B2W1 Mtc Enzyme Catalysis

Front 1

What is affected by enzymes?

Back 1

Rate/kinetics of reaction

NOT thermodynamics (i.e. Keq)

Front 2

Name five ways that enzymes affect a reaction

Back 2

1. stabilization of transition state

2. proximity effects

3. microenvironmental effects

4. acid base catalysis

5. covalent catalysis

Front 3

How do catalysts reduce the free energy of activation of the reaction?

Back 3

Stabilizing the transition state

Front 4

Keq

Back 4

how much substrate and product are present at equillibrium (steady state, will not change)

Keq=product/substrate

Front 5

Free energy equation

Back 5

Front 6

Variables in free energy equation

Back 6

R=1.98 x 10^-3 Kcal/mol K

1 Kcal=4.2 kJoules

T=temp in Kelvins

G=kilocalories/mol

Front 7

What does Keq mean?

Back 7

Keq=10^-4: means 10,000 substrate to 1 product, NOT favorable reaction, free energy is positive

Keq=10^4: means 10,000 product to 1 substrate, favorable reaction, free energy is negative

Keq=1: free energy is zero

*can couple unfavorable reactions with favorable to make work

Front 8

Free energy term

Back 8

Describes amount of energy absorbed or released in reaction

Front 9

What must be true in a thermodynamically favorable reaction?

Back 9

Substrate must be less stable than the product, i.e. bond energies within substrate are weaker than product

Example: CO2 is stable, glucose bonds are less stable, glucose to CO2 is from less stable to more stable

Bond energy differences=major force of a reaction and towards entropy

Front 10

Rate constant (kr)

Back 10

Determined by the free energy of activation (which is reduced by catalysts)

Amount of substrate concentration also influences

Catalysts need to bind to substrate and via bond energy make it more unstable; it will lower Ea

Front 11

What is true about reversible reactions?

Back 11

Usually have to add ATP to make it work

This occurs even though final state more stable than initial state

Example: oxidation and resynthesis of phosphoenolpyruvate

Front 12

What happens as you lower activation energy?

Back 12

Rae increases, larger turnover number (kCat)

Front 13

Numbering classes of enzymes

Back 13

First number=one of six major classes

Second and third=subclass and sub-subclasses

Fourth number=accession number, showing order in which enzyme was accepted into nomenclature

Front 14

Six major classes enzymes

Back 14

Oxidoreductases

Transferases

Hydrolases

Lyases

Isomerases

Ligases

Front 15

Oxidoreductases

Back 15

Oxidation-Reduction reaction

Ex. Lactate dehydrogenase

Front 16

Transferases

Back 16

Group transfer

Ex. hexokinase

Front 17

Hydrolyases

Back 17

Hydrolysis reactions (water coming in and out)

Ex. chymotrypsin

Front 18

Lyases

Back 18

Addition and removal of groups from double bonds

Ex. fumarase

Front 19

Isomerases

Back 19

Isomerization (intramolecular group transfer)

--changing groups within same molecule (i.e. ketose to aldetose)

Example: Triose phosphate isomerase

Front 20

Ligases

Back 20

Ligation of two substrates at expense of ATP

Example: Aminoacyl-tRNA synthetase

Front 21

How do we avoid the problem of water in reactions?

Back 21

Put in organic solvents so we can get A and B together in the right orientations so they can create C

This is what an enzyme does...tries to get water out of system (desolvation) and create right orientation for catalysis, as well as putting strain in the bonds

Front 22

Proximity effects

Back 22

Enzyme helps put substrates together so they can react

Example: succinic acid to succinyl anhydride vs acetic acid to acetic anhydride

When water taken out of system and succinic acid esterified together, can work better

Front 23

Transition state

Back 23

When enzyme binds to a compound and makes it into a condition where it will be easy to move to the next step

Usually tetrahedral

All has to do with bond energies

Front 24

What do drugs do?

Back 24

Mimic transition state

Example: HIV protease inhibitors

becomes tetrahedral so protease can't work anymore because it binds to enzyme, bond energy stabilized

Another example--Serrin gas

Front 25

What are ways to increase the pKa of an enzyme?

Back 25

Put in organic solvent/hydrophobic environment; H2O not there, nothing to pull the proton off

This is how you make a conjugate base

Front 26

What are ways to lower the pKa of an enzyme

Back 26

Use charges or polar amino acids in process