Editing Chloroplast (section)

== Structure ==
[[File:Chloroplast in leaf of Anemone sp TEM 12000x.png|thumb|right|[[Transmission electron microscope]] image of a chloroplast. Grana of [[thylakoid]]s and their connecting lamellae are clearly visible.]]

In [[Embryophyte|land plants]], chloroplasts are generally lens-shaped, 3–10 μm in diameter and 1–3 μm thick.<ref name="Wise-2007b">{{cite book| vauthors=Wise RR, Hoober JK |year=2007|title=The Structure and Function of Plastids|publisher=Springer|isbn=978-1-4020-6570-5|url=https://books.google.com/books?id=FKeCVPbJ3asC|pages= 32–33}}</ref><ref name="Milo"/> Corn seedling chloroplasts are ≈20 μm<sup>3</sup> in volume.<ref name="Milo"/> Greater diversity in chloroplast shapes exists among the [[algae]], which often contain a single chloroplast<ref name="Kim-2009" /> that can be shaped like a net (e.g., ''[[Oedogonium]]''),<ref>{{cite web|title=Oedogonium Link ex Hirn, 1900: 17|url=http://www.algaebase.org/search/genus/detail/?genus_id=43424|publisher=algaeBASE|access-date=19 May 2013}}</ref> a cup (e.g., ''[[Chlamydomonas]]''),<ref>{{cite web|title=Chlamydomonas Ehrenberg, 1833: 288|url=http://www.algaebase.org/search/genus/detail/?genus_id=43319|publisher=algaeBASE|access-date=19 May 2013}}</ref> a ribbon-like spiral around the edges of the cell (e.g., ''[[Spirogyra]]''),<ref>{{cite web|title=Spirogyra Link, 1820: 5|url=http://www.algaebase.org/search/genus/detail/?genus_id=43564|publisher=algaeBASE|access-date=19 May 2013}}</ref> or slightly twisted bands at the cell edges (e.g., ''[[Sirogonium]]'').<ref>{{cite web|title=Sirogonium Kützing, 1843: 278|url=http://www.algaebase.org/search/genus/detail/?genus_id=43563|publisher=algaeBASE|access-date=19 May 2013}}</ref> Some algae have two chloroplasts in each cell; they are star-shaped in ''[[Zygnema]]'',<ref>{{cite web|title=Zygnema C.Agardh, 1817: xxxii, 98|url=http://www.algaebase.org/search/genus/detail/?genus_id=43566|publisher=algaeBASE|access-date=19 May 2013}}</ref> or may follow the shape of half the cell in [[order (biology)|order]] [[Desmidiales]].<ref>{{cite web|title=Micrasterias C.Agardh ex Ralfs, 1848: 68|url=http://www.algaebase.org/search/genus/detail/?genus_id=43536|publisher=algaeBASE|access-date=19 May 2013}}</ref> In some algae, the chloroplast takes up most of the cell, with pockets for the [[Cell nucleus|nucleus]] and other organelles,<ref name="Kim-2009">{{cite book |doi=10.1007/978-3-540-68696-5_1 |chapter=Diversity and Evolution of Plastids and Their Genomes |title=The Chloroplast |series=Plant Cell Monographs |year=2009 | vauthors=Kim E, Archibald JM |isbn=978-3-540-68692-7 |volume=13 |pages=1–39 |s2cid=83672683 |editor1-first=Anna Stina |editor1-last=Sandelius |editor2-first=Henrik |editor2-last=Aronsson }}</ref> for example, some species of ''[[Chlorella]]'' have a cup-shaped chloroplast that occupies much of the cell.<ref>{{cite book | vauthors=John DM, Brook AJ, Whitton BA |title=The freshwater algal flora of the British Isles: an identification guide to freshwater and terrestrial algae |year=2002 |publisher=Cambridge University Press |location=Cambridge |isbn=978-0-521-77051-4 |page=335 |url=https://books.google.com/books?id=Sc4897dfM_MC&pg=PA335 }}</ref>

All chloroplasts have at least three membrane systems—the outer chloroplast membrane, the inner chloroplast membrane, and the [[thylakoid]] system. The two innermost [[cell membrane|lipid-bilayer membranes]]<ref name="Fuks-1996">{{cite journal |vauthors=Fuks B, Homblé F |date=October 1996 |title=Mechanism of proton permeation through chloroplast lipid membranes |journal=Plant Physiology |volume=112 |issue=2 |pages=759–66 |doi=10.1104/pp.112.2.759 |pmc=158000 |pmid=8883387}}</ref> that surround all chloroplasts correspond to the outer and inner [[cell membrane|membranes]] of the ancestral cyanobacterium's [[gram negative]] cell wall,<ref name="Keeling-2004" /><ref>{{cite journal |vauthors=Joyard J, Block MA, Douce R |date=August 1991 |title=Molecular aspects of plastid envelope biochemistry |journal=European Journal of Biochemistry |volume=199 |issue=3 |pages=489–509 |doi=10.1111/j.1432-1033.1991.tb16148.x |pmid=1868841 |doi-access=free}}</ref><ref>{{cite encyclopedia |title=Chloroplast |encyclopedia=Encyclopedia of Science |url=http://www.daviddarling.info/encyclopedia/C/chloroplasts.html |access-date=27 December 2012}}</ref> and not the [[phagosomal]] membrane from the host, which was probably lost.<ref name="Keeling-2004" /> Chloroplasts that are the product of [[#Endosymbiosis|secondary endosymbiosis]] may have additional membranes surrounding these three.<ref name="Chaal-2005" /> Inside the outer and inner chloroplast membranes is the chloroplast [[stroma (fluid)|stroma]], a semi-gel-like fluid<ref name="Wise-2006b">{{cite book|last1=Wise|first1=Robert R.|last2=Hoober|first2=J. Kenneth|name-list-style=vanc|title=The structure and function of plastids|year=2006|publisher=Springer|location=Dordrecht|isbn=978-1-4020-4061-0|pages=3–21|url=http://www.uwosh.edu/biology/faculty-and-staff/faculty/wise/publications/wise-the-diversity-of-plastid|access-date=21 May 2013|archive-date=8 March 2016|archive-url=https://web.archive.org/web/20160308205912/http://www.uwosh.edu/biology/faculty-and-staff/faculty/wise/publications/wise-the-diversity-of-plastid|url-status=dead}}</ref> that makes up much of a chloroplast's volume, and in which the thylakoid system floats.

