Catalysis by enzymes

Essentially all reactions that occur in biological systems are reactions of organic compounds. These reactions almost always require a catalyst. Most biological catalysts are proteins called enzymes. Each biological reaction is catalyzed by a different enzyme. 

The reactant of an enzyme-catalyzed reaction is called a substrate. The enzyme binds the substrate in a pocket of the enzyme called the active site. All the bond-making and bond-breaking steps of the reaction occur while the substrate is bound to the active site. 

Unlike nonbiological catalysts, enzymes are specific for the substrate whose reaction they catalyze (Section 6.17). All enzymes, however, do not have the same degree of specificity. Some are specific for a single compound and will not tolerate even the shghtest variation in stmcture, whereas some catalyze the reaction of a family of compounds with related stmctures. The specificity of an enzyme for its substrate is an exan le of the phenomenon known as molecular recognition—the ability of one molecule to recognize another molecule as a result of intermolecular interactions (see the introduction to Chapter 21). 

The specificity of an enzyme for its substrate results from the particular amino acid side chains that reside at the active site (Section 22.1). The side chains bind the substrate to the active site using hydrogen bonds, van der Waals forces, and dipole-dipole interactions— the same intermolecular interactions that hold molecules together (Section 3.9). A more in-depth discussion of the interaction between the enzyme and the substrate can be found in Section 23.8. 

The side chains at the active site of the enzyme hold the substrate in the precise position necessary for reaction. 

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O2, Mn, pH, and solid concentrations indicates that the character of the solid is important partly because some surfaces bind Mn " more strongly and partly because they facilitate the electron transfer differently. Catalysis by enzymes is clearly the most effective oxidation enhancing process as indicated by the laboratory studies with spores and material from the O2/H2S interface of Saanich Inlet. Microbial catalysis in this environment reduces the oxidation lifetime of Mn to about one day. This example illustrates... 

Catalysis by enzymes that proceeds via a unique reaction mechanism typically occurs when the transition state intermediate forms a covalent bond with the enzyme (covalent catalysis). The catalytic mechanism of the serine protease chymotrypsin (Figure 7-7) illustrates how an enzyme utilizes covalent catalysis to provide a unique reaction pathway. 

Biocatalysis refers to catalysis by enzymes. The enzyme may be introduced into the reaction in a purified isolated form or as a whole-cell micro-organism. Enzymes are highly complex proteins, typically made up of 100 to 400 amino acid units. The catalytic properties of an enzyme depend on the actual sequence of amino acids, which also determines its three-dimensional structure. In this respect the location of cysteine groups is particularly important since these form stable disulfide linkages, which hold the structure in place. This three-dimensional structure, whilst not directly involved in the catalysis, plays an important role by holding the active site or sites on the enzyme in the correct orientation to act as a catalyst. Some important aspects of enzyme catalysis, relevant to green chemistry, are summarized in Table 4.3. 

To date, most theozymes have been used to quantitate the effects of noncovalent interactions on catalysis by enzymes and catalytic antibodies (abzy-mes).131 Theozymes have provided insight into the... 

A second use of this type of analysis has been presented by Stewart and Benkovic (1995). They showed that the observed rate accelerations for some 60 antibody-catalysed processes can be predicted from the ratio of equilibrium binding constants to the catalytic antibodies for the reaction substrate, Km, and for the TSA used to raise the antibody, Kt. In particular, this approach supports a rationalization of product selectivity shown by many antibody catalysts for disfavoured reactions (Section 6) and predictions of the extent of rate accelerations that may be ultimately achieved by abzymes. They also used the analysis to highlight some differences between mechanism of catalysis by enzymes and abzymes (Stewart and Benkovic, 1995). It is interesting to note that the data plotted (Fig. 17) show a high degree of scatter with a correlation coefficient for the linear fit of only 0.6 and with a slope of 0.46, very different from the theoretical slope of unity. Perhaps of greatest significance are the... 

R. L. Schowen, Structural and Energetic Aspects of Proteolytic Catalysis by Enzymes Charge-Relay Catalysis in the Function of Serine Proteases , in Mechanistic Principles of Enzyme Activity , Eds. J. F. Liebman, A. Greenberg, VCH, New York, 1988, p. 119 — 165. 

Schowen, R.L. (1988). Structural and energetic aspects of protolytic catalysis by enzymes charge-relay catalysis in the function of serine proteases. In Mechanistic Principles of Enzyme Activity, Liebman, J.P. and Greenberg, A. (eds), pp. 119-168. VCH Publishers, New York... 

