Catalytic processes enzymes

The small molecules that assist in the catalytic processes enzymes promote and that are not themselves proteins are called coenzymes. Again, it will be recalled that these molecules are used to help consummate the reactions between substrates. So, for example, the coenzyme pyridoxal (vitamin Bg, Table 12.2) can (among other functions already discussed in Chapter 11) be utilized by a transaminase enzyme to help move a nitrogen from an amino acid (via initial reaction at an active-site lysine in the active site of the enzyme) to the a-carbonyl of an a-ketocarboxylic acid and vice versa (the process is called transamination). The pyridoxal (Table 12.2) has served as a catalytic nitrogen carrier. In some cases where pyridoxal (vitamin Bg) is used as a coenzyme, it is altered in the process. Thus, for example, in amino acid decarboxylation, pyridoxamine (HC=0 replaced by H2CNH2) can result and an additional step is required to reconvert it to pyridoxal. Indeed, such changes are common among coenzymes. 

A catalyst is defined as a substance that influences the rate or the direction of a chemical reaction without being consumed. Homogeneous catalytic processes are where the catalyst is dissolved in a liquid reaction medium. The varieties of chemical species that may act as homogeneous catalysts include anions, cations, neutral species, enzymes, and association complexes. In acid-base catalysis, one step in the reaction mechanism consists of a proton transfer between the catalyst and the substrate. The protonated reactant species or intermediate further reacts with either another species in the solution or by a decomposition process. Table 1-1 shows typical reactions of an acid-base catalysis. An example of an acid-base catalysis in solution is hydrolysis of esters by acids. 

Catalytic processes frequently require more than a single chemical function, and these bifunctional or polyfunctional materials innst be prepared in away to assure effective communication among the various constitnents. For example, naphtha reforming requires both an acidic function for isomerization and alkylation and a hydrogenation function for aromati-zation and saturation. The acidic function is often a promoted porous metal oxide (e.g., alumina) with a noble metal (e.g., platinum) deposited on its surface to provide the hydrogenation sites. To avoid separation problems, it is not unusual to attach homogeneous catalysts and even enzymes to solid surfaces for use in flow reactors. Although this technique works well in some environmental catalytic systems, such attachment sometimes modifies the catalytic specifici-... 

Water molecules or anions close to the active sites in the protease enzymes, mentioned above, may not be considered circumstantial, but may effectively contribute to the removal of the surplus proton from the imidazolium cation before the actual catalytic event. They could serve well to create the initial ion/neutral form of the Aspl02-His57 couple which is important for the initial step of the catalytic process in most discussions 11611 .13i. such a proton removal may be caused by the productive binding of a true substrate (or inhibitor) of the enzyme to the neighboring recognition clefts of the active site. 

Homogeneous catalytic processes are those in which the catalyst is dissolved in a liquid reaction medium. There are a variety of chemical species that may act as homogeneous catalysts (e.g., anions, cations, neutral species, association complexes, and enzymes). All such reactions appear to involve a chemical interaction between the catalyst and the substrate (the substance undergoing reaction). The bulk of the material in this section will focus on acid-base and enzyme catalysis. Students interested in learning more about these subjects and other aspects of homogeneous catalysis should consult appropriate texts (11-12, 16-29) or the original literature. 

Enzymes are protein molecules that possess exceptional catalytic properties. They are essential to plant and animal life processes. Enzymes are remarkable catalysts in at least three respects activity, specificity, and versatility. 

Rhin(bpy)3]3+ and its derivatives are able to reduce selectively NAD+ to 1,4-NADH in aqueous buffer.48-50 It is likely that a rhodium-hydride intermediate, e.g., [Rhni(bpy)2(H20)(H)]2+, acts as a hydride transfer agent in this catalytic process. This system has been coupled internally to the enzymatic reduction of carbonyl compounds using an alcohol dehydrogenase (HLADH) as an NADH-dependent enzyme (Scheme 4). The [Rhin(bpy)3]3+ derivative containing 2,2 -bipyridine-5-sulfonic acid as ligand gave the best results in terms of turnover number (46 turnovers for the metal catalyst, 101 for the cofactor), but was handicapped by slow reaction kinetics, with a maximum of five turnovers per day.50... 

It has been said above that cyt c was one of the most important and extensively studied electron-transfer proteins with active heme centers. Thus, cyt c was widely used in enzyme-based biosensors and to study the mechanism of the catalytic process between redox enzyme and substrate. 

Although not all facets of the reactions in which complexes function as catalysts are fully understood, some of the processes are formulated in terms of a sequence of steps that represent well-known reactions. The actual process may not be identical with the collection of proposed steps, but the steps represent chemistry that is well understood. It is interesting to note that developing kinetic models for reactions of substances that are adsorbed on the surface of a solid catalyst leads to rate laws that have exactly the same form as those that describe reactions of substrates bound to enzymes. In a very general way, some of the catalytic processes involving coordination compounds require the reactant(s) to be bound to the metal by coordinate bonds, so there is some similarity in kinetic behavior of all of these processes. Before the catalytic processes are considered, we will describe some of the types of reactions that constitute the individual steps of the reaction sequences. 

