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MIT Biology Hypertextbook: Enzyme Mechanisms

2 Enzyme Mechanisms

Most biological enzymes are proteins . They perform the chemical reactions in cells. Not all proteins are enzymes, but most enzymes are proteins (the exception is catalytic RNA). A catalyst is a molecule which increases the rate of a reaction but is not the substrate or product of that reaction. A substrate is a molecule upon which an enzyme acts to yield a product.

A ------>  B	
The free energy of this reaction is not changed by the presence of the enzyme, but, for a favored reaction (where delta G is negative), the enzyme can speed it up.
Graph the free energy against the reaction progress:

Delta G* is the activation energy
Delta G is negative overall for forward reaction

Enzymes Catalyze Reactions

Enzymes have affinity for the substrate in a transition state. They get the substrate into the right conformation which will lead to the breakdown into products.
Alternatively, for a reaction such as the one shown below, the enzyme may increase the local concentration of the two substrates A and B, driving the reaction forward:

A  +  B  --->  C  
The part of the enzyme that does the work is called the active site . The residues in this site are in the right 3D conformation to accomplish the enzyme's work.


Enzymes are named in a variety of ways. Several of the general rules of enzyme nomenclature are listed below.

  1. Named for its substrate: substrate-ase
    ex. lactase catalyzes
    lactose --> glucose + galactose
    If you are lactose intolerant, you can buy lactase in a powdered form to help you digest the food. (An enzyme with this function, produced by the bacterium E. coli is called b-galactosidase.)
  2. Named for its action
    ex. Deoxyribonuclease, or DNase catalyzes
    DNA ---> dNMP nucleotides
    the enzyme might be an endonuclease or an exonuclease

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