{{plain image with caption|File:Chloroplast structure.svg|'''Chloroplast ultrastructure''' ''(interactive diagram)'' Chloroplasts have at least three distinct membrane systems, and a variety of things can be found in their [[stroma (fluid)|stroma]].|500px|left|bottom|triangle|#3cb14d|image override=<div style="position: relative; left: 2px;">{{Chloroplast structure}}</div>}}

{{See also|Chloroplast membrane}}

There are some common misconceptions about the outer and inner chloroplast membranes. The fact that chloroplasts are surrounded by a double membrane is often cited as evidence that they are the descendants of endosymbiotic [[cyanobacteria]]. This is often interpreted as meaning the outer chloroplast membrane is the product of the host's [[cell membrane]] infolding to form a vesicle to surround the ancestral [[cyanobacterium]]—which is not true—both chloroplast membranes are [[Homology (biology)|homologous]] to the cyanobacterium's original double membranes.<ref name="Keeling-2004" />

The chloroplast double membrane is also often compared to the [[Mitochondrion|mitochondrial]] double membrane. This is not a valid comparison—the inner mitochondria membrane is used to run [[proton pumps]] and carry out [[oxidative phosphorylation]] across to generate [[Adenosine triphosphate|ATP]] energy. The only chloroplast structure that can be considered [[analogy (biology)|analogous]] to it is the internal thylakoid system. Even so, in terms of "in-out", the direction of chloroplast [[hydronium|H{{sup|+}}]] ion flow is in the opposite direction compared to oxidative phosphorylation in mitochondria.<ref name="Wise-2006b" /><ref name="Campbell-2009b">{{cite book | vauthors=Campbell NA, Reece JB, Urry LA, Cain ML, Wasserman, Minorsky PV, Jackson RB |title=Biology | edition=8th | year=2009 |publisher=Benjamin Cummings (Pearson) | pages=196–197 | isbn=978-0-8053-6844-4 }}</ref> In addition, in terms of function, the inner chloroplast membrane, which regulates metabolite passage and synthesizes some materials, has no counterpart in the mitochondrion.<ref name="Wise-2006b" />
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=== Outer chloroplast membrane ===

{{main|Chloroplast membrane}}

The outer chloroplast membrane is a semi-porous membrane that small molecules and [[ions]] can easily diffuse across.<ref>{{cite journal | vauthors=Koike H, Yoshio M, Kashino Y, Satoh K | title=Polypeptide composition of envelopes of spinach chloroplasts: two major proteins occupy 90% of outer envelope membranes | journal=Plant & Cell Physiology | volume=39 | issue=5 | pages=526–32 | date=May 1998 | pmid=9664716 | doi=10.1093/oxfordjournals.pcp.a029400 | doi-access=free }}</ref> However, it is not permeable to larger [[protein]]s, so chloroplast [[polypeptides]] being synthesized in the cell [[cytoplasm]] must be transported across the outer chloroplast membrane by the [[TOC complex]], or ''[[translocon|'''t'''ranslocon]] on the '''o'''uter '''c'''hloroplast'' membrane.<ref name="Soll-2004" />

The chloroplast membranes sometimes protrude out into the cytoplasm, forming a [[stromule]], or [[stroma (fluid)|'''strom'''a]]-containing tub'''ule'''. Stromules are very rare in chloroplasts, and are much more common in other [[plastids]] like [[chromoplasts]] and [[amyloplasts]] in petals and roots, respectively.<ref name="Köhler-2000">{{cite journal | vauthors=Köhler RH, Hanson MR | title=Plastid tubules of higher plants are tissue-specific and developmentally regulated | journal=Journal of Cell Science | volume=113 | issue=Pt 1 | pages=81–9 | date=January 2000 | doi=10.1242/jcs.113.1.81 | pmid=10591627 | url=http://jcs.biologists.org/cgi/pmidlookup?view=long&pmid=10591627 | url-status=live| archive-url=https://web.archive.org/web/20160920012721/http://jcs.biologists.org/cgi/pmidlookup?view=long&pmid=10591627 | archive-date=20 September 2016 }}</ref><ref name="Gray-2001">{{cite journal |vauthors=Gray JC, Sullivan JA, Hibberd JM, Hansen MR |title=Stromules: mobile protrusions and interconnections between plastids |journal=Plant Biology |volume=3 |issue=3|pages=223–33 |year=2001 |doi=10.1055/s-2001-15204|bibcode=2001PlBio...3..223G |s2cid=84474739 }}</ref> They may exist to increase the chloroplast's [[surface area to volume ratio|surface area]] for cross-membrane transport, because they are often branched and tangled with the [[endoplasmic reticulum]].<ref name="Schattat-2011">{{cite journal | vauthors=Schattat M, Barton K, Baudisch B, Klösgen RB, Mathur J | title=Plastid stromule branching coincides with contiguous endoplasmic reticulum dynamics | journal=Plant Physiology | volume=155 | issue=4 | pages=1667–77 | date=April 2011 | pmid=21273446 | pmc=3091094 | doi=10.1104/pp.110.170480 }}</ref> When they were first observed in 1962, some plant biologists dismissed the structures as artifactual, claiming that stromules were just oddly shaped chloroplasts with constricted regions or [[dividing chloroplasts]].<ref name="Schattat-2012">{{cite journal | vauthors=Schattat MH, Griffiths S, Mathur N, Barton K, Wozny MR, Dunn N, Greenwood JS, Mathur J | display-authors=6 | title=Differential coloring reveals that plastids do not form networks for exchanging macromolecules | journal=The Plant Cell | volume=24 | issue=4 | pages=1465–77 | date=April 2012 | pmid=22474180 | pmc=3398557 | doi=10.1105/tpc.111.095398 | bibcode=2012PlanC..24.1465S }}</ref> However, there is a growing body of evidence that stromules are functional, integral features of plant cell plastids, not merely artifacts.<ref>{{cite journal | vauthors=Brunkard JO, Runkel AM, Zambryski PC | title=Chloroplasts extend stromules independently and in response to internal redox signals | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=112 | issue=32 | pages=10044–9 | date=August 2015 | pmid=26150490 | pmc=4538653 | doi=10.1073/pnas.1511570112 | bibcode=2015PNAS..11210044B | doi-access=free }}</ref>

=== Intermembrane space and peptidoglycan wall ===
[[File:Glaucocystis sp.jpg|thumb|Instead of an intermembrane space, [[glaucophyte algae]] have a [[peptidoglycan wall]] between their inner and outer chloroplast membranes.]]

Usually, a thin intermembrane space about 10–20 [[nanometers]] thick exists between the outer and inner chloroplast membranes.<ref name="Burgess-1989a">{{cite book|last=Burgess|first=Jeremy | name-list-style=vanc |title=An introduction to plant cell development|year=1989|publisher=Cambridge university press|location=Cambridge|isbn=0-521-31611-1|page=46|url=https://books.google.com/books?id=r808AAAAIAAJ&pg=PA46|edition=Pbk.}}</ref>

[[Glaucophyte algal]] chloroplasts have a [[peptidoglycan]] layer between the chloroplast membranes. It corresponds to the [[peptidoglycan cell wall]] of their [[cyanobacterial]] ancestors, which is located between their two cell membranes. These chloroplasts are called ''muroplasts'' (from Latin ''"mura"'', meaning "wall"). Other chloroplasts were assumed to have lost the cyanobacterial wall, leaving an intermembrane space between the two chloroplast envelope membranes,<ref name="Wise-2006b" /> but has since been found also in moss, lycophytes and ferns.<ref>[https://academic.oup.com/plphys/article/190/1/165/6574362 Plant peptidoglycan precursor biosynthesis: Conservation between moss chloroplasts and Gram-negative bacteria]</ref>

