Fig. 16. Electron flow in oxygenic photosynthesis.

Dark reaction

The use of RUBP carboxylase and the Calvin cycle is the most common mechanism for CO₂ fixation among autotrophs. Indeed, RUBP carboxylase is said to be the most abundant enzyme on the planet (nitrogenase, which fixes N₂ is second most abundant). This is the only mechanism of autotrophic CO₂ fixation among eucaryotes, and it is used, as well, by all cyanobacteria and purple bacteria. Lithoautotrophic bacteria also use this pathway. But the green bacteria and the methanogens, as well as a few isolated groups of procaryotes, have alternative mechanisms of autotrophic CO₂ fixation and do not possess RUBP carboxylase.

RUBP carboxylase ( ribulose bisphosphate carboxylase ) uses ribulose bisphosphate (RUBP) and CO₂ as co-substrates. In a complicated reaction the CO₂ is "fixed" by addition to the RUBP, which is immediately cleaved into two molecules of 3-phosphoglyceric acid (PGA). The fixed CO₂ winds up in the -COO group of one of the PGA molecules. Actually, this is the reaction which initiates the Calvin cycle (Fig. 3).

The Calvin cycle is concerned with the conversion of PGA to intermediates in glycolysis that can be used for biosynthesis, and with the regeneration of RUBP, the substrate that drives the cycle. After the initial fixation of CO₂, 2 PGA are reduced and combined to form hexose-phosphate by reactions which are essentially the reverse of the oxidative Embden-Meyerhof pathway. The hexose phosphate is converted to pentose-phosphate, which is phosphorylated to regenerate RUBP. An important function of the Calvin cycle is to provide the organic precursors for the biosynthesis of cell material. Intermediates must be constantly withdrawn from the Calvin cycle in order to make cell material. In this regard, the Calvin cycle is an anabolic pathway. The fixation of CO₂ to the level of glucose (C₆H₁₂O₆) requires 18 ATP and 12 NADPH₂.

Fig. 17. The Calvin cycle and its relationship to the synthesis of cell materials.