Chapter 7: Basic Concepts of Enzyme Action

enzymes

• proteins (some others like RNA) with catalytic properties

• accelerate rxn by lowering activation energy

• not degraded or destroyed (typically)

• specific for substrate

catalyst

speeds up chemical rxn without being consumed

substrate

reactant enzymes bind to

proteases

• group of enzymes catalyzing proteolysis → hydrolysis of a peptide bond

• use water

• vary in substrate specificity

proteases: papain

cleaves any peptide bond, regardless of the side chains

proteases: trypsin

digestive enzyme → only cleaves peptide bonds on carbonyl side of lysine or arganine

proteases: thrombin

cleaves arg-gly peptide bonds on specific peptide sequences only

why are some enzymes more soecific than others

specificity dictated by the 3D structure of the enzyme

which direction do enzymes catalyze reactions

both forward and reverse rxn

7 major classes of enzymes

• oxidoreductases

• transferases

• hydrolyases

• lyases

• isomerases

• ligases

• translocases

7 major classes of enzymes: oxidoreductases

catalyze oxidation reduction rxns

7 major classes of enzymes: Transferases

move functional groups between molecules

7 major classes of enzymes: Hydrolases

hydrolysis → bond clevage by adding water

7 major classes of enzymes: lyases

add/remove atoms to form double bonds

7 major classes of enzymes: isomerases

move functional groups within a molecule

7 major classes of enzymes: Ligases

join two molecules by consuming ATP

7 major classes of enzymes: Translocases

facilitate molecule movement across or within biological membranes

enzyme nomenclature

• suffix -ase typically

• name based on substrate/rxn

• some have comon names

• systematic naming system → “EC” and 4 numbers

cofactor

small ions/molecule required for catalytic activity. 2 types: coenzymes and metals

apoenzyme

enzyme without its cofactor

holoenzyme

complete, catalysically active enzyme with any necessary cofactors

coenzyme

• type of cofactor → organic molecule derived from vitamins

• can be tight (prothetic group) or loosely associated

prosthetic group

• tightly bound coenzyme that continuously associates with an enzyme (doesn’t easily dissociate)

• considered catalytic (unchanged in rxn)

stoichiometric coenzymes

• loosely associated conenzymes

• behave like second substrates (cosubstrates) → can bind to enzyme, be changes, and then dissociate

how do stoichiometric coenzymes differ from actual substrates

coenzymes can be used by many enzymes, and those enzymes usually perform catalysis by similar mechanisms

gibbs free energy

measure of energy capable of doing work (useful energy)

what determines spontaneity of a rxn

free-energy difference (ΔG) between the products and the reactants → must be negative (exergonic rxn)

how do catalysts affect gibbs free energy of a rxn

• ΔG is unchanged

• doesn’t change rxn equilibrium

• free energy of activation (ΔG‡) changes

ΔG^‡

free energy of activation → difference between transition state G and substrate G

ΔG

free energy difference

• positive → rxn is not spantaneous (endergonic)

• negative → rxn is spantaneous (exergonic)

• 0 → rxn is at equilibrium

ΔG°

free-energy change of a reaction under standard conditions

• each reactant [ ] = 1M

• gases at 1 atmosphere

• T = 298K, 25C

what dertemines the rate of a rxn

free energy required to initiate the conversion of reactants into products → activation energy

ΔG°’

• used in biochem

• standard free energy change at pH 7 → if H+ or water are reactants, their [ ] is 1

• unchanged for a given rxn

• CAN NOT predict spontaneity, only ΔG can

if ΔG°’ is >/= 0, how can the rxn be made spontaneous?

change ΔG → change concentrations of the reactants and products

K′_eq

equilibrium constant under standard conditions and pH 7

important relationship between enzyme and ΔG on reaction kinetics

enymes make rxns reach equilibrium faster without altering what the equilibrium position is. only ΔG can define equilibrium position

transition state

in between stage where molecule is not longer a reactant but not yet a product

X^‡

transition state of a rxn

how do enzymes accelerate rxns

lower the activation energy → more molecules have enough energy to transition → faster rxn rate

what is an active site

• 3d cleft/crevice

• small part of the total enzyme

• catalytic site

unique microenvironment of active site

• close association of substrate and enzyme means excluding water → non polar active site

• can also have polar residues → exception bc usually on protein surface

what does the active site of an enzyme bind

the substrate and any cofactors

catalytic groups

amino acids in the active site that directly make and break bonds in catalysis

what attractions encompas substrate-enzyme binding

lots of weak attractions → ionic, VDF, hydrophobic effect

what makes enzymes specific

• shape of active site

• size

• charge/polarity

lock and key model

active site and substrate are complementary shapes

induced fit model

enzyme changes shape when its substrate binds, forming a complementary shape after binding

conformational selection

substrate only binds to certain conformations of an enzyme

binding energy

energy released when weak bonds form between an enzyme and substrate → makes up the energy to lower activation energy

how does binding energy help explain enzyme specificity

only the right substrate shape can participate in all the ES interactions and produce sufficient binding energy

at what point during a rxn is the active site fully complementary to the substrate

when substrate is in transition state → releases lots of binding E, lowering activation E

how does enzyme lowering transition energy affect direction of a rxn

decreases activation energy both ways → accelerates both forward and backward rxn

what does the unstablility of the transition state cause

random colllapse into either substrate or product → one active site can reach the transition state multiple times and bouncing back to substrate before making product

if the transition state can randomly collapse into substrate or product, how can one still to accumulate?

different activation energies between forward and backward rxn: lower AE → reaching transition state more → more chances to flip into the other

*the other will be flipped back at a much lower rate bcz it has a higher AE

transition state analogs

compound resembling transition state of a rxn → potent competetive inhibitors

catalytic antibodies/abzymes

antibodies that reconizes transition states → function like enzymes