BIOCHEM ENZYMES FLASHCARDS (EXAM 2)

Enzymes

tools that allow biochemical processes, which do not occur spontaneously to occur

Enzymes are biological catalysts

- increase reaction rates of biochemical reactions

- are not consumed in reaction and do not alter chemical equilibria

- facilitate processes that would otherwise occur too slowly

Enzymes are proteins that

Some RNA molecules could also catalyze chemical reactions

What happens if the protein is denatured

Catalytic activity of the enzyme is lost

Advantages of Enzymes over Inorganic Solvents

- Milder reaction conditions

- higher reaction rates

- capacity for regulation control

- greater reaction specificity

Are Enzymes more selective for the substrate (true or false)

true

L-phenylalanine

l-tyrosine

D-phenylalanine

No binding

Epinephrine

binding, no reaction

Active Site

pocket on enzyme where reactions occur

Substrate (S)

molecule that binds to active site and is modified in a reaction

Product (P)

altered form of substrate that is generated by a reaction

Transition state

Transient higher-ending configuration (decays to S and P)

What do enzymes use?

Cofactors

Inorganic Ions

Usually, metals that bind electro-statistically or participate in redox reactions

Coenzymes

- organic molecules often derived from vitamins, that "move" chemical substituents

Prosthetic Groups

co-enzymes that are permanently (usually covalently) altered to an enzyme

Energetics of an Enzyme- Catalytic Reactions

transition between a substrate and produced is by an equilibrium constant

If delta G is negative

reaction will proceed spontaneously

what does delta G equal

activation energy

As activation energy decreases

Reaction rate of enzyme increases

what do binding interactions produce?

negative free energy

biomolecular reactions

highest entrop

unimolecular with rotational freedom

lower entropy

unimolecular with rotational constraint

lowest entropy

uncatalyzed biomolecular reactions

two free reactants-------> single restricted transition state

Conversion is entropically unfavorable

Uncatalyzed unimolecular reactions

A flexible reactant------> rigid transition state conversion is entropically unfavorable for flexible reactants

Catalyzed Reactions

- enzyme uses the binding energy of substrates to organize the reactants to a fairly rigid ES complex

- entropy cost is paid during binding

- rigid reactant complex----> transition conversion is entropically ok

desolvation

displacement of the molecules that would impede reaction

compensation for bond distortion

multiple transition-state interactions offset electron redistribution costs

Induced Fit

confirmational changes in enzyme maximize interaction in transition state

Active Participation in reaction mechanism

transient covalent interaction or group transfer to/from substrate

Factors Affecting Activity of Enzymes

- Temperature: enzymes denatured at high temperatures

- pH: enzymes need their functional group in

- Ionic strength

- Presence of cofactors and prosthetic groups

acid-base catalysis

give and take protons

covalent catalysis

- change reaction paths

- requires a nucleophile on the enzyme

Metal Ion Catalysis

Use redox cofactors, pka shifters, enzyme functional groups

involves metal ion tightly bounded to the enzyme or complexes with substrate

Enhanced in low-water environments of enzyme active sites

Electrostatic Catalysis

preferential interactions with TS

Chymotrypsin Mechanism

1. Substrate Binding

2. nucleophilic attack

3. substrate cleavage

4. water comes in

5. water attacks

6. break off from the enzyme

7. product dissociates

nucleophiles

Ser 195 (first) and H2O (second)

Leaving Groups

amine group (first) and carboxylate (second)

Kinetics

the study of the rate at which compounds react

Rate

amount of product accumulated or substrate consumed per unit of time

What is rate of enzymatic reaction affected by

- enzyme concentration

- substrate concentration

- temp

-pH

- ionic strength

- regulators (effectors)

Lineweaver- Burk Plot

-confirms to the expression y=ax+b

- double reciprocal coordinates

- linearized

Michaelis Constant, Km

- Km

- concentration of the substrate at which velocity is 50% of the maximum

- (K2

Kcat - turnover number

number of substrate molecules converted to a product in a given unit of time on a single enzyme molecule when the enzyme is saturated with substrate

Specificity constant Kcat/Km

reflects its cellular environment, [S] and mechanism and the ratio of both is the measure of substrate conversion efficiency

What is the outcome of two-substrate reactions

-different kinetic mechanisms are possible

Kinetic Mechanism

The order of binding of substrates and release of products

Sequential Mechanism

ternary complex forms

Ping-Pong Mechanism

no ternary complex forms

Ternary Kinetic Mechanism in terms of Lineweaver Burk plot

- lines INTERSECT

- ternary complex is formed

Non-Ternary Kinetic Mechanism in terms of Lineweaver Burk plot

-parallel lines

- ternary complex is not formed

Enzyme Inhibition

inhibitors are compounds that decrease an enzymes activity

Irreversible Inhibition

- chemically react with the enzyme

- causes irreversible inactivation of the enzyme

- destroys functional group in the active site

- one inhibitor molecule can permanently shut off one enzyme molecule

- usually powerful toxins

- could be used as drugs

Reversible Inhibitors

Bind to and can dissociate from the enzyme

- can be structurally similar to substrates or products

- could be used as drugs to slow down particular enzyme

Types of reversible Inhibitors

- competitive inhibitors

- noncompetitive inhibitors

- uncompetitive inhibitors

competitive inhibitors

- inhibit substrate binding and does not affect catalysis. competes for the active site

- V max with respect to inhibitor stays the same and Km with respect to inhibitor increases

Noncompetitive inhibitor

dos not affect substrate binding and inhibits catalytic function. It also alters confirmation of enzyme so active site is no longer fully functional

V max with respect to inhibitor decreases and km with respect to inhibitor stays the same

Uncompetitive Inhibitors

- increases substrate binding

- does not affect catalysis

- V max and Km with respect to inhibitor both decrease

Mixed inhibitors

- bind to enzyme with or without bound substrate

- bind to regulatory site

- inhibit substrate binding

- inhibit catalytic function

- Vmax with respect to inhibitor decreases and Km with respect to inhibitor increases