View source for Chloroplast

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{{Short description|Plant organelle that conducts photosynthesis}}
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[[File:Chloroplast II (cropped).svg|thumb|upright=1.35|Structure of a typical higher-plant chloroplast. The green [[chlorophyll]] is contained in stacks of disk-like [[thylakoid]]s.]]
[[File:Bryum capillare leaf cells showing chloroplasts.jpg|thumb|upright=1.35|Chloroplasts, containing thylakoids, visible in the cells of ''[[Rosulabryum capillare]]'', a type of [[moss]]]]
A '''chloroplast''' ({{IPAc-en|ˈ|k|l|ɔːr|ə|ˌ|p|l|æ|s|t|,_|-|p|l|ɑː|s|t|}}){{refn|{{cite book |last=Jones |first=Daniel |author-link=Daniel Jones (phonetician) |title=English Pronouncing Dictionary | veditors=Roach P, Hartmann J, Setter J |place=Cambridge |publisher=Cambridge University Press |orig-date=1917 |year=2003 |isbn=3-12-539683-2 }}}}{{refn|{{MerriamWebsterDictionary|Chloroplast}}}} is a type of [[membrane-bound organelle|organelle]] known as a [[plastid]] that conducts [[photosynthesis]] mostly in [[plant cell|plant]] and [[algae|algal cells]]. Chloroplasts have a high concentration of [[chlorophyll]] pigments which capture the [[Radiant energy|energy from sunlight]] and convert it to [[chemical energy]] and release [[oxygen]]. The chemical energy created is then used to make sugar and other organic molecules from carbon dioxide in a process called the [[Calvin cycle]]. Chloroplasts carry out a number of other functions, including [[fatty acid synthesis]], [[amino acid]] synthesis, and the [[immune response]] in plants. The number of chloroplasts per cell varies from one, in some unicellular algae, up to 100 in plants like ''[[Arabidopsis]]'' and [[wheat]].

Chloroplasts are highly dynamic—they circulate and are moved around within cells. Their behavior is strongly influenced by environmental factors like light color and intensity. Chloroplasts cannot be made anew by the plant cell and must be inherited by each daughter cell during cell division, which is thought to be inherited from their ancestor—a photosynthetic [[cyanobacterium]] that was [[symbiogenesis|engulfed]] by an early [[eukaryotic]] cell.<ref>{{cite web | author= Basic Biology | title= Bacteria | date= 18 March 2016 | url=https://basicbiology.net/micro/microorganisms/bacteria}}</ref> 

Chloroplasts evolved from an ancient cyanobacterium that was engulfed by an early eukaryotic cell. Because of their endosymbiotic origins, chloroplasts, like [[mitochondria]], contain their own [[DNA]] separate from the [[cell nucleus]]. With one exception (the [[amoeboid]] ''[[Paulinella]] chromatophora''), all chloroplasts can be traced back to a single [[endosymbiotic event]]. Despite this, chloroplasts can be found in extremely diverse organisms that are not directly related to each other—a consequence of many [[secondary endosymbiotic events|secondary]] and even [[tertiary endosymbiotic events]].

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== Discovery and etymology ==

