Exam 2 Flashcards
Cooperativity
occurs when the change in one parameter influences the change in similar parameters.
This term is most often applied to macromolecular interactions [binding] where the binding of one molecule changes the binding characteristics of the second molecule.
allosteric site
the location on an enzyme which is separate from the substrate biding site(s) and catalytic site(s) to which molecules bind and alter the activity of the enzyme
active site
that portion of an enzyme which is responsible for enzyme activity.
It includes the substrate binding site(s), allosteric site(s) and catalytic site(s).
catalytic site
the location on an enzyme where the substrate(s) react with each other and/or portions of the enzyme.
daltons
a unit of molecular weight where one mole of hydrogen atoms is 1 dalton
enzymology
the study of enzymes and their properties by measuring enzyme activity (kinetics).
Vo (initial velocity)
the rate of change in the concentration of substrate or product per unit time at the beginning of the reaction, where little product is formed and when the back reaction is negligible.
Vo (3 equibars)= d[P]/dt = - d[S]/dt when t = 0
isozymes
one of two or more enzymes which catalyze the same biochemical reaction and can be separated by some physical method, e.g. electrophoresis or chromatography.
Ki
inhibition constant
Ki (3 equibars)= [E][I]/[[EI] E + I EI
Km
is the concentration of substrate which yields half of the maximum velocity [Vmax] for an enzyme catalyzed reaction or is the concentration when the intitial velocity is equal to half of the maximum velocity.
Defined mathematically as Km (3 equibars)= (k-1+kcat)/k1
specificity constant
kcat/Km (not memorable)
substrate binding site
the location on the enzyme where the substrate binds to the enzyme.
This binding occurs through a variety of forces and determines the specificity of the enzyme for different substrates.
Vmax
the rate of the enzyme catalyzed reaction with saturating concentrations of substrate(s) and is the product of the catalytic rate constant or turnover number and the total enzyme concentration.
In practice, the actual measured enzyme rate may never reach Vmax
Vmax (3 equibars)= k2[E]t
Zymogen
a inactive precursor of an enzyme.
To become active, the peptide chain is cleaved at particular site(s) with the possible loss of one or more peptide segments.
cofactor
a non-protein component which is required for enzyme activity.
It is usually copurified with the enzyme.
coenzyme
an organic cofactor
prosthetic group
a coenzyme which is tightly bound to an enzyme and which is not consumed by the reaction.
It usually is temporarily changed during the course of the reaction
transition state
the fleeting and unstable state of a substrate as it is converted into product.
It is characterized by distorted bond angles and lengths and cannot be detected or isolated.
Acid-base catalysis
a type of enzyme mechanism when a proton is transferred from one substrate to another, from a substrate to an enzyme, or from an enzyme to a substrate.
This provides an alternative path and hopefully more rapid rate of conversion of substrate to product.
Covalent catalysis
a type of enzyme mechanism when a covalent bond is formed between a substrate and a substrate or a substrate and an enzyme which does not involve a proton.
This provides an alternative path and hopefully more rapid rate of conversion of substrate to product.
Intermediate
a quasi-stable step between a substrate and product.
It can be detected and occasionally isolated.
intermediate formation
a type of enzyme mechanism when intermediates are formed in between the transition from a substrate to product.
By breaking up a reaction into a series of smaller steps, there is a decrease in the activation energy and an increase in the rate of reaction.
Proximity Effect
a type of enzyme mechanism which involves limiting the movement and orientation [translation and rotation] of the substrate(s) with respect to each other or to the enzyme.
This has the net effect of increasing the concentration which in turn increases the number and effectiveness of collisions and thereby increasing the rate of the reaction.
transition state analog
a stable molecule which resembles a proposed transition state.
It normally is an effective inhibitor.
apoenzyme
the protein component of an enzyme which requires a cofactor for activity
cosubstrate
a coenzyme which is loosely bound to an enzyme and is consumed during the reaction.
Typically this molecule is regenerated by another reaction(s) within the cell.
holoenzyme
an apoenzyme plus its cofactor(s)
metalloenzymes
an enzyme which contains one or more tightly bound metal ions which are essential for activty.
Some examples include catalase, superoxide dimutase, aconitase and cytochrom C oxidase.
simple enzymes
an enzyme which does not require a cofactor for activity
Transition State Stabilization
A type of enzyme mechanism in which there is an increase interaction between the enzyme and transition state which lowers the activation energy and thereby increases the rate of the reaction.
F
F (3 equibars) = 1 + [I]/Ki
Domain
A substructure of the tertiary structure that can evolve, function, and exist independently of the rest of the protein chain.
Motif
A unique combination and folding of secondary structures