=== Inner chloroplast membrane ===

{{main|Chloroplast membrane}}

The inner chloroplast membrane borders the stroma and regulates passage of materials in and out of the chloroplast. After passing through the [[TOC complex]] in the outer chloroplast membrane, [[polypeptides]] must pass through the [[TIC complex]] ''([[translocon|'''t'''ranslocon]] on the '''i'''nner '''c'''hloroplast membrane)'' which is located in the inner chloroplast membrane.<ref name="Soll-2004" />

In addition to regulating the passage of materials, the inner chloroplast membrane is where [[fatty acid]]s, [[lipid]]s, and [[carotenoid]]s are synthesized.<ref name="Wise-2006b" />

==== Peripheral reticulum ====

Some chloroplasts contain a structure called the [[chloroplast peripheral reticulum]].<ref name="Burgess-1989a" /> It is often found in the chloroplasts of [[C4 plant|{{C4}} plants]], though it has also been found in some {{C3}} [[angiosperms]],<ref name="Wise-2006b" /> and even some [[gymnosperm]]s.<ref name="Whatley-1994">{{cite journal|last=Whatley|first=Jean M | name-list-style=vanc |title=The occurrence of a peripheral reticulum in plastids of the gymnosperm Welwitschia mirabilis|journal=New Phytologist|date=5 July 1994|volume=74|issue=2|pages=215–220|doi=10.1111/j.1469-8137.1975.tb02608.x|doi-access=free}}</ref> The chloroplast peripheral reticulum consists of a maze of membranous tubes and vesicles continuous with the [[inner chloroplast membrane]] that extends into the internal [[stroma (fluid)|stromal]] fluid of the chloroplast. Its purpose is thought to be to increase the chloroplast's [[surface area to volume ratio|surface area]] for cross-membrane transport between its stroma and the cell [[cytoplasm]]. The small vesicles sometimes observed may serve as [[transport vesicles]] to shuttle stuff between the [[thylakoid]]s and intermembrane space.<ref name="Wise-2007a" />

=== Stroma ===

{{Main|Stroma (fluid)|l1=Stroma}}

The [[protein]]-rich,<ref name="Wise-2006b" /> [[alkaline]],<ref name="Campbell-2009b" /> [[aqueous]] fluid within the inner chloroplast membrane and outside of the thylakoid space is called the stroma,<ref name="Wise-2006b" /> which corresponds to the [[cytosol]] of the original [[cyanobacterium]]. [[Nucleoid]]s of [[chloroplast DNA]], chloroplast [[ribosome]]s, the thylakoid system with [[plastoglobuli]], [[starch]] granules, and many [[protein]]s can be found floating around in it. The [[Calvin cycle]], which fixes [[CO2|CO{{sub|2}}]] into [[Glyceraldehyde 3-phosphate|G3P]] takes place in the stroma.

==== Chloroplast ribosomes ====

{{plain image with caption|File:Chloroplast and bacterial ribosome comparison.png|'''Chloroplast ribosomes''' Comparison of a chloroplast ribosome (green) and a bacterial ribosome (yellow). Important features common to both ribosomes and chloroplast-unique features are labeled.|300px|right|bottom|triangle|#7ccc1b}}
Chloroplasts have their own ribosomes, which they use to synthesize a small fraction of their proteins. Chloroplast ribosomes are about two-thirds the size of [[Eukaryotic Ribosome (80S)|cytoplasmic ribosomes]] (around 17 [[Nanometre|nm]] vs 25 [[Nanometre|nm]]).<ref name="Burgess-1989a" /> They take [[mRNAs]] transcribed from the [[chloroplast DNA]] and [[translation (biology)|translate]] them into protein. While similar to [[bacterial ribosomes]],<ref name="Campbell-2009c" /> chloroplast translation is more complex than in bacteria, so chloroplast ribosomes include some chloroplast-unique features.<ref name="Manuell-2007">{{cite journal | vauthors=Manuell AL, Quispe J, Mayfield SP | title=Structure of the chloroplast ribosome: novel domains for translation regulation | journal=PLOS Biology | volume=5 | issue=8 | pages=e209 | date=August 2007 | pmid=17683199 | pmc=1939882 | doi=10.1371/journal.pbio.0050209 | doi-access=free }}</ref><ref name="Bieri-2017">{{cite journal |last1=Bieri |first1=P |last2=Leibundgut |first2=M |last3=Saurer |first3=M |last4=Boehringer |first4=D |last5=Ban |first5=N |title=The complete structure of the chloroplast 70S ribosome in complex with translation factor pY. |journal=The EMBO Journal |date=15 February 2017 |volume=36 |issue=4 |pages=475–486 |doi=10.15252/embj.201695959 |pmid=28007896 |pmc=5694952}}</ref>

Small subunit [[ribosomal RNA]]s in several [[Chlorophyta]] and [[euglenid]] chloroplasts lack motifs for [[Shine-Dalgarno sequence]] recognition,<ref name="Lim-2014">{{cite journal | vauthors=Lim K, Kobayashi I, Nakai K | title=Alterations in rRNA-mRNA interaction during plastid evolution | journal=Molecular Biology and Evolution | volume=31 | issue=7 | pages=1728–40 | date=July 2014 | pmid=24710516 | doi=10.1093/molbev/msu120 | doi-access=free }}</ref> which is considered essential for [[Translation (biology)|translation]] initiation in most chloroplasts and [[prokaryote]]s.<ref>{{cite journal | vauthors=Hirose T, Sugiura M | s2cid=10774032 | title=Functional Shine-Dalgarno-like sequences for translational initiation of chloroplast mRNAs | journal=Plant & Cell Physiology | volume=45 | issue=1 | pages=114–7 | date=January 2004 | pmid=14749493 | doi=10.1093/pcp/pch002 | doi-access=free }}</ref><ref>{{cite journal | vauthors=Ma J, Campbell A, Karlin S | title=Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures | journal=Journal of Bacteriology | volume=184 | issue=20 | pages=5733–45 | date=October 2002 | pmid=12270832 | pmc=139613 | doi=10.1128/JB.184.20.5733-5745.2002 }}</ref> Such loss is also rarely observed in other [[plastid]]s and prokaryotes.<ref name="Lim-2014"/><ref>{{cite journal | vauthors=Lim K, Furuta Y, Kobayashi I | title=Large variations in bacterial ribosomal RNA genes | journal=Molecular Biology and Evolution | volume=29 | issue=10 | pages=2937–48 | date=October 2012 | pmid=22446745 | pmc=3457768 | doi=10.1093/molbev/mss101 }}</ref> An additional 4.5S rRNA with homology to the 3' tail of 23S is found in "higher" plants.<ref name="Bieri-2017"/>

