Ch 2: Enzymes (14%)

Oxidoreductases

Name the Enzyme Class

WORD BANK: Transferases, Lyases, Hydrolases, Oxidoreductases, Ligases, Isomerases

——

Catalyze oxidation-reduction reactions

Often have a cofactor that acts as an electron carrier, such as NAD+ or NADP+

Include dehydrogenases, reductases, and oxidases

Transferases

Name the Enzyme Class

WORD BANK: Transferases, Lyases, Hydrolases, Oxidoreductases, Ligases, Isomerases

——

Catalyze the movement of a functional group from one molecule to another

Includes kinases → catalyze the transfer of a phosphate group (generally from ATP) to another molecule

Hydrolases

Name the Enzyme Class

WORD BANK: Transferases, Lyases, Hydrolases, Oxidoreductases, Ligases, Isomerases

——

Catalyze the breaking of a compound into two molecules using the addition of water

Includes phosphatase, peptidases, nucleases, and lipases

Lyases

Name the Enzyme Class

WORD BANK: Transferases, Lyases, Hydrolases, Oxidoreductases, Ligases, Isomerases

——

Catalyze the cleavage of a single molecule into two products

Do not require water

Can also catalyze the synthesis of two molecules into a single molecule, but they are referred to as synthases in this case

Isomerases

Name the Enzyme Class

WORD BANK: Transferases, Lyases, Hydrolases, Oxidoreductases, Ligases, Isomerases

——

Catalyze the rearrangement of bonds within a molecule

Catalyze reactions between stereoisomers and constitutional isomers

Ligases

Name the Enzyme Class

WORD BANK: Transferases, Lyases, Hydrolases, Oxidoreductases, Ligases, Isomerases

——

Catalyze addition or synthesis reactions generally between large similar molecules

Often require ATP

Most likely to be encountered in nucleic acid synthesis and repair on Test Day

overall change in free energy, equilibrium

What 2 things in a reaction do enzymes NOT change?

lower the activation energy to increase reaction rate (make it easier for the substrate to reach the transition state)

What do enzymes do in reactions?

B complex vitamins, vitamin C (ascorbic acid)

WORD BANK: Vitamin K, Vitamin D, Vitamin C (ascorbic acid), Vitamin D, Vitamin A, Vitamin E, B Complex Vitamins

——

name the 2 types of water-soluble vitamins that can act as cofactors

vitamin A, vitamin D, vitamin E, vitamin K

WORD BANK: Vitamin K, Vitamin D, Vitamin C (ascorbic acid), Vitamin D, Vitamin A, Vitamin E, B Complex Vitamins

——

name the 4 types of fat-soluble vitamins that can act as cofactors

temperature, pH, salinity

name the 3 environmental factors that influence enzyme activity

Feedback Inhibition (Negative Feedback Regulation)

when the concentration of a product LATER in the metabolic pathway inhibits an enzyme EARLIER in the pathway

increase temperature, decrease activation energy

What are the 2 ways to increase the rate of a reaction?

activation energy

the minimum amount of energy it takes to pass over the transition state, meaning the reaction can proceed

increase, lowering

Enzymes ________ reaction rates by _________ transition state energies

both directions

A catalyst lowers the activation energy in _____ __________

Vmax

Enzyme Kinetics

The maximum rate of the reaction achieved when all enzyme active sites are saturated with substrate

Appears as a horizontal asymptote on a Michaelis-Menten plot

total amount of enzyme

Enzyme Kinetics

What does V_max depend on?

Km

Enzyme Kinetics

Michaelis constant

A measure of the affinity of an enzyme for its substrate

Measures how easily an enzyme-substrate complex forms

The substrate concentration required for the reaction rate to = ½ V_max

lower/weaker, it requires a higher substrate concentration to be half-saturated

Enzyme Kinetics

Do enzymes with HIGH K_m’s have a HIGHER/STRONGER or LOWER/WEAKER affinity for its substrate?

Why?

higher/stronger, it requires a lower substrate concentration to be half-saturated

Enzyme Kinetics

Do enzymes with LOW K_m’s have a HIGHER/STRONGER or LOWER/WEAKER affinity for its substrate?

