Free energy, Enzyme + Kinetics

Potential vs kinetic energy

PE: energy stored in an object

KE: energy of motion, includes motion at the molecular scale

Energy is the potential to do work

what is free energy

energy that can be used to do work

high free energy is less stable, more concentrated, more ordered, and has greater work capacity

low free energy is more stable, less concentrated, less ordered, less work capacity

objects tend to move from high to low free energy

the reason molecules move down a concentration gradient is that each molecule at a high concentration has a higher free energy

exergonic vs endergonic

energy releasing reactions are exergonic/spontaneous. Reactants have more energy than products, ∆G < 0

energy consuming reactions are endergonic/non-spontaneous. Reactants have less energy than products, ∆G > 0

Equilibrium constant

Keq = [B] / [A] (how much product do we have/how much reactant do we have)

Keq > 1 is exergonic

Keq < 1 is endergonic

The equilibrium constant is the proportion of products over reactants when the reaction reaches equilibrium

Equilibrium is when the forward and reverse reactions have the same rate (A goes to B as frequently as B goes to A)

how to interpret an equilibrium constant numerically

Keq = 140 means for every 1 reactant there are 140 products

Keq = 1/5 means for every 5 reactants there will be 1 product

Activation energy

spontaneous reactions are not actually spontaneous; they need a trigger. The activation energy is the energy required for reactions to reach the transition state (the unstable intermediate where covalent bonds can be rearranged)

The requirement for a transition state can greatly impede exergonic reactions

effect of a catalyst on a reaction

does not change the amount of energy released

does not change Keq

does lower E_a, the rxn reaches the transition state at a lower free energy

does increase the rate of reaction.

is not itself changed by the reaction

active site

where the substrate binds and where catalysis occurs. Binding between enzyme and substrate can cause a shape change in the enzyme protein (induced fit)

Substrates match shape and chemistry of the enzymes they bind to

what interacts when substrates bind

the enzyme’s R groups with the substrate, which stabilizes the transition state

binding destabilizes chemical bonds in substrate which lowers the activation energy which makes the reaction go faster

basic enzymatic reaction

substrate + enzyme ←> enzyme-substrate complex ←> enzyme + product

reaction rate and factors that affect it

amount of product formed/time

substrate/enzyme concentration, temperature, pH, the presence/concentration of other ions

explain temperature’s effect on rxn rate

there is an optimum temperature where rxn rate is highest. Too hot = denaturation, too cold = lower kinetic energy, fewer collisions, and protein is too rigid to take substrates

explain ph’s effect on rxn rate

pH can change amino acid protonation.

Enzymes from different organisms may function best at different pHs

How does substrate/enzyme concentration affect reaction rate

rate of reaction increases as substrate concentration increases to a maximum velocity rate (V_max). Adding more substrates = faster/more products, but is saturable because there can be more substrate than the enzyme can handle

What is V_max and what is Km in terms of values

V_max: enzyme is processing substrate to product as fast as it can

Km: the substrate concentration at which V_max is at half maxiumum

What does Km mean

describes the affinity of an enzyme for its substrate. A low Km means that the enzyme holds the substrate tightly (high affinity). A high Km means that the enzyme holds the substrate more loosely (lower affinity) because they need more substrate to get to the same amount of reaction.

What does less enzyme do to Vmax and Km

Vmax lowers, Km is unchanged

irreversible inhibition

inhibiting the enzyme in an irreversible way. Changes the shape/chemistry of the enzyme to control its activity, and typically involves covalent modification of the enzyme

reversible regulation

a molecule binds to an enzyme in a non-covalent manner and alters enzyme confirmation. Changes the shape/chemistry but in a reversible way.

reversible small molecule inhibition involves something binding to but not covalently altering the target enzyme, making it reversible

2 types of reversible small molecule inhibition

competitive inhibitor: binds to the active site and mimics the substrate to compete for the active site. Affected by substrate concentration because high [S] means it’s less likely for the inhibitor to bind to enzyme

noncompetitive inhibitor: binds away from the active site but alters the conformation of the enzyme so that the active site is no longer fully functional. Not affected by [S]

what happens to Vmax and Km with competitive and noncompetitive inhibitors

Competitive - Vmax stays the same, Km is higher

Noncompetitive - Vmax lowers, even at very high [S]