Calvin cycle

Overview
The Calvin cycle (or Calvin-Benson-Bassham cycle or carbon fixation) is a series of biochemical reactions that takes place in the stroma of chloroplasts in photosynthetic organisms. It was discovered by Melvin Calvin, James Bassham and Andrew Benson at the University of California, Berkeley. It is one of the light-independent reactions or dark reactions.

Overview
During photosynthesis, light energy is used to generate chemical free energy, stored in glucose. The light-independent Calvin cycle, also (misleadingly) known as the "dark reaction" or "dark stage", uses the energy from short-lived electronically-excited carriers to convert carbon dioxide and water into organic compounds that can be used by the organism (and by animals which feed on it). This set of reactions is also called carbon fixation. The key enzyme of the cycle is called RuBisCO. In the following equations, the chemical species (phosphates and carboxylic acids) exist in equilibria among their various ionized states as governed by the pH.

The enzymes in the Calvin cycle are functionally equivalent to many enzymes used in other metabolic pathways such as  gluconeogenesis and the pentose phosphate pathway, but they are to be found in the chloroplast stroma instead of the cell cytoplasm, separating the reactions. They are activated in the light (which is why the name "dark reaction" is misleading), and also by products of the light-dependent reaction. These regulatory functions prevent the Calvin cycle from operating in reverse to respiration, which would create a continuous cycle of carbon dioxide being reduced to carbohydrates, and carbohydrates being respired to carbon dioxide. Energy (in the form of ATP) would be wasted in carrying out these reactions that have no net productivity.

The sum of reactions in the Calvin cycle is the following:
 * 3 CO2 + 6 NADPH + 5 H2O + 9 ATP → C3H5O3-PO32- + 2 H+ + 6 NADP+ + 9 ADP + 8 Pi
 * OR
 * 3 CO2 + 6 C21H29N7O17P3 + 5 H2O + 9 C10H16N5O13P3 → C3H5O3-PO32- + 2 H+ + 6 NADP+ + 9 C10H15N5O10P2 + 8 Pi

It should be noted that hexose (six carbon) sugars are not a product of the Calvin cycle. Although many texts list a product of photosynthesis as C6H12O6, this is mainly a convenience to counter the equation of respiration, where six-carbon sugars are oxidized in mitochondria. The carbohydrate products of the Calvin Cycle are three-carbon sugar phosphate molecules, or "triose phosphates," specifically, glyceraldehyde-3-phosphate.

Steps of the Calvin cycle

 * 1) The enzyme RuBisCO catalyses the carboxylation of Ribulose-1,5-bisphosphate, a 5 carbon compound, by carbon dioxide (a total of 6 carbons) in a two-step reaction . Rubisco is a large, slow enzyme averaging 3 substrate per second compared to 1000/s for most other enzymes in the Calvin cycle. Two molecules of glycerate 3-phosphate, a 3-carbon compound, are created. (also: 3-phosphoglycerate, 3-phosphoglyceric acid, 3PGA)
 * 2) The enzyme phosphoglycerate kinase catalyses the phosphorylation of 3PGA by ATP (which was produced in the light-dependent stage). 1,3-bisphosphoglycerate (glycerate-1,3-bisphosphate) and ADP are the products. (However, note that two PGAs are produced for every CO2 that enters the cycle, so this step utilizes 2ATP per CO2 fixed.
 * 3) The enzyme G3P dehydrogenase catalyses the reduction of 1,3BPGA by NADPH (which is another product of the light-dependent stage). Glyceraldehyde 3-phosphate (also G3P, GP) is produced, and the NADPH itself was oxidized and becomes NADP+. Again, two NADPH are utilized per CO2 fixed.

(Simplified versions of the Calvin cycle integrate the remaining steps, except for the last one, into one general step - the regeneration of RuBP - also, one G3P would exit here.)


 * 1) Triose phosphate isomerase converts some G3P reversibly into dihydroxyacetone phosphate (DHAP), also a 3-carbon molecule.
 * 2) Aldolase and fructose-1,6-bisphosphatase convert a G3P and a DHAP into fructose-6-phosphate (6C). A phosphate ion is lost into solution.
 * 3) Then fixation of another CO2 generates two more G3P.
 * 4) F6P has two carbons removed by transketolase, giving erythrose-4-phosphate. The two carbons on transketolase are added to a G3P, giving the ketose xylulose-5-phosphate (Xu5P).
 * 5) E4P and a DHAP (formed from one of the G3P from the second CO2 fixation) are converted into sedoheptulose-1,7-bisphosphate (7C) by aldolase enzyme.
 * 6) Sedoheptulose-1,7-bisphosphatase (one of only three enzymes of the Calvin cycle which are unique to plants) cleaves sedoheptulose-1,7-bisphosphate into sedoheptulose-7-phosphate, releasing an inorganic phosphate ion into solution.
 * 7) Fixation of a third CO2 generates two more G3P. The ketose S7P has two carbons removed by transketolase, giving ribose-5-phosphate (R5P), and the two carbons remaining on transketolase are transferred to one of the G3P, giving another Xu5P. This leaves one G3P as the product of fixation of 3 CO2, with generation of three pentoses which can be converted to Ru5P.
 * 8) R5P is converted into ribulose-5-phosphate (Ru5P, RuP) by phosphopentose isomerase. Xu5P is  converted into RuP by phosphopentose epimerase.
 * 9) Finally, phosphoribulokinase (another plant unique enzyme of the pathway) phosphorylates RuP into RuBP, ribulose-1,5-bisphosphate, completing the Calvin cycle. This requires the input of one ATP.

Thus, of 6 G3P produced, three RuBP (5C) are made totalling 15 carbons, with only one available for subsequent conversion to hexose. This required 9 ATPs and 6 NADPH per 3 CO2.

RuBisCO also reacts competitively with O2 instead of CO2 in photorespiration. The rate of photorespiration is higher at high temperatures. "photorespiration" turns RuBP into 3PGA and 2-phosphoglycolate, a 2-carbon molecule which can be converted via glycolate and glyoxalate to glycine. Via the glycine cleavage system and tetrahydrofolate, two glycines are converted into serine +CO2. Serine can be converted back to 3-phosphoglycerate. Thus, only 3 of 4 carbons from two phosphoglycolates can be converted back to 3PGA. Obviously photorespiration has very negative consequences for the plant, because rather than fixing CO2, this process leads to loss of CO2. C4 carbon fixation evolved to circumvent photorespiration, but can only occur in certain plants living in very warm or tropical climates.

Products of the Calvin cycle
The immediate product of the Calvin cycle is glyceraldehyde-3-phosphate (G3P) and water. Two G3P molecules (or one F6P molecule) that have exited the cycle are used to make larger carbohydrates. In simplified versions of the Calvin cycle they may be converted to F6P or F5P after exit, but this conversion is also part of the cycle.

Hexose isomerase converts about half of the F6P molecules in to glucose-6-phosphate. These are phosphorescent and the glucose can be used to form starch, which is stored in, for example, potatoes, or cellulose used to build up cell walls. Glucose, with fructose, forms sucrose, a non-reducing sugar which is a stable storage sugar, unlike glucose.