Enzymes intermediary metabolism

The net reaction catalyzed by this enzyme depends upon coupling between the two reactions shown in Equations (3.26) and (3.27) to produce the net reaction shown in Equation (3.28) with a net negative AG°. Many other examples of coupled reactions are considered in our discussions of intermediary metabolism (Part III). In addition, many of the complex biochemical systems discussed in the later chapters of this text involve reactions and processes with positive AG° values that are driven forward by coupling to reactions with a negative AG°. ... 

University of Illinois, isolated Just 30 mg of lipoic acid from approximately 10 tons of liver No evidence exists of a dietary lipoic acid requirement by humans stricdy speaking, it is not considered a vitamin. Nevertheless, it is an essential component of several enzymes of intermediary metabolism and is present in body tissues in small amounts. 

Biotin is involved in carboxylation and decarboxylation reactions. It is covalently bound to its enzyme. In the carboxylase reaction, C02 is first attached to biotin at the ureido nitrogen, opposite the side chain in an ATP-dependent reaction. The activated C02 is then transferred from carboxybiotin to the substrate. The four enzymes of the intermediary metabolism requiring biotin as a prosthetic group are pyruvate carboxylase (pyruvate oxaloacetate), propionyl-CoA-carboxylase (propionyl-CoA methylmalonyl-CoA), 3-methylcroto-nyl-CoA-carboxylase (metabolism of leucine), and actyl-CoA-carboxylase (acetyl-CoA malonyl-CoA) [1]. 

Several enzymes of the intermediary metabolism require thiaminpyrophosphate (TPP, Fig. 1) as coenzyme, e.g., enzymes of the pyruvate dehydrogenase complex, a-ketoglutarate dehydrogenase complex, or pentose phosphate pathway. 

This system displays a two-enzyme kinetic model in which bioconversion is controlled by the interaction between the two reactions and the mass transfer. This situation offers a more realistic model for the conditions occurring in vivo, in which some pathways of intermediary metabolism consist of linear sequences of reactions. These pathways take place in highly organized compartments. 

FIGURE 28-5 Schematic illustration of the movement of cytoskeletal elements in slow axonal transport. Slow axonal transport represents the movement of cytoplasmic constituents including cytoskeletal elements and soluble enzymes of intermediary metabolism at rates of 0.2-2 mm/day which are at least two orders of magnitude slower than those observed in fast axonal transport. As proposed in the structural hypothesis and supported by experimental evidence, cytoskeletal components are believed to be transported down the axon in their polymeric forms, not as individual subunit polypeptides. Cytoskeletal polypeptides are translated on cytoplasmic polysomes and then are assembled into polymers prior to transport down the axon in the anterograde direction. In contrast to fast axonal transport, no constituents of slow transport appear to be transported in the retrograde direction. Although the polypeptide composition of slow axonal transport has been extensively characterized, the motor molecule(s) responsible for the movement of these cytoplasmic constituents has not yet been identified. 

Cytoplasmic and cytoskeletal elements move coherently at slow transport rates. Two major rate components have been described for slow axonal transport, representing movement of cytoplasmic constituents including cytoskeletal elements and soluble enzymes of intermediary metabolism [3]. Cytoplasmic and cytoskeletal elements in axonal transport move with rates at least two orders of magnitude slower than fast transport. 

While the enzymes involved in detoxication processes are nonspecific in the classical sense of intermediary metabolism, they often have distinct specificities both for organic functional groups and for the electronic, steric, and stereochemical environments where these functional groups are located. Enzyme specificity based on organic functional groups and their environments leads to a wide diversity in the alkaloid substrates possible and therefore the products obtained from biotransformation. This section of the chapter will concentrate principally on the enzymes themselves, including general concepts of substrate specificity and mechanism. 

THE TYPES OF REACTION CATALYSED BY ENZYMES OF INTERMEDIARY METABOLISM... 

Many enzymes involved in the pathways of intermediary metabolism are Mg2+ dependent, as are a great many of the enzymes involved in nucleic acid metabolism. Of the ten enzymes involved in the glycolytic pathway (see Chapter 5), five are Mg2+ dependent. 

Phosphoryl group transfer reactions add or remove phosphoryl groups to or from cellular metabolites and macromolecules, and play a major role in biochemistry. Phosphoryl transfer is the most common enzymatic function coded by the yeast genome and, in addition to its importance in intermediary metabolism (see Chapter 5), the reaction is catalysed by a large number of central regulatory enzymes that are often part of signalling cascades, such as protein kinases, protein phosphatases, ATPases and GTPases. 

We begin this overview of manganese biochemistry with a brief account of its role in the detoxification of free radicals, before considering the function of a dinuclear Mn(II) active site in the important eukaryotic urea cycle enzyme arginase. We then pass in review a few microbial Mn-containing enzymes involved in intermediary metabolism, and conclude with the very exciting recent results on the structure and function of the catalytic manganese cluster involved in the photosynthetic oxidation of water. 

The Types of Reaction Catalysed by Enzymes of Intermediary Metabolism... 

