Biochemical reactions - examples

In biological systems molecular assemblies connected by non-covalent interactions are as common as biopolymers. Examples arc protein and DNA helices, enzyme-substrate and multienzyme complexes, bilayer lipid membranes (BLMs), and aggregates of biopolymers forming various aqueous gels, e.g, the eye lens. About 50% of the organic substances in humans are accounted for by the membrane structures of cells, which constitute the medium for the vast majority of biochemical reactions. Evidently organic synthesis should also develop tools to mimic the Structure and propertiesof biopolymer, biomembrane, and gel structures in aqueous media. 

In most biochemical reactions the pH of the medium is close to 7 At this pH car boxylic acids are nearly completely converted to their conjugate bases Thus it is common practice m biological chemistry to specify the derived carboxylate anion rather than the carboxylic acid itself For example we say that glycolysis leads to lactate by way of pyruvate... 

Among the biochemical reactions that ammo acids undergo is decarboxylation to amines Decarboxylation of histidine for example gives histamine a powerful vasodila tor normally present m tissue and formed m excessive amounts under conditions of trau matic shock... 

Enzyme-Catalyzed Reactions Enzymes are highly specific catalysts for biochemical reactions, with each enzyme showing a selectivity for a single reactant, or substrate. For example, acetylcholinesterase is an enzyme that catalyzes the decomposition of the neurotransmitter acetylcholine to choline and acetic acid. Many enzyme-substrate reactions follow a simple mechanism consisting of the initial formation of an enzyme-substrate complex, ES, which subsequently decomposes to form product, releasing the enzyme to react again. 

Lethal Synthesis. This is a process in which the toxic substance has a close stmctural similarity to normal substrates in biochemical reactions. As a result, the material may be incorporated into the biochemical pathway and metabolized to an abnormal and toxic product. A classic example is... 

Mercerized cellulose fibers have improved luster and do not shrink further. One of the main reasons for mercerizing textiles is to improve their receptivity to dyes. This improvement may result more from the dismption of the crystalline regions rather than the partial conversion to a new crystal stmcture. A good example of the fundamental importance of the particular crystal form is the difference in rate of digestion by bacteria. Bacteria from cattle mmen rapidly digest Cellulose I but degrade Cellulose II very slowly (69). Thus aHomorphic form can be an important factor in biochemical reactions of cellulose as well as in some conventional chemical reactions. 

Optically inactive starting materials can give optically active products only if they are treated with an optically active reagent or if the reaction is catalyzed by an optically active substance. The best examples are found in biochemical processes. Most biochemical reactions are catalyzed by enzymes. Enzymes are chiral and enantiomerically homogeneous they provide an asymmetric environment in which chemical reaction can take place. Ordinarily, enzyme-catalyzed reactions occur with such a high level of stereoselectivity that one enantiomer of a substance is formed exclusively even when the substrate is achiral. The enzyme ftimarase, for example, catalyzes hydration of the double bond of fumaric acid to malic acid in apples and other fruits. Only the S enantiomer of malic acid is formed in this reaction. 

Among the biochemical reactions that anino acids undergo is decarboxylation to fflnines. Decar boxylation of histidine, for example, gives histamine, a powerful vasodilator nonnally present in tissue and fonned in excessive fflnounts under conditions of traumatic shock. 

Most of the biochemical reactions that take place in the body, as well as many organic reactions in the laboratory, yield products with chirality centers. Fo example, acid-catalyzed addition of H2O to 1-butene in the laboratory yield 2-butanol, a chiral alcohol. What is the stereochemistry of this chiral product If a single enantiomer is formed, is it R or 5 If a mixture of enantiomers i formed, how much of each In fact, the 2-butanol produced is a racemic mix ture of R and S enantiomers. Let s see why. 

Elucidating the stereochemistry of reaction at prochirality centers is a powerful method for studying detailed mechanisms in biochemical reactions. As just one example, the conversion of citrate to (ds)-aconitate in the citric acid cycle has been shown to occur with loss of a pro-R hydrogen, implying that the reaction takes place by an anti elimination mechanism. That is, the OH and H groups leave from opposite sides of the molecule. 

