM the effect of the inhibitor is minimal because as [S] decreases, V approaches Vmax[S]/KM. 4) At [S] > KM the effect of the inhibitor on reducing Vmax is apparent because as [S] increases, V approaches Vmax/α′.

3 and 4

Enalaprilat is a competitive inhibitor of the angiotensin-converting enzyme (ACE), which cleaves the blood-pressure regulating peptide angiotensin I. ACE has a KM = 12 μM for angiotensin I, which is present in plasma at a concentration of 75 μM. When enalaprilat is present at 2.4 nM, the activity of ACE in plasma is 10% of its uninhibited activity. What is the value of KI for enalaprilat?

3.7 x 10^-11 M

Arrange the events for the hydrolysis of amide bonds by chymotrypsin in their correct order. 1) attack by Ser 195 to give a tetrahedral intermediate 2) enzyme returns to initial state 3) protonation by His 57 and then cleavage of the C-N bond release the C-terminal fragment 4) protonation by His 57 and then cleavage of the C-O bond release the N-terminal fragment 5) attack by water, leading to formation of a tetrahedral intermediate 6) binding of substrate to properly position the scissile bond for cleavage

6 1 3 5 4 2

Suggest the effects of each of the following mutations on the physiological role of chymotrypsinogen: R15S A) Activation of the molecule will be greatly reduced due to removal of the R that is binded in its active site. B) Automodification of π-chymotrypsin to α-chymotrypsin could be reduced, the effect on activation might be slight. C) If activation occurs, the N-terminal peptide will no longer be constrained by an SS bond and may be released. --------- C1S A) Activation of the molecule will be greatly reduced due to removal of the R that is binded in its active site. B) Automodification of π-chymotrypsin to α-chymotrypsin could be reduced, the effect on activation might be slight. C) If activation occurs, the N-terminal peptide will no longer be constrained by an SS bond and may be released. --------- T147S A) Activation of the molecule will be greatly reduced due to removal of the R that is binded in its active site. B) Automodification of π-chymotrypsin to α-chymotrypsin could be reduced, the effect on activation might be slight. C) If activation occurs, the N-terminal peptide will no longer be constrained by an SS bond and may be released.

A C B

Which of the following statements BEST describes the Michaelis-Menton constant KM? A) It is a measure of enzyme efficiency. B) It is numerically equal to the substrate concentration required to reach half maximal velocity for an enzyme-catalyzed reaction. C) It has units of concentration. D) It is numerically equal to the affinity between the enzyme and its substrate. E) It is a measure of the rate of a catalytic process.

B

You have added an irreversible inhibitor to a sample of enzyme and substrate. At this point, the reaction has stopped completely. What can you do to regain the activity of the enzyme? A) Removing the irreversible inhibitor should get the reaction working again. B) The enzyme is inactive at this point. New enzyme must be added to regain enzyme activity. C) Adding more substrate will increase the rate of reaction. D) Adding more inhibitor should get the reaction up to speed again.

B

You have an enzymatic reaction proceeding at the optimum pH and optimum temperature. You add a competitive inhibitor to the reaction and notice that the reaction slows down. What can you do to speed the reaction up again? a) Add more inhibitor to speed up the reaction. b) Add more substrate; it will outcompete the inhibitor and increase the reaction rate. c) Increase the temperature. d) Increase the pH.

B

Show that the half-life for a first-order reaction is inversely proportional to the rate constant, and determine the constant of proportionality. Choose the equation for a first-order reaction. A) [A]o[A]t / [A]t−[A]o = kt B) ln ( [A]t / [A]o ) = −kt C) log ( [A]t / [A]o ) = −kt D) 1/[A]t − 1/[A]o = −kt -------------- When t = t1/2, what is the value of −kt1/2? -------------- What is the expression for the half-life for a first-order reaction? a) t1/2 = 0.693k b) t1/2 = 0.693k c) t1/2 = −k0.693 d) t1/2 = −0.693k --------------- Based on the half-life expression for a first-order reaction, determine its constant of proportionality?"