The first definitive description of a chloroplast (''Chlorophyllkörnen'', "grain of chlorophyll") was given by [[Hugo von Mohl]] in 1837 as discrete bodies within the green plant cell.<ref>von Mohl, H. (1835/1837). [https://www.biodiversitylibrary.org/item/928#page/3/mode/1up Ueber die Vermehrung der Pflanzen-Zellen durch Teilung]. Dissert. Tubingen 1835. ''Flora'' 1837, .</ref> In 1883, [[Andreas Franz Wilhelm Schimper]] named these bodies as "chloroplastids" (''Chloroplastida'').<ref name="Schimper-1883">{{cite journal| last=Schimper |first=AF |author-link=Andreas Franz Wilhelm Schimper |title=Über die Entwicklung der Chlorophyllkörner und Farbkörper |trans-title=About the development of the chlorophyll grains and stains |language=de |journal=Bot. Zeitung |year=1883 |volume=41 |pages=105–14, 121–31, 137–46, 153–62 |url=http://publikationen.stub.uni-frankfurt.de/frontdoor/index/index/docId/19551 |archive-url=https://web.archive.org/web/20131019121025/http://publikationen.stub.uni-frankfurt.de/frontdoor/index/index/docId/19551 |archive-date=19 October 2013}}</ref> In 1884, [[Eduard Strasburger]] adopted the term "chloroplasts" (''Chloroplasten'').<ref>{{cite book | vauthors=Strasburger E | date=1884 | title=Das botanische Praktikum | url=https://archive.org/details/b28101455 | edition=1st | publisher=Gustav Fischer | location=Jena }}</ref><ref>{{cite book | vauthors=Gunning B, Koenig F, Govindjee P | date=2006 | chapter=A dedication to pioneers of research on chloroplast structure | veditors=Wise RR, Hoober JK | chapter-url=https://books.google.com/books?id=FKeCVPbJ3asC | title=The structure and function of plastids | publisher=Springer | location=Netherlands | pages=xxiii–xxxi | isbn=978-1-4020-6570-5 }}</ref><ref>{{cite book | vauthors=Hoober JK | date=1984 | url=https://books.google.com/books?id=OT8GCAAAQBAJ | title=Chloroplasts | publisher=Plenum | location=New York | isbn=978-1-4613-2767-7 }}</ref>

The word ''chloroplast'' is derived from the [[Greek language|Greek]] words ''chloros'' (χλωρός), which means green, and ''plastes'' (πλάστης), which means "the one who forms".<ref name="OED">{{cite encyclopedia |title=chloroplast |dictionary=[[Online Etymology Dictionary]] |url=http://www.etymonline.com/index.php?term=chloroplast&allowed_in_frame=0}}</ref>

== Endosymbiotic origin of chloroplasts ==
{{main|Plastid evolution}}
{{See also|Cyanobacteria|Symbiogenesis}}
Chloroplasts are one of many types of organelles in photosynthetic eukaryotic cells. They evolved from [[cyanobacteria]] through a process called [[Symbiogenesis|organellogenesis]].<ref name="Moore-2019">{{cite journal | vauthors=Moore KR, Magnabosco C, Momper L, Gold DA, Bosak T, Fournier GP | title=An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids | language=en | journal=Frontiers in Microbiology | volume=10 | article-number=1612 | date=2019 | pmid=31354692 | pmc=6640209 | doi=10.3389/fmicb.2019.01612 | doi-access=free }}</ref> Cyanobacteria are a diverse [[phylum]] of [[Gram-negative bacteria|gram-negative]] [[bacteria]] capable of carrying out [[photosynthesis|oxygenic photosynthesis]]. Like chloroplasts, they have [[thylakoid]]s.<ref name="Campbell-2009g">{{cite book |title=Biology |vauthors=Campbell NA, Reece JB, Urry LA, Cain ML, Wasserman, Minorsky PV, Jackson RB |publisher=Benjamin Cummings (Pearson) |year=2009 |isbn=978-0-8053-6844-4 |edition=8th |pages=186–187}}</ref> The thylakoid membranes contain [[photosynthetic pigment]]s, including [[chlorophyll a|chlorophyll ''a'']].<ref name="Kim-2009" /><ref>{{cite journal  | vauthors=Bryant DA, Guglielmi G, de Marsac NT, Castets AM, Cohen-Bazire G |doi=10.1007/BF00446810 |title=The structure of cyanobacterial phycobilisomes: A model |year=1979 |journal=Archives of Microbiology |volume=123 |issue=2 |pages=311–34 |bibcode=1979ArMic.123..113B |s2cid=1589428 }}</ref> This origin of chloroplasts was first suggested by the Russian biologist [[Konstantin Mereschkowski]] in 1905<ref>{{cite journal |author=Mereschkowsky K |author-link=Konstantin Mereschkowski |title= Über Natur und Ursprung der Chromatophoren im Pflanzenreiche |trans-title=About the nature and origin of chromatophores in the vegetable kingdom |language=de|journal= Biol Centralbl|year=1905|volume=25|pages=593–604 |url=https://archive.org/details/cbarchive_51353_bernaturundursprungderchromato1881}}</ref> after [[Andreas Franz Wilhelm Schimper]] observed in 1883 that chloroplasts closely resemble [[cyanobacteria]].<ref name="Schimper-1883" /> Chloroplasts are only found in [[plant]]s, [[algae]],<ref name="Alberts-2002a">{{cite book |last=Alberts|first=Bruce| name-list-style=vanc |title=Molecular biology of the cell|year=2002|publisher=Garland|location=New York [u.a.]|isbn=0-8153-4072-9|url=https://www.ncbi.nlm.nih.gov/books/NBK26819/|edition=4.}}</ref> and some species of the [[amoeba|amoeboid]] ''[[Paulinella]]''.<ref name="Gabr-2020">{{cite journal |vauthors=Gabr A, Grossman AR, Bhattacharya D |title=Paulinella, a model for understanding plastid primary endosymbiosis |journal=J Phycol |volume=56 |issue=4 |pages=837–843 |date=August 2020 |pmid=32289879 |pmc=7734844 |doi=10.1111/jpy.13003 |bibcode=2020JPcgy..56..837G |url=}}</ref>

