How does Enzymatic catalysis work?

Question 1

acid base catalysis

Answer 1

uses acidic and basic side chains… asp, glu, his, lys, arg, tyr, cys…

Question 2

covalent catalysis

Answer 2

forms covalent bonds btween the enzyme/coenzyme and the substrates
- uses nucleophilic side chain interactions between lys, his, cys, asp, glu, ser
- could also use the nucleophilic part of PLP and TPP

ex: chymotypsin mech…. you form a TI by serine

Question 3

metalloenzymes

Answer 3

have coordinate covalent bonds (ligand provides both electrons) to metal ion cofactors
- often d block metals
- several oxidation states

4 major functions:
1. binding something else other than the protein
2. allows for changing of oxidation states of metals that are used in the mechanism
3. shield charges.
4. alter the nucleophilicity or electrophilicity… (carbonix anhydrase use zinc to make water act like hydroxide)

Question 4

electrostatic

Answer 4

arranging the position of active site charges from AA/cofactors/etc so that you can stabilize/destabilize mechanism steps,

• the charges in the active sites are quite strong, because even though the AS is exposed to aqueous environment, the tunnel leading to the active site as a “stripping mechanism” that removes the H2Os off of the substrate as it is coming in.
  Now, substrate has exposed charges with no water shield, which allows charges to become strong and alter pka values.
• stripping of water ALLOWS:
  approximation of our active sites as being in organic solvents

Question 5

proximity and orientation

Answer 5

freeze and bind substrates in the correct proximity and orientation.
thinking more of the entropy as you achieve TS, more important than thinking of entropy as you are freezing and binding.
orientation more important than proximity:
proximity, yes there is a possibility for a reaction, but actually orienting in the correct position for the reaction to occur is more important

Question 6

preferential TS complex binding

Answer 6

binding to the TS the best

Question 7

look through chymotrypsin mech and see where these are except for metalloenzymes