B -0.693 A 0.693

TPCK and TLCK are irreversible inhibitors of serine proteases. One of these inhibits trypsin and the other chymotrypsin. Which is which? A) TPCK inhibits trypsin, TLCK inhibits chymotrypsin. B) TLCK inhibits trypsin, TPCK inhibits chymotrypsin. ---------- Explain your reasoning. a) TPCK is an analog of Val and therefore a better inhibitor of chymotrypsin, whereas TLCK is an analog of Ala and therefore a better inhibitor of trypsin. b) TPCK is an analog of Lys and therefore a better inhibitor of chymotrypsin, whereas TLCK is an analog of Phe and therefore a better inhibitor of trypsin. c) TPCK is an analog of Phe and therefore a better inhibitor of chymotrypsin, whereas TLCK is an analog of Lys and therefore a better inhibitor of trypsin. d) TPCK is an analog of Ala and therefore a better inhibitor of chymotrypsin, whereas TLCK is an analog of Leu and therefore a better inhibitor of trypsin.

B C

An enzyme _____. a) is a source of energy for endergonic reactions b) is a inorganic catalyst c) is an organic catalyst d) can bind to nearly any molecule e) increases the EA of a reaction

C

Enalapril is administered in pill form, but enalaprilat must be administered intravenously. Why do you suppose enalapril works as a pill, but enalaprilat does not? a) Enalaprilat has a larger size than enalapril and cannot cross membranes to get from the gut to circulation. b) Enalaprilat has a larger mass than enalapril and cannot cross membranes to get from the gut to circulation. c) Enalaprilat is too polar to cross membranes, whereas enalapril can cross membranes to get from the gut to circulation. d) Enalaprilat is not flexible enough to get into pores, whereas enalapril can cross membranes to get from the gut to circulation.

C

On the basis of these data, suggest what features of amino acid sequence dictate the specificity of proteolytic cleavage by elastase. Fill in the blanks: large small C-terminal N-terminal A hydrophobic residue seems to be favored at the position ________ to the site of bond cleavage. Elastase always requires a ________ residue (like Ala) to the ___________ side.

C-terminal small N-terminal

Which of the following describes a mechanism that enzymes use to achieve their rate enhancement of reactions? A) preferential binding to the transition state through complementary non-covalent interactions B) altering the reaction pathway to include intermediate states C) distortion of the substrate or active site, which, in effect, lowers the energy of activation D) All of the listed choices describe mechanisms used by enzymes to achieve their rate enhancement of reactions.

D

If a mixture of these three substrates was presented to elastase with the concentration of each peptide equal to 0.5 {\rm mm}, which would be digested most rapidly? Which most slowly? (Assume enzyme is present in excess.) Rank from most rapidly to most slowly. PAPA!F PAPA!G PAPA!A

PAPA!F PAPA!A PAPA!G

Which of the following statements about the oxyanion hole is NOT true? a) This preformed loop is properly positioned to stabilize the negatively charged tetrahedral intermediate involved in amide bond hydrolysis. b) The backbone NH bonds of S195 and G193 create H-bonding interactions with the developing negative charge as Ser 195 attacks the scissile carbon bond. c) It represents an electrostatic interaction that leads to a lower energy state. d) It represents an enthalpic interaction that helps stabilize the transition state.

a

Which of the following statements about the various methods of enzyme inhibition is NOT true? a) Competitive inhibitors bind at a different site than substrate, altering the ability of the enzyme to bind its native target. b) Noncompetitive inhibitors bind at a different site than substrate, altering the ability of the enzyme to bind its native target. c) Irreversible inhibitors, primarily because they covalently modify an enzyme, are often toxic. d) Uncompetitive inhibitors bind at a different site than substrate but only after enzyme has bound its native target.

a

Which of the following statements are true with respect to enzyme activity? Check all that apply. a) Enzymes are regenerated when the reaction is completed. b) Enzymes affect the reaction pathway by forming an enzyme-substrate complex. c) The activation energy of a reaction increases when an enzyme is used to catalyze the reaction. d) Enzymes speed up the reaction rate. e) Enzyme reactivity is not affected by change in pH and temperature.

a b d

Explain the shape of the curve in panel (b). Why does v0 increase initially, before decreasing at higher [succinate]? Check all that apply. a) As the [succinate] increases, succinate will bind to T-state ATCase and promote the T → R switch. This accounts for the decrease of v0 in plot (b). b) As the [succinate] increases, it blocks more active sites from binding the true substrate (Asp), and the turnover of Asp decreases (as shown in plot (b)). c) At low [succinate], succinate blocks more active sites from binding the true substrate (Asp). This accounts for the initial rise in v0 in plot (b). d) At low [succinate], succinate will bind to T-state ATCase and promote the T → R switch, thereby activating the ATCase. This accounts for the initial rise in v0 in plot (b).

