Enzymes in biochemical reactions

Catalysis A process by which the rate of a chemical reaction is increased by a substance (namely enzymes in biochemical reactions) that remains chemically unchanged at the end of the reaction. 

Enzymes are proteins that act as biological catalysts. They facilitate chemical modification of substrate molecules by virtue of their specific binding properties, which arise from particular combinations of functional groups in the constituent amino acids at the so-called active site. In many cases, an essential cofactor, e.g. NAD+, PLP, or TPP, may also be bound to participate in the transformation. The involvement of enzymes in biochemical reactions has been a major theme throughout this book. The ability of enzymes to carry out quite complex chemical reactions, rapidly, at room temperature, and under essentially neutral conditions is viewed with envy by synthetic chemists, who are making rapid progress in harnessing this ability for their own uses. Several enzymes are currently of importance commercially, or for medical use, and... 

Reactions can be catalyzed using the metabolic pathways in microorganisms or the direct use of enzymes in biochemical reactors. The use of enzymes directly can have... 

Bioorganic components in soil include those organic molecules that participate in biochemical reactions, initiate reactions, inhibit the action of other biochemical, or act as antibiotics. Bioorganic chemistry also uses synthesized molecules to study biological processes such as enzyme activity. Often these studies are undertaken to develop a mechanism for the reactions of interest. Bioorganic molecules will be present either as components of the synthesis chain or as part of the degradation products. Whenever a cell lyses, its compounds will be released into the soil solution. 

Figure 6. Enzymes act as recycling catalysts in biochemical reactions. A substrate molecule binds (reversible) to the active site of an enzyme, forming an enzyme substrate complex. Upon binding, a series of conformational changes is induced that strengthens the binding (corresponding to the induced fit model of Koshland [148]) and leads to the formation of an enzyme product complex. To complete the cycle, the product is released, allowing the enzyme to bind further substrate molecules. (Adapted from Ref. 1). See color insert.

Different from conventional chemical kinetics, the rates in biochemical reactions networks are usually saturable hyperbolic functions. For an increasing substrate concentration, the rate increases only up to a maximal rate Vm, determined by the turnover number fccat = k2 and the total amount of enzyme Ej. The turnover number ca( measures the number of catalytic events per seconds per enzyme, which can be more than 1000 substrate molecules per second for a large number of enzymes. The constant Km is a measure of the affinity of the enzyme for the substrate, and corresponds to the concentration of S at which the reaction rate equals half the maximal rate. For S most active sites are not occupied. For S >> Km, there is an excess of substrate, that is, the active sites of the enzymes are saturated with substrate. The ratio kc.AJ Km is a measure for the efficiency of an enzyme. In the extreme case, almost every collision between substrate and enzyme leads to product formation (low Km, high fccat). In this case the enzyme is limited by diffusion only, with an upper limit of cat /Km 108 — 109M. v 1. The ratio kc.MJKm can be used to test the rapid... 

Besides the enzyme, the superoxide ion can also be an electron donor. The ion arises as a result of detoxication of xenobiotics (xenobiotics are outsiders, which are involved in the chain of metabolism). Xenobiotics yield anion-radicals by the neutralizing influence of redox proteins. Oxygen (inhaled with air) takes an unpaired electron off from a part of these anion radicals and forms the superoxide ion. The superoxide ion plays its own active role in biochemical reactions. 

So the idea, the concept of enzyme action as a general principle in biochemical reactions was that of Berthelot in the 1850 s, as to the priority. The experimental verification however was Buchner s work, and he earned the merit for it. 

While some enzymes, such as sucrase, split substrate molecules apart, others join substrate molecules together. In all cases, enzymes are so efficient that a single enzyme molecule may act on thousands or even millions of substrate molecules per second. Without enzymes, most biochemical reactions would not occur at rates fast enough to support life. 

The most exciting applications of esr are in the study of radical intermediates in organic reactions. Considerable use has been made of the technique in biochemical reactions and it has been shown that radicals are generated and decay in oxidations brought about by enzymes. Radicals also have been detected by esr measurements in algae that fix carbon dioxide in photosynthesis. The character of the radicals formed has been found to depend upon the wavelength of the light supplied for photosynthesis. 

Traditionally when considering catalysis in biological systems primary emphasis has been placed on the enzymes—very high-molecular-weight proteins. However, recently there has been growing interest in the role of the transition metals, particularly as found in coenzymes such as BI2, in biochemical reactions. 

Eight B vitamins are important in poultry nutrition. In general they participate in biochemical reactions as enzyme cofactors that mostly affect the transfer of energy. 

Consider enzymes. Enzymes are proteins that act as catalysts in biochemical reactions. They are able to do this because enzyme molecules contain one or more active sites, regions with a characteristic shape designed to fit some particular molecule (the substrate) on which the enzyme operates. Suppose the function of the enzyme is to break apart a large molecule. That reaction is made possible when the large molecule "docks in the active site, prompting some chemical mechanism in or around the active site that cleaves it. If the function of the enzyme is to join two small molecules, the reaction takes place when both small molecules take their places in the active site, which generates chemical bonds between the two molecules. 

When you shake a can of soda and open the lid, usually you get soaked by a spray of liquid. The spray is powered by the sudden release of carbon dioxide gas that had been dissolved in the liquid. Some carbon dioxide is also dissolved in cellular fluid (although an animal usually doesn t fizz when shaken) and can be used in biochemical reactions. That s good, because the next step in the synthesis of AMP needs carbon dioxide. In the reaction the gas molecule (actually its water-logged counterpart, bicarbonate) is placed by Enzyme VII onto carbon 3 to make Intermediate VIII. An energy pellet of ATP powers this step.4... 

Biotin is an enzyme cofactor that activates and transports CO2 for use as a electrophile in biochemical reactions. 

When an enzyme-catalyzed biochemical reaction operating in an isothermal system is in a non-equilibrium steady state, energy is continuously dissipated in the form of heat. The quantity J AG is the rate of heat dissipation per unit time. The inequality of Equation (4.13) means that the enzyme can extract energy from the system and dissipate heat and that an enzyme cannot convert heat into chemical energy. This fact is a statement of the second law of thermodynamics, articulated by William Thompson (who was later given the honorific title Lord Kelvin), which states that with only a single temperature bath T, one may convert chemical work to heat, but not vice versa. 

Another motif recurs in this activation reaction. The enzyme-hound acyl-adenylate intermediate is not unique to the synthesis of acyl CoA. Acyl adenylates are frequently formed when carboxyl groups are activated in biochemical reactions. Amino acids are activated for protein synthesis hy a similar mechanism (Section 29.2.1). although the enzymes that catalyze this process are not homologous to acyl CoA synthetase. Thus, activation by adenylation recurs in part because of convergent evolution. 

---