biochem6

enzyme

A biomolecules, either protein or RNA, that catalyzes a specific chemical reaction. It doe not affect the equilibrium of the catalyzed reaction; it enhances the rate of the reaction by providing a reaction path with a lower activation energy

cofactor

an inorganic ion or a coenzyme required for enzyme activity

coenzyme

an organic cofactor required for the action of certain enzymes; often has a vitamin component

prosthetic group

a metal ion or an organic compound (other than an amino acid) that is covalently bound to a protein and is essential to its activity

holoenzyme

a catalytically active enzyme, including all necessary subunits, prosthetic groups, and cofactors

apoenzyme

the protein portion of an enzyme, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for catalytic activity

apoprotein

the protein portion of a protein, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for activity

active site

the region of an enzyme surface that binds the substrate molecule and catalytically transforms it; also known as the catalytic site

substrate

the specific compound acted upon by an enzyme

ground state

the normal, stable form of an atom or molecule; as distinct from the excited state

standard free energy change (delta G degree)

the free-energy change for a reaction occurring under a set of standard conditions: temperature, 298 K; pressure, 1 atm or 101.3 kPa; and all solutes at 1M concentration. denotes the standard free-energy change at pH 7 in 55.5M water

activation energy (delta G double-cross)

the amount of energy (in joules) required to convert all the molecules in 1 mol of a reacting substance from the ground state to the transition state

reaction intermediate

any chemical species in a reaction pathway that has a finite chemical lifetime

transition state

an activated form of a molecule in which the molecule has undergone a partial chemical reaction; the highest point on the reaction coordinate

rate-limiting step

(1) generally, the step in an enzymatic reaction with the greatest activation energy or the transition state of highest free energy (2) the slowest step in a metabolic pathway

equilibrium constant (K sub-eq)

a constant, characteristic for each chemical reaction, that relates the specific concentrations of all reactants and products as equilibrium at a given temperature and pressure

rate constant

the proportionality constant that relates the velocity of a chemical reaction to the concentration(s) of the reactant(s)

binding energy (delta G sub-B)

the energy derived from noncovalent interactions between enzyme and substrate or receptor and ligand

specificity

the ability of an enzyme or receptor to discriminate among competing substrates or ligands

induced fit

a change in the conformation of an enzyme in response to substrate binding that renders the enzyme catalytically active; also used to denote changes in the conformation of any macromolecule in response to ligand binding such that the binding site of the macromolecule better conforms to the shape of the ligand

specific acid-base catalysis

acid or bas catalysis involving the constituents of water (hydroxide or hydronium ions)

general acid-base catalysis

catalysis involving proton transfer(s) to or from a molecule other than water

covalent catalysis

a transient covalent bond is formed between the enzyme and the substrate

initial rate (V sub-0)

initial velocity

V sub-max

the maximum velocity of an enzymatic reaction when the binding site is saturated with substrate

pre-steady state

when the enzyme is first mixed with a large excess of substrate, the initial period during which the concentration of ES builds up

steady state

a nonequilibrium state of a system through which matter is flowing and in which all components remain at a constant concentration

Michaelis constant (K sub-M)

the substrate concentration at which an enzyme-catalyzed reaction proceeds at one-half its max velocity

Michaelis-Menten equation
V0=Vmax[S]/km+[S]

the equation describing the hyperbolic dependence of the initial reaction velocity, V sub0, on substrate concentration, [S], in many enzyme-catalyzed reactions

Lineweaver-Burk equation
1/Vo=(Km/Vmax[S])+(1/Vmax)

an algebraic transform of the Michaelis-Menten equation, allowing determination of Vmax and Km by extrapolation of [S] to infinity

dissociation constant (K sub-d)

an equilibrium constant for the dissociation of a complex of two or more biomolecules into its components; ex, dissociation of a substrate from an enzyme

turnover number

the number of times an enzyme molecule transforms a substrate molecule per unit time, under conditions giving maximal activity at substrate concentrations that are saturating

competitive inhibition

a type of enzyme inhibition reversed by increasing the substrate concentration; a competitive inhibitor generally competes with the normal substrate or ligand for a protein's binding site

uncompetitive inhibition

the reversible inhibition pattern resulting when an inhibitor molecule can bind to the enzyme-substrate complex but not to the free enzyme

mixed inhibition

the reversible inhibition pattern resulting when an inhibitor molecule can bind to either the freen enzyme or the enzyme-substrate complex (not necessarily with the same affinity)

irreversible inhibitor

binds covalently with or destroys a functional group on an enzyme that is essential for the enzyme's activity,or forms a particularly stable noncovalent association

suicide inactivator

a relatively inert molecule that is transformed by an enzyme, at its active site, into a reactive substance that irreversibly inactivates the enzyme

regulatory enzyme

an enzyme with a regulatory function, through its capacity to undergo a change in catalytic activity by allosteric mechanisms or by covalent modification

allosteric enzyme

a regulatory enzyme with catalytic activity modulated by the noncovalent binding of a specific metabolite at a site other than the active site

feedback inhibition

inhibition of an allosteric emzyme at the beginning of a metabolic sequence by the end product of the sequence

protein kinases

enzymes that transfer the terminal phosphoryl group of ATP or another nucleoside triphosphate to a Ser, Thr, Tyr, Asp, or His side chain in a target protein, thereby regulating the activity or other properties of that protein

zymogen

an inactive precursor of an enzyme; ex) pepsinogen, the precursor of pepsin