Why?

greater

(*** at low concentrations (< Km), the reaction rate is very sensitive to changes in [S])

Enzyme Kinetics

Will changes in substrate concentration have a GREATER or LESSER effect on reaction rate when the substrate concentration is less than K_m ([S] < K_m)?

lesser

(*** at high concentrations (> Km), the reaction rate is less responsive to changes in [S])

Enzyme Kinetics

Will changes in substrate concentration have a GREATER or LESSER effect on reaction rate when the substrate concentration is more than K_m ([S] > K_m)?

pic

Enzyme Kinetics

What is the general enzyme-substrate complex formula? (answer in pic)

(rate of substrate/enzyme complex dissociation + rate of product formation) / rate of enzyme/substrate complex formation

Enzyme Kinetics

write out the formula for K_m using the rate constants

high, saturated, [S]»Km

Enzyme Kinetics

Does V_max occur at low or high substrate concentration?

In this state, is the enzyme saturated or unsaturated?

In this state, what is the relationship between [S] and K_m?

(Vmax x [S]) / (Km + [S])

Enzyme Kinetics

write out the Michaelis-Menten equation

properties, enzyme

Enzyme Kinetics

The unknowns V_max and K_m are ____________ of the particular __________

Km = [S]

Enzyme Kinetics

write out the relationship between K_m and [S] when the reaction velocity = ½ V_max

higher, lower

Enzyme Kinetics

More efficient enzymes have ________ V_max’s and _______ K_m’s which gives you a faster reaction rate for a given level of substrate

Michaelis-Menten

Enzyme Kinetics

Michaelis-Menten vs. Lineweaver-Burk Plot

displays a hyperbolic curve

Lineweaver-Burk

Enzyme Kinetics

Michaelis-Menten vs. Lineweaver-Burk Plot

displays a linear function

Km/Vmax

Enzyme Kinetics

write out the formula for calculating the slope of a Lineweaver-Burk plot

1/Vmax

Enzyme Kinetics

write out the formula for calculating the y-intercept of a Lineweaver-Burk plot

-1/Km

Enzyme Kinetics

write out the formula for calculating the x-intercept of a Lineweaver-Burk plot

cooperativity

Enzyme Kinetics

enzymes that display THIS characteristic (ex: hemoglobin) have a sigmoidal (S-shaped) Michaelis-Menten graph

cooperativity

Enzyme Kinetics

the phenomenon where the binding of a substrate molecule to one subunit of a multi-subunit enzyme influences the enzyme's affinity for additional substrates

>1

Enzyme Kinetics: <1 vs. =1 vs. >1

Hill’s coefficient when POSITIVE cooperative binding is occurring → After one ligand is bound the affinity of the enzyme for further ligands increases

<1

Enzyme Kinetics: <1 vs. =1 vs. >1

Hill’s coefficient when NEGATIVE cooperative binding is occurring → After one ligand is bound the affinity of the enzyme for further ligands decreases

= 1

Enzyme Kinetics: <1 vs. =1 vs. >1

Hill’s coefficient when the enzyme does NOT exhibit cooperative binding

Michaelis-Menten graph

Michaelis-Menten Graph vs. Lineweaver-Burk Plot

What is this a picture of?

Lineweaver-Burk plot

Michaelis-Menten Graph vs. Lineweaver-Burk Plot

What is this a picture of?

inhibitor

Enzyme Kinetics

Molecules that reduce the activity of an enzyme by combining it with a way that either affects substrate binding or affects conversion of substrate to product (can be a small molecule or a protein)

competitive inhibition

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

When inhibitor and substrate compete for the same active site

Can be overcome by adding more substrate

no

Enzyme Kinetics - Competitive Inhibition

Does competitive inhibition affect V_max?

If so, does it INCREASE or DECREASE it?

no, yes

Enzyme Kinetics - Competitive Inhibition

Does competitive inhibition change the y-intercept?

Does competitive inhibition change the x-intercept?

low

Enzyme Kinetics - Competitive Inhibition

High vs. Low

Competitive inhibition has more of an effect at _____ levels of substrate concentration

yes, increase, decrease

Enzyme Kinetics - Competitive Inhibition

Does competitive inhibition affect K_m?

If so, does it INCREASE or DECREASE it?

Does this mean an INCREASE or DECREASE in binding affinity for the substrate?

competitive

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

competitive

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

uncompetitive

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

When inhibitor binds to the enzyme-substrate complex (not the free enzyme) and prevents the conversion of substrate to product

Can be interpreted as an increase in binding affinity between the enzyme and substrate

yes, decrease

Enzyme Kinetics - Uncompetitive Inhibition

Does uncompetitive inhibition affect V_max?

If so, does it INCREASE or DECREASE it?

yes, decrease, increase

Enzyme Kinetics - Uncompetitive Inhibition

Does uncompetitive inhibition affect K_m?

If so, does it INCREASE or DECREASE it?

