Chapter 6: Enzymes and Catalytic Principles
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182 Terms
What is an enzyme?
A biomolecule, either a protein or RNA, that speeds up a specific chemical reaction without being used up.
What does an enzyme do to a reaction?
It speeds up the reaction by providing a pathway with a lower activation energy.
Why do enzymes speed up reactions?
They lower the activation energy needed for the reaction to occur.
What happens to the rate of a reaction when an enzyme is present?
The reaction reaches equilibrium faster.
Are enzymes used up during a reaction?
No. The enzyme is not used up.
What type of biological molecules are most enzymes?
Proteins
What is a cofactor?
An inorganic ion or a coenzyme that is required for enzyme activity.
What is a coenzyme?
An organic cofactor required for the action of certain enzymes.
What are coenzymes often made from?
Vitamins
What are two important coenzymes?
NAD+ and coenzyme A.
How do NAD+ and coenzyme A bind to enzymes?
They bind reversibly.
What is a prosthetic group?
A cofactor that is tightly bound to an enzyme, such as a tightly bound coenzyme or metal ion.
What is an apoenzyme?
The protein portion of an enzyme without its required cofactors or prosthetic groups.
What is an example of a cofactor that is NOT a coenzyme?
A Mn ion.
Where does an enzyme-catalyzed reaction take place?
In a pocket on the enzyme called the active site.
What is the active site?
The part of an enzyme where the substrate binds and the reaction takes place.
What is a substrate?
The molecule that is acted on by an enzyme.
What happens when a substrate binds to an enzyme?
They temporarily form an enzyme-substrate complex.
What is an enzyme-substrate complex (ES complex)?
The temporary complex formed when a substrate binds to an enzyme.
What is the general reaction involving an enzyme, substrate, and product?
E + S ⇄ ES ⇄ EP ⇄ E + P
What does E represent?
Enzyme.
What does S represent?
Substrate
What does P represent?
Product.
What do ES and EP represent?
Short-lived complexes.
What allows protein enzymes to form active sites that can promote catalysis in multiple ways?
They are made up of amino acids.
If an enzyme catalyzes S → P, can it also catalyze P → S?
Yes. The same enzyme can catalyze the reaction in either direction.
What determines the rate of a reaction?
The energy of the transition state.
What determines equilibrium?
The difference in free energy between the products and reactants.
What is activation energy?
The energy barrier that must be overcome for a reaction to occur.
How can enzymes lower a large activation-energy barrier?
They can divide one high-activation-energy reaction into multiple reactions with lower activation energies.
What is a reaction intermediate?
A chemical species in a reaction pathway that has a finite chemical lifetime.
What is a rate-limiting step?
The step in a reaction with the greatest activation energy or highest-free-energy transition state.
What is the rate-limiting step in a metabolic pathway?
The slowest step.
What does a reaction coordinate diagram show?
The free energy of a system as a reaction progresses.
What does the equilibrium constant (Keq) describe?
The equilibrium of a reaction.
For the reaction S ⇄ P, what is Keq?
Keq = [P]/[S]
What does V represent in a reaction?
The velocity, or rate, of the reaction.
What does the velocity (V) tell you?
The amount of substrate that reacts per unit of time.
What is the equation for a first-order reaction?
V = k[S]
What does a first-order reaction depend on?
The concentration of one molecule, S.
What happens if two different substrate molecules are required for a reaction?
The reaction is second order.
What is the rate equation for a second-order reaction involving S1 and S2?
V = k[S1][S2]
What does k represent in the rate equation?
The rate constant.
What is enzyme specificity?
The ability of an enzyme to recognize and act on a specific substrate or a few closely related substrates.
What does an enzyme’s active site need to be complementary to?
The transition state of the reaction
Why does an enzyme bind strongly to the transition state?
The binding energy helps lower the activation barrier and speed up the reaction.
What is binding energy?
The energy gained from strong interactions between an enzyme and its substrate that helps overcome factors that slow the reaction.
How does enzyme specificity help the reaction?
It allows the enzyme to distinguish its substrate from competing molecules.
What is a transition state?
The unstable, highest-energy point between the substrate and product.
Which molecule does an enzyme usually bind most tightly?
A molecule that resembles the transition state.
What is a transition state analog?
A molecule that resembles the transition state and can bind tightly to the enzyme and inhibit it.
How can inhibiting an enzyme help in medicine?
Blocking the active site can prevent the enzyme from carrying out its reaction.
What is the most common type of reaction in biochemistry?
Proton transfer.
What is general acid-base catalysis?