==== Plastoglobuli ====

Plastoglobuli ('''singular''' ''plastoglobulus'', sometimes spelled ''plastoglobule(s)''), are spherical bubbles of [[lipid]]s and [[protein]]s<ref name="Wise-2006b" /> about 45–60 nanometers across.<ref name="Austin-2006" /> They are surrounded by a [[lipid monolayer]].<ref name="Austin-2006" /> Plastoglobuli are found in all chloroplasts,<ref name="Burgess-1989a" /> but become more common when the chloroplast is under [[oxidative stress]],<ref name="Austin-2006">{{cite journal | vauthors=Austin JR, Frost E, Vidi PA, Kessler F, Staehelin LA |author5-link=Lucas Andrew Staehelin | title=Plastoglobules are lipoprotein subcompartments of the chloroplast that are permanently coupled to thylakoid membranes and contain biosynthetic enzymes | journal=The Plant Cell | volume=18 | issue=7 | pages=1693–703 | date=July 2006 | pmid=16731586 | pmc=1488921 | doi=10.1105/tpc.105.039859 |bibcode=2006PlanC..18.1693A }}</ref> or when it ages and transitions into a [[gerontoplast]].<ref name="Wise-2006b" /> Plastoglobuli also exhibit a greater size variation under these conditions.<ref name="Austin-2006" /> They are also common in [[etioplasts]], but decrease in number as the etioplasts mature into chloroplasts.<ref name="Austin-2006" />

Plastoglobuli contain both structural proteins and enzymes involved in [[lipid synthesis]] and [[metabolism]]. They contain many types of [[lipid]]s including [[plastoquinone]], [[vitamin E]], [[carotenoid]]s and [[chlorophylls]].<ref name="Austin-2006" />

Plastoglobuli were once thought to be free-floating in the [[stroma (fluid)|stroma]], but it is now thought that they are permanently attached either to a [[thylakoid]] or to another plastoglobulus attached to a thylakoid, a configuration that allows a plastoglobulus to exchange its contents with the thylakoid network.<ref name="Austin-2006" /> In normal green chloroplasts, the vast majority of plastoglobuli occur singularly, attached directly to their parent thylakoid. In old or stressed chloroplasts, plastoglobuli tend to occur in linked groups or chains, still always anchored to a thylakoid.<ref name="Austin-2006" />

Plastoglobuli form when a bubble appears between the layers of the [[lipid bilayer]] of the thylakoid membrane, or bud from existing plastoglobuli—though they never detach and float off into the stroma.<ref name="Austin-2006" /> Practically all plastoglobuli form on or near the highly curved edges of the [[thylakoid]] disks or sheets. They are also more common on stromal thylakoids than on [[granum|granal]] ones.<ref name="Austin-2006" />

{{plain image with caption|File:Chlamydomonas TEM 07.jpg|[[Transmission electron micrograph]] of ''[[Chlamydomonas reinhardtii]]'', a green alga that contains a pyrenoid surrounded by starch.|300px|right|bottom|triangle|#aaa}}

==== Starch granules ====

[[Starch granules]] are very common in chloroplasts, typically taking up 15% of the organelle's volume,<ref name="Crumpton-Taylor-2012" /> though in some other plastids like [[amyloplasts]], they can be big enough to distort the shape of the organelle.<ref name="Burgess-1989a" /> Starch granules are simply accumulations of starch in the stroma, and are not bounded by a membrane.<ref name="Burgess-1989a" />

Starch granules appear and grow throughout the day, as the chloroplast synthesizes [[sugars]], and are consumed at night to fuel [[Cellular respiration|respiration]] and continue sugar export into the [[phloem]],<ref name="Zeeman-2007">{{cite journal | vauthors=Zeeman SC, Delatte T, Messerli G, Umhang M, Stettler M, Mettler T, Streb S, Reinhold H, Kötting O |s2cid=15995416 |doi=10.1071/FP06313 |title=Starch breakdown: Recent discoveries suggest distinct pathways and novel mechanisms |year=2007  |journal=Functional Plant Biology |volume=34 |issue=6 |pages=465–73|pmid=32689375 |bibcode=2007FunPB..34..465Z }}</ref> though in mature chloroplasts, it is rare for a starch granule to be completely consumed or for a new granule to accumulate.<ref name="Crumpton-Taylor-2012">{{cite journal | vauthors=Crumpton-Taylor M, Grandison S, Png KM, Bushby AJ, Smith AM | title=Control of starch granule numbers in Arabidopsis chloroplasts | journal=Plant Physiology | volume=158 | issue=2 | pages=905–16 | date=February 2012 | pmid=22135430 | pmc=3271777 | doi=10.1104/pp.111.186957 }}</ref>

Starch granules vary in composition and location across different chloroplast lineages. In [[red algae]], starch granules are found in the [[cytoplasm]] rather than in the chloroplast.<ref name="Rochaix-1998">{{cite book | vauthors=Rochaix JD |title=The molecular biology of chloroplasts and mitochondria in Chlamydomonas|year=1998|publisher=Kluwer Acad. Publ.|location=Dordrecht [u.a.]|isbn=978-0-7923-5174-0|pages=550–565|url=https://books.google.com/books?id=apv1hktfq_8C&pg=PA550}}</ref> In [[C4 plant|{{C4}} plants]], [[mesophyll tissue|mesophyll]] chloroplasts, which do not synthesize sugars, lack starch granules.<ref name="Wise-2006b" />

==== RuBisCO ====
{{main|RuBisCO}}
{{plain image with caption|File:Rubisco.png|'''RuBisCO''', shown here in a [[space-filling model]], is the main enzyme responsible for [[carbon fixation]] in chloroplasts.|300px|right|top|triangle|#aaa}}

The chloroplast stroma contains many proteins, though the most common and important is [[RuBisCO]], which is probably also the most abundant protein on the planet.<ref name="Campbell-2009b" /> [[RuBisCO]] is the enzyme that fixes [[CO2|CO{{sub|2}}]] into sugar molecules. In [[C3 plant|{{C3}} plants]], RuBisCO is abundant in all chloroplasts, though in [[C4 plant|{{C4}} plants]], it is confined to the [[bundle sheath]] chloroplasts, where the [[Calvin cycle]] is carried out in {{C4}} plants.<ref name="Gunning-1996a" />

=== Pyrenoids ===
{{main|Pyrenoid}}

The chloroplasts of some [[hornworts]]<ref>{{cite journal |doi=10.1071/PP01210 |year=2002 |last1=Hanson |first1=David |last2=Andrews |first2=T. John |last3=Badger |first3=Murray R. | name-list-style=vanc |journal=Functional Plant Biology |volume=29 |issue=3 |pages=407–16 |title=Variability of the pyrenoid-based CO<sub>2</sub> concentrating mechanism in hornworts (Anthocerotophyta)|pmid=32689485 |bibcode=2002FunPB..29..407H }}</ref> and algae contain structures called [[pyrenoid]]s. They are not found in higher plants.<ref name="Ma-2011">{{cite journal | vauthors=Ma Y, Pollock SV, Xiao Y, Cunnusamy K, Moroney JV | title=Identification of a novel gene, CIA6, required for normal pyrenoid formation in Chlamydomonas reinhardtii | journal=Plant Physiology | volume=156 | issue=2 | pages=884–96 | date=June 2011 | pmid=21527423 | pmc=3177283 | doi=10.1104/pp.111.173922 }}</ref> Pyrenoids are roughly spherical and highly refractive bodies which are a site of starch accumulation in plants that contain them. They consist of a matrix opaque to electrons, surrounded by two hemispherical starch plates. The starch is accumulated as the pyrenoids mature.<ref name="Retallack-1970" /> In algae with [[Photosynthesis#Carbon concentrating mechanisms|carbon concentrating mechanisms]], the enzyme [[RuBisCO]] is found in the pyrenoids. Starch can also accumulate around the pyrenoids when CO<sub>2</sub> is scarce.<ref name="Ma-2011" /> Pyrenoids can divide to form new pyrenoids, or be produced [[De novo synthesis|"de novo"]].<ref name="Retallack-1970">{{cite journal | vauthors=Retallack B, Butler RD | title=The development and structure of pyrenoids in Bulbochaete hiloensis | journal=Journal of Cell Science | volume=6 | issue=1 | pages=229–41 | date=January 1970 | doi=10.1242/jcs.6.1.229 | pmid=5417694 }}</ref><ref name="Brown-1970">{{cite journal|last1=Brown|first1=Malcolm R| first2=Howard J | last2=Arnott | name-list-style=vanc |title=Structure and Function of the Algal Pyrenoid|journal=Journal of Phycology|year=1970|url=http://www.botany.utexas.edu/mbrown/papers/hreso/h26.pdf|access-date=31 December 2012|doi=10.1111/j.1529-8817.1970.tb02350.x|volume=6|pages=14–22|s2cid=85604422|url-status=dead|archive-url=https://web.archive.org/web/20130531182224/http://www.botany.utexas.edu/mbrown/papers/hreso/h26.pdf|archive-date=31 May 2013}}</ref>