[[Mitochondrion|Mitochondria]] are thought to have come from a similar [[endosymbiosis]] event, where an [[Aerobic organism|aerobic]] [[prokaryote]] was engulfed.<ref name="Campbell-2009c">{{cite book |title=Biology |vauthors=Campbell NA, Reece JB, Urry LA, Cain ML, Wasserman, Minorsky PV, Jackson RB |publisher=Benjamin Cummings (Pearson) |year=2009 |isbn=978-0-8053-6844-4 |edition=8th |page=516}}</ref> 

=== Primary endosymbiosis ===

{{Plain image with caption|Chloroplast endosymbiosis simple.svg|'''Primary endosymbiosis'''<br />A eukaryote with [[Mitochondrion|mitochondria]] engulfed a [[cyanobacterium]] in an event of [[Serial endosymbiosis|serial]] primary endosymbiosis, creating a [[Archæplastida|lineage]] of cells with both organelles.<ref name="Campbell-2009c" />|400px|right|bottom|triangle|#1abc31}}

Approximately two{{Nbsp}}billion years ago,<ref name="Milo" /><ref name="Sánchez-Baracaldo-2017">
{{cite journal | vauthors=Sánchez-Baracaldo P, Raven JA, Pisani D, Knoll AH | title=Early photosynthetic eukaryotes inhabited low-salinity habitats | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=114 | issue=37 | pages=E7737–E7745 | date=September 2017 | pmid=28808007 | pmc=5603991 | doi=10.1073/pnas.1620089114 | bibcode=2017PNAS..114E7737S | doi-access=free }}</ref><ref>{{Cite journal |last1=Falcón |first1=Luisa I |last2=Magallón |first2=Susana |last3=Castillo |first3=Amanda |date=4 March 2010 |title=Dating the cyanobacterial ancestor of the chloroplast |url=https://academic.oup.com/ismej/article/4/6/777/7588052 |journal=The ISME Journal |language=en |volume=4 |issue=6 |pages=777–783 |doi=10.1038/ismej.2010.2 |pmid=20200567 |bibcode=2010ISMEJ...4..777F |issn=1751-7362|url-access=subscription }}</ref> a free-living [[cyanobacterium]] entered an early [[eukaryotic]] cell, either as food or as an internal [[parasite]],<ref name="Campbell-2009c" /> but managed to escape the [[phagocytic vacuole]] it was contained in and persist inside the cell.<ref name="Kim-2009" /> This event is called ''[[endosymbiosis]]'', or "cell living inside another cell with a mutual benefit for both". The external cell is commonly referred to as the ''host'' while the internal cell is called the ''endosymbiont''.<ref name="Campbell-2009c" /> The engulfed cyanobacteria provided an advantage to the host by providing sugar from photosynthesis.<ref name="Campbell-2009c" /> Over time, the cyanobacterium was assimilated, and many of its genes were lost or transferred to the [[nuclear genome|nucleus]] of the host.<ref name="Nakayama-2012">{{cite journal |vauthors=Nakayama T, Archibald JM |date=April 2012 |title=Evolving a photosynthetic organelle |journal=BMC Biology |volume=10 |issue=1 |article-number=35 |doi=10.1186/1741-7007-10-35 |pmc=3337241 |pmid=22531210 |doi-access=free}}</ref> Some of the cyanobacterial proteins were then synthesized by host cell and imported back into the chloroplast (formerly the cyanobacterium), allowing the host to control the chloroplast.<ref name="Nakayama-2012" /><ref name="McFadden-2001" />

