enzyme mech and catalysis

Question 1

why are enzymes central to all biochemical processes?

Answer 1

enzymes show greater substrate specificity, have optimal arrangement of catalytic groups, and increase reaction rates

Question 2

Although most enzymes are proteins, what can also catalyze reactions?

Answer 2

RNA molecules

Question 3

how are enzymes named?

Answer 3

adding “ase” to substrate or words describing reaction
ex) DNA polymerase catalyzes the polymerization of nucleotides to form DNA

Question 4

what chemically reactive groups do enzymes contain that help catalyze reactions?

Answer 4

amino acid side-chains and N-terminal -NH2 and C-terminal -COOH

Question 5

what do enzyme cofactors do?

Answer 5

do chemistry impossible with usual functional groups

Question 6

what can cofactors be?

Answer 6

metal ions or organic molecules

Question 7

what do enzymes catalyze the conversion of?

Answer 7

substrates to products

Question 8

in the simple enzymatic reaction, what are transient complexes(reaction intermediates)?

Answer 8

ES and EP

Question 9

what does the equilibrium between S and P reflect?

Answer 9

the difference in the free energies of their ground states

Question 10

because the ground state of P is lower than S, hence delta G for the reaction is…

Answer 10

negative and favors P

Question 11

enzymes accelerate reaction rates by lowering the activation energy barrier, but do not affect…

Answer 11

reaction equlibria

Question 12

what is the equilibrium constant, Keq?

Answer 12

describes relative amounts of substrates and products present at equilibrium in a biochemical reaction

Question 13

what is the rate constant, k?

Answer 13

measure of how fast (velocity) a reaction can occur

Question 14

what happens to delta G when k is larger?

Answer 14

it is smaller (inverse exponential relationship)

Question 15

what does an enzyme’s tertiary structure create?

Answer 15

unique microenvironment for ES-intermediate substrate binding

Question 16

what is the interaction between substrate and enzyme mediated by?

Answer 16

the same non-covalent forces that stabilize protein structure

Question 17

transition state stabilization

Answer 17

lowers energy of transition state making it easier to form

Question 18

orientation

Answer 18

arranges atoms for optimal activity

Question 19

desolvation

Answer 19

binding removes interactions with solvent (water)

Question 20

induced fit

Answer 20

substrate binding changes conformation of enzyme

Question 21

acid-base catalysis

Answer 21

push or pull a proton

Question 22

covalent catalysis

Answer 22

adducts or intermediates

Question 23

metal ion catalysis

Answer 23

lewis acids and redox agents

Question 24

binding energy

Answer 24

energy derived from ES interaction

Question 25

what do enzymes use binding energy for?

Answer 25

to achieve substrate specificity and to stabilize the transition states through non-covalent interactions

Question 26

what do the non-covalent interactions allow the enzyme to do?

Answer 26

bind substrates, bind and stabilize the transition-state

Question 27

what is important to remember about the mechanism of enzyme binding?

Answer 27

NOT A LOCK-AND-KEY

Question 28

what do enzymes bind with a greater affinity to?

Answer 28

bind the transition state over either substrates or products

Question 29

important corollary about binding

Answer 29

good substrates don’t necessarily bind extremely tightly to enzyme; do not want to get stuck in an ES complex

Question 30

what are good inhibitors of enzymes

Answer 30

transition state analogs (rational basis for drug design)