Exam 2

Question 1

Cooperativity

Answer 1

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.

Question 2

allosteric site

Answer 2

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

Question 3

active site

Answer 3

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).

Question 4

catalytic site

Answer 4

the location on an enzyme where the substrate(s) react with each other and/or portions of the enzyme.

Question 5

daltons

Answer 5

a unit of molecular weight where one mole of hydrogen atoms is 1 dalton

Question 6

enzymology

Answer 6

the study of enzymes and their properties by measuring enzyme activity (kinetics).

Question 7

Vo (initial velocity)

Answer 7

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

Question 8

isozymes

Answer 8

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.

Question 9

Ki

Answer 9

inhibition constant

Ki (3 equibars)= [E][I]/[[EI] E + I EI

Question 10

Km

Answer 10

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

Question 11

specificity constant

Answer 11

kcat/Km (not memorable)

Question 12

substrate binding site

Answer 12

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.

Question 13

Vmax

Answer 13

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

Question 14

Zymogen

Answer 14

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.

Question 15

cofactor

Answer 15

a non-protein component which is required for enzyme activity.

It is usually copurified with the enzyme.

Question 16

coenzyme

Answer 16

an organic cofactor

Question 17

prosthetic group

Answer 17

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

Question 18

transition state

Answer 18

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.

Question 19

Acid-base catalysis

Answer 19

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.

Question 20

Covalent catalysis

Answer 20

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.

Question 21

Intermediate

Answer 21

a quasi-stable step between a substrate and product.

It can be detected and occasionally isolated.

Question 22

intermediate formation

Answer 22

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.

Question 23

Proximity Effect

Answer 23

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.

Question 24

transition state analog

Answer 24

a stable molecule which resembles a proposed transition state.

It normally is an effective inhibitor.

Question 25

apoenzyme

Answer 25

the protein component of an enzyme which requires a cofactor for activity

Question 26

cosubstrate

Answer 26

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.

Question 27

holoenzyme

Answer 27

an apoenzyme plus its cofactor(s)

Question 28

metalloenzymes

Answer 28

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.

Question 29

simple enzymes

Answer 29

an enzyme which does not require a cofactor for activity

Question 30

Transition State Stabilization

Answer 30

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.

Question 31

F

Answer 31

F (3 equibars) = 1 + [I]/Ki

Question 32

Domain

Answer 32

A substructure of the tertiary structure that can evolve, function, and exist independently of the rest of the protein chain.

Question 33

Motif

Answer 33

A unique combination and folding of secondary structures