A detailed understanding of the mechanism of DHFR at the molecular level enabled the identification of critical interactions between the substrate and the enzyme during the catalytic process. This information is ultimately expected to be useful in the design of potent and specific inhibitors of DHFR. 

In the foregoing sections, the rate-enhancing effect of alkylammonium micelles has been extensively described. Similar effects can be expected for bilayer membranes of dialkylammonium salts. In addition, specific catalytic processes may be realized in this new system by taking advantage of the peculiar membrane structure. For example, catalyst molecules which are anisotropically bound to the membrane may act in very specific manners, and the liquid-crystalline nature of the bilayer membrane should provide unique microenvironments for catalysis. These are particularly interesting in relation to the mode of action of membrane-bound enzymes. 

In pressure experiments one has to be very careful about the enzyme concentration. Usually, this concentration must be held within a narrow interval. If [E]o is too high, the catalytic process may proceed too rapidly to give linear rate curves. The substrate is quickly destroyed and the rate falls off at an early stage in the experiment, perhaps too early to get reliable measurements. It takes some time to put the pressure equipment together, and the measurement should last 5-10 times this dead-time. If the enzyme concentration is too low, the slope of the rate curve may be so small that it falls to practically zero while pressure is applied. 

Pressure may cause several changes in enzymes, as well as some changes which are not directly associated with the catalytic process. These changes may include conformational changes and subunit dissociation-association processes. Pressures above 4000 bar may induce conformational changes to such an extent that the enzyme in effect becomes irreversibly denatured. These are dealt with in the next section. In this section we will deal with lower pressures and reversible processes, namely, interactions between subunits in quaternary structures. For most multimeric enzymes, the maintenance of... 

In a pressure study involving a multimeric enzyme, it will in general not be possible to decide how much of the effect is due to direct influence of pressure on the catalytic process and how much of it is due to indirect influence through subunit dissociation and accompanying deactivation. Generally, a self-association reaction may be expressed in either of two equivalent forms ... 

One of the important consequences of studying catalysis by mutant enzymes in comparison with wild-type enzymes is the possibility of identifying residues involved in catalysis that are not apparent from crystal structure determinations. This has been usefully applied (Fersht et al., 1988) to the tyrosine activation step in tyrosine tRNA synthetase (47) and (49). The residues Lys-82, Arg-86, Lys-230 and Lys-233 were replaced by alanine. Each mutation was studied in turn, and comparison with the wild-type enzyme revealed that each mutant was substantially less effective in catalysing formation of tyrosyl adenylate. Kinetic studies showed that these residues interact with the transition state for formation of tyrosyl adenylate and pyrophosphate from tyrosine and ATP and have relatively minor effects on the binding of tyrosine and tyrosyl adenylate. However, the crystal structures of the tyrosine-enzyme complex (Brick and Blow, 1987) and tyrosyl adenylate complex (Rubin and Blow, 1981) show that the residues Lys-82 and Arg-86 are on one side of the substrate-binding site and Lys-230 and Lys-233 are on the opposite side. It would be concluded from the crystal structures that not all four residues could be simultaneously involved in the catalytic process. Movement of one pair of residues close to the substrate moves the other pair of residues away. It is therefore concluded from the kinetic effects observed for the mutants that, in the wild-type enzyme, formation of the transition state for the reaction involves a conformational change to a structure which differs from the enzyme structure in the complex with tyrosine or tyrosine adenylate. The induced fit to the transition-state structure must allow interaction with all four residues simultaneously. 

The catalysis takes place in a specific region of the enzyme named the active site or catalytic cavity. This active site involves those amino acid residues (i.e., side chains) directly implicated in the mode of binding and the specificity of the substrate, as well as in the catalytic process itself. 

So far the debate is still hot, but it can be stated that most likely a protein activity is required for palmitoylation. However, it still has to be elucidated if this protein activity is required in a chaperone-like way that is not involved in the catalytic process or if the palmitate transfer is enzyme mediated. ... 

In MET, a low-molecular-weight, redox-active species, referred to as a mediator, is introduced to shuttle electrons between the enzyme active site and the electrode.In this case, the enzyme catalyzes the oxidation or reduction of the redox mediator. The reverse transformation (regeneration) of the mediator occurs on the electrode surface. The major characteristics of mediator-assisted electron transfer are that (i) the mediator acts as a cosubstrate for the enzymatic reaction and (ii) the electrochemical transformation of the mediator on the electrode has to be reversible. In these systems, the catalytic process involves enzymatic transformations of both the first substrate (fuel or oxidant) and the second substrate (mediator). The mediator is regenerated at the electrode surface, preferably at low overvoltage. The enzymatic reaction and the electrode reaction can be considered as separate yet coupled. 

Despite the diverse chemical nature of side groups of amino acids in the active site, compounds other than amino acids may be co-opted to provide additional reactive groups. Such compounds play a part in the catalytic mechanism, so that they remain unchanged at the end of the catalytic process. Those that remain bound to the enzyme, even when catalysis is not occurring, are known as prosthetic groups (Figure 3.4). Compounds that have a similar... 

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