BioChem Chapter 6

Which of the following statements about a plot of V0 vs. [S] for an enzyme that follows Michaelis-Menten kinetics is false? a. As [S] increases, the initial velocity of reaction V0 also increases. b. At very high [S], the velocity curve becomes a horizontal line that intersects the y-axis at Km. c. Km is the [S] at which V0 = 1/2 Vmax. d. The shape of the curve is a hyperbola. e. The y-axis is a rate term (velocity)

b. At very high [S], the velocity curve becomes a horizontal line that intersects the y-axis at Km.

A good transition-state molecule/species:

binds to the enzyme more tightly than the substrate.

How does an amino acid act as a nucleophile?

by donating a "R" "O" anything but a proton ("H")

The steady state assumption, as applied to enzyme kinetics, implies: a. Km = Ks. b. the enzyme is regulated. c. the ES complex is formed and broken down at equivalent rates. d. the Km is equivalent to the cellular substrate concentration. e. the maximum velocity occurs when the enzyme is saturated.

c. the ES complex is formed and broken down at equivalent rates.

covalent catalysis

change reaction paths

Some enzymes require another organic molecules to function. These helper molecules are called ___________. If that molecule is covalently or tightly bound to the enzyme, it is called a __________________ group. An enzyme with that molecule attached is called a __________, while an enzyme minus its extra component is called an __________.

coenzyme prothetic holoenzyme apoenzyme

Does the Michaelis-Menten equation equation apply to all enzymes? If not, to which kind does it not apply?

does not apply to enzymes that display sigmoidal V0 vs. [S] curves

the process of general base catalysis is illustrated by

donating electrons to "H"

The higher the Kcat the ________ the reaction

faster

Acid-base Catalysis

give and take protons

How does an amino acid act as a base or acid-base catalysis?

gives protons

Identify the type of enzyme catalyzing the following reaction:

https://o.quizlet.com/lb5BMB0s62a7ivyFld7yvw.png B. Isomerase

What kind of interaction would this modification may affect?

ionic interactions (salt bridges)

What is the best way to compare the catalytic efficiencies of different enzymes or the specificity of different substrates by the same enzyme?

kcat/Km

What relative values of Km, and kcat would describe an enzyme with a high catalytic efficiency/ substrate efficiency?

low Km, and high kcat

Enzymes are potent catalysts because they:

lower the activation energy for the reactions they catalyze

Lower Km means

more affinity

A competitive inhibitor binds to ________________, while an uncompetitive inhibitor binds to ________________.

only to the enzyme; only to the enzyme-substrate complex

What is the common type of covalent modification?

phosphorylation

Enzymes organize reactive groups into ___________ _________and________ _______

proper orientation ; close proximity

What breaks down proteins?

protease

The concept of "induced fit" refers to the fact that

substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper orientation.

What does Kcat/Km tell us?

the efficiency

Explain how a biochemist might discover that a certain enzyme is allosterically regulated.

the graph would be sigmoidal, not hyperbolic.

When 10 ug of an enzyme of Mr 50,000 is added to a solution containing its substrate at a concentration one hundred times the Km, it catalyzes the conversion of 75 umol of substrate into product in 3 min. What is the enzyme's turnover number?

total enzyme = 10x10^-6 / 5x10^9 = 2x10^-10 Vmax= 75umol/3min= 25um/min (25x10^-6umol/min) / (2x10^-10)= 12.5x10^4min

Enzymes bind __________ ________ _______ better than substrates

transition state intermediates

How does the total enzyme concentration affect turnover number and Vmax?

turnover number is not affected by the total enzyme concentration

How would the addition of a catalyst to the reaction S⇋P affect the difference between the free energies of S and P in their ground states (∆G'°)?

∆G'° would not change

How do you calculate x-intercept

-1/Km

explain how enzyme catalysis overcomes the thermodynamic barriers from above

1. Binding energy holds the substrates in the proper orientation to react 2. enzyme also undergo conformational changes to align specific functional groups on the enzyme into the proper position to catalyze the reaction 3. binding energy helps to compensate thermodynamically for any distortion 4. Enzyme-substrate interactions replace most or all of the hydrogen bonds between the substrate and water that would otherwise impede reaction.

What are the four ways in which enzymes are regulated? Which of these regulation is irreversible?

1. Covalent modification 2. Allosteric modulation 3. Proteolytic cleavage: irreversible 4. Interaction with other regulatory proteins

What are the four concepts that we need to know for amino acid function?

