Dark Reaction or C3 Cycle or Biosynthetic Phase or Photosynthetic Carbon Reduction (PCR) Cycle

The dark reaction (also called the biosynthetic phase, or the Photosynthetic Carbon Reduction, PCR, cycle) is where the ATP and NADPH+H+ generated during the light reaction are finally put to use: fixing and reducing carbon dioxide into carbohydrate. Because this phase does not itself require light directly, it is named the dark reaction, but its rate is strongly temperature-dependent, which is why it is also described as a thermochemical (rather than photochemical) process. The cycle's CO2 acceptor is ribulose 1,5-bisphosphate (RuBP), a 5-carbon compound, and the enzyme that actually attaches CO2 onto it is RuBP carboxylase-oxygenase, universally abbreviated RuBisCO. Because the very first stable product of this fixation step is a 3-carbon compound, phosphoglyceric acid (PGA), the whole pathway is also called the C3 cycle, and it runs entirely within the chloroplast stroma. M. Calvin, A. Benson and their co-workers worked out this pathway in 1957 (earning Calvin the 1961 Nobel Prize), so it is also frequently called the Calvin-Benson cycle. The cycle proceeds through three linked phases. In carboxylation (fixation), RuBisCO attaches one molecule of CO2 onto RuBP (5C), momentarily forming an unstable 6-carbon intermediate that immediately splits into two molecules of the 3-carbon compound PGA: $RuBP\ (5C) + CO_2 \xrightarrow{Rubisco} 2\ PGA\ (3C)$. In reduction (also called the glycolytic reversal), each PGA molecule is first phosphorylated by ATP (via the enzyme PGA kinase) to form 1,3-bisphosphoglyceric acid, which is then reduced using the reducing power NADPH+H+ into glyceraldehyde-3-phosphate (G3P); G3P readily isomerises into its structural isomer, dihydroxyacetone phosphate (DHAP). In regeneration, the bulk of this G3P/DHAP pool is recycled back into RuBP through a sequence of intermediate sugar-phosphates spanning 4-carbon, 5-carbon, 6-carbon and 7-carbon skeletons (including erythrose-4-phosphate, sedoheptulose-1,7-bisphosphate/7-phosphate, ribose-5-phosphate and xylulose-5-phosphate), with the final step being an ATP-driven phosphorylation of ribulose-5-phosphate (RU5P) back into RuBP, closing the cycle; only a small, net fraction of the G3P produced overall is diverted out of this recycling to build hexose sugars and starch. Because six turns of the cycle are needed to net one hexose sugar, the overall stoichiometry for fixing six CO2 molecules is $6CO_2 + 18ATP + 12NADPH+H^+ \rightarrow C_6H_{12}O_6 + 6H_2O + 18ADP + 18P_ …