Enzymes and Coenzymes

Unlike many of the catalysts that chemists use in the laboratory, enzymes are usually specific in their action. Often, in fact, an enzyme will catalyze only a single reaction of a single compound, called the enzyme s substrate. For example, the enzyme amylase, found in the human digestive tract, catalyzes only the hydrolysis of starch to yield glucose. Cellulose and other polysaccharides are untouched by amylase. 

Different enzymes have different specificities. Some, such as amylase, are specific for a single substrate, but others operate on a range of substrates. Papain, for instance, a globular protein of 212 amino acids isolated from papaya fruit, catalyzes the hydrolysis of many kinds of peptide bonds. In fact, it s this ability to hydrolyze peptide bonds that makes papain useful as a meat tenderizer and a cleaner for contact lenses. 

Enzymes function through a pathway that involves initial formation of an enzyme-substrate complex E S, followed by a multistep chemical conversion of the enzyme-bound substrate into enzyme-bound product E P and final release of product from the complex. 

The overall rate constant for conversion of the E S complex to products E -I- P is called the turnover number because it represents the number of substrate molecules a single enzyme molecule turns over into product per unit time. A value of about 10 per second is typical. 

FIGURE 19.8 Energy diagrams for uncatalyzed (red) and enzyme-catalyzed (blue) processes. The enzyme makes available an alternative, lower-energy pathway. Rate enhancement is due to the ability of the enzyme to bind to the transition state for product formation, thereby lowering its energy. 

The chemical reactions that are observed in biosynthesis (or biogenesis) are essentially the same as those the synthetic organic chemist uses to produce materials in the reaction flask. The key difference between natural and synthetic chemistry, lies in the catalytic systems found in nature. The catalysts which drive biochemical reactions are known as enzymes. These are globular proteins, i.e. proteins that prefer to adopt globular shapes, rather than those that remain linear or form into sheets or helices. The role of enzymes is to make biochemical reactions faster and much more selective. 

Occasionally, enzymes require coenzymes, also known as co-factors, to take part in a reaction. For example, in a reduction or oxidation reaction, the coenzyme may provide the reducing or oxidising power to drive the reaction. The coenzyme is then recycled by being re-oxidised or re-reduced, as appropriate, in a subsequent cycle or even in a different enzyme system. There are three coenzymes that are particularly important in the biosynthesis of terpenoids and it is worth looking at them in a little more detail before we move on to the main topic. 

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Compared with the extensive application of NMR procedures, electron paramagnetic resonance (EPR) is used less frequently except for analysis of the state of metals in enzymes and coenzymes. There has, however, been increasing awareness of the role of radical-mediated reactions and some examples are used to illustrate its potential. 

Chistoserdova L, JA Vorholt, RK Thauer, ME Lidstrom (1998) Cl transfer enzymes and coenzymes linking methylotrophic bacteria and methanogenic archaea. Science 281 99-102. 

The microbes use two general strategies to synthesize ATP respiration and fermentation. A respiring microbe captures the energy released when electrons are transferred from a reduced species in the environment to an oxidized species (Fig. 18.1). The reduced species, the electron donor, sorbs to a complex of redox enzymes, or a series of such complexes, located in the cell membrane. The complex strips from the donor one or more electrons, which cascade through a series of enzymes and coenzymes that make up the electron transport chain to a terminal enzyme complex, also within the cell membrane. 

In accordance with the recommendation of the Commission of the International Union of Biochemistry [R. H. S. Thompson, Classification and nomenclature of enzymes and coenzymes, Nature 193, 1227 (1902)] the terms NAD and NADP have been used instead of DPN and TPN, except in Fig. 4. The generic term nicotinamide nucleotides is used with the same significance as pyridine nucleotides. 

C. Schelp, T. Scheper, F. Buckmann, and K. F. Reardon, Two fibre-optic sensors with confined enzymes and coenzymes Development and applications, Anal Chim Acta 255, 223-229 (1991). 

The next part presents the reactions involved in the interconversion of these compounds—the part of biochemistry that is commonly referred to as metabolism (pp. 88-195). The section starts with a discussion of the enzymes and coenzymes, and discusses the mechanisms of metabolic regulation and the so-called energy metabolism. After this, the central metabolic pathways are presented, once again arranged according to the class of metabolite (pp. 150-195). 

Bugg, T. (1997) An Introduction to Enzyme and CoEnzyme Chemistry, Blackwell, Oxford. 

Table 20 Some well-known enzymes and coenzymes active in alkaloid biogenesis...

Enzymes and Coenzymes Electrochemical behavior of bovine erythrocyte superoxide dismutase adsorbed on Hg electrode has been studied by Qian... 

