9.8 Enzyme Mechanism and Catalysis I

Enzymatic reaction mechanisms are similar to non-enzymatic mechanisms, but enzymes show greater

specificity

Enzymatic reaction mechanisms have an optimal arrangement of

catalytic groups for chemical reaction

Enzymes ____ reaction rates but not reaction equilibria

increase

Most enzymes are

proteins

___ molecules can also catalyze reactions

RNA

Enzymes are classified according to

the reactions catalyzed

Enzymes contain ____ _____ groups that help catalyze reactions

chemically reactive (amino acid side-chains and n-terminal NH2 & C terminal -COOH)

Enzymes use ________ to do chemistry impossible with usual functional groups

cofactors (group transfer reactions and redox reactions)

Cofactors can be

metal ions or organic molecules

Coenzyme

Complex organic or metalloorganic molecule that act as transient carriers of specific functional groups

Enzymes catalyze conversion of

substrates to products

Prosthetic group

Coenzyme or metal ion that is very tightly or covalently bound to the enzyme protein (ex. heme)

Catalytic activity depends on

Integrity of native protein conformation

Molecular weight of enzymes

12,000 to >1 million daltons

Holoenzyme

Complete catalytically active enzyme together with its bound coenzyme and/or metal ions

Apoenzyme or apoprotein

Protein part of a holoenzyme (inactive)

What type of reaction are catalyzed by these enzymes: Oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases, translocases

Oxidoreductases: Transfer of electron (Hydride/H atoms)

Transferases: Group transfer

Hydrolases: Hydrolysis (Transfer of functional groups to water)

Lyases: Cleave bonds via elimination, often leaving behind double bonds/rings, or add a group to double bonds

Isomerases: Transfer/rearrangement of groups within molecules to yield isomeric forms

Ligases: Form bonds by condensation with the help of ATP or similar cofactors

Translocases: Facilitate the movement/separation of molecules or ions across membranes

Active site

Where catalyzed reaction takes place; provides specific environment and protein domain in which a given reaction can occur more rapidly

T/F: Catalysts (enzymes) do not change

TRUE

ES and EP are ____ complexes

transient

Reactants (substrate and product) must overcome an ____ ______ for a reaction to occur

energy barrier, deltaG

The equilibrium between S and P reflects the difference in

the free energies of their ground states

Ground state

Starting point for either the forward or reverse reaction

The ground state of ___ is lower than ___, hence DeltaG’ for the reaction is…

P is lower than S; negative and favors P

Energy barrier reflects the energy required for

molecular alignment, formation of charges, bond rearrangement, and other transformations

Transition state

Point at which decay to substrate or product are equally likely

Enzymes accelerate reactions rates by lowering the

activation energy barrier (Via temp or pressure), this does not affect reaction equilibria

Rate limiting step

The step with the highest activation energy and the slowest rate

Position and direction of the equilibrium are/are not affected by the enzyme (catalyst)

ARE NOT

Rates of the forward and reverse reactions increase by

the same amount

Equilibrium constant, K’_eq, describes

the relative amounts of substrates and products present at the equilibrium in a biochemical reaction

K’eq =

P / S

∆G^o =

-RT Ln K’_eq

Δ𝐺 can/cannot influence kinetics of a reaction

cannot; it only shows which direction the equilibrium favors

Rate constant k, is a measure of how fast (velocity) a

reaction can occur

velocity of the forward reaction

v forward = k forward (S; concentration of substrate)

First-order reaction

Uses units of reciprocal time s^-1, only depends on concentration of one substrate

Second-order reaction

Depends on concentration of two substrate

Velocity for second-order reaction

V = k[S₁][S₂]

velocity of the reverse reaction

v reverse = k reverse (P)

k is larger when DeltaG is

smaller (inverse exponential relationship_)

Enzymes can perform

great stereo-specific catalytic reactions

Enzyme’s tertiary structure creates a unique microenvironment for

ES-intermediate substrate binding

Interaction between substrate and enzyme is mediated by

the same non-covalent forces that stabilize protein structure

Binding Energy, ∆G_B

Energy derived from noncovalent enzyme-substrate interaction; mediated by weaker interactions; major source of free energy used by enzymes to lower activation energy

Covalent interactions between enzyme and substrate _______ activation energy

lower

Noncovalent interactions between enzyme and substrate are optimized in

Transition state; Complementary shape of a substrate and its binding partner

Reaction transition state

Enzymes are complementary to this state; full complement of enzyme is only reaches when substrate reaches transition state

Transition-state stabilization

lowers energy of transition state making it easier to form

Orientation

arranges atoms for optimal activity

Desolvation

binding removes interactions with solvent (water)

Induced fit

substrate binding changes conformation of enzyme

Acid-base catalysis

push or pull a proton

Covalent catalysis

adducts or intermediates

Enzymes use binding energy to achieve

substrate specificity and to stabilize the transition states through non-covalent interactions

Non-covalent interactions allow the enzyme to

bind to substrates

Non-covalent interactions also allow enzyme to bind and stabilize the

transition state

Non-covalent interactions with the transition-state are stronger than

the substrate

Mechanism of enzyme bonding is or is not lock and key

NOT

Enzymes bind the transition state with ____ affinity than either substrates or products

greater, increases forward and backward rates equally

Important corollary - good substrates don’t necessarily…

bind extremely tightly to enzyme, don’t want to be stuck in ES complex

Nu vs E

Nucleophile vs electrophile; Electron rich that donates e^- pair vs electron deficient that accepts e^-

AA can function both as a

general acid or base

General acid catalyst

Partial proton donation from AA stabilizes negative charge that forms in transition state

General base catalyst

Partial proton attraction by AA helps form negative charge and stabilizes transition state

Covalent catalyst

Transient covalent bond can form between E and S

Metal ion catalyst

Depends on ability of ion to serve as template; binds and orient substrate; also shield/stabilizes charge formed in transition state; increases acidity of bound water/alcohol

Nearly ____ of all known enzymes require ____ ___ for catalytic activity

1/3; metal ions