Overall process of photosynthesis The chloroplast is involved in both stages of photosynthesis. The light reaction takes place in the thylakoid discs. There, water (H20) is oxidized, and oxygen (O2) is released. The electrons freed up from water are transferred to ATP and NADPH. The dark reaction occurs outside of the thylakoids. In this reaction, the energy from ATP and NADPH are used to fix carbon dioxide (C02). The products of this reaction are sugar molecules and other organic molecules necessary for cell function and metabolism. Note that the dark reaction takes place in the stroma (aqueous fluid surrounding the stacks of thylakoids) and the cytoplasm. Calvin Cycle: (Also referred as – Light–Independent Reactions of Photosynthesis, Carbon Fixation) The high–energy molecules ATP and NADPH, synthesized in the light–dependent reactions of photosynthesis, are used to synthesize carbohydrates from carbon dioxide – hence the term carbon fixation.
The carbon fixation cycle, also called the Calvin cycle, is a 3–phase cycle that occurs in the stroma and that converts CO2 into carbohydrates using the energy of ATP and the oxidation of NADPH.
Carbon enters the Calvin cycle in the form of CO2 and leaves in the form of sugar. The cycle spends ATP as an energy source and consumes NADPH as reducing power for adding high–energy electrons to make the sugar. The carbohydrate produced directly from the Calvin cycle is actually not glucose, but a three–carbon sugar named glyceraldehyde–3–phosphate (G3P). For the net synthesis of one molecule of this sugar, the cycle must take place three times, fixing three molecules of CO2 . As we trace the steps of the cycle, keep in mind that we are following three molecules of CO2 through the reactions.
Sequential steps involved in Dark reactions/Calvin cycle/ Carbon fixation
The carbon fixation cycle has three phases: phase I is carbon fixation (each molecule of ribulose
1,5– biphosphate + CO2 
2 molecules of 3–phosphoglycerate);
phase II is reduction (each molecule of 3–phosphoglycerate + ATP + NADPH
glyceraldehyde 3–phosphate + ADP + Pi + NADP+); and phase III is regeneration of
ribulose 1,5–biphosphate (5 molecules of glyceraldehyde 3–phosphate + 3ATP
3 molecules of ribulose 1,5–biphosphate + 3ADP + 3Pi.)
For each molecule of CO2 fixed, 3 ATPs and 2 NADPH's are consumed. Phase I: Carbon fixation. The Calvin cycle incorporates each CO2 molecule, one at a time, by attaching it to a five–carbon sugar named ribulose bisphosphate (RuBP). The enzyme that catalyzes this first step is RuBP carboxylase, or rubisco. (It is the most abundant protein in the chloroplast and probably the most abundant protein on Earth). The product of the reaction is a six–carbon intermediate, so unstable that it immediately splits in half, forming two molecules of 3–phospoglycerate ( for each CO2 ).
Phase II: Reduction. Each molecule of 3–phosphoglycerate receives an additional phosphate group from ATP, becoming 1,3– Bisphosphoglycerate. Next, a pair of electrons donated from NADPH reduces 1,3–bisphosphoglycerate to G3P. Specifically, the electrons from NADPH reduce the carboxyl group of 3–phosphoglycerate to the aldehyde group of G3P, which stores more potential energy. G3P is a sugar– the same three–carbon sugar formed in glycolysis by the splitting of glucose. Notice in the figure that for every three molecules of CO2 , there are six molecules of G3P. But only one molecule of this three–carbon sugar can be counted as a net gain of carbohydrate. The cycle began with 15 carbons worth of carbohydrate in the form of three molecules of the five–carbon sugar RuBP. Now there are 18 carbons' worth of carbohydrate in the form of six molecules of G3P. One molecule exists the cycle to be used by the plant cell, but the other five molecules must be recycled to regenerate the three molecules of RuBP.
Phase III Regeneration of the CO2 acceptor (RuBP) : In a complex series of reactions, the carbon skeletons of five molecules G3P are rearranged by the last steps of the Calvin cycle into three molecules of RuBP. To accomplish this, the cycle spends three more molecules of ATP. The RuBP is now prepared to receive CO2 again, and the cycle continues. For the net synthesis of one G3P molecule, the Calvin cycle consumes a total of nine molecules of ATP and six molecules of NADPH. The light reactions regenerate the ATP and NADPH. The G3P spun off from the Calvin cycle becomes the starting material for metabolic pathways that synthesize other organic compounds, including glucose and other carbohydrates. Neither the light reactions nor the Calvin cycle alone can make sugar from CO2 . Photosynthesis is an emergent property of the intact chloroplast, which integrates the two stages of photosynthesis.