Phosphorylation-dephosphorylation biochemical cycle

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. 

If we concentrate on one particular component of this map - the phosphorylation of PI(4,5)P2 to PI(3,4,5)P3 by PI3K and the dephosphorylation of PI(3,4,5)P3 to PI(4,5)P2 by F TEN, we can study the detailed enzyme kinetic scheme of this so-called phosphorylation-dephosphorylation cycle, which is illustrated in Figure 5.2. This illustrated cycle represents a ubiquitous module in biochemical signaling, ft could, for example, represent the phosphorylation of mitogen-activation protein kinase (MAPK) by MAPK kinase (MAPKK) and dephosphorylation of MAPK by MAPK phosphatase (MKP). 

Figure 5.2 A typical cellular biochemical switch consisting of a phosphorylation-dephosphorylation cycle. The substrate molecule S may be a protein or other signaling molecule. If S is a protein then the phosphorylation of S is catalyzed by a protein kinase (K) and the dephosphorylation is catalyzed by a protein phosphatase (P). The entire cycle is accompanied by the reaction ATP ADP+PI. In the context of mitogen-activation protein kinase pathway, S, K, and P correspond to MAPK, MAPKK, and MKP, respectively. In the context of the example from the PIP3 pathway, the kinase is PI3K and the phosphatase is PTEN.

Figure 5.4 Switch-like behavior of the phosphorylation-dephosphorylation cycle. The left panel illustrates the off position (unphosphorylated) of the biochemical switch, in which the phosphatase activity is higher than the kinase activity. When the kinase activity exceeds the phosphatase activity, as in the right panel, the biochemical switch is in the opposite state.

In analyzing the temporal behavior of a biochemical switching molecule, we can study either of the equivalent models of the phosphorylation-dephosphorylation cycle or the GTPase signaling module. In particular, we are interested in the duration of each activation event at the single-molecule level. 

Consider a chemical system as shown in fig. 7.1. Mechanisms of this type are common in biochemical networks. For example, the subnetwork of fig. 7.1 containing S3 to S5 is based on a simple model of fructose interconversion in glycolysis [2] (see fig. 1.2) and the subnetwork composed of Se to S7 is similar to the phosphorylation/dephosphorylation cycles found in cyclic cascades [3,4]. As an aside, this mechanism performs the function... 

Phosphate esters play an essential part in photosynthesis, carbohydrate and lipid metabolism, the nitrogen cycle and in many other biochemical reactions where they are the principal source of energy transfer. Most, if not all enzyme action, is associated with phosphorylation-dephosphorylation mechanisms. 

The sodium and calcium pumps can be isolated to near purity and still exhibit most of the biochemical properties of the native pump. Some kinetic properties of these pumps in native membranes are altered or disappear as membrane preparations are purified. For example, when measured in intact membranes, the time-dependencies of phosphorylation and dephosphorylation of the pump catalytic sites exhibit biphasic fast to slow rate transition this characteristic progressively disappears as the membranes are treated with mild detergents. One suggested explanation is that, as the pumps begin to cycle, the catalytic subunits associate into higher oligomers that may permit more efficient transfer of the energy from ATP into the ion transport process [29, 30], Some structural evidence indicates that Na,K pumps exist in cell membranes as multimers of (a 3)2 [31]. 

Figure 53. Half cycles in dissipative maintenance metabolism with steady state ATP turnover, decoupled by futile cycling. The fhictose 6-phosphate/fructose 1,6-bisphosphate cycle is shown as an example. The net enthalpy change is calculated from the net biochemical change which, at steady state levels of ATP and all anabolic intermediates, is exclusively due to the catabolic half cycle reaction, equivalent to uncoupled catabolism (oxycaloric equivalent), Enthalpy is intermittently conserved in endothermic half cycles (p, phosphorylation a, anabolic), but an equivalent amount of enthalpy is exothermic in the reversed exergonic half cycles (-p, dephosphorylation d, dissipative). Therefore, ATP turnover and futile cycling raise the heat flux strictly proportional to the catabolic flux which, however, can be augmented by anaerobic catabolism with a corresponding anaerobic contribution to total heat flux (Reproduced from Reference [25] with permission).

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