Editing Calvin cycle (section)

==Calvin cycle==
{{Citations needed|section|date=December 2023}}
[[Image:Calvin-cycle4.svg|thumb|300px|class=skin-invert-image|Overview of the Calvin cycle and [[carbon fixation]]]]

The '''Calvin cycle''', '''Calvin–Benson–Bassham (CBB) cycle''', '''reductive pentose phosphate cycle (RPP cycle)''' or '''C3 cycle''' is a series of [[biochemistry|biochemical]] [[redox]] reactions that take place in the [[stroma (fluid)|stroma]] of [[chloroplast]] in [[photosynthesis|photosynthetic]] [[organism]]s. The cycle was discovered in 1950 by [[Melvin Calvin]], [[James Bassham]], and [[Andrew Benson]] at the [[University of California, Berkeley]] by using the [[radioactive]] [[isotope]] [[carbon-14]].<ref>{{cite journal |vauthors=Bassham J, Benson A, Calvin M |year=1950 |title=The path of carbon in photosynthesis |url=http://www.jbc.org/cgi/reprint/185/2/781.pdf |url-status=dead |journal=J Biol Chem |volume=185 |issue=2 |pages=781–7 |doi=10.2172/910351 |pmid=14774424 |archive-url=https://web.archive.org/web/20090219123745/http://www.jbc.org/cgi/reprint/185/2/781.pdf |archive-date=2009-02-19 |access-date=2013-07-03}}</ref>

Photosynthesis occurs in two stages in a cell. In the first stage, light-dependent reactions capture the energy of light and use it to make the energy-storage molecule [[Adenosine triphosphate|ATP]] and the moderate-energy hydrogen carrier [[NADPH]]. The Calvin cycle uses these compounds to convert [[carbon dioxide]] and [[water]] into [[organic compound]]s<ref>{{cite book | last = Campbell | first = Neil A. |author2=Brad Williamson |author3=Robin J. Heyden | title = Biology: Exploring Life | publisher = Pearson Prentice Hall | year = 2006 | location = Boston, Massachusetts | url = http://www.phschool.com/el_marketing.html | isbn = 0-13-250882-6 }}</ref> that can be used by the organism (and by animals that feed on it). This set of reactions is also called ''carbon fixation''. The key [[enzyme]] of the cycle is called [[RuBisCO]]. In the following biochemical equations, the chemical species (phosphates and carboxylic acids) exist in equilibria among their various ionized states as governed by the [[pH]].{{Citation needed|date=December 2023}}

The enzymes in the Calvin cycle are functionally equivalent to most enzymes used in other metabolic pathways such as  [[gluconeogenesis]] and the [[pentose phosphate pathway]], but the enzymes in the Calvin cycle are found in the chloroplast stroma instead of the cell [[cytosol]], 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 being respired to carbon dioxide. Energy (in the form of ATP) would be wasted in carrying out these reactions when they have no [[primary production|net productivity]].{{Citation needed|date=December 2023}}

The sum of reactions in the Calvin cycle is the following:{{Citation needed|date=December 2023}}
:3 {{chem|CO|2}} + 6 [[Nicotinamide adenine dinucleotide phosphate|NADPH]] + 9 [[Adenosine triphosphate|ATP]] + 5 {{chem|H|2|O}} → [[glyceraldehyde-3-phosphate]] (G3P)  + 6 [[Nicotinamide adenine dinucleotide phosphate|NADP<sup>+</sup>]] + 9 [[Adenosine diphosphate|ADP]] + 8 P<sub>i</sub> &nbsp;&nbsp;(P<sub>i</sub> = inorganic [[phosphate]])
[[Hexose]] (six-carbon) sugars are not products of the Calvin cycle. Although many texts list a product of photosynthesis as {{chem|C|6|H|12|O|6}}, this is mainly for convenience to match the equation of [[aerobic 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", namely, [[glyceraldehyde-3-phosphate]] (G3P).{{Citation needed|date=December 2023}}

