BIO 361 Test 2

cooperativity

binding of one ligand affects binding of other ligands

T state

low affinity for oxygen (high kd), predominates when oxygen is not bound, stabilized by ionic interactions, puckered heme

R state

high affinity for oxygen (low kd), predominates when oxygen is bound, planar heme

allostery

regulatory mechanism where molecule (or ligand) binds to one site on a protein and changes the activity at a distant site

nH=1

no cooperatibity

nH>1

positive cooperativity

nH<1

negative cooperativity

MWC model (concerted model)

1. Only two conformations of the tetramer exist (T and R)

2. T and R conformations are in equilibrium

3. All subunits undergo transition simultaneously

4. Ligand can bind to both T and R states but has higher affinity for R

5. Each successive ligand binding increases the likelihood of T to R transition

Binding curve is described by ratio of affinities for ligand and position of equilibrium in absence of ligand

No intermediate conformations have been observed in crystal structures

KNF Model (Sequential Model)

1. Ligand can bind to both T and R states

2. Ligand binding induces T to R in a single subunit

3. Transition in one subunit increases the likelihood of transition in adjacent subunit

4. Requires existence of many mixed state tetramer conformations

Compatible with negative cooperativity

apoenzyme

inactive enzyme that requires a cofactor to be bound to become active

holoenzyme

active enzyme that required a cofactor to become active

prosthetic group

coenzyme that binds to protein molecules irreversibly (i.e. heme)

cosubstrates

coenzymes that reversibly bind to protein and usually undergo 2 rounds of catalysis (i.e. ATP)

rate of enhancement

ratio of catalyzed reaction and the uncatalyzed reaction

first order

velocity proportional to concentration of reactants, half-life is independent of concentration of reactants

second order

velocity proportional to the concentration of the reactants squared, half-life is dependent on substrate concentration, half-life becomes longer

zero order

velocity is independent of concentration of substrate

kcat

the number of substrates turned over to product per enzyme molecules per second