BI25M7 - 1.4-1.6 - Enzymes

Energy for life

cofactor

non-protein chemical compound that is necessary for enzyme activity

coenzyme

an organic molecule type of cofactor that assists enzymes in catalyzing chemical reactions, usually produced from a vitamin

coenzyme examples and their derivatives

FAD from riboflavin, NAD+ from niacin, Coenzyme A from pantothenate

prosthetic group

cofactor covalently bound to the enzyme or very tightly associated with the enzyme

apoenzyme

the protein component of an enzyme that contains a cofactor

holoenzyme

whole enzyme, apoenzyme plus the cofactor(s)

six classes of enzymes

oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases

oxidoreductases function

transfer electrons

transferases function

group transfer

hydrolases function

hydrolysis (transfer chemical groups to water)

lyases function

form, or add groups to double bonds

isomerases function

transfer groups within molecules (form isomers)

ligases function

formation of C-C, C-S, C-O, C-N bonds (coupled to ATP cleavage)

enzyme function

Increase rates of spontaneous reactions

Lower the activation energy of biochemical reactions

Accelerate movement towards reaction equilibrium

Gibbs free energy equation

ΔG = ΔH - ΔTS

spontaneous reactions

decrease enthalpy (H) and or increase entropy (S)

energy barrier

energy required to position chemical groups correctly, bond rearrangements, electron rearrangements, etc..

entropy reduction

Enzymes “force” the substrate(s) to be correctly orientated by binding them in the formation they need to be in for the reaction to proceed

desolvation

Weak bonds between the substrate and enzyme essentially replace most or all of the H-bonds between substrate and aqueous solution

induced fit

Conformational changes occur in the protein structure when the substrate binds

catalysis occurs when …

Active site is complementary to transition state

more substrate =

higher initial rate of reaction

low substrate concentration

almost a linear increase in V0 as ↑ [S]

michaelis-menten equation importance

crucial in enzyme kinetics to determine the rate of enzyme-catalyzed reactions and the affinity of an enzyme for its substrate.

michaelis-menten equation basis

E + S ↔ ES ↔ E + P

The Michaelis constant (K_m) can be defined as

the sum of the rate constants for the (part) reactions in which the enzyme-substrate complex decays, divided by the rate constant of the (part) reaction in which enzyme-substrate complex is formed.

Km

equivalent to the substrate concentration at which the initial reaction rate is half of the maximum reaction rate

Km tells us…

a clue to the affinity of the enzyme with it’s substrate

Vmax tells us

fast a reaction is proceeding when the enzyme is saturated with substrate

high Km, high Vmax

poor fit and fast enzyme

low Km, low Vmax

tight fit, slow enzyme

Lineweaver-Burk equation

linear equation

glucokinase

high Km, high Vmax, poor fit but fast enzyme. so when blood glucose goes up after a meal, the glucokinase activity increases

hexokinase

low Km, low Vmax, tight fit but slow enzyme. so when blood glucose is low, it’s active

Enzymes and two or more substrates

different Km values

Allosteric enzymes

change shape when bound to a specific molecule, impacting their activity and have a site separate from the active site

pH effect on enzymes

charge of amino acids changed, enzyme doesn’t function correctly, extremes can denature enzyme, affect the substrates of the reaction, some of which may require H+ or OH- groups to be involved in the reaction

inhibitors

competitive, non-competitive, uncompetitive

competitive inhibitors

increased Km, Vmax unchanged, reduces the affinity but doesn’t effect enzyme speed

AZT drug

competitive inhibitor of reverse transcriptase, used to treat AIDS

Transition state analouges

inhibitor to mimic transition state of enzyme

catalytic antibdies

specific to to transition state molecule

non-competitive antibodies

Km unchanged, Vmax decreased, affinity unchanged and speed of reaction decreased

ways regulatory enzyme modulate reactions

allosteric enzymes, covalently modified enzymes

feedback inhibition

product can inhibit enzymes

allosteric control

effectors that activate and inhibit enzymes

allosteric enzyme kinetics

initial low [S] sensitises the enzyme so it responds more efficiently at higher [S]

allosteric enzyme kinetics models

concerted model, sequential model

concerted model

allosteric activators and inhibitors

sequential model

substrate binding causes a change in one sub-unit which causes a change in another sub-unit allowing it to bind S more readily

reversible covalent modification

phosphorylation - Enzymes catalyse the phosphorylation of enzymes: Protein kinases (add phosphoryl groups to proteins) Protein phosphatases (remove phosphoryl groups)

multiple phosphorylation sites

These allow very fine control of enzyme function depending on the requirement of the particular enzyme at a given time - enzyme activity depends on signals

proteolytic cleavage

Enzymes can exist as an inactive precursor protein,called a proprotein or proenzyme. Proproteins can be cleaved to give active enzyme by proteases