{{clear}}

=== Thylakoid system ===
{{Main|Thylakoid}}
[[File:Lettuce Chloroplast STEM.jpg|thumb|660px|'''Scanning transmission electron microscope imaging of a chloroplast'''<br />(Top) 10-nm-thick STEM tomographic slice of a lettuce chloroplast. Grana stacks are interconnected by unstacked stromal thylakoids, called "stroma lamellae". Round inclusions associated with the thylakoids are plastoglobules. Scalebar=200&nbsp;nm. See.<ref name="Bussi-2019" />
<br />(Bottom) Large-scale 3D model generated from segmentation of tomographic reconstructions by STEM. grana=yellow; stroma lamellae=green; plastoglobules=purple; chloroplast envelope=blue. See.<ref name="Bussi-2019" /> ]]

Thylakoids (sometimes spelled ''thylakoïds''),<ref>{{cite journal | vauthors=Infanger S, Bischof S, Hiltbrunner A, Agne B, Baginsky S, Kessler F | title=The chloroplast import receptor Toc90 partially restores the accumulation of Toc159 client proteins in the Arabidopsis thaliana ppi2 mutant | journal=Molecular Plant | volume=4 | issue=2 | pages=252–63 | date=March 2011 | pmid=21220583 | doi=10.1093/mp/ssq071 | url=http://doc.rero.ch/record/278856/files/Infanger_S.-Chloroplast_Import-20170222160947-YL.pdf }}</ref> are small interconnected sacks which contain the membranes that the [[light reactions]] of photosynthesis take place on. The word ''thylakoid'' comes from the Greek word ''thylakos'' which means "sack".<ref>{{cite web|title=thylakoid|url=http://www.merriam-webster.com/dictionary/thylakoid|work=Merriam-Webster Dictionary|publisher=Merriam-Webster|access-date=19 May 2013}}</ref>

Suspended within the chloroplast stroma is the [[thylakoid]] system, a highly dynamic collection of membranous sacks called [[thylakoid]]s where [[chlorophyll]] is found and the [[light reactions]] of [[photosynthesis]] happen.<ref name="Campbell-2009g" />
In most [[vascular plant]] chloroplasts, the thylakoids are arranged in stacks called grana,<ref name="Mustárdy-2008" /> though in certain [[C4 plant|{{C4}} plant]] chloroplasts<ref name="Gunning-1996a" /> and some [[algal]] chloroplasts, the thylakoids are free floating.<ref name="Kim-2009" />

==== Thylakoid structure ====

[[File:Thylakoid Structure.jpg|thumb|660px|'''Granum-stroma assembly structure''' The prevailing model of the granum-stroma assembly is stacks of granal thylakoids wrapped by right-handed helical stromal thylakoids which are connected to large parallel sheets of stromal thylakoids and adjacent right-handed helices by left-handed helical structures. (Based on<ref name="Bussi-2019" />).]]

Using a [[light microscope]], it is just barely possible to see tiny green granules—which were named [[Thylakoid|grana]].<ref name="Burgess-1989a" /> With [[electron microscopy]], it became possible to see the thylakoid system in more detail, revealing it to consist of stacks of flat [[thylakoid]]s which made up the grana, and long interconnecting stromal thylakoids which linked different grana.<ref name="Burgess-1989a" />
In the [[transmission electron microscope]], thylakoid membranes appear as alternating light-and-dark bands, 8.5 nanometers thick.<ref name="Burgess-1989a" />

The three-dimensional structure of the thylakoid membrane system has been disputed. Many models have been proposed, the most prevalent being the [[Helix|helical]] model, in which granum stacks of thylakoids are wrapped by helical stromal thylakoids.<ref name="Paolillo-1970">{{cite journal | author1=Paolillo Jr, DJ | title=The three-dimensional arrangement of intergranal lamellae in chloroplasts | journal= J Cell Sci | year=1970 | pmid=5417695 | volume=6 | issue=1| pages=243–55| doi=10.1242/jcs.6.1.243 }}</ref> Another model known as the 'bifurcation model', which was based on the first electron tomography study of plant thylakoid membranes, depicts the stromal membranes as wide lamellar sheets perpendicular to the grana columns which bifurcates into multiple parallel discs forming the granum-stroma assembly.<ref name="Reich Z-2005">{{cite journal | title=Three-dimensional organization of higher-plant chloroplast thylakoid membranes revealed by electron tomography | journal=Plant Cell | volume=17 | issue=9 | pages=2580–6 | year=2005 | pmid=16055630 | doi=10.1105/tpc.105.035030 | author1=Shimoni E | author2=Rav-Hon O | author3=Ohad I | author4=Brumfeld V | author5=Reich Z | pmc=1197436| bibcode=2005PlanC..17.2580S }}</ref> The helical model was supported by several additional works,<ref name="Mustárdy-2008">{{cite journal | vauthors=Mustárdy L, Buttle K, Steinbach G, Garab G | title=The three-dimensional network of the thylakoid membranes in plants: quasihelical model of the granum-stroma assembly | journal=The Plant Cell | volume=20 | issue=10 | pages=2552–7 | date=October 2008 | pmid=18952780 | pmc=2590735 | doi=10.1105/tpc.108.059147 | bibcode=2008PlanC..20.2552M }}</ref><ref name="Austin-2011">{{cite journal | vauthors=Austin JR, Staehelin LA | title=Three-dimensional architecture of grana and stroma thylakoids of higher plants as determined by electron tomography | journal=Plant Physiology | volume=155 | issue=4 | pages=1601–11 | date=April 2011 | pmid=21224341 | pmc=3091084 | doi=10.1104/pp.110.170647 }}</ref> but ultimately it was determined in 2019 that features from both the helical and bifurcation models are consolidated by newly discovered left-handed helical membrane junctions.<ref name="Bussi-2019">{{cite journal | title=Fundamental helical geometry consolidates the plant photosynthetic membrane | journal=Proc Natl Acad Sci USA | volume=116 | issue=44 | pages=22366–22375 | year=2019 | pmid=31611387 | doi=10.1073/pnas.1905994116 | author1=Bussi Y | author2=Shimoni E | author3=Weiner A | author4=Kapon R | author5=Charuvi D | author6=Nevo R | author7=Efrati E | author8=Reich Z | pmc=6825288| bibcode=2019PNAS..11622366B | doi-access=free }}</ref> Likely for ease, the thylakoid system is still commonly depicted by older "hub and spoke" models where the grana are connected to each other by tubes of stromal thylakoids.<ref>{{cite web | url=https://www.sciencephoto.com/media/911533/view/chloroplast-in-a-plant-cell | title=Chloroplast in a plant cell | publisher=TUMEGGY / SCIENCE PHOTO LIBRARY | access-date=19 August 2020}}</ref>

