Editing Chloroplast (section)

==== Dark reactions ====
{{Main|Dark reactions}}

{{Plain image with caption|File:Calvin-cycle4.svg|'''The Calvin cycle''' ''(Interactive diagram)'' The [[Calvin cycle]] incorporates carbon dioxide into sugar molecules.|435px|right|top|triangle|#ccc|image override=}}
<!--{{Calvin cycle}}-->

The [[Calvin cycle]], also known as the [[dark reactions]], is a series of biochemical reactions that fixes [[CO2|CO<sub>2</sub>]] into [[Glyceraldehyde 3-phosphate|G3P]] sugar molecules and uses the energy and electrons from the [[Adenosine triphosphate|ATP]] and [[NADPH]] made in the light reactions. The Calvin cycle takes place in the stroma of the chloroplast.<ref name="Campbell-2009d" />

While named ''"the dark reactions"'', in most plants, they take place in the light, since the dark reactions are dependent on the products of the light reactions.<ref name="Campbell-2009g" />

===== Carbon fixation and G3P synthesis =====

The Calvin cycle starts by using the enzyme [[RuBisCO]] to fix CO<sub>2</sub> into five-carbon [[Ribulose bisphosphate]] (RuBP) molecules. The result is unstable six-carbon molecules that immediately break down into three-carbon molecules called [[3-phosphoglyceric acid]], or 3-PGA.
The [[Adenosine triphosphate|ATP]] and [[NADPH]] made in the light reactions is used to convert the 3-PGA into [[glyceraldehyde-3-phosphate]], or G3P sugar molecules. Most of the G3P molecules are recycled back into RuBP using energy from more ATP, but one out of every six produced leaves the cycle—the end product of the dark reactions.<ref name="Campbell-2009d" />

===== Sugars and starches =====

{{Plain image with caption|File:Saccharose2.svg|Sucrose is made up of a [[glucose]] monomer (left), and a [[fructose]] monomer (right).|width=220px|align=left|caption position=top|triangle=triangle|triangle color=#aaa}}

Glyceraldehyde-3-phosphate can double up to form larger sugar molecules like [[glucose]] and [[fructose]]. These molecules are processed, and from them, the still larger [[sucrose]], a [[disaccharide]] commonly known as table sugar, is made, though this process takes place outside of the chloroplast, in the [[cytoplasm]].<ref name="Berg-2002a">{{cite book| first1=Jeremy M | last1=Berg | first2=John L | last2=Tymoczko | first3=Lubert | last3=Stryer | name-list-style=vanc |title=Biochemistry|year=2002|publisher=W. H. Freeman|location=New York, NY [u.a.]|isbn=0-7167-3051-0|pages=Section 20.1|edition=5. ed., 4. print.|url=https://archive.org/details/biochemistrychap00jere| url-access=registration }}</ref>

Alternatively, glucose [[monomers]] in the chloroplast can be linked together to make [[starch]], which accumulates into the [[chloroplast starch granule|starch grains]] found in the chloroplast.<ref name="Berg-2002a" />
Under conditions such as high atmospheric CO<sub>2</sub> concentrations, these starch grains may grow very large, distorting the grana and thylakoids. The starch granules displace the thylakoids, but leave them intact.<ref name="Wample-1983" />
Waterlogged [[root]]s can also cause [[starch]] buildup in the chloroplasts, possibly due to less [[sucrose]] being exported out of the chloroplast (or more accurately, the [[plant cell]]). This depletes a plant's [[free phosphate]] supply, which indirectly stimulates chloroplast starch synthesis.<ref name="Wample-1983">{{cite journal | vauthors=Wample RL, Davis RW | title=Effect of Flooding on Starch Accumulation in Chloroplasts of Sunflower (Helianthus annuus L.) | journal=Plant Physiology | volume=73 | issue=1 | pages=195–8 | date=September 1983 | pmid=16663176 | pmc=1066435 | doi=10.1104/pp.73.1.195 }}</ref>
While linked to low photosynthesis rates, the starch grains themselves may not necessarily interfere significantly with the efficiency of photosynthesis,<ref>{{cite journal| vauthors=Carmi A, Shomer I |year=1979|title=Starch Accumulation and Photosynthetic Activity in Primary Leaves of Bean (''Phaseolus vulgaris'' L.)|journal=Annals of Botany|volume=44|issue=4|pages=479–484|doi=10.1093/oxfordjournals.aob.a085756 }}</ref> and might simply be a side effect of another photosynthesis-depressing factor.<ref name="Wample-1983" />

===== Photorespiration =====

[[Photorespiration]] can occur when the oxygen concentration is too high. RuBisCO cannot distinguish between oxygen and carbon dioxide very well, so it can accidentally add O<sub>2</sub> instead of CO<sub>2</sub> to [[RuBP]]. This process reduces the efficiency of photosynthesis—it consumes ATP and oxygen, releases CO<sub>2</sub>, and produces no sugar. It can waste up to half the carbon fixed by the Calvin cycle.<ref name="Pearson-2009" /> Several mechanisms have evolved in different lineages that raise the carbon dioxide concentration relative to oxygen within the chloroplast, increasing the efficiency of photosynthesis. These mechanisms are called [[carbon dioxide concentrating mechanism]]s, or CCMs. These include [[Crassulacean acid metabolism]], [[C4 carbon fixation|{{C4}} carbon fixation]],<ref name="Pearson-2009" /> and [[pyrenoid]]s. Chloroplasts in {{C4}} plants are notable as they exhibit a distinct [[#Specialized chloroplasts in C4 plants|chloroplast dimorphism]].