# Structural Biochemistry/Enzyme/Acid-Base Catalysis
## General acid/base catalysis and its effectiveness

General acid/base catalysis' rate determining step is the proton transfer step. Therefore, general acid catalysis has its reaction rate depending on all the acids present; similarly, the general base catalysis has its reaction rate depending on all the bases present. The preferred reaction environment is neutral PH for both reactions, because high concentration of H+ or OH- can damp out the catalytic contributions from other acids and bases, thus, turning the "general" acid or base reaction into "specific" acid or base catalysis.
Since the proton transfer step determines the rate of the reaction, it is important to examine the effectiveness of the general catalysis. The effectiveness of the general catalysis can be determined from Bronsted equation, which is written as,
       $\log k_{\text{HA}}=\alpha \log K_{\text{HA}}+{\text{Constant}}$
       $k_{HA}$, the rate constant of the catalysis
       $K_{HA}$, the dissociation constant of HA
       $\alpha$, the sensitivity of the catalytic step to the acid dissociation step.
The relationship can be easily seen by graphing logk(HA) vs. log K(HA), and so the slope, which is the alpha, can be analyzed graphically. Each dot on the graph represents different acids. Since efficiency cannot exceed 1, the rage of the slope is bounded between 0 and 1. A slope of 1 indicates that the rate increases with every acid dissociation and that the proton transfer is effective. A slope of zero means every acid dissociation contributes the same effect to the catalysis, and the transfer of proton is not effective. On the other hand, the sensitivity graph for the specific acid/base catalysis may appear as a nonlinear relationship between k(HA) and K(HA).

## Overview

General acid-base catalysis involves a molecule besides water that acts as a proton donor or acceptor during the enzymatic reaction. Acid-base catalysis facilitates a reaction by stabilizing the charges in the transition state through the use of an acid or base, which donates protons or accepts them, respectively. Nucleophilic and electrophilic groups are activated as a result of the proton addition or removal and causes the reaction to proceed. Many acid-base catalysis reactions involve histidine because it has a pKa close to 7, allowing it to act as both an acid and a base. When a functional group accepts a proton, it will release or donate a proton by the end of the catalytic cycle, and vice versa. Functional groups that participate in reaction are His imidazole, alpha-amino group, alpha-carboxyl group, thiol of Cys, R group of carboxyls of Glu and Asp, aromatic OH of Tyr, and guanidino group of ARG. The protonation of these functional groups are dependent on the pH, therefore the enzymatic catalytic activity is sensitive to the pH level.
General acid-base catalysis is involved in a majority of enzymatic reactions, wherein the side chains of various amino acids act as general acids or general basis. General acid–base catalysis needs to be distinguished from specific acid–base catalysis.
Specific acid–base catalysis means specifically, –OH or H+ accelerates the reaction. The reaction rate is dependent on pH only (which of course is a function of –OH and H+ concentrations), and not on buffer concentration. General acid - partial transfer of a proton from a Brønsted acid lowers the free energy of the transition state rate of reaction increases with decrease in pH and increase in [Brønsted acid].
-Specific acid - protonation lowers the free energy of the transition state, rate of reaction increases with decrease in pH.
-Specific base - abstraction of a proton (or nucleophilic attack) by OH$^-$ lowers the free energy of the transition state, rate of reaction increases with increase in pH.
In General acid–base catalysis, the buffer aids in stabilizing the transition state via donation or removal of a proton. Therefore, the rate of the reaction is dependent on the buffer concentration, as well as the appropriate protonation state. -General base - partial abstraction of a proton by a Brønsted base lowers the free energy of the transition state rate of reaction increases with increase in pH and increase in Brønsted base.

## Example

An example of acid-base catalysis is peptide hydrolysis by chymotrypsin. Chymotrypsin uses a histidine residue as a base catalyst to increase the nucleophilicity of serine. Chymotrypsin uses a histindine residue as a base catalyst to help to strengthen the nucleophillic property of serine, whereas a histindine residue in carbonic anhydrase helps the removal of hydrogen ion from zinc bound water molecule to generate OH$^-$.
The pKa of Histidine is close to neutral thus making it the most effective candidate for general acid or base because it can either donate or accept protons. His 119 in Ribonuclease A plays the role of a general acid that donates a proton to 5'-hydroxyl of nucleoside. On the other hand, His 12 acts as a general base which accepting a proton from the 2'-hydroxyl of 3'-nucleotide. As a result, a 2’-3’ cyclic phosphate intermediate is formed. When water replaces the nucleoside, the roles of His 119 and His 12 are reversed. In the end, the original Histidine protonation states are restored.
File:ProtonAcceptingDonating.png His 119 is the acid and His 12 is the base. File:2’-3’ cyclic phosphate intermediate .png A 2'-3' cyclic phosphate intermediate is formed. File:ProtonAcceptingDonatingReversed.png Reversely, His 119 is the base and His 12 is the acid. File:OriginalStateofHis.png His 119 and His 12 return to their initial states.
In the picture, serine acts as a nucleophile and attacks the carbonyl group of the substrate, while histidine accepts the proton from serine and the tetrahedral intermediate is formed. The collapse of the tetrahedral intermediate forms the acyl enzyme. Water loses a proton to histidine and attacks the acyl enzyme and the oxyanion hole is formed. The reaction ends with the release of a carboxylic acid. The cycle then continues with a new substrate.
Another example of acid-base catalysis is the reaction with carbonic anhydrase. His residues in carbonic anhydrase facilitates the removal of a hydrogen ion from zinc-bound water to generate a hydroxide ion.

## Reference

Berg, Jeremy M. John L. Tymoczko. Lubert Stryer. Biochemistry Sixth Edition. New York: W.H. Freeman, and Company 2007.
http://www.chem.uwec.edu/Chem352_S09/pages/lecture_materials/unit_II/lecture-4/overheads/Chem352_lecture-4_Part-II.pdf
http://biochemistry.wur.nl/Biochem/educatio/Colleges/Maurice/ppt_Ch2.ppt