Chloroplasts which can be traced back directly to a cyanobacterial ancestor (i.e. without a subsequent endosymbiotic event) are known as '''''primary plastids''''' ("[[plastid]]" in this context means almost the same thing as chloroplast<ref name="Campbell-2009c" />).<ref name="Wise-2006b" /> Chloroplasts that can be traced back to another photosynthetic eukaryotic endosymbiont are called '''''secondary plastids''''' or '''''tertiary plastids''''' (discussed below).

Whether primary chloroplasts came from a single endosymbiotic event or multiple independent engulfments across various eukaryotic lineages was long debated. It is now generally held that with one exception (the amoeboid ''Paulinella chromatophora''), chloroplasts arose from a single endosymbiotic event around two{{Nbsp}}billion years ago and these chloroplasts all share [[monophyly|a single ancestor]].<ref name="Sánchez-Baracaldo-2017" /> It has been proposed this the closest living relative of the ancestral engulfed cyanobacterium is ''[[Gloeomargarita lithophora]].''<ref>{{cite journal |vauthors=Ponce-Toledo RI, Deschamps P, López-García P, Zivanovic Y, Benzerara K, Moreira D |date=February 2017 |title=An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids |journal=Current Biology |volume=27 |issue=3 |pages=386–391 |bibcode=2017CBio...27..386P |doi=10.1016/j.cub.2016.11.056 |pmc=5650054 |pmid=28132810}}</ref><ref>{{cite journal |vauthors=de Vries J, Archibald JM |date=February 2017 |title=Endosymbiosis: Did Plastids Evolve from a Freshwater Cyanobacterium? |journal=Current Biology |volume=27 |issue=3 |pages=R103–R105 |bibcode=2017CBio...27.R103D |doi=10.1016/j.cub.2016.12.006 |pmid=28171752 |doi-access=free}}</ref><ref name="López-García-2017">{{cite journal |vauthors=López-García P, Eme L, Moreira D |date=December 2017 |title=Symbiosis in eukaryotic evolution |journal=Journal of Theoretical Biology |volume=434 |pages=20–33 |bibcode=2017JThBi.434...20L |doi=10.1016/j.jtbi.2017.02.031 |pmc=5638015 |pmid=28254477}}</ref> Separately, somewhere about 90–140&nbsp;million years ago, this process happened again in the [[amoeboid]] ''[[Paulinella]]'' with a cyanobacterium in the genus ''[[Prochlorococcus]]''. This independently evolved chloroplast is often called a ''chromatophore'' instead of a chloroplast.<ref name="Macorano-2021">{{Cite journal |last1=Macorano |first1=Luis |last2=Nowack |first2=Eva C.M. |date=13 September 2021 |title=Paulinella chromatophora |journal=Current Biology |language=en |volume=31 |issue=17 |pages=R1024–R1026 |doi=10.1016/j.cub.2021.07.028|pmid=34520707 |bibcode=2021CBio...31R1024M |doi-access=free }}</ref><ref group="Note" name=":0">Not to be confused with [[chromatophore]]—the pigmented cells in some animals—or [[Chromatophore (bacteria)|chromatophore]]—the membrane associated vesicle in some bacteria.</ref>