b and d

Is the effect of the mutation what you would expect for a residue that makes up part of the oxyanion hole? How do the reported values of and support your answer? Check all that apply. a) kcat should be reduced due to the gain of enthalpic stabilization of the transition state. b) For a mutation of a residue that only interacts with the oxyanion intermediate, one would not expect Km to change significantly. c) The oxyanion is formed after S binds. d) For a mutation of a residue that only interacts with the oxyanion intermediate, one would expect Km to change significantly. e) The oxyanion is formed after S goes away. f) kcat should be reduced due to the loss of enthalpic stabilization of the transition state.

b c f

Enzymes can accelerate reactions by: a) lowering the energy for activation. b) correctly positioning a metal ion for catalysis. c) promoting the removal or addition of protons. d) binding a substrate or substrates. e) all of the above.

e

Which of the following statements about the proposed mechanisms of action for hen egg white lysozyme does NOT support either model? a) A water molecule is deprotonated, which then attacks C1 of the substrate. b) The active site glutamic acid changes between being protonated and deprotonated. C) Glycosidic bond cleavage occurs by general acid/base catalysis. d) A covalent intermediate is formed between an active site aspartate and C1 of the substrate. e) The active site aspartic acid changes between being protonated and deprotonated.

e

Electrostatic catalysis proceeds via covalent bonding interactions. True False

false

Non-catalyzed biochemical reactions always occur at physiological useful timescales. True False

false

In an enzyme-catalyzed reaction, the reactant species to which the enzyme binds is called the substrate. The substrate is then converted into products by a series of steps. The lock-and-key model explains the steps involved in an enzyme-catalyzed reaction. Label the following diagram that illustrates the lock-and-key model of enzyme activity. Drag the appropriate labels to their respective targets. active site enzyme-substrate complex products enzyme

left to right active site enzyme-substrate complex products (top) enzyme (bottom)

In a favorable reaction the free energy of the products is ________ than the free energy of the reactants.

less

Classify each of the characteristics as lock-and-key model or induced-fit model or both. a) active site is rigid. b) active site is flexible c) substrate shape is modified d) enzyme is substrate specific e) active site-substrate interaction induces an optimal fit for catalysis f) enzyme returns to its initial state after catalysis

lock-and-key model: A induced-fit model: B, C, E both: D, F

Fill in the blanks with the following: His 57 gain loss N-terminus C-terminus Asp 102 Ser 195 The change in between 6 and 7 must involve _______ of a proton in the active site. The best candidate is _______. The increase in at higher must involve a change in the binding site. The group involved is probably the __________ at Ile 16, created by the cleavage that activates chymotrypsin.

loss His 57 N-terminus

Which myoglobin is more thermodynamically stable, the mutant or the wild-type? mutant myoglobin wild-type myoglobin

mutant myoglobin

In general, an enzyme has one active site at which catalysis can occur. When the substrates are bound to the active site, the enzyme will catalyze the reaction. As the concentration of substrate increases, the reaction rate increases, until the point where the active site is saturated with substrate. When the enzyme is saturated, the rate of the reaction will not increase with the concentration of substrates. ******* Look at the graph of reaction rate versus substrate concentration for an enzyme. (Figure 1) In which region does the reaction rate remain constant? region A region B region C ---------- Refer again to the graph. (Figure 1) In which region is the enzyme saturated with substrate? region A region B region C --------- Consider a situation in which the enzyme is operating at optimum temperature and pH, and has been saturated with substrate. What is your best option for increasing the rate of the reaction? A) Increase the pH. B) Increase the temperature. C) Increase the enzyme concentration. D) Increase the substrate concentration.

region C region C C

The graph presents three activation energy profiles for a chemical reaction (the hydrolysis of sucrose): an uncatalyzed reaction, and the same reaction catalyzed by two different enzymes. Rank these by reaction rate, as measured by the rate of product formation (from the most product formed to the least product formed). To rank items as equivalent, overlap them. rxn catalyzed by enzyme A rxn catalyzed by enzyme B uncatalyzed rxn

rxn catalyzed by enzyme B rxn catalyzed by enzyme A uncatalyzed rxn

What name is given to the reactants in an enzymatically catalyzed reaction? EA products reactors substrate active sites

substrate