BIOC192 - Module 1 (enzymes)

Lectures 7-12

if delta G is less than 0

the reaction is spontaneous and energy is released

if delta G is greater than 0

the reaction is non-spontaneous and energy is required

if delta G is = 0

the reaction is at equilibrium

enzyme catalysed reactions must be

in balance so there’s constant flow through the reaction pathways

reactions pass through

high energy transition states

what’s required to reach the transition state?

activation energy

activation energy

the energy barrier to get from reactants to products

how do enzymes contribute to a reaction

they lower the activation energy, decreasing the amount of energy needed in the reaction to get to the transition state and the product

by decreasing delta G…

enzymes accelerate the forward and reverse reactions equally

oxidoreductases function

catalysis of redox reactions (transfer of electrons)

Transferases function

transfer of functional groups

hydrolase function

hydrolysis reactions using water

lyase function

non-hydrolytic breaking or making of bonds

isomerase function

transfer of atoms/groups to yield an isomeric form

ligase function

joining two molecules together (forming bonds, ATP cleavage)

co-factors

non-protein “factors” that give more chemical diversity to the enzyme

metal ions (co-factor) - location

sit in active site

co-enzyme (co-factor)

a subset - small organic molecules derived from vitamins

metal ions are lewis ___ which allows them to participate in ___ ____ ____

acids, acid-base catalysis

why are metal ions useful cofactors?

they form coordination compounds with specific bonding geometry which is good for positioning reactants exactly where they need to be

what is the location of the PLP co-factor?

found at the active site of glycogen phosphorylase

how is PLP connected to the active site of glycogen phosphorylase?

covalently linked to a lysine residue in the active site

reaction coupling

coupling a non-spontaneous reaction with a spontaneous reaction

what does lowering the activation energy of a reaction allow an enzyme to do?

catalyse thermodynamically favourable reactions

how do enzymes lower delta G?

creating an alternate reaction pathway with a lower energy transition state

how can ground state destabilisation and transition state stabilisation be achieved?

by having the active site be more complementary to the transition state rather than the substrate

the destabilisation of the ground state brings

the energy of the reactants up

the active site provides…

a chemical environment that stabilises the transition state

the active site of an enzyme has diversity because of…

it has the same backbone so diversity comes from the amino acids protruding into it

the active site binds substrate through

multiple weak interactions that generate specificity for the substrate

weaker interactions of the enzyme with substrate allow for

the breaking and forming of bonds more easily

enzyme-substrate bond: ionic bonds

salt bridges making use of charged side chains

enzyme-substrate bond: hydrogen bonds

O and N from the side chains or backbone can form H bonds

advantage of hydrogen bonds

they are directional allowing for correct alignment to get effective binding

enzyme-substrate bond: Van der Waals interactions

between any protein and substrate atoms in close proximity, very weak

enzyme-substrate bond: covalent bonds

strongest bond type but very rare to find at active site

enzyme substrate complex

where we first get binding of the substrate to the active site

why does the ES complex have to have lower energy than S by itself

makes it more favourable to get to this state

many weak interactions ensure…

specificity and reversibility

molecular complementarity between E and S is critical because

weak bonds can only form if relevant atoms are precisely positioned

lock and key model (for E&S binding)

substrate meets geometry and the active site accommodates the shape of the substrate

induced fit model (for E&S binding)

enzyme active site doesn’t perfectly match the shape of the substrate until the substrate binds — complete complementarity to form enzyme-substrate complex

prediction of preferential binding of the transition state

enzymes are evolved to effectively bind the transition state of the reaction

problem of preferential binding of the transition state

the transition state is transient and can’t be isolated

transition state analogues

mimic the transition state so the enzyme is more likely to take it up as it is more energy efficient

for two molecules to react they need to be

close together and at the correct orientation

acid-base catalysis

different reaction pathways involving proton transfer

metal ion catalysts provide

substrate orientation due to specific coordination geometry, act as lewis acids, good sites for oxidation-reduction reactions