In addition to effects on biochemical reactions, the inhibitors may influence the permeability of the various cellular membranes and through physical and chemical effects may alter the structure of other subcellular structures such as proteins, nucleic acid, and spindle fibers. Unfortunately, few definite examples can be listed. The action of colchicine and podophyllin in interfering with cell division is well known. The effect of various lactones (coumarin, parasorbic acid, and protoanemonin) on mitotic activity was discussed above. Disturbances to cytoplasmic and vacuolar structure, and the morphology of mitochondria imposed by protoanemonin, were also mentioned. Interference with protein configuration and loss of biological activity was attributed to incorporation of azetidine-2-carboxylic acid into mung bean protein in place of proline. 

A second theoretical inconsistency with a radical mechanism for the biochemical reaction was described by Finke. Although cleavage of the methyl-Co(II) bond is very efficient and rapid process, he argued that homolysis of methyl-Co does not occur in enzymes because reduction of CHs-Co requires too low a potential for biochemically relevant electron donors (<-1.0 V vs NHE) (195). For example, the mid-... 

Although the restrictions of constant T and P are stringent, they apply to many important chemical processes, including reactions that occur in the human body, which has a nearly constant temperature of 37 °C and nearly constant pressure of 1 bar. Any biochemical reaction that occurs in the body occurs under conditions in which the immediate surroundings are at constant T and P. Figure 14-16 shows three examples of systems at constant T and P. 

The energy for the fission of the covalent bond in organic contaminants is normally supplied thermally using thermodynamically accessible chemical or biochemical reactions, or by the introduction of catalysts to lower the activation energy of the reactions. There has been interest, however, in using electrical energy in a number of forms to carry out these reactions. A selection of processes for the destruction of contaminant is noted with some illustrative examples. 

There are situations where such a macroscopic description of reaction dynamics will break down. For instance, biochemical reactions in the cell may involve only small numbers of molecules of certain species that participate in the mechanism. An example is gene transcription where only tens of free... 

Once the product specifications have been fixed, some decisions need to be made regarding the reaction path. There are sometimes different paths to the same product. For example, suppose ethanol is to be manufactured. Ethylene could be used as a raw material and reacted with water to produce ethanol. An alternative would be to start with methanol as a raw material and react it with synthesis gas (a mixture of carbon monoxide and hydrogen) to produce the same product. These two paths employ chemical reactor technology. A third path could employ a biochemical reaction (or fermentation) that exploits the metabolic processes of microorganisms in a biochemical reactor. Ethanol could therefore also be manufactured by fermentation of a carbohydrate. 

For biochemical reactions, the performance of the reactor will normally be dictated by laboratory results, because of the difficulty of predicting such reactions theoretically6. There are likely to be constraints on the reactor performance dictated by the biochemical processes. For example, in the manufacture of ethanol using microorganisms, as the concentration of ethanol rises, the microorganisms multiply more slowly until at a concentration of around 12% it becomes toxic to the microorganisms. 

Initially, most theoretical methods calculated the properties of molecules in the gas phase as isolated species, but chemical reactions are most often carried out in solution. Biochemical reactions normally take place in water. Consequently, there is increasing interest in methods for including solvents in the calculations. In the simplest approach, solvents are treated as a continuum, whose average properties are included in the calculation. Explicit inclusion of solvent molecules in the calculation greatly expands the size of the problem, but newer approaches do this for at least those solvent molecules next to the dissolved species of interest. The detailed structures and properties of these solvent molecules affect their direct interaction with the dissolved species. Reactions at catalytic surfaces present an additional challenge, as the theoretical techniques must be able to handle the reactants and the atoms in the surface, as well as possible solvent species. The first concrete examples of computationally based rational catalyst design have begun to appear in publications and to have impact in industry. 

The stoichiometric matrix N consists of m rows, corresponding to m metabolic reactants, and r columns, corresponding to r biochemical reactions or transport processes (see Fig. 5 for an example). Within a metabolic network, the number of reactions (columns) is usually of the same order of magnitude as the number of metabolites (rows), typically with slightly more reactions than metabolites [138]. Due to conservation relationships, giving rise to linearly dependent rows in N, the stoichiometric matrix is usually not of full rank, but... 

One of the most distinguishing features of metabolic networks is that the flux through a biochemical reaction is controlled and regulated by a number of effectors other than its substrates and products. For example, as already discovered in the mid-1950s, the first enzyme in the pathway of isoleucine biosynthesis (threonine dehydratase) in E. coli is strongly inhibited by its end product, despite isoleucine having little structural resemblance to the substrate or product of the reaction [140,166,167]. Since then, a vast number of related... 

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