Does this mean an INCREASE or DECREASE in binding affinity for the substrate?

high

Enzyme Kinetics - Uncompetitive Inhibition

High vs. Low

Uncompetitive inhibition has more of an effect at _____ substrate concentration

yes, yes

Enzyme Kinetics - Uncompetitive Inhibition

Does uncompetitive inhibition change the y-intercept?

Does uncompetitive inhibition change the x-intercept?

uncompetitive

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

uncompetitive

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

mixed

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

When the inhibitor binds to both the enzyme/substrate complex and the free enzyme, but has different affinities for each

competitive

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

prevents substrate binding to the enzyme

uncompetitive

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

prevents conversion of substrate to product

mixed

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

prevents both substrate binding & conversion of substrate to product

yes, decrease

Enzyme Kinetics - Uncompetitive Inhibition

Does uncompetitive inhibition affect V_max?

If so, does it INCREASE or DECREASE it?

yes (the change depends on whether or not affinity for the substrate is increased or decreased)

Enzyme Kinetics - Mixed Inhibition

Does mixed inhibition affect K_m?

yes, yes

Enzyme Kinetics - Mixed Inhibition

Does mixed inhibition change the y-intercept?

Does mixed inhibition change the x-intercept?

mixed

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

noncompetitive

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

When the inhibitors bind to an allosteric site instead of the active site, which leads to a change in enzyme conformation

When the inhibitor binds to the enzyme and the enzyme-substrate complex with equal affinity

A specific type of mixed inhibition

yes, decrease

Enzyme Kinetics - Noncompetitive Inhibition

Does noncompetitive inhibition affect V_max?

If so, does it INCREASE or DECREASE it?

no

Enzyme Kinetics - Noncompetitive Inhibition

Does noncompetitive inhibition affect K_m?

If so, does it INCREASE or DECREASE it?

Does this mean an INCREASE or DECREASE in binding affinity for the substrate?

yes, no

Enzyme Kinetics - Noncompetitive Inhibition

Does noncompetitive inhibition change the y-intercept?

Does noncompetitive inhibition change the x-intercept?

noncompetitive

Enzyme Kinetics

Competitive vs. Uncompetitive vs. Noncompetitive vs. Mixed Inhibition

C, F

Select all of the following that would INCREASE the rate of a reaction:

A. decreasing the free energy (G) of the substrate

B. decreasing the free energy (G) of the product

C. increasing the temperature

D. decreasing the temperature

E. increasing the free energy of activation (delta G naught cross)

F. decreasing the free energy of activation (delta G naught cross)

D

A reaction proceeds at a rate ≈ Vmax. What is the substrate concentration [S]?

A. [S] = [E]_T

B. [S] = Km

C. [S] = 2 x Km

D. [S] » Km

B

For the type of inhibition shown, what does the inhibitor bind to?

A. the enzyme only (E)

B. the enzyme:substrate complex only (ES)

C. Both the enzyme (E) and the enzyme:substrate complex (ES)

D. none of the choices are correct

B

The graph shows a special type of mixed inhibition where the inhibitor binds both E and ES with equal affinity. How does the presence of this inhibitor change the EFFECTIVENESS of both Vmax and Km?

A. decreases Km; decreases Vmax

B. no change to Km; decreases Vmax

C. increases Km; decreases Vmax

D. no change to Km; increases Vmax

E. increases Km; no change to Vmax

C

Catalysts primarily work by:

A. providing additional kinetic energy for a substrate to overcome free energy barriers

B. increasing the free energy of the substrate

C. stabilizing the transition state of a reaction

D. decreasing the free energy of the product

C

In the case of competitive inhibition, which of the following statements about the Lineweaver-Burk plot is TRUE?

A. The slope does not change as inhibitor is added

B. The intersection point as inhibitor is added is given by [-1/α, 1/α]

C. The y intercept does not change as inhibitor is added

D. The x intercept does not change as inhibitor is added

A

In the case of uncompetitive inhibition, which of the following statements about the Lineweaver-Burk plot is TRUE?

A. The slope does not change as inhibitor is added

B. The x intercept does not change as inhibitor is added

C. The y intercept does not change as inhibitor is added

D. The intersection point as inhibitor is added is given by [-1/α', 1/α']

D

If a Lineweaver-Burk plot of a reaction is not linear, which of the following is TRUE?

A. The reaction is performed with a competitive inhibitor

B. The reaction is performed with an uncompetitive inhibitor

C. The reaction is performed with a mixed inhibitor

D. The reaction does not obey Michaelis-Menten kinetics