how enzymes work

Question 1

What are enzymes?

Answer 1

protein catalysts!!

Question 2

what are three ways to increase the rate of chemical reactions?

Answer 2

increase the temperature
increase the concetration
add a catalyst

Question 3

Do enzymes alter the equilibrium?

Answer 3

NO, just the speed of the reaction

Question 4

What part of enzymes is involved in the chemistry?

Answer 4

the active site

Question 5

are enzymes normally present in high amounts compared to the substrates?

Answer 5

NO

Question 6

what do enzymes lower?

Answer 6

the free energy of activation for a reaction

Question 7

how do enzymes lower the free energy?

Answer 7

residues at the active site bind the substrates and put them in proximity (the correct orientation), and provide functional groups for catalysis

Question 8

What do enzymes preferentially bind and stabilize?

Answer 8

the transition state (induced fit)

Question 9

what is the time to catalyze on reaction called?

Answer 9

turn over time

Question 10

what are the mechanisms of catalysts?

Answer 10

acid-base: transfer or removal of H+ lowers the ∆Gt

covalent: transient formation of reversible covalent bond between an enzyme and a substrate
metal: indirect or direct; red/ox reactions

Question 11

do the AA side chains often play a direct role in acid-base and covalent catalysis at the active site?

Answer 11

YES

Question 12

What is something that some catalytic mechanisms require?

Answer 12

enzyme co-factors (organic co-enzymes or metal ions)
with cofactor= holoenzyme
w/out cofactor= apoenzyme

Question 13

nucleophiles in enzymes (5)

Answer 13

ser, tyr, cys, lys, his

Question 14

how do metal ions catalyze reactions?

Answer 14

metal ions at the active site can mediate oxidation/reduction reactions, promote further reactivity of other functional groups, or interact directly with the reacting substrate

Question 15

what type of catalysis does chymotrypsin use?

Answer 15

acid-base and covalent in the hydrolysis of a peptide bond

Question 16

what does chymotrypsin prefer as residues on the carbonyl side of the peptide bond?

Answer 16

bulky non-polar, part of the serine protease family

Question 17

what form the catalytic triad?

Answer 17

asp 102, his 57, ser 195

Question 18

what is serines role?

Answer 18

acts as nucleophile

Question 19

what is histidines role?

Answer 19

act as a general base

Question 20

what is asparagines role?

Answer 20

anchor

Question 21

what happens if you use mutations to affect chymotrypsin?

Answer 21

if you replace Asp you decrease rate by 1000x, replace ser decrease by 10^6x BUT it still acts as a catalyst because of the specificity of the active site

Question 22

is chymotrypsin flexible? How so?

Answer 22

Yes, it adopts slightly different conformations as it goes through the catalytic cycle (induced fit)

Question 23

How does chymotrypsin preferentially stabilize the transition state?

Answer 23

through gly 193 and a backbone amide (oxyanion hole)

Question 24

how do different proteases have different specificities at the active site?

Answer 24

different residues lining the substrate binding pocket

despite similar tertiary structure (divergent evolution)

Question 25

what is an example of convergent evolution with enzymes?

Answer 25

some proteases that are not homologous to the serine proteases and have little sequence and 3D structure similarities but use a similar catalytic mechanism involving a triad

Question 26

What is a zymogin?

Answer 26

an inactive pre-cursor protease that needs to be activated by cleavage by other proteases

Question 27

are some proteases regulated by specific inhibitors?

Answer 27

YES

Question 28

what are isozymes?

Answer 28

a set of different enzymes which catalyze the same reaction, they different primary structure

Question 29

what are cyclooxegenases?

Answer 29

catalyze the first step in the synthesis of prostaglandins

AKA COX and they are isoenzymes

Question 30

what is COX-1 required for?

Answer 30

required for basal PG production

Question 31

what is COX-2 required for?

Answer 31

it is inducible and involved in pain and inflammation

Question 32

what is the advantage of COX-2?

Answer 32

it has a slightly larger active site due to val instead of ile at position 523 which has allowed for the development of COX 2 specific drugs such as vioxx and celebrex