Lecture 7 - Enzyme Classification and Mechanism Of Catalysis

enzymes are ___

catalysts

increase rate of reaction w/out being used

most enzymes are ___ proteins

globular

some RNA also catalyze reactions

why are enzymes needed

• greater reaction specificity (avoids side prods)

• milder rxn conditions (conducive to conds in cells)

• higher rxn rates

• capacity for regulation (control of biological pathways)

• they choose the fastest and most favorable rxn pathway

enzyme substrate selectivity

• L and D amino acids

• Enzymes evolved to bind L-amino acids

• substrates with D-amino acids usually don’t fit

• enzymes highly stereospecific

enzymatic cofactor

• some enzymes need a cofactor

• help enzymes perform catalysis

types of enzymatic cofactors

• inorganic (Mg2+, Zn2+, Mn2+) bring a charge to help bind to substrate

• organic, also called coenzymes

• prosthetic groups, cofactor or coenzyme covalently bound to protein

• apoenzyme, without coenzyme

• haloenzyme, with coenzyme

enzymes classified based on rxns they catalyze

• oxirdoeductases (trasnfer of e- or H+)

• transferases (group transfer rxns)

• hydrolases (hydrolysis rxns)

• lyases (cleavage of c-c, c-o, or c-n bonds… by elim, leaves double bond)

• isomerases (transfer of groups w/in molecules to yield isomers)

• ligases (formation of c-c, c-s, c-o, c-n bonds through condensation)

enzymatic catalysis

• E + S ⇋ ES ⇋ EP ⇋ E + P

• substrate enters active site

• forms enzyme substrate complex

• creates enzyme product complex (always exists)

• products leave active site of enzyme

what contributes to specificity and catalysis

binding energy

binding energy in specificity and catalysis

• enzyme substrate binding lowers entropy

• enzyme substrate biding results in desolvation (replacement of ho bonds between enzyme and substrate)

• Binding energy from weak interactions in the transition state offsets the unfavorable free-energy cost of substrate distortion

• enzyme undergoes change in conformation (induced fit)

enzyme graph

see photo

enzyme catalyzed reaction graph

see graph

enzymes dont affect…

equilibirum (Keq) and free energy (ΔG)

enzymes do affect…

rate of reaction and activation energy

how is activation energy lowered

• enzymes organize reactive groups into proximity and proper orientation

• uncatalyzed rxns: transition state conversion is entropically unfavored

• catalyzed rxns: enzymes use binding energy of substrates to organize reactants to a rigid ES complex (entropy cost paid during binding)

enzymes binds ___ states best

transition

why do enzymes bind transition states best

• active sites complimentary to transition state of rxn

• enzymes bind transition states better than subtrates

• stronger/additional interactions w/ transition state compare to ground state lower the activation barrier

catalytic mechanisms

• acid base catalysis

• covalent catalysis

• metal ion catalysis

acid base catalysis

• give/take protons

• presence of alternative proton donors/acceptors accelerate rxn

• amino acid side chains act as donor/acceptor

covalent catalysis

• transient covalent bond between enzyme and substrate

• changes reaction pathway

• requires nucleophile on enzyme (can be reactive serine, thiolate, amine, or carboxylate)

metal ion catalysis

• involves metal ion bound to enzyme

• interacts with substrate to facilitate binding

• stabilizes -ve charge

• participates in oxidation reactions

chymotropsin

• protease

• break peptide bonds

• cleaves peptide bonds next to aromatic amino acids

• during digestion, proteins must be broken into smaller peptides by proteases

• uses most of the catalytic mechanisms

• 1st, acylation, a fast reaction

• 2nd deacylation, a slow reaction

Catalysis of peptide bond by chymotrypsin

• Enzyme–substrate complex:

• Polypeptide substrate binds noncovalently in the enzyme’s hydrophobic pocket.

• First transition state

• Serine (Ser195) attacks the peptide bond → tetrahedral intermediate forms, stabilized by His57 and Asp102.

• Acyl-enzyme intermediate

• Peptide bond is cleaved.

• C-terminal fragment leaves; N-terminal fragment stays covalently attached to Ser195.

• Water binding:

• A water molecule enters and takes the place of the departed peptide fragment.

• Second transition state:

• Water donates a proton to His57 and attacks the acyl-enzyme bond → new tetrahedral intermediate forms.

• Product release:

• N-terminal fragment is released.

• Enzyme returns to its original state, ready for another cycle.