Enzyme Mechanisms Flashcards
what are the five catalytic mechanisms in biology?
- acid base catalysis
- metal ion catalysis
- catalysis via proximity and orientation
- covalent catalysis
- catalysis by preferential transition state binding
what is acid base catalysis?
transferring of protons to or from the substrate-acting as an acid, base, or both
what is metal ion catalysis?
metal ions act either through oxidation or forming favorable interactions to the transition state
what is catalysis via proximity and orientation?
enzymes orient the molecule and places it so that they’re optimal to carry out for catalysis to occur
what is covalent catalysis?
reactions are accelerated by a transient formation of covalent complex between the enzyme and the substrate
what is catalysis by preferential transition state binding?
particular energetically favorable interactions to the transition state
what principle do biological catalysts follow?
they low the activation energy barrier to speed up the reaction
what do catalysts (i.e. enzymes) not affect?
they don’t effect the equilibrium of a reaction
what does ribonuclease A do generally?
it’s an endonuclease that cleaves single-stranded RNA
how many products does ribonuclease A catalysis form?
2
true of false: his12 only acts as a base and his119 only acts as an acid
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
which element carries out a nucleophilic attack on the adjacent phosphorous in the RNA?
2’-OH
which element carries out a nucleophilic attack on the phosphorous of the intermediate?
water OH
what is the name of the specific example of metal ion catalysis we learned?
carbonic anhydrase
what element ionizes a water molecule?
Zn2+
what does the OH- do to the C atoms of the CO2 substrate?
perform a nucleophilic attack
what is the structure of trypsin, a serine protease?
an all B protein
which amino acids are in the catalytic triad?
serine, histidine, and aspartate
which 3 of the 5 catalytic mechanisms do serine proteases use?
- covalent catalysis
- concerted acid-base catalysis
- transition state stabilization
what does Asp102 do?
orients His57
what does His57 do?
acts as a general acid and base
what does Ser195 do?
form a covalent bond with peptide to be cleaved i.e. perform nucleophilic attack
what does the covalent bond formation do?
transiently turns trigonal C into a tetrahedral C of an intermediate
what is the tetrahedral oxyanion intermediate stabilize by?
main chain NHs of Gly193 and Ser195: the oxyanion hole
what carries out the nucleophilic attack on the carbonyl carbon in serine proteases?
water OH
in which type of catalysis is a bicarbonate ion formed?
metal ion catalysis
in the serine proteases, the role of Ser195 is __ and the role of His57 is __
nucleophilic attack; acid/base catalysis