1. base 2. acid 3. electrophile 4. Nucleophile

Name the six types of enzymes classified based on the types of reaction catalyzed by them

1. oxideoreductases 2. transferases 3. hydrolases 4. lyases 5. isomerases 6. ligases

Describe four thermodynamic barriers to reactions

1. the entropy (freedom of motion) of molecules in solution, which reduces the possibility that they will react together 2. the need for proper alignment of catalytic functional groups on the enzyme 3. the distortion of substrates that must occur in many reactions 4. the solvation shell of hydrogen-bonded water that surrounds and helps to stabilize most biomolecules in aqueous solution

How do you calculate Vo

1/2 VMax

How do you calculate y-intercept

1/VMax

At a substrate concentration of 5 mM, what is the velocity of an enzymatic reaction given a Vmax of 25 mM/min and a Km of 0.5 mM?

25[5] / 0.5 + 5 = 23

The following data were obtained in a study of an enzyme known to follow Michaelis-Menten kinetics: V0 Substrate (mmol/min) (mM) ————————————— 217 0.8 325 2 433 4 488 6 550 10 649 1,000 650 2,000 ————————————— The Km for this enzyme is approximately:

2mM

Which aspect of a reaction can an enzyme alter?

Activation Energy (ΔG‡)

Which term quantitatively determine the reaction rate reaction of conversion of S to P?

Activation Energy (ΔG‡)

the process of covalent catalysis is illustrated by

An "O" or "OH" group donating to a "C"

Which of the following statements about a plot of V0 vs. [S] for an enzyme that follows Michaelis-Menten kinetics is false? -The shape of the curve is a hyperbola. -At very high [S], the velocity curve becomes a horizontal line that intersects the y-axis at Km. -As [S] increases, the initial velocity of reaction V0 also increases until it plateaus. -Km is the [S] at which V0 = 1/2 Vmax.

At very high [S], the velocity curve becomes a horizontal line that intersects the y-axis at Km.

___________is the free energy released in forming many weak bonds and interactions between an enzyme and its substrate. This contributes to specificity as well as to catalysis.

Binding energy

S-Adenosyl methionine (SAM) is an organic molecule bound to various metabolic enzyme and functions transfer methyl groups from SAM to an acceptor. What is the proper designation of SAM?

Co-enzyme and Co-factor

What are the functions of coenzymes? Note that many of them are vitamins

Co-enzymes are complex organic or metallo-organic molecules that function as transient carriers of specific functional groups. They are derived from vitamins, organic nutrients required in small amounts in the diet.

What components besides amino acids residues are sometimes necessary for an enzyme to be active?

Co-factors like metal ions and co-enzymes

What is the specific source of energy for lowering the activation energy barriers on the enzyme-catalyzed reactions?

Covalent interactions between enzymes and substrates lower the activation energy by providing an alternative, lower-energy reaction path. much of the energy required to lower activation energies is derived from weak, noncovalent interactions between substrate and enzyme called binding energy.

Methanol (wood alcohol) is highly toxic because it is converted to formaldehyde in a reaction catalyzed by the enzyme alcohol dehydrogenase: NAD+ + methanol -> NADH + H+ + formaldehyde Part of the medical treatment for methanol poisoning is to administer ethanol (ethyl alcohol) in amounts large enough to cause intoxication under normal circumstances. Explain this in terms of what you know about examples of enzymatic reactions.

Ethanol is a structural analog of methanol, and competes with methanol for the binding site of alcohol dehydrogenase, slowing the conversion of methanol to formaldehyde, and allowing its clearance by the kidneys. The effect of ethanol is that of a competitive inhibitor.

The enzymatic activity of lysozyme is optimal at pH 5.2 and decreases above and below this pH value. Lysozyme contains two amino acid residues in the active site essential for catalysis: Glu35 and Asp52. The pK value for the carboxyl side chains of these two residues are 5.9 and 4.5, respectively. What is the ionization state of each residue at the pH optimum of lysozyme? How can the ionization states of these two amino acid residues explain the pH-activity profile of lysozyme?

For the enzyme to be active, it is likely that Asp52 is unprotonated and Glu35 is protonated. When the pH is below 4.5, Asp52 becomes protonated, and when it is above 5.9, Glu35 is deprotonated, either of which decreases the activity of the enzyme.

What is the function of cysteine residue in the active site of the following enzyme catalyzed reaction?

Functioning as nucleophile, which attacks the electrophilic carbonyl center of substrate

Which term quantitatively determine the reaction equilibrium between S and P?

Gibbs Free Energy (ΔG'˚)

Which of the following is true of enzymes? I. They increase the rate of reaction by forming lower energy transition state II. They raise activation energy to shift the equilibrium to favor the products III. They lower activation energy of the reaction they catalyze.