Grana consist of a stacks of flattened circular granal thylakoids that resemble pancakes. Each granum can contain anywhere from two to a hundred thylakoids,<ref name="Burgess-1989a" /> though grana with 10–20 thylakoids are most common.<ref name="Mustárdy-2008" /> Wrapped around the grana are multiple parallel right-handed helical stromal thylakoids, also known as frets or lamellar thylakoids. The helices ascend at an angle of ~20°, connecting to each granal thylakoid at a bridge-like slit junction.<ref name="Mustárdy-2008" /><ref name="Austin-2011" /><ref name="Bussi-2019" />

The stroma lamellae extend as large sheets perpendicular to the grana columns. These sheets are connected to the right-handed helices either directly or through bifurcations that form left-handed helical membrane surfaces.<ref name="Bussi-2019" /> The left-handed helical surfaces have a similar tilt angle to the right-handed helices (~20°), but ¼ the pitch. Approximately 4 left-handed helical junctions are present per granum, resulting in a pitch-balanced array of right- and left-handed helical membrane surfaces of different radii and pitch that consolidate the network with minimal surface and bending energies.<ref name="Bussi-2019" /> While different parts of the thylakoid system contain different membrane proteins, the thylakoid membranes are continuous and the thylakoid space they enclose form a single continuous labyrinth.<ref name="Mustárdy-2008" />

====Thylakoid composition====

Embedded in the thylakoid membranes are important [[protein complexes]] which carry out the [[light reactions]] of [[photosynthesis]]. [[Photosystem II]] and [[photosystem I]] contain [[light-harvesting complexes]] with [[chlorophyll]] and [[carotenoid]]s that absorb light energy and use it to energize electrons. Molecules in the thylakoid membrane use the energized electrons to pump [[hydrogen ions]] into the thylakoid space, decreasing the [[pH]] and turning it acidic. [[ATP synthase]] is a large protein complex that harnesses the [[concentration gradient]] of the hydrogen ions in the thylakoid space to generate [[Adenosine triphosphate|ATP]] energy as the hydrogen ions flow back out into the stroma—much like a dam turbine.<ref name="Campbell-2009b" />

There are two types of thylakoids—granal thylakoids, which are arranged in grana, and stromal thylakoids, which are in contact with the [[stroma (fluid)|stroma]]. Granal thylakoids are pancake-shaped circular disks about 300–600 nanometers in diameter. Stromal thylakoids are [[helicoid]] sheets that spiral around grana.<ref name="Mustárdy-2008" /> The flat tops and bottoms of granal thylakoids contain only the relatively flat [[photosystem II]] protein complex. This allows them to stack tightly, forming grana with many layers of tightly appressed membrane, called granal membrane, increasing stability and [[surface area]] for light capture.<ref name="Mustárdy-2008" />

In contrast, [[photosystem I]] and [[ATP synthase]] are large protein complexes which jut out into the stroma. They can't fit in the appressed granal membranes, and so are found in the stromal thylakoid membrane—the edges of the granal thylakoid disks and the stromal thylakoids. These large protein complexes may act as spacers between the sheets of stromal thylakoids.<ref name="Mustárdy-2008" />

The number of thylakoids and the total thylakoid area of a chloroplast is influenced by light exposure. Shaded chloroplasts contain larger and more [[Thylakoid|grana]] with more thylakoid membrane area than chloroplasts exposed to bright light, which have smaller and fewer grana and less thylakoid area. Thylakoid extent can change within minutes of light exposure or removal.<ref name="Wise-2007a" />

=== Pigments and chloroplast colors ===
Inside the photosystems embedded in chloroplast thylakoid membranes are various [[photosynthetic pigment]]s, which absorb and transfer [[light energy]]. The types of pigments found are different in various groups of chloroplasts, and are responsible for a wide variety of chloroplast colorations. Other [[plastid]] types, such as the [[leucoplast]] and the [[chromoplast]], contain little chlorophyll and do not carry out photosynthesis.

<div style="position: relative; margin-left: 5px; margin-right: 10px; width: 100px; height: 491px; float: left; <!--border: 1px rgba(0,0,0,0.2) solid;--> box-shadow: 1px 1px 3px rgba(0,0,0,0.2);">
<div style="position: absolute;" >[[File:Chromatography.jpg|[[Paper chromatography]] of some [[spinach]] leaf extract shows the various pigments present in their chloroplasts.|100px]]</div>
<div style="position: absolute; width: 90px; font-size: 90%; line-height: 120%; margin: 5px;" >[[Paper chromatography]] of some [[spinach]] leaf extract shows the various pigments present in their chloroplasts.</div>

<div style="position:absolute; width:100px; left:0; font-size:90%; line-height:120%; text-align:center; top:245px;">[[Xanthophylls|<span style="color:#e2c000;">'''Xanthophylls'''</span>]]</div>
<div style="position:absolute; width:100px; left:0; font-size:90%; line-height:120%; text-align:center; top:272px;">[[Chlorophyll a|<span style="color:#00bb90;">'''Chlorophyll ''a'''''</span>]]</div>
<div style="position:absolute; width:100px; left:0; font-size:90%; line-height:120%; text-align:center; top:300px;">[[Chlorophyll b|<span style="color:#00bb34;">'''Chlorophyll ''b'''''</span>]]</div>
</div>

==== Chlorophylls ====
[[Chlorophyll a|Chlorophyll ''a'']] is found in all chloroplasts, as well as their [[cyanobacterial]] ancestors. Chlorophyll ''a'' is a [[blue-green]] pigment<ref name="Campbell-2009e">{{cite book | vauthors=Campbell NA, Reece JB, Urry LA, Cain ML, Wasserman, Minorsky PV, Jackson RB |title=Biology | edition=8th | year=2009 |publisher=Benjamin Cummings (Pearson) | pages=190–193 | isbn=978-0-8053-6844-4 }}</ref> partially responsible for giving most cyanobacteria and chloroplasts their color. Other forms of chlorophyll exist, such as the [[accessory pigments]] [[chlorophyll b|chlorophyll ''b'']], [[Chlorophyll c|chlorophyll ''c'']], [[chlorophyll d|chlorophyll ''d'']],<ref name="Kim-2009" /> and [[chlorophyll f|chlorophyll ''f'']].

