Enzyme interconversion cycles

An important extended example of enzyme interconversion cycles is the reciprocal control of glycogen metabolism involving glycogen synthase and glycogen phosphorylase (Section 11.5). The activities of both enzymes are regulated in concert by phosphorylation and dephosphorylation reactions so that when the synthetic pathway is in operation, the degradative pathway is reciprocally r uced. 

The topic of interconversion cycles in providing inhibition or activation of a target enzyme, the activity of which regulates the flux through a pathway, is discussed above. In brief, an enzyme exists in two forms, conventionally designated a and b, one being a covalent modification of the other. This is brought about, for example, by phosphorylation with ATP, so that one form is a phos-... 

Pyruvate dehydrogenase, the activity of which is affected by a number of factors the ATP/ADP, the NADH/NAD+ and the acetyl-CoA/CoASH concentration ratios. It is also activated by Ca ions. These factors change the enzyme activity via an interconversion cycle (Fignre 6.16(b)). 

Since the enzyme glycogen synthase catalyses the rate-limiting step in glycogen synthesis, it is the activity of this enzyme that must be increased as the blood glucose concentration increases. This is achieved via an interconversion cycle (i.e. reversible phosphorylation). A protein kinase phosphorylates it, which inactivates the enzyme, whereas a protein phosphatase dephosphorylates it, which... 

There are only five key biochemical factors that provide for the regnlation (i) snbstrate cycles (ii) regulation of phosphofrncto-2-kinase (PFK-2) (iii) phosphorylation/ dephosphorylation interconversion cycles (i.e. reversible phosphorylation) (iv) gene expression of gluconeogenic enzymes (v) concentrations of precnrsors in the blood. 

Two key enzymes in the pathway are regnlated by interconversion cycles they are the regnlatory enzyme PFK-2, and the glycolytic enzyme pyruvate kinase. There are two separate protein kinases that phosphorylate these enzymes and they both resnlt in activation of these enzymes. Dephosphorylation inactivates them. 

As indicated above, the flux-generating step for fatty acid synthesis is the conversion of acetyl-CoA to malonyl-CoA, catalysed by acetyl-CoA carboxylase. Consequently, regulation of the rate of synthesis is achieved via changes in the activity of this enzyme. The properties of the carboxylase identify three mechanisms for regulation allosteric regulation, reversible phosphorylation (an interconversion cycle) and changes in the concentration of the enzyme. (The principles underlying the first two mechanisms are discussed in Chapter 3.)... 

The principle underlying the changes in activity of a G-protein is similar to that of an interconversion cycle (Chapter 3). The classic example of an interconversion cycle is that between the two forms of the enzyme phos-phorylase phosphorylase a and b. The interconversions between b and a are catalysed by a protein kinase and a protein phosphatase. The similarities are as follows. 

As might be expected from other mechanisms of regulation described in this text, phosphorylation and dephosphorylation of key proteins is the main mechanism for regulating the cycle, i.e. reversible phosphorylation, also known as interconversion cycles (discussed in Chapter 3). In the cell cycle, several of these interconversion cycles play a role in control at the checkpoints. Two important terms must be appreciated to help understand the mechanism of regulation of the cycle the phosphorylation of proteins is catalysed by specific protein kinases, known as cell-division kinases (cdck) or cell cycle kinases (cck) and these enzymes are activated by specific proteins, known as cyclins. 

Figure 20.31 The principle of interconversion cycles in regulation of protein activity or changes in protein concentration as exemplified by translation/proteolysis or protein kinase/protein phosphatase. They result in very marked relative changes in regulator concentration or enzyme activity. The significance of the relative changes (or sensitivity in regulation) is discussed in Chapter 3. The principle of regulation by covalent modihcation is also described in Chapter 3. The modifications in cyclin concentration are achieved via translation and proteolysis, which, in effect, is an interconversion cycle. For the enzyme, they are achieved via phosphorylation and dephosphorylation reactions. In both cases, the relative change in concentration/activity by the covalent modification is enormous. This ensures, for example, that a sufficient increase in cyclin can occur so that an inactive cell cycle kinase can be converted to an active cell cycle kinase, or that a cell cycle kinase can be completely inactivated. Appreciation of the common principles in biochemistry helps in the understanding of what otherwise can appear to be complex phenomena.

