Chapter 6: Enzyme Kinetics

What is an enzyme?

A biocatalyst that speeds up a reaction by lowering activation energy between reactants and products.

Is a reaction spontaneous or non spontaneous when the products are at a lower ΔG than the reactants?

Spontaneous

Can enzymes change ΔG or K?

NO

What is a substrate?

A molecule converted into product

What benefits does using enzymes have on reactions?

1. They can function at physiologic pH and temp

2. Increase reaction rates

3. Can be highly specific

4. Ability to regulate

What type of reactions do oxidoreductase enzymes catalyze?

Redox

What type of reactions do transferase enzymes catalyze?

Transfer of functional groups

What type of reactions do hydrolyase enzymes catalyze?

Hydrolysis

What type of reactions do lyases enzymes catalyze?

Group elimination to form double bonds; cleavage of C-C, C-O, C-N, elimination of CO₂

What type of reactions do isomerase enzymes catalyze?

Isomerization

What type of reactions do ligase enzymes catalyze?

Bond formation coupled with ATP hydrolysis; forms C-C, C-O, C-N, C-S, phosphoric ester

Difference between lock & key and induced fit

Lock & key: substrate and binding site match exactly

Induced fit: binding site is not exact but binding of a molecule causes a conformational change to make it bind better

What is a cofactor?

A small molecule required for an enzyme to function

What is a holoenzyme?

enzyme/cofactor complex (active)

What is a apoenzyme?

No cofactor (inactive)

Why do enzymes require cofactors?

1. Proteins can do acid-base chemistry (protonate/deprotonate)

2. Proteins cannot do redox reactions readily

What is an exergonic reaction?

ΔG < 0, spontaneous

What is an endergonic reaction?

ΔG > 0, process requires energy input

Is FAD to FADH₂ oxidized or reduced?

Reduced

Is FMN to FMNH₂ oxidized or reduced?

Reduced

Is NAD⁺ to NADH oxidized or reduced?

Reduced

What is an intermediate?

A lower energy state between reactants and products

What is the transition state?

unstable at high energy states

What is a rate-limiting step?

the step with highest activation energy

What is ΔG⁺⁺_cat?

Activation energy with catalyst/enzyme

What is ΔΔG⁺⁺_cat?

The difference in activation energy

What is ΔG⁺⁺?

Activation energy

What is [X]⁺⁺?

Transition state that occurs at the highest G

What is the intermediate in a reaction coordinate diagram?

A lower energy state between reactants and products

What is the transition state?

Highest energy state (peak)

What is the rate-limiting step?

The step with the higher activation energy

What is acid-base catalysis?

The transfer of protons from acid or proton abstraction by a base to lower the reaction TS free energy

What is covalent catalysis?

Formation of a catalyst-substrate covalent bond

What is metal-ion catalysis?

A metal binds to a substrate to orient/position reaction, mediate redox reactions, stabilize or shield negative charges in the site

What is a nucleophile attack?

A nucleophile that has free electrons with an arrow drawn to an electrophile (not a H)

What is an abstraction?

A base removes a hydrogen from a substrate

What is loss of leaving group?

Bonded electrons move to an atom, resulting in a bond being broken

What is an example of acid/base catalysis?

Hydrolysis of RNA

What are the amino acids that participate in acid/base catalysis?

1. Glu

2. Asp

3. Lys

4. Arg

5. Cys

6. His

7. Tyr

What is a nucleophile?

A molecule with a free pair of electrons that attack something else to form new bonds

What is an electrophile?

A molecule that accepts protons

• Often will be P of a phosphate or C of carbonyl

How can metal ions contribute to reactions?

1. Position and orient

2. Transfer electrons

3. Shield negative charges

4. Change pka of water

In what three ways do enzymes help facilitate reactions?

1. Proximity

2. Proper orientation

3. Preferential binding of TS complex