I and III

Enzymes with a kcat / Km ratio of about 10^8 M-1 s-1 are considered to show optimal catalytic efficiency. Fumarase, which catalyzes the reversible dehydration reaction fumarate + H2O -->malate has a ratio of turnover number to the Michaelis-Menten constant, (kcat / Km) of 1.6 X 10^8 for the substrate fumarate and 3.6 X 10^7 for the substrate malate. Because the turnover number for both substrates is nearly identical what factors might be involved that explain the different ratio for the two substrates?

If the turnover number is nearly identical for both substrates, then the Km for malate must be much larger than for fumarate

Describe the difference between lock and key hypothesis and induced fit mechanism of enzyme kinetics

Induced fit model states that the enzyme itself usually undergoes a change in conformation while the lock and key states that the enzymes were structurally complementary to their substrates

Which of the following is true of the binding energy derived from enzyme-substrate interactions? -It is the result of covalent bonds formed between enzyme and substrate. -It is sometimes used to hold two substrates in the optimal orientation for reaction. -It is the result of covalent bonds formed between enzyme and transition state. -It cannot provide enough energy to explain the large rate accelerations brought about by enzymes.

It is sometimes used to hold two substrates in the optimal orientation for reaction.

How can the Michaelis-Menten constant, be derived from this Lineweaver-Burk plot?

Km = (-1)/ (x-intercept)

How do you calculate slope

Km/Vmax

Which of the following correctly matches the enzyme class with the type of reaction it catalyzes?

Oxidoreductase: transfer of electrons

A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein is called a

Prosthetic group

Among the following types of enzyme if regulation, which is irreversible? -Allosteric modulation -Phosphorylation of enzymes (covalent modification) -Proteolytic cleavage -Both 1 and 3

Proteolytic cleavage

What makes mRNA

RNA polymerase

Which amino acid residues are involved in these modifications?

Serine Theronine Tyrosine

Which of the following statements is FALSE regarding a Lineweaver-Burk plot? -The line has an intercept of -1/Km on the 1/[S] axis. -The line has an intercept of 1/Vmax on the 1/V0 axis. -It is a plot of 1/V0 versus 1/[S]. -The line has a slope of Vmax / Km.

The line has a slope of Vmax / Km

Sometimes the difference in (standard) free-energy content, ΔG'°, between a substrate S and a product P is very large, yet the rate of chemical conversion, S ------>P, is quite slow. Why?

The rate of conversion from substrate to product does not depend on the free-energy difference between them. It depends on the activation energy of the reaction.

At a substrate concentration that is greater than the Km for the reaction, which statement below is true (assuming the enzyme obeys Michaelis-Menten kinetics).

The reaction velocity is > ½ Vmax

Why does pH affect the activity of an enzyme?

The state of ionization of several amino acid side chains is affected by pH, and the activity of many enzymes requires that certain of the amino acid residue side chains be in a specific ionization state

What is the difference between transition state and reaction intermediate?

The transition state is not a chemical species with any significant stability. Reaction intermediates are more stable and have normal bonds

What does K'eq mean in terms of standard free energy change of the reaction?

The value of Keq' reflects the difference between the free energy content of S and P. Free energy and equilibrium constant are related by the expression: delta G'° = -RT ln Keq'

Why is a transition-state analog not necessarily the same as a competitive inhibitor?

Their competitive inhibitor cannot communicate with the enzyme at the active site.

Which of the following statement is true regarding allosteric inhibition? -They are generally less complex than nonallosteric enzymes. -They have one or more regulatory sites for binding modulators. -They function through irreversible, covalent binding of regulatory compounds. -They are generally smaller than nonallosteric enzymes.

They have one or more regulatory sites for binding modulators.

Stronger/additional interactions with the ______ ______as compared to the ground state (or substrate) lower the activation barrier.

Transition state

Which statement is incorrect regarding uncompetitive inhibitors? -Uncompetitive inhibitions results in the change of the Km. -Uncompetitive inhibitions results in the change of the Vmax. -Uncompetitive inhibitions results in the change of the Km/Vmax. -Uncompetitve inhibitors binds to the enzyme-substrate complex only

Uncompetitive inhibitions results in the change of the Km/Vmax.

Metal Ions in Catalysis

Use redox cofactors

Give the Michaelis-Menten equation and define each term in it.

V0 = Vmax [S]/( Km + [S]), V0-initial velocity at any given concentration of S Vmax- velocity when all enzyme molecules are saturated with S [S] is the concentration Km is a constant

How do you calculate Kcat

VMax/Total enzyme

For the reaction E + S ->ES -> E + P the Michaelis-Menten constant, Km, Describe the constant. How can it be determined graphically?

When k2 is rate-limiting, k2 << k-1 and Km reduces to k-1/k1 -1/ Km