===Steps===
In the first stage of the Calvin cycle, a {{CO2}} molecule is incorporated into one of two three-carbon molecules ([[glyceraldehyde 3-phosphate]] or G3P), where it uses up two molecules of [[Adenosine triphosphate|ATP]] and two molecules of [[NADPH]], which had been produced in the light-dependent stage. The three steps involved are:{{Citation needed|date=December 2023}}
[[Image:Calvin cycle step 1.svg|thumb|450px|class=skin-invert-image|Calvin cycle step 1 (black circles represent carbon atoms)]]
[[Image:Calvin cycle step 2 (doubled).svg|thumb|532px|class=skin-invert-image|Calvin cycle steps 2 and 3 combined]]
# The enzyme [[RuBisCO]] catalyses the carboxylation of [[ribulose-1,5-bisphosphate]], RuBP, a 5-carbon compound, by carbon dioxide (a total of 6 carbons) in a two-step reaction.<ref>{{cite book |author=Farazdaghi H |title=Photosynthesis in silico |chapter=Modeling the Kinetics of Activation and Reaction of Rubisco from Gas Exchange |series=Advances in Photosynthesis and Respiration |volume=29 |issue=IV |pages=275–294 |year=2009 |doi=10.1007/978-1-4020-9237-4_12 |isbn=978-1-4020-9236-7 }}</ref> The product of the first step is enediol-enzyme complex that can capture {{chem|CO|2}} or {{chem|O|2}}. Thus, enediol-enzyme complex is the real carboxylase/oxygenase. The {{chem|CO|2}} that is captured by enediol in second step produces an unstable six-carbon compound called 2-carboxy 3-keto 1,5-biphosphoribotol (CKABP<ref name="lorimer86">{{cite journal|last1=Lorimer|first1=G.H.|last2=Andrews|first2=T.J.|last3=Pierce|first3=J.|last4=Schloss|first4=J.V.|title=2´-carboxy-3-keto-D-arabinitol 1,5-bisphosphate, the six-carbon intermediate of the ribulose bisphosphate carboxylase reaction|date=1986|doi=10.1098/rstb.1986.0046|url=https://royalsocietypublishing.org/doi/10.1098/rstb.1986.0046|journal=Phil. Trans. R. Soc. Lond. B|volume=313|issue=1162 |pages=397–407|bibcode=1986RSPTB.313..397L |url-access=subscription}}</ref>) (or 3-keto-2-carboxyarabinitol 1,5-bisphosphate) that immediately splits into 2 molecules of [[3-phosphoglycerate]] (also written as 3-phosphoglyceric acid, PGA, 3PGA, or 3-PGA), a 3-carbon compound.<ref>Campbell, and Reece Biology: 8th Edition, page 198. Benjamin Cummings, December 7, 2007.</ref>
# The enzyme [[phosphoglycerate kinase]] catalyses the phosphorylation of 3-PGA by ATP (which was produced in the light-dependent stage). [[1,3-Bisphosphoglycerate]] (glycerate-1,3-bisphosphate) and [[Adenosine diphosphate|ADP]] are the products. (However, note that two 3-PGAs are produced for every {{chem|CO|2}} that enters the cycle, so this step utilizes two [[Adenosine triphosphate|ATP]] per {{chem|CO|2}} fixed.){{Citation needed|date=December 2023}}
# The enzyme [[Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)|glyceraldehyde 3-phosphate dehydrogenase]] catalyses the [[redox|reduction]] of 1,3BPGA by [[NADPH]] (which is another product of the light-dependent stage). [[Glyceraldehyde 3-phosphate]] (also called G3P, GP, TP, PGAL, GAP) is produced, and the [[NADPH]] itself is oxidized and becomes [[NADP+|NADP<sup>+</sup>]]. Again, two [[NADPH]] are utilized per {{chem|CO|2}} fixed.{{Citation needed|date=December 2023}}

[[Image:Calvin cycle step 3.svg|thumb|535px|class=skin-invert-image|Regeneration stage of the Calvin cycle]]
The next stage in the Calvin cycle is to regenerate [[RuBP]]. Five G3P molecules produce three [[RuBP]] molecules, using up three molecules of ATP. Since each {{CO2}} molecule produces two G3P molecules, three {{CO2}} molecules produce six G3P molecules, of which five are used to regenerate [[RuBP]], leaving a net gain of one G3P molecule per three {{CO2}} molecules (as would be expected from the number of carbon atoms involved).{{Citation needed|date=December 2023}}
[[File:V2 (Фаза регенерации цикл Кальвина).svg|thumb|270x270px|class=skin-invert-image|The regeneration stage of Calvin's cycle. Substances and their parts are outlined in colors: green - carbon accepting aldoses, pink - ketoses-donors of three-carbon groups, yellow - parts of ketoses remaining after donation of two-carbon keto-groups highlighted in orange. Enzymes are also highlighted: aldolases in purple and transketolases in red.]]
[[File:Calvin cycle.svg|thumb|class=skin-invert-image|Simplified C3 cycle with structural formulas]]
The regeneration stage can be broken down into a series of steps.
# [[Triose phosphate isomerase]] converts one of the G3P reversibly into [[dihydroxyacetone phosphate]] (DHAP), also a 3-carbon molecule.{{Citation needed|date=December 2023}}
# [[Aldolase]] and [[fructose-1,6-bisphosphatase]] convert a G3P and a DHAP into [[fructose 6-phosphate]] (6C). A phosphate ion is lost into solution.{{Citation needed|date=December 2023}}
# Then fixation of another {{chem|CO|2}} generates two more G3P.{{Citation needed|date=December 2023}}
# F6P has two carbons removed by [[transketolase]], giving [[erythrose-4-phosphate]] (E4P). The two carbons on [[transketolase]] are added to a G3P, giving the ketose [[xylulose-5-phosphate]] (Xu5P).{{Citation needed|date=December 2023}}
# E4P and a DHAP (formed from one of the G3P from the second {{chem|CO|2}} fixation) are converted into [[sedoheptulose-1,7-bisphosphate]] (7C) by aldolase enzyme.{{Citation needed|date=December 2023}}
# [[Sedoheptulose-bisphosphatase|Sedoheptulose-1,7-bisphosphatase]] (one of only three enzymes of the Calvin cycle that are unique to plants) cleaves [[sedoheptulose-1,7-bisphosphate]] into [[sedoheptulose-7-phosphate]], releasing an inorganic phosphate ion into solution.{{Citation needed|date=December 2023}}
# Fixation of a third {{chem|CO|2}} 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 {{chem|CO|2}}, with generation of three pentoses that can be converted to Ru5P.{{Citation needed|date=December 2023}}
# R5P is converted into [[ribulose-5-phosphate]] (Ru5P, RuP) by [[phosphopentose isomerase]]. Xu5P is converted into RuP by [[phosphopentose epimerase]].{{Citation needed|date=December 2023}}
# 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.{{Citation needed|date=December 2023}}