Other enzyme reaction cycles, most of the interconversions take place without a change in free energy, i.e., near equilibrium. This ensures minimal thermal losses. 

If a response involves an interconversion cycle its eflFect must be included in the catalystic component of the intrinsic sensitivity of the pathway enzyme to X, i.e., in r pc) (Section III,B,2). Moreover, since it represents an independent route of communication from X to pathway enzyme, a function such as must be added to any other catalystic components of the response (Section... 

The citric acid cycle is the final common pathway for the aerobic oxidation of carbohydrate, lipid, and protein because glucose, fatty acids, and most amino acids are metabolized to acetyl-CoA or intermediates of the cycle. It also has a central role in gluconeogenesis, lipogenesis, and interconversion of amino acids. Many of these processes occur in most tissues, but the hver is the only tissue in which all occur to a significant extent. The repercussions are therefore profound when, for example, large numbers of hepatic cells are damaged as in acute hepatitis or replaced by connective tissue (as in cirrhosis). Very few, if any, genetic abnormalities of citric acid cycle enzymes have been reported such ab-normahties would be incompatible with life or normal development. 

As an illustration, we briefly discuss the SCC-DFTB/MM simulations of carbonic anhydrase II (CAII), which is a zinc-enzyme that catalyzes the interconversion of CO2 and HCO [86], The rate-limiting step of the catalytic cycle is a proton transfer between a zinc-bound water/hydroxide and the neutral/protonated His64 residue close to the protein/solvent interface. Since this proton transfer spans at least 8-10 A depending on the orientation of the His 64 sidechain ( in vs. out , both observed in the X-ray study [87]), the transfer is believed to be mediated by the water molecules in the active site (see Figure 7-1). To carry out meaningful simulations for the proton transfer in CAII, therefore, it is crucial to be able to describe the water structure in the active site and the sidechain flexibility of His 64 in a satisfactory manner. 

The Enzyme Aconitase. The enzyme aconitase catalyzes the elimination or addition of water in the second step of the citric acid (Krebs) cycle, catalyzing the interconversion of citrate and isocitrate via cix-aconitate. See reference 8, pages 190-196, Figure 7.49, and equation 7.13. 

The progression of the cell cycle is regulated by interconversion processes, in each phase, special Ser/Thr-specific protein kinases are formed, which are known as cyclin-depen-dent kinases (CDKs). This term is used because they have to bind an activator protein (cyclin) in order to become active. At each control point in the cycle, specific CDKs associate with equally phase-specific cyclins. if there are no problems (e.g., DNA damage), the CDK-cyclin complex is activated by phosphorylation and/or dephosphorylation. The activated complex in turn phosphorylates transcription factors, which finally lead to the formation of the proteins that are required in the cell cycle phase concerned (enzymes, cytoskeleton components, other CDKs, and cyclins). The activity of the CDK-cyclin complex is then terminated again by proteolytic cyclin degradation. 

Mitochondrial fractions may be characterized by testing for the presence of known enzyme activities as previously discussed. The relative purity of each fraction can be estimated by measuring the specific activity of marker enzymes. Table El0.1 identifies marker enzymes for the matrix and membranes. Malate dehydrogenase, the tricarboxylic acid cycle enzyme that catalyzes the interconversion of malate and oxaloacetate (Equation E10.1), serves as a marker for the matrix enzymes. 

Many of the enzymes participating in de novo synthesis of deoxyribonucleotide triphosphates, as well as those responsible for interconversion of deoxyribonucleotides, increase in activity when cells prepare for DNA synthesis. The need for increased DNA synthesis occurs under three circumstances (1) when the cell proceeds from the G0, or resting, stage of the cell cycle to the S, or synthetic or replication, stage (fig. 23.26) (2) when it performs repair after extensive DNA damage and (3) after infection of quiescent cells with virus. When cells leave G0, for example, enzymes such as thymidylate synthase and ribonucleotide reductase, increase as well as the corresponding mRNAs. These increases in enzyme amount supplement allosteric controls that increase the activity of each enzyme molecule. Corresponding decreases in amounts of these enzymes and their mRNAs occur when DNA synthesis is completed. 

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