[[Chlorophyll b|Chlorophyll ''b'']] is an [[olive green]] pigment found only in the chloroplasts of [[plant]]s, [[green algae]], any secondary chloroplasts obtained through the [[secondary endosymbiosis]] of a green alga, and a few [[cyanobacteria]].<ref name="Kim-2009" /> It is the chlorophylls ''a'' and ''b'' together that make most plant and green algal chloroplasts green.<ref name="Campbell-2009e" />

[[Chlorophyll c|Chlorophyll ''c'']] is mainly found in secondary endosymbiotic chloroplasts that originated from a [[red alga]], although it is not found in chloroplasts of red algae themselves. Chlorophyll ''c'' is also found in some [[green algae]] and [[cyanobacteria]].<ref name="Kim-2009" />

Chlorophylls [[chlorophyll d|''d'']] and [[chlorophyll f|''f'']] are pigments found only in some cyanobacteria.<ref name="Kim-2009" /><ref name="UniSydney-2010">{{cite web|url=http://www.usyd.edu.au/news/84.html?newsstoryid=5463|title=Australian scientists discover first new chlorophyll in 60 years|date=20 August 2010|publisher=University of Sydney}}</ref>

==== Carotenoids ====
{{plain image with caption|File:Delesseria sanguinea Helgoland.JPG|''[[Delesseria sanguinea]]'', a [[red alga]], has chloroplasts that contain red pigments like [[phycoerytherin]] that mask their blue-green [[chlorophyll a|chlorophyll ''a'']].<ref name="Campbell-2009f" />|250px|right|bottom|triangle|#aa2040}}

In addition to chlorophylls, another group of [[yellow]]–[[orange (colour)|orange]]<ref name="Campbell-2009e" /> pigments called [[carotenoid]]s are also found in the photosystems. There are about thirty photosynthetic carotenoids.<ref name="Takaichi-2011">{{cite journal | vauthors=Takaichi S | title=Carotenoids in algae: distributions, biosyntheses and functions | journal=Marine Drugs | volume=9 | issue=6 | pages=1101–18 | date=15 June 2011 | pmid=21747749 | pmc=3131562 | doi=10.3390/md9061101 | doi-access=free }}</ref> They help transfer and dissipate excess energy,<ref name="Kim-2009" /> and their bright colors sometimes override the chlorophyll green, like during the [[autumn|fall]], when the leaves of [[Deciduous tree|some land plants]] change color.<ref>{{cite web|last=Shapley|first=Dan| name-list-style=vanc |title=Why Do Leaves Change Color in Fall?|url=http://www.thedailygreen.com/environmental-news/latest/why-do-leaves-change-color-0909|work=News Articles|access-date=21 May 2013|date=15 October 2012}}</ref> [[β-carotene]] is a bright red-orange carotenoid found in nearly all chloroplasts, like [[chlorophyll a|chlorophyll ''a'']].<ref name="Kim-2009" /> [[Xanthophylls]], especially the orange-red [[zeaxanthin]], are also common.<ref name="Takaichi-2011" /> Many other forms of carotenoids exist that are only found in certain groups of chloroplasts.<ref name="Kim-2009" />

==== Phycobilins ====
[[Phycobilin]]s are a third group of pigments found in [[cyanobacteria]], and [[glaucophyte]], [[red algal]], and [[Cryptomonad|cryptophyte]] chloroplasts.<ref name="Kim-2009" /><ref name="Howe-2008">{{cite journal | vauthors=Howe CJ, Barbrook AC, Nisbet RE, Lockhart PJ, Larkum AW | title=The origin of plastids | journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume=363 | issue=1504 | pages=2675–85 | date=August 2008 | pmid=18468982 | pmc=2606771 | doi=10.1098/rstb.2008.0050 }}</ref> Phycobilins come in all colors, though [[phycoerytherin]] is one of the pigments that makes many red algae red.<ref>{{cite web|title=Introduction to the Rhodophyta|url=http://www.ucmp.berkeley.edu/protista/rhodophyta.html|publisher=University of California Museum of Paleontology|access-date=20 May 2013}}</ref> Phycobilins often organize into relatively large protein complexes about 40 nanometers across called [[phycobilisome]]s.<ref name="Kim-2009" /> Like [[photosystem I]] and [[ATP synthase]], phycobilisomes jut into the stroma, preventing thylakoid stacking in red algal chloroplasts.<ref name="Kim-2009" /> [[Cryptomonad|Cryptophyte]] chloroplasts and some cyanobacteria don't have their phycobilin pigments organized into phycobilisomes, and keep them in their thylakoid space instead.<ref name="Kim-2009" />

{| cellpadding="4" style="text-align: center; margin-left:auto; margin-right: auto; margin-bottom: 20px;"
|-
| colspan=10 | '''Photosynthetic pigments.''' Presence of pigments across chloroplast groups and cyanobacteria.
Colored cells represent pigment presence. Chl = chlorophyll<ref name="Kim-2009" /><ref name="Takaichi-2011" /><ref name="Howe-2008" />
|-
|
| style="border-bottom: 2px solid #00bb90;"| [[Chlorophyll a|<span style="color:#00bb90;">'''Chl&nbsp;''a'''''</span>]]
| style="border-bottom: 2px solid #00bb34;"| [[Chlorophyll b|<span style="color:#00bb34;">'''Chl&nbsp;''b'''''</span>]]
| style="border-bottom: 2px solid #d3cf00;"| [[Chlorophyll c|<span style="color:#d3cf00;">'''Chl&nbsp;''c'''''</span>]]
| style="border-bottom: 2px solid #00d30c; color: #00d30c;"| '''[[Chlorophyll|<span style="color:#00d30c;">Chl</span>]]&nbsp;''[[Chlorophyll d|<span style="color:#00d30c;">d</span>]]'' and ''[[Chlorophyll f|<span style="color:#00d30c;">f</span>]]'''''

| style="border-bottom: 2px solid #e2c000;"| [[Xanthophylls|<span style="color:#e2c000;">'''Xanthophylls'''</span>]]
| style="border-bottom: 2px solid #ff9e00;"| [[Alpha carotene|<span style="color:#ff9e00;">'''α-carotene'''</span>]]
| style="border-bottom: 2px solid #ff6000;"| [[Beta carotene|<span style="color:#ff6000;">'''β-carotene'''</span>]]

| style="border-bottom: 2px solid #ff0040;"| [[Phycobilins|<span style="color:#ff0040;">'''Phycobilins'''</span>]]
<!--
| bgcolor="#ff8700" style="color: #fff;"|'''Phycourobilin'''
| bgcolor="#ff0040" style="color: #fff;"|'''Phycoerythrobilin'''
| bgcolor="#00c4ff" style="color: #fff;"|'''Phycocyanobilin'''
-->
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| style="text-align: right; padding-right: 10px; border-right: 4px solid #24d12b;"| '''[[Land plants|<span style="color:#24d12b;">Land plants</span>]]'''
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| style="text-align: right; padding-right: 10px; border-right: 4px solid #24d14e;"| '''[[Green algae|<span style="color:#24d14e;">Green algae</span>]]'''
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| style="text-align: right; padding-right: 10px; border-right: 4px solid #24d16d; color: #24d16d" rowspan="2"| '''[[Euglenophyta|<span style="color:#24d16d;">Euglenophytes</span>]]''' and <br />'''[[Chlorarachniophyta|<span style="color:#24d16d;">Chlorarachniophytes</span>]]'''
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| style="background:#ff6000; color:#fff; border-right:2px solid white;"|

