07: Enzyme Mechanisms

Induced fit model

As substrate and enzyme bind, there will be conformational changes in the substrate and enzyme to match better and facilitate the reaction

Binding site

The portion of the enzyme where the substrate binds

Catalytic site

Where reaction occurs

Types of enzyme regulation

Bioavailability and catalytic efficiency

What functional group is required for phosphorylation to happen

Alcohol

Which AA can undergo phosphorylation

Serine, Threonine, Tyrosine

Catalytically perfect enzymes

They can’t get any faster, the reaction is the most efficient it will ever be

How do enzymes speed up a reaction

Lowering the activation energy (delta G double dagger)

How do enzymes facilitate a faster reaction

• Increases the chance of a productive collision (proximity, orientation, energy)

• Stabilizes the transition state

• Provides an alternate path

• Decreases entropy in active site, increases entropy of solvent

• Mimics an increase in substrate concentration

How do enzymes stabilize the transition state

Producing IMFs and salt bridges, which releases energy

Binding energy (G_B)

The energy difference/released between the transition state of the uncatalyzed reaction and the catalyzed reaction. Represents the energy released from the formation of favorable IMFs by the ES complex and the increase in solvent entropy

Cofactor

Small inorganic molecule that helps enzymes or proteins

Coenzyme

Larger, organic cofactor

Prosthetic group

A coenzyme permanently associated with the enzyme

NAD/NADH

B3, redox reactions

FAD/FADH2

B2, redox reactions

Thiamine Pyrophosphate (TPP)

B1, aldehyde group transfer

Biotin

B7, carboxylation

Coenzyme A

Pantothenic acid, acyl group transfer

Tetrahydrofolate

Folic acid, single carbon transfer

Pyridoxal Phosphate

B6, amine group transfer

Lipoamide

Lipoic acid, two carbon transfer

Cobalamin

B12, alkyl group transfer

Holoenzyme

Enzyme with cofactor or coeznyme

Apoenzyme

enzyme without cofactor or coenzyme

Enzyme class 1

Oxoreductase, redox, transfers H or O (dehydrogenase)

Enzyme class 2

Transferase, moves functional groups (kinase)

Enzyme class 3

Hydrolase, uses water to break bonds (lipase)

Enzyme class 4

Lyase, cuts bonds in a way other than redox or hydrolysis (de/carboxylases)

Enzyme class 5

Isomerase, intramolecular rearrangements (mutases)

Enzyme class 6

Lyase, forms bonds using ATP cleavage (synthetases)