Enzymes

Question 1

enthalpy

Answer 1

the total energy in a system

Question 2

free energy

Answer 2

the amount of energy that is AVAILABLE in a system to use

Question 3

entropy

Answer 3

the tendency for ordered things to become random

Question 4

how do enzymes serve as catalysts?

Answer 4

they speed up chemical reactions (increase the rate of reaction) by lowering the activation energy; ex: the enzyme glucokinase holds ATP and glucose together which stabilizes it so the enzyme can place the phosphate onto glucose

Question 5

activation energy

Answer 5

the minimum amount of energy required to overcome the energy barrier and achieve transition state

part of the transition state complex which is where the energy required to raise the substrate energy to the transition state

the minimum amount of energy required to convert a normal stable molecule into a reactive molecule

Question 6

transition state

Answer 6

a high energy state; the apex when the molecules have the highest potential energy; the most unstable point for the molecules

Question 7

transition state complex

Answer 7

specifically while the substrate is held in its active site, since substrates need to be activated; after binding and before it’s released

inversely proportional to the rate of the reaction

Question 8

substrate binding site

Answer 8

where the substrate binds (the whole “mouth” that also contains the active site)

Question 9

lock and key

Answer 9

substrate binding site creates a 3-D shape that is complementary to the substrate (ensures a perfect match since enzymes are so specific)

Question 10

induced fit

Answer 10

substrate binding to the enzyme induces a conformational change; this still relies on complementarity

helps to reposition the functional groups to promote the reaction

Question 11

when is a reaction exergonic

Answer 11

if the product (P) has less free energy than the starting reagents (A and B), the G is (-), reaction will go forward spontaneously, and energy is released

Question 12

when is a reaction endergonic

Answer 12

if the product P has more free energy than A and B, the G is (+), reaction will not occur spontaneously, and energy needs to be added for the reaction to occur

Question 13

what does delta G predict?

Answer 13

it predicts the DIRECTION of a reaction; it does not affect the rate at which the reaction occurs!!!!!

Question 14

what does the RATE of a reaction depend on?

Answer 14

the activation energy! the lower the activation energy, the faster the rate of reaction

Question 15

why is ATP used so much?

Answer 15

it is highly exergonic because ripping off that third phosphate group releases a lot of energy, and we can couple this exergonic reaction with endergonic ones so the overall G for the coupled reaction remains negative

Question 16

where do the functional groups in the active site come from?

Answer 16

they can be from the protein (enzyme) itself or from other bound cofactors (coenzymes)

Question 17

what kind of bonds form between the substrate and the substrate binding site?

Answer 17

non covalent bonds with the amino acids from the enzyme or cofactors

Question 18

why are additional bonds formed with the enzyme?

Answer 18

to stabilize the substrate in its transition state; adding bonds increases the stability of the substrate which directly relates to a lower activation energy

Question 19

how do enzymes lower the activation energy?

Answer 19

by stabilization! (a.k.a. more chemical bonds with the substrate, which makes it more stable and ready to proceed in the reaction)

Question 20

what kind of non covalent interactions occur between the enzyme amino acids and / or cofactors with the substrate?

Answer 20

hydrophobic, electrostatic, H-bonds, etc

Question 21

what does “lowering the amount of energy” mean?

Answer 21

in the transition state complex, it means more molecules at any given time are more apt to reach the transition state so the reaction can occur

Question 22

functional groups found in the active site

Answer 22

amino acid side chains, coenzymes, metal ions

Question 23

covalent catalysis amino acids

Answer 23

serine, cysteine, lysine, histidine

Question 24

polar amino acids in the side chains of functional groups

Answer 24

nucleophilic catalysis (an electron rich molecule that donates electrons)

Question 25

coenzymes

Answer 25

non-protein organic molecules (vitamins)

Question 26

what processes do coenzymes do to the substrate?

Answer 26

activation transfer or oxidation-reduction

Question 27

activation transfer

Answer 27

form covalent bond with substrate it, then activate it for transfer

Question 28

activation transfer (remember…this is how vitamins / coenzymes work)

Answer 28

form covalent bond with substrate it, then activate it for transfer

ex: biotin - uses N to attach to CO2 groups in carboxylases
coenzyme A - uses its sulfhydryl group (in the cysteine) to do nucleophilic attacks
thiamine pyrophosphate - contains carbon with dissociable proton

Question 29

oxidation-reduction

Answer 29

functional groups accept or donate electrons

similar to activation transfer, but no covalent bond is formed

Question 30

metal ions

Answer 30

electrophiles (they are positively charged, so they liked to accept electrons)

participate in substrate binding, stabilizing anions, and donating/accepting electrons in redox reactions

Question 31

inhibitors

Answer 31

compounds that decrease the rate of an enzymatic reaction

Question 32

types of inhibitors

Answer 32

covalent inhibitor, transition state analogs, non-covalent

Question 33

covalent inhibitor

Answer 33

form covalent (very tight) bond with functional groups in the active site

Question 34

transition state analogs

Answer 34

bind more tightly to the enzyme than substrates or products; the best kind of inhibitors and often used in medicine

Question 35

why are transition state analogs so effective?

Answer 35

more bonds are being made (can be covalent or not) so it’s harder to rip apart