Fluorescence determinations are important to analyze cysteine, guanidine, proteins, (LSD), steroids, a number of enzymes and coenzymes, and some vitamins, as well as several hundred more substances. A fluorometer can be used to verify conformational changes in multipartite operator recognition by. -repressor as explained in a journal article by Deb et al. (2000). Upon titration with single operators site, the tryptophan fluorescence quenches to different degrees, suggesting different conformations of the DNA-protein complexes. 

Eugene Kennedy and Albert Lehninger showed in 1948 that, in eulcaiyotes, the entire set of reactions of the citric acid cycle takes place in mitochondria. Isolated mitochondria were found to contain not only all the enzymes and coenzymes required for the citric acid cycle, but also all the enzymes and proteins necessaiy for the last stage of respiration—electron transfer and ATP synthesis by oxidative phosphoiylation. As we shall see in later chapters, mitochondria also contain the enzymes for the oxidation of fatty acids and some amino acids to acetyl-CoA, and the oxidative degradation of other amino acids to a-ketoglutarate, succinyl-CoA, or oxaloacetate. Thus, in nonphotosynthetic eulcaiyotes, the mitochondrion is the site of most energy-yielding... 

The dehydrogenases discussed in this section catalyze the oxidation of alcohols to carbonyl compounds. They utilize either NAD+ or NADP+ as coenzymes. The complex of the enzyme and coenzyme is termed the holoenzyme the free enzyme is called the apotnzyme. Some dehydrogenases are specific for just one of the coenzymes a few use both. The reactions are readily reversible, so that carbonyl compounds may be reduced by NADH or NADPH. The rates of reaction in either direction are conveniently measured by the appearance or disappearance of the reduced coenzyme, since it has a characteristic ultraviolet absorbance at 340 nm. The reduced coenzymes also fluoresce when they are excited at 340 nm, which provides an even more sensitive means of assay. 

Bugg, T.D. An Introduction la Enzyme and Coenzyme Chemistry. Blackwell Science. Inc.. Malden. MA. 1997. 

Before discussing the specific aspects of regulation of fatty acid metabolism, let us review the main steps in fatty acid synthesis and degradation. Figure 18.18 illustrates these processes in a way that emphasizes the parallels and differences. In both cases, two-carbon units are involved. However, different enzymes and coenzymes are utilized in the biosynthetic and degradative processes. Moreover, the processes take place in different compartments of the cell. The differences in the location of the two processes and in the... 

The photosynthetic apparatus is found in and on membrane structures, which, in plant cells and algae, are located in chloroplasts and are called thylakoids. In bacteria the photosynthetic membrane is derived by complex invagination of the cytoplasmic membrane. The photosynthetic apparatus is made up of antennae, which contain light-harvesting pigment molecules (usually chlorophylls or bacteriochlorophylls) and photochemical reaction centres, which also contain pigments, together with the necessary enzymes and coenzymes. 

Slany, R. K., Kersten, H. Genes, enzymes and coenzymes of queuosine biosynthesis in procaryotes. Biochimie 1994, 76, 1178-1182. 

An Introduction to Enzyme and Coenzyme Chemistry, T. Bugg, Blackwell Stience 1997, 247 pp., ISBN 0-86542-793-3 (paperback). This is a superb undergraduate/ postgraduate textbook about enzymes. It is well written and illustrated, with interesting examples and well-thought-out exercises. 

In addition to their role in genetics, nucleotides play other important roles in biochemistry. Key enzymes and coenzymes such as nicotinamide adenine dinucleotide (NAD), flavin adenine dinucleotide (FAD), and vitamin B12 also include nucleotides as part of their structures. Also, the major component of viruses is DNA. 

Sulphate is the form in which S is normally absorbed by plant roots and the reduction of sulphate for the synthesis of sulphur-containing compounds is universal for plants. Sulphur occurs in some amino acids, proteins and also in the oils of some plants such as cabbages and turnips. The S—H group is very important for the action of some enzymes and coenzymes. S is also a constituent of ferredoxins. A deficiency leads to stunting and yellowing but can be cured. A classical case of S deficiency known as tea yellows was identified in 1933 by Storey and Leach (reported in Hewitt and Smith, 1975). Sulphur deficiency leads to accumulation of amine and ammonia nitrogen, with little change in the total. 

Biomimetic chemistry not only provides means of elucidating enzyme and coenzyme functions through manipulation of model systems, but also opens a way to the development of novel polyfunctional catalysts and materials that may or may not exist in nature. On the basis of the advancement of research described in this book, we now stand on the edge of an interdisciplinary valley so that the jump beyond the mimetic chemistry becomes possible in the future. 

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