Glycolysis biochemical mechanism

I would like to comment on the theoretical analysis of two systems described by Professor Hess, in order to relate the phenomena discussed by Professor Prigogine to the nonequilibrium behavior of biochemical systems. The mechanism of instability in glycolysis is relatively simple, as it involves a limited number of variables. An allosteric model for the phosphofrucktokinase reaction (PFK) has been analyzed, based on the activation of the enzyme by a reaction product. There exists a parameter domain in which the stationary state of the system is unstable in these conditions, sustained oscillations of the limit cycle type arise. Theoretical... 

Systems of biochemical reactions like glycolysis, the citric acid cycle, and larger and smaller sequential and cyclic sets of enzyme-catalyzed reactions present challenges to make calculations and to obtain an overview. The calculations of equilibrium compositions for these systems of reactions are different from equilibrium calculations on chemical reactions because additional constraints, which arise from the enzyme mechanisms, must be taken into account. These additional constraints are taken into account when the stoichiometric number matrix is used in the equilibrium calculation via the program equcalcrx, but they must be explicitly written out when the conservation matrix is used with the program equcalcc. The stoichiometric number matrix for a system of reactions can also be used to calculate net reactions and pathways. 

Glycolysis involves 10 biochemical reactions and 16 reactants. Water is not counted as a reactant in writing the stoichiometric number matrix or the conservation matrix for reasons described in Section 6.3. Thus there are six components because C = N — R = 16 — 10 = 6. From a chemical standpoint this is a surprise because the reactants involve only C, H, O, N, and P. Since H and O are not conserved at specified pH in dilute aqueous solution, there are only three conservation equations based on elements. Thus three additional conservation relations arise from the mechanisms of the enzyme-catalyzed reactions in glycolysis. Some of these conservation relations are discussed in Alberty (1992a). At specified pH in dilute aqueous solutions the reactions in glycolysis are... 

Glycolysis, a series of reactions that occurs in almost every living cell, is believed to be among the oldest of all the biochemical pathways. Both the enzymes and the number and mechanisms of the steps in the pathway are highly homologous in prokaryotes and eukaryotes. Also, glycolysis is an anaerobic process, which it would have had to be in the oxygen-poor atmosphere of pre-eukaryotic Earth. 

Consider the biochemical reaction mechanism shown in fig. 4.8, which occurs in glycolysis [7] note the similarity in the structure of this mechanism to that of a model of a chemical neuron shown in fig. 4.1. Calculations of the stable stationary states of the biochemical system of fig. 4.8 are plotted in fig. 4.9. The change from high to low concentration of either compound is not as abrupt as that in fig. 4.2 for the chemical model, but is clearly present. We have identified a computational element, a fuzzy chemical neuron, in a biochemical reaction. 

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... 

Biochemically, cyanide affects the citric acid cycle, strongly inhibits catalases and pro-teinases, induces glycolysis in protozoans, fish, and mammals, produces vitamin B12 deficiency, and modifies the phosphorylation mechanism of respiratory mitochondrial enzymes, causing arrested respiration due to... 

Satoh H, Mino T, Matsuo T (1992) Uptake of organic substrates and accumulation of polyhy-droxyalkanoates linked with glycolysis of intracellular carbohydrates under anaerobic conditions in the biological excess phosphate removal processes. Water Sd Technol 26 933-942 Savenkova L, Gercberga Z, Bibers I, Kalnin M (2000) Effect of 3-hydroxy valerate content on some physical and mechanical properties of polyhydioxyaUcanoates produced by Azotobacter chroococcum. Process Biochem 36 445-450... 

As well as being of biochemical interest glycolysis is commercially important it is used in the production of bread, beer, and wine. For a constant rate of glucose input, oscillation is observed in the rate of CO2 production as well as in the concentrations of many reaction intermediates.There are multiple feedback loops the control mechanism is far more elaborate than in any of the physicochemical oscillators discussed previously. We shall sketch some of the results to indicate the complexity of even a rather simple biochemical pathway. 

Consider the following model for the reaction mechanism of the beginning part of glycolysis (Fig. 16.3) [6] for the production of the energy rich chemical species ATP (adenosine triphosphate), which is the universal energy coinage in biochemical reactions. 

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