Chloroplasts are believed to have arisen after [[Mitochondrion|mitochondria]], since all [[eukaryote]]s contain mitochondria, but not all have chloroplasts.<ref name="Campbell-2009c" /><ref>{{cite journal |vauthors=Archibald JM |date=January 2009 |title=The puzzle of plastid evolution |journal=Current Biology |volume=19 |issue=2 |pages=R81-8 |bibcode=2009CBio...19..R81A |doi=10.1016/j.cub.2008.11.067 |pmid=19174147 |s2cid=51989 |doi-access=free}}</ref> This is called ''[[serial endosymbiosis]]''—where an early eukaryote engulfed the [[mitochondrion]] ancestor, and then descendants of it then engulfed the chloroplast ancestor, creating a cell with both chloroplasts and mitochondria.<ref name="Campbell-2009c" />

=== Secondary and tertiary endosymbiosis ===

{{plain image with caption|File:Chloroplast secondary endosymbiosis.svg|Secondary endosymbiosis consisted of a [[eukaryote|eukaryotic]] [[Algae|alga]] being engulfed by another eukaryote, forming a chloroplast with three or four membranes.|600px|right|bottom|triangle|#71d7ff}}

Many other organisms obtained chloroplasts from the primary chloroplast lineages through secondary endosymbiosis—engulfing a red or green alga with a primary chloroplast. These chloroplasts are known as '''secondary plastids'''.<ref name="Wise-2006b" />

As a result of the secondary endosymbiotic event, secondary chloroplasts have additional membranes outside of the original two in primary chloroplasts.<ref name="Keeling-2004">{{cite journal |vauthors=Keeling PJ |date=October 2004 |title=Diversity and evolutionary history of plastids and their hosts |journal=American Journal of Botany |volume=91 |issue=10 |pages=1481–93 |doi=10.3732/ajb.91.10.1481 |pmid=21652304 |bibcode=2004AmJB...91.1481K |s2cid=17522125 |doi-access=free}}</ref> In secondary plastids, typically only the chloroplast, and sometimes its [[cell membrane]] and [[Cell nucleus|nucleus]] remain, forming a chloroplast with three or four membranes<ref name="Chaal-2005">{{cite journal |vauthors=Chaal BK, Green BR |date=February 2005 |title=Protein import pathways in 'complex' chloroplasts derived from secondary endosymbiosis involving a red algal ancestor |journal=Plant Molecular Biology |volume=57 |issue=3 |pages=333–42 |doi=10.1007/s11103-004-7848-y |pmid=15830125 |bibcode=2005PMolB..57..333C |s2cid=22619029}}</ref>—the two cyanobacterial membranes, sometimes the eaten alga's cell membrane, and the [[phagosomal vacuole]] from the host's cell membrane.<ref name="Keeling-2004" />

The genes in the phagocytosed eukaryotes nucleus are often transferred to the secondary host's nucleus.<ref name="Keeling-2004" /> [[Cryptomonad|Cryptomona]]s and [[chlorarachniophyte]]s retain the phagocytosed eukaryotes nucleus, an object called a [[nucleomorph]],<ref name="Keeling-2004" /> located between the second and third membranes of the chloroplast.<ref name="Kim-2009" /><ref name="McFadden-2001" />

All secondary chloroplasts come from [[green algae|green]] and [[red algae]]. No secondary chloroplasts from [[glaucophytes]] have been observed, probably because glaucophytes are relatively rare in nature, making them less likely to have been taken up by another eukaryote.<ref name="Keeling-2004" />

Still other organisms, including the dinoflagellates ''[[Karlodinium]]'' and ''[[Karenia (dinoflagellate)|Karenia]],'' obtained chloroplasts by engulfing an organism with a secondary plastid. These are called '''tertiary plastids'''.<ref name="Wise-2006b" />
[[File:Chloroplast Cladogram.svg|alt=Cladogram of chloroplast evolution|center|thumb|800x800px|'''Possible cladogram of chloroplast evolution'''<ref name="Keeling-2004" /><ref name="McFadden-2004">{{cite journal |last1=McFadden |first1=Geoffrey I. |last2=Van Dooren |first2=Giel G. |date=2004 |title=Evolution: Red Algal Genome Affirms a Common Origin of All Plastids |journal=Current Biology |volume=14 |issue=13 |pages=R514–R516 |bibcode=2004CBio...14.R514M |doi=10.1016/j.cub.2004.06.041 |pmid=15242632}}</ref><ref name="Keeling-2010" /> Circles represent [[endosymbiotic]] events. For clarity, [[dinophyte]] tertiary endosymbioses and many nonphotosynthetic lineages have been omitted.
----<small><sup>'''a'''</sup> It is now established that [[Chromalveolata]] is [[paraphyletic]] to [[Rhizaria]].<ref name="Keeling-2010" /></small>]]