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| style="text-align: right; padding-right: 10px; border-right: 4px solid #dc003e;"| '''[[Red algae|<span style="color:#dc003e;">Multicellular red algae</span>]]'''
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| style="background:#e2c000; color:#fff;"|
| style="background:#ff9e00; color:#fff; opacity:0.5;"|
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| style="background:#ff0040; color:#fff;"|

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| style="text-align: right; padding-right: 10px; border-right: 4px solid #dc0052;"| '''[[Red algae|<span style="color:#dc0052;">Unicellular red algae</span>]]'''
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| style="text-align: right; padding-right: 10px; border-right: 4px solid #b13b00; color: #b13b00" rowspan="2"| '''[[Haptophyta|<span style="color:#b13b00;">Haptophytes</span>]]''' and <br />'''[[Dinophyta|<span style="color:#b13b00;">Dinophytes</span>]]'''
| style="background:#00bb90; color:#fff;"|
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| style="text-align: right; padding-right: 10px; border-right: 4px solid #ca4300;"| '''[[Cryptomonad|<span style="color:#ca4300;">Cryptophytes</span>]]'''
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| style="text-align: right; padding-right: 10px; border-right: 4px solid #00ca9b;"| '''[[Glaucophytes|<span style="color:#00ca9b;">Glaucophytes</span>]]'''
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| style="text-align: right; padding-right: 10px; border-right: 4px solid #00c9be;"| '''[[Cyanobacteria|<span style="color:#00c9be;">Cyanobacteria</span>]]'''
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| style="background:#00bb34; color:#fff; opacity:0.5;"|
| style="background:#d3cf00; color:#fff; opacity:0.3;"|
| style="background:#00d30c; color:#fff; border-right:2px solid white; opacity:0.5;"|
| style="background:#e2c000; color:#fff; opacity:1;"|
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=== Specialized chloroplasts in {{C4}} plants ===
{{See also|Photosynthesis|C4 carbon fixation|label 2={{C4}} photosynthesis}}
{{Plain image with caption|File:C4 photosynthesis is less complicated.svg|Many [[C4 plant|{{C4}} plants]] have their [[Mesophyll tissue|mesophyll cells]] and [[bundle sheath cells]] arranged radially around their [[leaf veins]]. The two types of cells contain different types of chloroplasts specialized for a particular part of [[photosynthesis]].|500px|right|bottom|triangle|#00cd4c}}

To fix [[carbon dioxide]] into sugar molecules in the process of [[photosynthesis]], chloroplasts use an enzyme called [[RuBisCO]]. RuBisCO has trouble distinguishing between [[carbon dioxide]] and [[oxygen]], so at high oxygen concentrations, RuBisCO starts accidentally adding oxygen to sugar precursors. This has the result of [[Adenosine triphosphate|ATP]] energy being wasted and {{CO2}} being released, all with no sugar being produced. This is a big problem, since O{{sub|2}} is produced by the initial [[light reactions]] of photosynthesis, causing issues down the line in the [[Calvin cycle]] which uses RuBisCO.<ref name="Campbell-2009d">{{cite book | vauthors=Campbell NA, Reece JB, Urry LA, Cain ML, Wasserman, Minorsky PV, Jackson RB |title=Biology | edition=8th | year=2009 |publisher=Benjamin Cummings (Pearson) | pages=200–201 | isbn=978-0-8053-6844-4 }}</ref>

[[C4 plants|{{C4}} plants]] evolved a way to solve this—by spatially separating the light reactions and the Calvin cycle. The light reactions, which store light energy in [[Adenosine triphosphate|ATP]] and [[NADPH]], are done in the [[mesophyll tissue|mesophyll]] cells of a {{C4}} leaf. The Calvin cycle, which uses the stored energy to make sugar using RuBisCO, is done in the [[bundle sheath cells]], a layer of cells surrounding a [[vein (botany)|vein]] in a [[leaf]].<ref name="Campbell-2009d" />

As a result, chloroplasts in {{C4}} mesophyll cells and bundle sheath cells are specialized for each stage of photosynthesis. In mesophyll cells, chloroplasts are specialized for the light reactions, so they lack [[RuBisCO]], and have normal [[Thylakoid|grana]] and [[thylakoid]]s,<ref name="Gunning-1996a">{{cite book| first1=Brian E S | last1=Gunning | first2=Martin W | last2=Steer | name-list-style=vanc |title=Plant cell biology: structure and function|year=1996|publisher=Jones and Bartlett Publishers|location=Boston, Mass.|isbn=0-86720-504-0|page=[https://archive.org/details/plantcellbiology00gunn_0/page/n137 24]|url=https://archive.org/details/plantcellbiology00gunn_0| url-access=registration }}</ref> which they use to make ATP and NADPH, as well as oxygen. They store {{CO2}} in a four-carbon compound, which is why the process is called [[C4 carbon fixation|''{{C4}} photosynthesis'']]. The four-carbon compound is then transported to the bundle sheath chloroplasts, where it drops off {{CO2}} and returns to the mesophyll. Bundle sheath chloroplasts do not carry out the light reactions, preventing oxygen from building up in them and disrupting RuBisCO activity.<ref name="Campbell-2009d" /> Because of this, they lack thylakoids organized into [[Thylakoid|grana]] stacks—though bundle sheath chloroplasts still have free-floating thylakoids in the stroma where they still carry out [[cyclic electron flow]], a light-driven method of synthesizing [[Adenosine triphosphate|ATP]] to power the Calvin cycle without generating oxygen. They lack [[photosystem II]], and only have [[photosystem I]]—the only protein complex needed for cyclic electron flow.<ref name="Gunning-1996a" /><ref name="Campbell-2009d" /> Because the job of bundle sheath chloroplasts is to carry out the Calvin cycle and make sugar, they often contain large [[starch]] grains.<ref name="Gunning-1996a" />

Both types of chloroplast contain large amounts of [[chloroplast peripheral reticulum]],<ref name="Gunning-1996a" /> which they use to get more [[surface area to volume ratio|surface area]] to transport stuff in and out of them.<ref name="Whatley-1994" /><ref name="Wise-2007a">{{cite book|last=Wise|first=Robert R | name-list-style=vanc |title=The Structure and Function of Plastids|year=2007|publisher=Springer|isbn=978-1-4020-6570-5|pages=17–18|url=https://books.google.com/books?id=FKeCVPbJ3asC&pg=PA17}}</ref> Mesophyll chloroplasts have a little more peripheral reticulum than bundle sheath chloroplasts.<ref name="Lawton-1988">{{cite journal|last=Lawton|first=June R | name-list-style=vanc |title=Ultrastructure of Chloroplast Membranes in Leaves of Maize and Ryegrass as Revealed by Selective Staining Methods|journal=New Phytologist|date=March 1988|volume=108|issue=3|pages=277–283|jstor=2433294|doi=10.1111/j.1469-8137.1988.tb04163.x|pmid=33873933 |doi-access=free|bibcode=1988NewPh.108..277L }}</ref>