Biochemistry - Chemical Reactions in Living Cells, Volume 2 - D. Metzler 1980

Biosynthesis; how new molecules are formed
Biosynthesis of monomers
Biosynthesis of glucose (gluconeogenesis)

In the preceding sections, we examined the biosynthetic pathways of three-carbon carbohydrate precursors. Triose phosphates are formed in the reductive pentose phosphate cycle (Fig. 11-4, B). The reductive Tricarboxylic Acid Cycle and the glyoxylate pathway yield oxaloacetate, which is readily converted into phosphoenolpyruvate. We will now examine the further conversion of PEP and triose phosphates into glucose-1-phosphate—a key intermediate in The Biosynthesis of the vast family of Sugars and Polysaccharides.

The conversion of PEP to glucose-1-phosphate represents the reversal of a portion of The Glycolytic Pathway. Therefore, it is logical to consider it alongside the Reversal of the entire Glycolysis sequence, starting from lactic acid. This reaction, known as Gluconeogenesis, is an essential component of the Cori cycle (Ch. 9, Sec. E). It can be utilized by the Organism to convert Pyruvate, formed As a result of the deamination of Alanine or Serine (Ch. 14), into CARBOHYDRATES.

¹⁾ It is interesting that all the genes encoding specific Enzymes of the glyoxylate pathway are clustered in a single region of the bacterial chromosome.

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Just as in the case of The pentose phosphate cycle, the exact reversal of the glycolysis reaction sequence [equation (11-18)] is thermodynamically unfavorable.

Even at very high values of R_p, it is unlikely that the reaction would proceed to completion. The actual pathways of gluconeogenesis [equation (11-19), dashed lines] apparently differ from the corresponding pathways in glycolysis [equation (11-19), solid lines]. 1) If Glycogen breakdown is initiated by the inorganic phosphate reaction catalyzed by phosphorylase [step a, equation (11-19)], the biosynthetic sequence from glucose-1-phosphate through uridine diphosphate glucose [equation (11-19), step b; see also Sec. E,1,b] is coupled with the Cleavage of an ATP molecule. 2) In catabolic processes (glycolysis), fructose-6-phosphate is converted into fructose-1,6-diphosphate by a specific kinase [equation (11-19), step c], after which the resulting fructose diphosphate is cleaved by aldolase, and the resulting triose phosphate undergoes further breakdown. In contrast, during gluconeogenesis, the Formation of fructose phosphate from fructose diphosphate is catalyzed by a specific phosphatase [equation (11-19), step d]. 3) In the course of glycolysis, phosphoenolpyruvate is converted into pyruvate by the action of a kinase, yielding ATP (Fig. 9-7, reaction 10). In gluconeogenesis, however, pyruvate is converted into phosphoenolpyruvate not directly, but via oxaloacetate [equation (11-20)]. This serves as another example of coupling an ATP cleavage reaction within a carboxylation-decarboxylation sequence. The net result of converting pyruvate to PEP is the consumption of not one, but two ATP molecules (effectively one ATP and one GTP molecule).

The overall reaction of reversed glycolysis is therefore characterized by a rather large negative Standard Free energy change [equation (11-21)].

¹⁾ However, the generally accepted view that pyruvate kinase does not catalyze the reverse reaction during gluconeogenesis has been questioned [17].

Two enzymes capable of directly converting pyruvate into PEP have been discovered in Bacteria and plants. In each of these cases, as in the animal enzyme systems discussed in previous sections, this conversion is accompanied by the expenditure of two high-energy ATP bonds. Phosphoenolpyruvate synthetase from E. coli apparently first transfers a pyrophosphate group from ATP to the Y-group of the enzyme [equation (11-22)], after which one phosphate group of this intermediate is removed by Hydrolysis [dashed line in equation (11-22), step b], ensuring The formation of an abundant E-Y-P intermediate that reacts with pyruvate to yield PEP [18]. A similar enzyme, pyruvate,phosphate dikinase, was first identified in tropical grasses and is now known to play a crucial role in the functioning of CO₂-concentrating systems in so-called C₄ plants (Ch. 13, Sec. D,9) [19, 20]. This same enzyme participates in gluconeogenesis in Acetobacter [20]. The Mechanism of this enzyme's action can be inferred from equation (11-22). Its only difference from E. coli phosphoenolpyruvate synthetase is that the attacking nucleophile [equation (11-22), step c] is inorganic phosphate rather than Water, yielding inorganic pyrophosphate as a product, which is presumably subsequently hydrolyzed by a phosphatase. The overall reaction ultimately proves to be the same as in the PEP synthetase reaction.

It is appropriate here to pose a question to the student. The point is that the exact same final result should have been obtained if the E—Y—P intermediate in equation (11-22) were formed by transferring a phosphate group from ATP to Y. The product in this case would be ADP. To drive the process to completion, this ADP molecule could be hydrolyzed to AMP and P_i by a specific phosphatase. Why is this process never utilized in nature?