Thus, of six G3P produced, five are used to make three RuBP (5C) molecules (totaling 15 carbons), with only one G3P available for subsequent conversion to hexose. This requires nine ATP molecules and six NADPH molecules per three {{chem|CO|2}} molecules. The equation of the overall Calvin cycle is shown diagrammatically below.{{Citation needed|date=December 2023}}
[[Image:Calvin cycle overall.svg|thumb|center|580px|class=skin-invert-image|The overall equation of the Calvin cycle (black circles represent carbon atoms)]]

[[RuBisCO]] also reacts competitively with {{chem|O|2}} instead of {{chem|CO|2}} in [[photorespiration]]. The rate of photorespiration is higher at high temperatures. Photorespiration turns RuBP into 3-PGA and 2-phosphoglycolate, a 2-carbon molecule that can be converted via glycolate and glyoxylate to glycine. Via the glycine cleavage system and tetrahydrofolate, two glycines are converted into serine plus {{chem|CO|2}}. Serine can be converted back to 3-phosphoglycerate. Thus, only 3 of 4 carbons from two phosphoglycolates can be converted back to 3-PGA. It can be seen that photorespiration has very negative consequences for the plant, because, rather than fixing {{chem|CO|2}}, this process leads to loss of {{chem|CO|2}}. [[C4 carbon fixation]] evolved to circumvent photorespiration, but can occur only in certain plants native to very warm or tropical climates—corn, for example. Furthermore, RuBisCOs catalyzing the light-independent reactions of photosynthesis generally exhibit an improved specificity for CO<sub>2</sub> relative to O<sub>2</sub>, in order to minimize the oxygenation reaction. This improved specificity evolved after RuBisCO incorporated a new protein subunit.<ref>{{cite journal |last1=Schulz |first1=L |last2=Guo |first2=Z |last3=Zarzycki |first3=J |last4=Steinchen |first4=W |last5=Schuller |first5=JM |last6=Heimerl |first6=T |last7=Prinz |first7=S |last8=Mueller-Cajar |first8=O |last9=Erb |first9=TJ |last10=Hochberg |first10=GKA |title=Evolution of increased complexity and specificity at the dawn of form I Rubiscos |url=https://www.science.org/doi/10.1126/science.abq1416 |journal=Science |pages=155–160 |language=en |doi=10.1126/science.abq1416 |date=14 October 2022|volume=378 |issue=6616 |pmid=36227987 |bibcode=2022Sci...378..155S |s2cid=252897276 |url-access=subscription }}</ref>

===Products===
The immediate products of one turn of the Calvin cycle are 2 glyceraldehyde-3-phosphate (G3P) molecules, 3 ADP, and 2 NADP<sup>+</sup>. (ADP and NADP<sup>+</sup> are not really "products". They are regenerated and later used again in the [[light-dependent reactions]]). Each G3P molecule is composed of 3 carbons. For the Calvin cycle to continue, RuBP (ribulose 1,5-bisphosphate) must be regenerated. So, 5 out of 6 carbons from the 2 G3P molecules are used for this purpose. Therefore, there is only 1 net carbon produced to play with for each turn. To create 1 surplus G3P requires 3 carbons, and therefore 3 turns of the Calvin cycle. To make one glucose molecule (which can be created from 2 G3P molecules) would require 6 turns of the Calvin cycle. Surplus G3P can also be used to form other carbohydrates such as starch, sucrose, and cellulose, depending on what the plant needs.<ref>Russell, Wolfe et al.''Biology: Exploring the Diversity of Life''.Toronto:Nelson College Indigenous,1st ed, Vol. 1, 2010, pg 151</ref>