ch 3

DRUG TARGETS: ENZYMESChapter 3 Naming enzymes Root + ase

ClassificationReaction Type CatalyzedOxidoreductasesOxidation Reduction ReactionsTransferasesGroup transfer ReactionsHydrolasesHydrolysis ReactionsLyasesAddition or removal of groups to form double bondsIsomerasesIntramolecular group transfersLigasesJoining two substrates

Structure and function of enzymes Globular proteins acting as the bodys catalysts Speed up time for reaction to reach equilibrium Lower the activation energy of a reaction

Example:LDH = Lactate dehydrogenase (enzyme)NADH2 = Nicotinamide adenosine dinucleotide (reducing agent & cofactor)Pyruvic acid = Substrate

Lowering the activation energy of reaction Structure and function of enzymesAct. energyTransition stateWITHOUT ENZYMEProductStartingmaterialEnergy

WITH ENZYMEProductStartingmaterialEnergyG

Newtransition stateGAct. energyEnzymes lower the activation energy of a reaction but DG remains the same

Methods of enzyme catalysis Provides a reaction surface (the active site)

Provides a suitable environment (hydrophobic)

Brings reactants together

Positions reactants correctly for reaction

Weakens bonds in the reactants

Provides acid / base catalysis

Provides nucleophilic groups Structure and function of enzymes The active site Hydrophobic hollow or cleft on the enzyme surface

Accepts reactants (substrates and cofactors)

Contains amino acids which:- bind reactants (substrates and cofactors)- catalyse the reactionENZYMEActive siteActive site Substrate binding Active site is nearly the correct shape for the substrate Binding alters the shape of the enzyme (induced fit) Binding strains bonds in the substrate Binding involves intermolecular bonds between functional groups in the substrate and functional groups in the active site Induced fitInduced fitSubstrate

S Substrate binding Ionic H-bonding van der Waals

Bonding forcesExample

SEnzymeActive sitevdwinteractionionicbondH-bondPhe

SerOH

AspCO2

Substrate binding Ionic H-bonding van der Waals

Bonding forcesExample - Binding of pyruvic acid in LDHH-BondPossible interactionsvdw-interactionsOHH3N

Ionic bondH-Bond

van der Waals

Ionic

Substrate binding Induced fit - Active site alters shape to maximise intermolecularbonding Bonding forcesIntermolecular bonds not optimum length for maximum bonding

Intermolecular bond lengths optimisedSusceptible bonds in substrate strainedSusceptible bonds in substrate more easily broken

SPhe

SerOH

AspCO2

Induced fitSPhe

SerOH

AspCO2

Substrate bindingExample - Binding of pyruvic acid in LDHOHH3N

OOO Substrate bindingExample - Binding of pyruvic acid in LDHOHH3N

p bondweakened

Catalysis mechanismsHistidine

Acid/base catalysisNucleophilic residues

Non-ionizedActs as a basic catalyst(proton 'sink')IonizedActs as an acid catalyst(proton source)

L-Serine

L-Cysteine Catalysis mechanismsOHSer

H2OOHSerHO

Serine acting as a nucleophile Catalysis mechanismsMechanism for chymotrypsin to hydrolyses peptide bondsCatalytic triad of serine, histidine and aspartateChymotrypsinNNOHHOOSerHisAsp..::Catalysis mechanismsMechanism for chymotrypsinProteinNHCOProtein::ChymotrypsinNNOHHOOSerHisAsp..:: Catalysis mechanismsMechanism for chymotrypsin

ChymotrypsinNNHHOOSerHisAsp:: Catalysis mechanismsMechanism for chymotrypsin

ChymotrypsinNHOOSerHisAsp:: Catalysis mechanismsMechanism for chymotrypsin

ChymotrypsinNNHOOSerHisAsp::: Catalysis mechanismsMechanism for chymotrypsin

ChymotrypsinNNHOOSerHisAsp::: Catalysis mechanismsMechanism for chymotrypsin

ChymotrypsinNHOOSerHisAsp:: Catalysis mechanismsMechanism for chymotrypsin

ChymotrypsinNNOHHOOSerHisAsp..:: Catalysis mechanismsMechanism for chymotrypsin

Overall process of enzyme catalysisSE

ESPE

EP

PEE + PESE + SE Binding interactions must be strong enough to hold the substrate sufficiently long for the reaction to occur Interactions must be weak enough to allow the product to depart Implies a fine balance Designing molecules with stronger binding interactions results in enzyme inhibitors which block the active site Regulation of enzymes Many enzymes are regulated by agents within the cell Regulation may enhance or inhibit the enzyme The products of some enzymes may act as inhibitors Usually bind to a binding site called an allosteric binding siteExample

ACTIVE SITE (open)ENZYMEEnzymeRegulation of enzymes Inhibitor binds reversibly to an allosteric binding site Intermolecular bonds are formed Induced fit alters the shape of the enzyme Active site is distorted and is not recognised by the substrate Increasing substrate concentration does not reverse inhibition Inhibitor is not similar in structure to the substrateAllostericbinding siteActive site (open)ENZYMEEnzyme

InducedfitActive siteunrecognisableAllostericinhibitor Regulation of enzymes Enzymes with allosteric sites are often at the start of a biosynthetic pathway Enzyme is controlled by the final product of the pathway Final product binds to the allosteric site and switches off enzyme

PPP

Biosynthetic pathwayFeedback controlInhibitionPS

(open)ENZYMEEnzymeProteinkinaseCell Regulation of enzymes External signals can regulate the activity of enzymes (e.g. neurotransmitters or hormones) Chemical messenger initiates a signal cascade which activates enzymes called protein kinases Protein kinases phosphorylate target enzymes to affect activity

Example

AdrenalineSignal cascade

Phosphorylase b (inactive)Phosphorylase a (active)

Glycogen

Glucose-1-phosphate