Biochemistry/Catalytic Strategies/Acid Base reactions

Introduction to acid base catalysis reactions
This type of catalysis involves proton donors or acceptors other than water. There is then a nucleophilic or electrophilic attack. Finally, the enzyme is then restored.

The donation or acceptance of protons is generally to stabilize the transition state. A corollary to this is metal ion catalysis which involves a metal ion that stabilizes the transition state with its positive charge. Some acid base catalysis reactions also use metal ions. One common amino acid present in most enzymes that acts as an acid or a base is histidine, since its pKa is close to that of the surrounding pH. Thus, it can act as either an acid or a base.

One example is with carbonic anhydrase that breaks down carbonic acid into a proton and a bicarbonate ion.

H2CO3 <-(with carbonic anhydrase)-> H+ HCO3-

There is a part at the active site of carbonic anhydrase that contains a Zinc ion (Zn2+) that is coordinated to a few histidine R groups. The Zinc also coordinates with the oxygen of a water molecule. When Zinc is coordinated with a water molecule, the pKa reduces from 15.7 to about 7. Thus, this means that at the physiological pH, the water molecule readily deprotonates. Now this Oxygen atom acts as a nucleophile, attacking the carbon of a carbon dioxide. This creates a complex coordination compound attached to the Zinc ion, resembling the bicarbonate ion. In the final step, another water molecule replaces the biocarbonate ion, and the enzyme is reformed, ready to react again.