Proton transfers are particularly common. This acid-base catalysis by enzymes is much more effective than the exchange of protons between acids and bases in solution. In many cases, chemical groups are temporarily bound covalently to the amino acid residues of the enzyme or to coenzymes during the catalytic cycle. This effect is referred to as covalent catalysis (see the transaminases, for example p. 178). The principles of enzyme catalysis sketched out here are discussed in greater detail on p. 100 using the example of lactate dehydrogenase. 

At one extreme diffusivity may be so low that chemical reaction takes place only at suface active sites. In that case p is equal to the fraction of active sites on the surface of the catalyst. Such a polymer-supported phase transfer catalyst would have extremely low activity. At the other extreme when diffusion is much faster than chemical reaction p = 1. In that case the observed reaction rate equals the intrinsic reaction rate. Between the extremes a combination of intraparticle diffusion rates and intrinsic rates controls the observed reaction rates as shown in Fig. 2, which profiles the reactant concentration as a function of distance from the center of a spherical catalyst particle located at the right axis, When both diffusion and intrinsic reactivity control overall reaction rates, there is a gradient of reactant concentration from CAS at the surface, to a lower concentration at the center of the particle. The reactant is consumed as it diffuses into the particle. With diffusional limitations the active sites nearest the surface have the highest turnover numbers. The overall process of simultaneous diffusion and chemical reaction in a spherical particle has been described mathematically for the cases of ion exchange catalysis,63 65) and catalysis by enzymes immobilized in gels 66-67). Many experimental parameters influence the balance between intraparticle diffusional and intrinsic reactivity control of reaction rates with polymer-supported phase transfer catalysts, as shown in Fig. 1. 

Enzymes represent a special case of protein function. Enzymes bind and chemically transform other molecules—they catalyze reactions. The molecules acted upon by enzymes are called reaction substrates rather than ligands, and the ligand-binding site is called the catalytic site or active site. In this chapter we emphasize the noncatalytic functions of proteins. In Chapter 6 we consider catalysis by enzymes, a central topic in biochemistry. You will see that the themes of this chapter—binding, specificity, and conformational change—are continued in the next chapter, with the added element of proteins acting as reactants in chemical transformations. 

The quantitative study of catalysis by enzymes, i.e., the study of enzyme kinetics, is a highly developed branch of biochemistry. It is one of our most important means of learning about the mechanisms of catalysis at the active sites of enzymes.1 13a By determining rate constants k under a variety of conditions we can learn just how fast an enzyme can act, how tightly it binds its substrates to form the enzyme-substrate (ES) complexes essential to catalysis, how specific it is with respect to substrate structure, and how it is affected by compounds that inhibit or activate the catalysis. 

Spector, L. B. (1982) Covalent Catalysis by Enzymes, Springer-Verlag, New York... 

This reaction is quite special in that it is an aldol-type addition in which a thioester is the donor (nucleophile) and a keto acid is the acceptor (electrophile). From the discussion in Section 18-8E, you will see that reactions of this kind involving an ester as the donor and an aldehyde or ketone as the acceptor can be achieved in the laboratory only under rather special conditions. For the thioester to function as a nucleophile at the a carbon under the restraints imposed by having the reaction occur at the physiological pH, the catalyzing enzyme almost certainly must promote formation of the enol form of the thioester. The enol then could add to the ketone carbonyl with the assistance of a basic group on the enzyme. This kind of catalysis by enzymes is discussed in Section 25-9C. 

The mechanisms outlined in equations 3-6 illustrate a basic feature Nucleophilic catalysis by enzymes involves the formation of an intermediate state in which the substrate... 

The catalysis of ester hydrolysis by other groups within the ester molecule (intramolecular catalysis) has been extensively studied (17,18). These reactions are important because they simulate catalysis by enzymes. Intramolecular catalysis of esters has been used as a model in drug discovery efforts... 

I. V. Berezin, and K. Martinek, Catalysis by enzymes entrapped into hydrated surfactant aggregates having lamellar or cylindrical (hexagonal) or ball-shaped (cubic) structure in organic solvents,... 

Kemp elimination was used as a probe of catalytic efficiency in antibodies, in non-specific catalysis by other proteins, and in catalysis by enzymes. Several simple reactions were found to be catalyzed by the serum albumins with Michaelis-Menten kinetics and could be shown to involve substrate binding and catalysis by local functional groups (Kirby, 2000). Known binding sites on the protein surface were found to be involved. In fact, formal general base catalysis seems to contribute only modestly to the efficiency of both the antibody and the non-specific albumin system, whereas antibody catalysis seems to be boosted by a non-specific medium effect. 

Catalysis by enzymes the biological ammonia synthesis. Top. Catal., 37, 55. 

Hinnemann B. Norskov J. K. Catalysis by enzymes The biological ammonia synthesis. 

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