What is the catalytic scheme adopted by Lys156 at the beginning (1) of the catalytic cycle?
- Lysine's side is mature (fully deprotonated) and hence very nucleophilic
- Lys156 is using general base catalysis it is accepting a proton from Ser226
Ser226 (serine alkoxide) one of the most potent biological ________. What are the two types of catalytic schemes adopted by Ser226 at the beginning (1) of the catalytic cycle? What is happening at (2) where Ser226 is linked to the tetrahedral carbon (ELTCI)
- Ser226 is in general acid catalysis (exchange of protons)
- Lys156 is in general basic catalysis (exchange of protons)
The tetrahedral carbon (ELTCI: Enzyme-linked tetrahedral covalent intermediate) is in covalent catalysis with Ser226, protons are not being exchanged instead a covalent bond ensues
What type of catalytic scheme is being utilized by Lys156 and Ser226 toward the end (4) of the catalytic cycle?
- Step 4 & 1 depict role reversal Lys156 is now general acid it donates a proton to Ser226, which is now general base because it receives a proton
- **Note: This process (1-4) is cyclic
a) With respect to His218, what is the catalytic scheme being utilized? (Explain)b) With respect to His56, what is the catalytic scheme being utilized? (Explain)
- a) With respect to His218, it is covalent catalysis. The reason is that we are seeing a transient covalent bond in the reaction mechanism scheme
- b) With respect to His56, we are observing a general acid catalysis. The reason is that we are observing the His56 residue lose or donate a proton
What is unique about water, as it pertains to acid base catalysis? What happens when two water molecules react with each other? How does water behave at the active site of an enzyme?
- Water can act as an acid or as a base (amphoteric).
- When two water molecules react with each other, they exchange protons: (equilibration between hydronium and hydroxide ions).
- When water is in an active site, it behaves as an acid
This is an example of metal ion-based catalysis utilized by the enzyme, carbonic anhydrase, a metalloenzyme. What is the function of the metal ion? What happens to the alkyloxonium's (water molecule derivative) proton?
- Zn activates the oxygen in water even more (nucleophilically) and after the hydrogen is lost, allows oxygen to bind to CO2
- His64 captures alkyloxonium's (water derivative's) proton with general base catalysis
How are reactions mechanism determined, in other words, how do researchers discover the mechanisms of enzymes and substrates? Do they use substrates in the process?
- They don't use a substrate, because the substrate will be immediately catalyzed into product by the enzyme
- Instead they use an analog which cannot be catalyzed by the enzyme, by using other enzymes like stereoisomerase/epimerase/racemase which flip stereochemistry of substrate L→D, R→S etc
- Substrate analog, which is NOT catalyzed serve as COMPETITIVE INHIBITORS and strongly binds to the enzyme active site halting all activity and allowing researchers to observe structure and mechanism as much as they want
Anytime a molecule resembles a substrate, it is likely a _______ _______ and thus it is likely a very effective _______ ______
- substrate analog
- competitive inhibitor