Catalysis that involves transferring protons to or from a molecule other than water.
What does an acid do?
Donates a proton
What does a base do?
Accepts a proton
What is covalent catalysis?
Catalysis in which a temporary covalent bond forms between the enzyme and the substrate.
What is metal-ion catalysis?
Catalysis that uses metal cofactors such as Fe²⁺, Mg²⁺, Mn²⁺, or Zn²⁺.
What happens during acid-base catalysis?
The enzyme moves H⁺ to or from the substrate, making it easier for the substrate to react and form products.
What is specific acid-base catalysis?
Acid-base catalysis involving H₃O⁺ or OH⁻, with the reaction being determined by the pH of the solution.
What is general acid-base catalysis?
Acid-base catalysis that uses weak acids or bases other than water to transfer protons.
In general acid-base catalysis, where do the proton-donating and proton-accepting groups come from?
Side chains of amino acid residues in the enzyme's active site.
What does a general acid do during catalysis?
Donates a proton
What does a general base do during catalysis?
Accepts a proton
Which amino acid residues can act as proton donors or acceptors in general acid-base catalysis?
Aspartate
Glutamate
Lysine
Arginine
Cysteine
Histidine
Serine
Tyrosine
What happens during covalent catalysis?
A temporary covalent bond forms between the enzyme and the substrate.
Why does forming a temporary covalent bond help?
It creates a new reaction pathway with a lower activation energy.
How many main steps does covalent catalysis have?
Two
What happens in step 1 of covalent catalysis?
A nucleophilic group from the enzyme forms a covalent bond with part of the substrate, releasing the first product.
What is the enzyme doing in step 1 of covalent catalysis?
Its nucleophilic group attacks the substrate and forms a temporary covalent bond.
What happens in step 2 of covalent catalysis?
Water helps break the temporary covalent bond, releasing the second product and restoring the enzyme.
What happens to the enzyme after covalent catalysis is complete?
The enzyme returns to its original form.
What amino acid side chain forms the covalent bond in the p-nitrophenylacetate example?
The hydroxyl (OH) group of serine.
What are the two products when p-nitrophenylacetate is hydrolyzed?
Acetate and p-nitrophenol.
Why is the covalent intermediate useful?
It is more reactive than the original substrate and creates an easier reaction pathway.
What reaction type is NADH/NAD⁺ involved in?
Oxidation-reduction reactions.
In the alcohol dehydrogenase reaction, what does NADH transfer to acetaldehyde?
A hydride ion.
What are the two forms an enzyme can exist in during a reaction?
Free enzyme (E) and enzyme-substrate complex (ES).
What is the pre-steady state?
The short period at the beginning of an enzyme reaction before the steady state is reached.
What happens to [ES] during the pre-steady state?
[ES] increases.
What is steady-state kinetics?
The period when the concentration of the enzyme-substrate complex (ES) stays approximately constant.
What happens during most of an enzyme-catalyzed reaction?
The reaction is in the steady state.
How does increasing substrate concentration affect the initial reaction rate?
The initial reaction rate increases.
What happens at low substrate concentration?
Most of the enzyme is free (E), so the reaction rate increases as substrate concentration increases.
What is V₀?
The initial rate of an enzyme-catalyzed reaction.
What is Vmax?
The maximum velocity of an enzyme-catalyzed reaction when all of the enzyme is in the ES complex.
What happens to the reaction rate as substrate concentration keeps increasing?
The rate increases and approaches Vmax.
What is the Michaelis-Menten equation?
V₀ = Vmax[S] / (Km + [S])
V₀ = Vmax[S] / (Km + [S])
The substrate concentration at which the reaction rate is one-half of Vmax.
What is true when V₀ = ½Vmax?
Km = [S].
What units does Km have?
Molarity (M), because Km is a substrate concentration.
Is Km always equal to Kd?
No
What is kcat?
The number of substrate molecules converted to product per unit of time by a given concentration of enzyme when the enzyme is operating at Vmax.
What does kcat describe?
How quickly an enzyme converts substrate to product when the enzyme is saturated with substrate.
What is the relationship between kcat and Vmax?
kcat = Vmax / [Et]
What does [Et] represent?
The total enzyme concentration.
What is catalytic efficiency?
The ratio kcat/Km.
What does a higher kcat/Km indicate?
Greater catalytic efficiency.
What is the upper limit for kcat/Km?
About 10⁸–10⁹ M⁻¹s⁻¹.
What does “catalytic perfection” mean?
An enzyme has a kcat/Km near the diffusion-controlled upper limit.