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In chemistry, a reaction coordinate [1] is an abstract one-dimensional coordinate chosen to represent progress along a reaction pathway. Where possible it is usually a geometric parameter that changes during the conversion of one or more molecular entities, such as bond length or bond angle. For example, in the homolytic dissociation of ...
A catalytic triad is a set of three coordinated amino acid residues that can be found in the active site of some enzymes. [1] [2] Catalytic triads are most commonly found in hydrolase and transferase enzymes (e.g. proteases, amidases, esterases, acylases, lipases and β-lactamases).
The active site consists of amino acid residues that form temporary bonds with the substrate, the binding site, and residues that catalyse a reaction of that substrate, the catalytic site. Although the active site occupies only ~10–20% of the volume of an enzyme, [ 1 ] : 19 it is the most important part as it directly catalyzes the chemical ...
An illustrative example is the effect of catalysts to speed the decomposition of hydrogen peroxide into water and oxygen: . 2 H 2 O 2 → 2 H 2 O + O 2. This reaction proceeds because the reaction products are more stable than the starting compound, but this decomposition is so slow that hydrogen peroxide solutions are commercially available.
This is also known as kinetic perfection or catalytic perfection. Since the rate of catalysis of such enzymes is set by the diffusion-controlled reaction, it therefore represents an intrinsic, physical constraint on evolution (a maximum peak height in the fitness landscape). Diffusion limited perfect enzymes are very rare.
Enzyme catalysis of chemical reactions occur with high selectivity and rate. The substrate is activated in a small part of the enzyme 's macromolecule called the active site . There, the binding of a substrate close to functional groups in the enzyme causes catalysis by so-called proximity effects.
While a number of inhibitory strategies exist such as high temperature treatments(70-90 °C) to eliminate catechol oxidase catalytic activity, [6] a popular strategy is decreasing the pH with citric acid. Catechol oxidase is more catalytically active in the pH 4-8 range due to coordination of the histidine residues to the catalytic copper centers.
Enzymes are evolved to catalyze a particular reaction on a particular substrate with high catalytic efficiency (k cat /K M, cf.Michaelis–Menten kinetics).However, in addition to this main activity, they possess other activities that are generally several orders of magnitude lower, and that are not a result of evolutionary selection and therefore do not partake in the physiology of the organism.