Common Mechanisms in Enzymatic Catalysis

Once the substrate is bound, other residues at the active site carry out the catalytic reaction. The elementary steps involved are similar to those we covered in Chapters 3 and 4. Broadly speaking, enzyme catalysis is divided into two common mechanisms Bronsted acid/base catalysis and nucleophilic catalysis [26]. 

Bronsted acid/base catalysis is the most common enzymatic mechanism, since nearly all enzymatic reactions involve a proton transfer. This means that nearly all enzymes have acidic and/or basic groups in their active site. In add catalysis, the substrate is protonated by one of the amino add residues at the active site (typically aspartic acid, glutamic acid, histidine, cysteine, lysine, or tyrosine). This residue itself must therefore be protonated at the readion pH (typically between pH 5 and 9), with a pKa just above this value. Conversely, in base catalysis, the pJCa of the deprotonating residue must be just below the physiological pH. Some enzymes can even carry out bifunctional catalysis, by protonating and deprotonating two different sites on the same substrate molecule simultaneously. 

In nucleophilic catalysis (sometimes called covalent catalysis), a nucleophilic 

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The formation of covalent substrate-catalyst adducts might occur, e.g., by single-step Lewis-acid-Lewis-base interaction or by multi-step reactions such as the formation of enamines from aldehydes and secondary amines. The catalysis of aldol reactions by formation of the donor enamine is a striking example of common mechanisms in enzymatic catalysis and organocatalysis - in class-I aldolases lysine provides the catalytically active amine group whereas typical organocatalysts for this purpose are secondary amines, the most simple being proline (Scheme 2.2). 

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