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How are enzymes suited to be catalysts?
There is a huge variety of enzymes in living organisms. Enzymes function as biological catalysts; almost all are proteins; they catalyse substrates in many different ways; and they speed up reactions enormously. For example, orotidine monophosphate decarboxylase increases the rate of reaction by a factor of 1.4x10^17. The power of enzyme catalysis is so important that life could not exist without it; many essential reactions that must be carried out in microseconds in the human body would take years if uncatalysed. The first way in which enzymes are suited to be catalysts is their selectiveness of substrate. Selectivity means each enzyme controls at most a few reactions; many catalysts only aid one reaction which gives the cell greater control over pathways carried out at any time. It results in fewer undesirable effects from enzymes catalysing the wrong reactions, and means a reaction can be initiated in response to one specific occurrence. Enzymes achieve specificity through their unique tertiary structures. Active sites, where catalysis occurs, are clefts or crevices on the protein which will only admit or catalyse select substrates. The reason for this is that firstly only molecules of a certain size will be able to enter the active site, and secondly the presence of an individual sequence of residues results in different conformations and arrays of functional groups to which a substrate must be complementary. Active sites bond with many weak non-covalent bonds to substrates to form an enzyme-substrate complex; these can be viewed using X-ray crystallography. The formation of complexes can also be detected by various means of spectroscopy, a striking example of which is that the enzyme tryptophan synthase changes in fluorescence intensity upon the consecutive addition of its substrates, serine and an indole derivative. The precise arrangement of functional groups, which can form a mixture of bonds such as ionic interactions, hydrogen bonds, disulfide bridges and hydrophobic interactions, determines what shape of substrate may, and how strongly it will, bind to the active site. These functional groups are also vital to the catalysis mechanism i.e. the formation of intermediates through reactions with the active site. This is demonstrated by the fact that some enzyme inhibitors - mechanism-based, or suicide, inhibitors - covalently modify an enzyme and render it inactive. An example is the inhibitor N,N-Dimethylpropargylamine, which upon oxidisation by the enzyme monoamine oxidase forms a covalent bond with MAO's flavin prosthetic group, meaning that no other substrates may enter MAO's active site to be catalysed. The importance of a complementary active site gives many enzymes a high degree of specificity. For example, thrombin will only cleave the peptide bond between the amino acids glycine and arginine in specific polypeptide sequences. Picture This is why there is a maximal rate in enzyme-catalysed reactions: the formation of ES complexes is the limiting factor in reaction velocity. However, ES Complexes speed up reaction rate in one or more of several ways. The chances of a collision and hence reaction between molecules in the aqueous environment of the cell may be very small, and greatly increased by substrates fixed onto proteins; even more so if they are fixed in complementary orientations as in a ternary complex. This strategic clamping of substrates by the enzyme is called entropy reduction, and can accelerate catalysis by many orders of magnitude, as seen in reaction rate differences between bimolecular reactions and reactions between two functional groups on the same molecule. In the latter, there is a much higher rate of reaction as the reactant groups are closer together and more likely to collide. Enzymes also increase the proportion of molecules attaining product by making the intermediate more energetically favourable. At its most thermodynamically unfavourable state, a reactant may decompose to
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