== Primary chloroplast lineages ==
All primary chloroplasts belong to one of four chloroplast lineages—the [[glaucophyte]] chloroplast lineage, the [[rhodophyte]] ("red") chloroplast lineage, and the [[chloroplastidan|chloroplastida]] ("green") chloroplast lineage, the amoeboid ''Paulinella chromatophora'' lineage.<ref name="Ball-2011" /> The glaucophyte, rhodophyte, and chloroplastidian lineages are all descended from the same ancestral endosymbiotic event and are all within the group [[Archaeplastida]].<ref name="Keeling-2004" />

=== Glaucophyte chloroplasts ===
{{See also|Glaucophyte|}}{{Plain image with caption|image=Woelfib cyanphoraparadoxa teilungsfigur 1 0632002 img 54414492 ude 20131024233254 small.jpg|caption=The glaucophyte ''[[Cyanophora paradoxa]]'' with two chloroplasts in the process of dividing.|align=right}}
The glaucophyte chloroplast group is the smallest of the three primary chloroplast lineages as there are only 25 described glaucophyte species.<ref>{{Cite journal |last=Guiry |first=Michael D. |date=2 January 2024 |title=How many species of algae are there? A reprise. Four kingdoms, 14 phyla, 63 classes and still growing |journal=Journal of Phycology |language=en |volume=60 |issue=2 |pages=214–228 |doi=10.1111/jpy.13431 |pmid=38245909 |bibcode=2024JPcgy..60..214G |issn=0022-3646|doi-access=free }}</ref> Glaucophytes diverged first before the red and green chloroplast lineages diverged.<ref>{{Cite journal |last=Archibald |first=John M. |date=27 January 2009 |title=The Puzzle of Plastid Evolution |journal=Current Biology |language=en |volume=19 |issue=2 |pages=R81–R88 |doi=10.1016/j.cub.2008.11.067|pmid=19174147 |bibcode=2009CBio...19..R81A |doi-access=free }}</ref> Because of this, they are sometimes considered intermediates between cyanobacteria and the red and green chloroplasts.<ref name="Miyagishima-2011">{{Cite journal |last=Miyagishima |first=Shin-ya |date=1 March 2011 |title=Mechanism of Plastid Division: From a Bacterium to an Organelle |journal=Plant Physiology |language=en |volume=155 |issue=4 |pages=1533–1544 |doi=10.1104/pp.110.170688 |issn=1532-2548 |pmc=3091088 |pmid=21311032}}</ref> This early divergence is supported by both [[Phylogenetics|phylogenetic]] studies and physical features present in glaucophyte chloroplasts and cyanobacteria, but not the red and green chloroplasts. First, glaucophyte chloroplasts have a [[peptidoglycan]] wall, a type of cell wall otherwise only in bacteria (including cyanobacteria).<ref group="Note">For this reason, glaucophyte chloroplasts are also known as 'muroplasts' from the Latin ''muro'' meaning wall.</ref> Second, glaucophyte chloroplasts contain [[concentric]] unstacked [[thylakoid]]s which surround a [[carboxysome]] – an [[icosahedral]] structure that contains the enzyme [[RuBisCO]] responsible for [[carbon fixation]]. Third, starch created by the chloroplast is collected outside the chloroplast.<ref name="Wise-2006">{{Cite book |url=http://link.springer.com/10.1007/978-1-4020-4061-0 |title=The Structure and Function of Plastids |date=2006 |publisher=Springer Netherlands |isbn=978-1-4020-4060-3 |editor-last=Wise |editor-first=Robert R. |series=Advances in Photosynthesis and Respiration |volume=23 |location=Dordrecht |doi=10.1007/978-1-4020-4061-0 |editor-last2=Hoober |editor-first2=J. Kenneth}}</ref> Additionally, like cyanobacteria, both glaucophyte and rhodophyte thylakoids are studded with light collecting structures called [[phycobilisome]]s. 

