Catalytic enzyme molecule

The turnover number of an enzyme, is a measure of its maximal catalytic activity, is defined as the number of substrate molecules converted into product per enzyme molecule per unit time when the enzyme is saturated with substrate. The turnover number is also referred to as the molecular activity of the enzyme. For the simple Michaelis-Menten reaction (14.9) under conditions of initial velocity measurements, Provided the concentration of... 

The catalytically active enzyme substrate complex is an interactive structure in which the enzyme causes the substrate to adopt a form that mimics the transition-state intermediate of the reaction. Thus, a poor substrate would be one that was less effective in directing the formation of an optimally active enzyme transition-state intermediate conformation. This active conformation of the enzyme molecule is thought to be relatively unstable in the absence of substrate, and free enzyme thus reverts to a conformationally different state. 

The catalytic capacity of the rate-fimiting reaction in a metabolic pathway is the product of the concentration of enzyme molecules and their intrinsic catalytic efficiency. It therefore follows that catalytic capacity can be... 

An enzyme consists of a polypeptide chain with a particular spatial configuration specific to that sequence of amino acids. The molecule twists and turns, forming structural features that are catalytically active, these being known as active sites. There may be more than one active site per enzyme molecule. Sometimes an auxiliary catalyst, known as a coenzyme, is also needed. Apparently, only the relevant active site of the enzyme comes into contact with the substrate and is directly involved in the catalysed reaction. The active site consists of only a few amino acid residues. These are not necessarily adjacent to one another in the peptide chain but may be brought into proximity by the characteristic folding of the enzyme structure. The active site may also include the coenzyme. The remainder of the enzyme molecule fulfils the essential function of holding the components of the active site in their appropriate relative positions and orientation. 

With the exception of a small group of catalytic RNA molecules, all the enzymes are proteins. Their molecular weights, as for other proteins, range from about 12,000 to over 1 million Dalton. 

Magnesium has its role intimately intertwined with phosphate in many phosphoryl transfer reactions, as Mg-ATP in muscle contraction, in the stabilization of nucleic acid structures as well as in the catalytic activity of ribozymes (catalytic RNA molecules). It also serves as a structural component of enzymes, and is found as the metal centre in chlorophylls, which absorbs light energy in photosynthesis. 

The interaction within the active site can be either in the form of covalent binding or in the form of quasi-irreversible (tight but slowly reversible) binding, and it can involve the protein residues, the porphyrin moiety or the catalytic center (heme iron) [8]. CYP inactivation follows a stoichiometry of one substrate molecule per enzyme molecule inactivated. To measure the stoichiometry of the inactivation, it is necessary to trap all molecules that are not specifically bound to the active site, by using an appropriate scavenger, normally GSH. 

We should also remember that not all of the states that we see when freezing the enzyme (Section 7.4) are necessarily part of the mechanism. The most stable enzyme molecule is a dead one, so we must be aware that some of the spectroscopic signals represent damaged molecules. In the [NiFe] hydrogenases, the NiA and NiB states probably are not involved in the catalytic cycle, because they react slowly, if at all, with H2. In the mechanism shown in Fig. 8.3, it is assumed that the relevant active states are NiSR, NiA and NiR. 

Although most catalysts in living systems are enzymes, they are not the only ones. Ribozymes are catalytic RNA molecules. These also play important roles in the metabolism of living organisms, including specifically the synthesis of proteins. 

Specific chemical modifications produce changes in the properties of the enzyme. When single modification of one group results in inactivation but does not change the conformation of the enzyme molecule, this indicates that the group is essential for the catalytic activity. In other cases, modification of the side chains in the enzymes may cause specific, and sometimes drastic changes in the catalytic properties and in thermal stability. 

Metal-dependent enzymes have been divided into two groups,80-83 the metalloenzymes and the enzyme-metal-ion complexes. Metalloenzymes are those that contain one or more functional metal atoms per enzyme molecule. The metal is firmly bound to the protein, and the enzyme can be purified without any loss in activity. The content of functional metal in the preparation approaches a limiting value during purification. Enzyme-metal-ion complexes are more readily dissociable than metalloenzymes. It is necessary to add the functional, metal ion during or after purification, in order to maintain or restore full catalytic activity. 

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