Virtually all biological reactions are stereospecific. This generalization applies not only to the enzyme-catalyzed reactions of intermediary metabolism, but also to the processes of nucleic acid synthesis and to the process of translation, in which the amino acids are linked in specific sequence to form the peptide chains of the enzymes. This review will be restricted mainly to some of the more elementary aspects of the stereospecificity of enzyme reactions, particularly to those features of chirality which have been worked out with the help of isotopes. 

The term intermediary metabolism is used to emphasize the fact that metabolic processes occur via a series of individual chemical reactions. Such chemical reactions are usually under the control of enzymes which act upon a substrate molecule (or molecules) and produce a product molecule (or molecules) as shown in Figure 1.1. The substrates and products are referred to collectively as intermediates or metabolites . The product of one reaction becomes the substrate for another reaction and so the concept of a metabolic pathway is created. 

Primary and secondary metabolites are made by a diverse range of bacteria and fimgi and their production is a conservative process that usually does not expend energy or nutrients to make compounds already available in the environment and does not overproduce components of intermediary metabolism. Coordination of metabolic functions ensures that, at any given moment, only the necessary enzymes, and the correct... 

Enzyme inhibitors are chemicals that may serve as a natural means of controlling metabolic activity by reducing the number of enzyme molecules available for catalysis. In many cases, natural or synthetic inhibitors have allowed us to unravel the pathways and mechanisms of intermediary metabolism. Enzyme inhibitors may also be used as pesticides or drugs. Such materials are designed so that they inhibit a specific enzyme that is peculiar to an organism or a disease state. For example, a good antibiotic may inhibit a bacterial enzyme, but it should have no effect on the host person or animal. 

The third type of inhibition is called allosteric inhibition, and is particularly important in the control of intermediary metabolism This refers to the ability of enzymes to change their shape (tertiary and quaternary structure, see Section 13.3) when exposed to certain molecules. This sometimes leads to inhibition, whereas in other cases it may actually activate the enzyme. The process allows subtle control of enzyme activity according to an organism s demands. Further consideration of this complex phenomenon is outside our immediate needs. 

As we look at some of the reactions of intermediary metabolism, we shall rationahze them in terms of the chemistry that is taking place. In general, we shall not consider here the involvement of the enzyme itself, the binding of substrates to the enzyme, or the role played by the enzyme s amino acid side-chains. In Chapter 13 we looked at specific examples where we know just how an enzyme is able to catalyse a reaction. Examples such as aldolase and those phosphate isomerase, enzymes of the glycolytic pathway, and citrate synthase from the Krebs cycle were considered in some detail. It may... 

Metabolism Bench-top or automated chemistry analyzer assays of cell lysates for key enzymes of intermediary metabolism, antioxidant system, ion transport... 

The nature of the substrate proteins of protein kinase of type A is very diverse the substrate may be, e.g., other proteins or enzymes of intermediary metabolism (see Chapter 7.2). 

Enzymes as elements of signal chains (Chapters 7, 8, 10, 13) and in enzymes of intermediary metabolism (Chapter 2)... 

Of the protein kinases, protein kinase A is the best investigated and characterized (review Francis and Corbin, 1994). The functions of protein kinase A are diverse. Protein kinase A is involved in the regulation of metabolism of glycogen, lipids and sugars. Substrates of protein kinase A may be other protein kinases, as well as enzymes of intermediary metabolism. Protein kinase A is also involved in cAMP-stimulated transcription of genes that have a cAMP-responsive element in their control region (review Montminy, 1997). An increase in cAMP concentration leads to activation of protein kinase A which phosphorylates the transcription factor CREB at Ser 133. CREB only binds to the transcriptional coactivator CBP in the phosphorylated state and stimulates transcription (see Chapter 1.4.4.2). 

The enzymes specifically involved in the metabolism of foreign compounds are necessarily often flexible, and the substrate specificity is generally broad. However, it follows from the above two conditions that if the structure of a foreign compound is similar to a normal endogenous molecule, then the foreign compound may be a suitable substrate for an enzyme primarily involved in intermediary metabolic pathways if the enzyme is present in the exposed tissue. Thus, foreign compounds are not exclusively metabolized by specific enzymes. 

Fluorocitrate is therefore a pseudosubstrate. As well as inhibiting cellular respiration, inhibition of the TCA cycle will also reduce the supply of 2-oxoglutarate. This may decrease the removal of ammonia via formation of glutamic acid and glutamine, and this might account for the convulsions seen in some species after exposure to fluoroacetate. The toxicity is manifested as a malfunction of the CNS and heart, giving rise to nausea, apprehension, convulsions, and defects of cardiac rhythm, leading to ventricular fibrillation. Fluoroacetate and fluorocitrate do not appear to inhibit other enzymes involved in intermediary metabolism, and the di- and trifluoroacetic acids are not similarly incorporated and therefore do not produce the same toxic effects. 

The reduction in protein synthesis obviously has other ramifications, such as a deficiency in hepatic enzymes and a consequent general disruption of intermediary metabolism. Methylation reactions are presumably also affected. 

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