Enzyme Mechanisms

Question 1

what are the five catalytic mechanisms in biology?

Answer 1

1. acid base catalysis
2. metal ion catalysis
3. catalysis via proximity and orientation
4. covalent catalysis
5. catalysis by preferential transition state binding

Question 2

what is acid base catalysis?

Answer 2

transferring of protons to or from the substrate-acting as an acid, base, or both

Question 3

what is metal ion catalysis?

Answer 3

metal ions act either through oxidation or forming favorable interactions to the transition state

Question 4

what is catalysis via proximity and orientation?

Answer 4

enzymes orient the molecule and places it so that they’re optimal to carry out for catalysis to occur

Question 5

what is covalent catalysis?

Answer 5

reactions are accelerated by a transient formation of covalent complex between the enzyme and the substrate

Question 6

what is catalysis by preferential transition state binding?

Answer 6

particular energetically favorable interactions to the transition state

Question 7

what principle do biological catalysts follow?

Answer 7

they low the activation energy barrier to speed up the reaction

Question 8

what do catalysts (i.e. enzymes) not affect?

Answer 8

they don’t effect the equilibrium of a reaction

Question 9

what does ribonuclease A do generally?

Answer 9

it’s an endonuclease that cleaves single-stranded RNA

Question 10

how many products does ribonuclease A catalysis form?

Answer 10

2

Question 11

true of false: his12 only acts as a base and his119 only acts as an acid

Answer 11

false. in the beginning his12 acts as a base and his119 acts as an acid, however after the first product leaves, his119 acts as a base and his12 acts as an acid

Question 12

which element carries out a nucleophilic attack on the adjacent phosphorous in the RNA?

Answer 12

2’-OH

Question 13

which element carries out a nucleophilic attack on the phosphorous of the intermediate?

Answer 13

water OH

Question 14

what is the name of the specific example of metal ion catalysis we learned?

Answer 14

carbonic anhydrase

Question 15

what element ionizes a water molecule?

Answer 15

Zn2+

Question 16

what does the OH- do to the C atoms of the CO2 substrate?

Answer 16

perform a nucleophilic attack

Question 17

what is the structure of trypsin, a serine protease?

Answer 17

an all B protein

Question 18

which amino acids are in the catalytic triad?

Answer 18

serine, histidine, and aspartate

Question 19

which 3 of the 5 catalytic mechanisms do serine proteases use?

Answer 19

1. covalent catalysis
2. concerted acid-base catalysis
3. transition state stabilization

Question 20

what does Asp102 do?

Answer 20

orients His57

Question 21

what does His57 do?

Answer 21

acts as a general acid and base

Question 22

what does Ser195 do?

Answer 22

form a covalent bond with peptide to be cleaved i.e. perform nucleophilic attack

Question 23

what does the covalent bond formation do?

Answer 23

transiently turns trigonal C into a tetrahedral C of an intermediate

Question 24

what is the tetrahedral oxyanion intermediate stabilize by?

Answer 24

main chain NHs of Gly193 and Ser195: the oxyanion hole

Question 25

what carries out the nucleophilic attack on the carbonyl carbon in serine proteases?

Answer 25

water OH

Question 26

in which type of catalysis is a bicarbonate ion formed?

Answer 26

metal ion catalysis

Question 27

in the serine proteases, the role of Ser195 is __ and the role of His57 is __

Answer 27

nucleophilic attack; acid/base catalysis