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=== Rhodophyta (red chloroplasts) ===
{{See also|Red algae}}
{{plain image with caption|File:Cyanidium O5A.jpg|'''Diversity of red algae''' Clockwise from top left: ''[[Bornetia secundiflora]]'', ''[[Peyssonnelia squamaria]]'', ''[[Cyanidium]]'', ''[[Laurencia]]'', ''[[Callophyllis laciniata]]''. Red algal chloroplasts are characterized by [[phycobilin]] pigments which often give them their reddish color.|400px|right|top|triangle|#ca004d|image override=
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The rhodophyte, or [[red algae]], group is a large and diverse lineage.<ref name="Keeling-2004" /> Rhodophyte chloroplasts are also called ''rhodoplasts'',<ref name="Wise-2006b" /> literally "red chloroplasts".<ref>{{cite web|url=http://www.thefreedictionary.com/rhodo-|title=rhodo-|work=The Free Dictionary|publisher=Farlex|access-date=7 June 2013}}</ref> Rhodoplasts have a double membrane with an intermembrane space and [[phycobilin]] pigments organized into [[phycobilisome]]s on the thylakoid membranes, preventing their thylakoids from stacking.<ref name="Kim-2009" /> Some contain [[pyrenoid]]s.<ref name="Wise-2006b" /> Rhodoplasts have [[chlorophyll a|chlorophyll ''a'']] and phycobilins<ref name="Keeling-2010" /> for photosynthetic pigments; the phycobilin [[phycoerythrin]] is responsible for giving many red algae their distinctive [[red]] color.<ref name="Campbell-2009f">{{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=582–92 | isbn=978-0-8053-6844-4 }}</ref> However, since they also contain the blue-green [[chlorophyll a|chlorophyll ''a'']] and other pigments, many are reddish to purple from the combination.<ref name="Wise-2006b" />{{dubious|date=January 2022|Subtractive pigments won't give purple}} The red phycoerythrin pigment is an adaptation to help red algae catch more sunlight in deep water<ref name="Wise-2006b" />—as such, some red algae that live in shallow water have less phycoerythrin in their rhodoplasts, and can appear more greenish.<ref name="Campbell-2009f" /> Rhodoplasts synthesize a form of starch called [[floridean starch]],<ref name="Wise-2006b" /> which collects into granules outside the rhodoplast, in the cytoplasm of the red alga.<ref name="Kim-2009" />

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=== Chloroplastida (green chloroplasts) ===
{{See also|Chloroplastida}}
{{plain image with caption|File:Micrasterias .jpg|'''Diversity of green algae''' Clockwise from top left: ''[[Scenedesmus]]'', ''[[Micrasterias]]'', ''[[Hydrodictyon]]'', ''[[Volvox]]'', ''[[Stigeoclonium]]''. Green algal chloroplasts are characterized by their pigments [[chlorophyll a|chlorophyll ''a'']] and [[chlorophyll b|chlorophyll ''b'']] which give them their green color.|425px|right|top|triangle|#3cca48|image override=
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The [[chloroplastida]] group is another large, highly diverse lineage that includes both [[green algae]] and [[land plants]].<ref name="Lewis-2004">{{cite journal | vauthors=Lewis LA, McCourt RM | title=Green algae and the origin of land plants | journal=American Journal of Botany | volume=91 | issue=10 | pages=1535–56 | date=October 2004 | pmid=21652308 | doi=10.3732/ajb.91.10.1535 | bibcode=2004AmJB...91.1535L }}</ref> This group is also called [[Viridiplantae]], which includes two core clades—[[Chlorophyta]] and [[Streptophyta]].

Most green chloroplasts are [[green]] in color, though some aren't due to accessory pigments that override the green from chlorophylls, such as in the resting cells of ''[[Haematococcus pluvialis]]''. Green chloroplasts differ from glaucophyte and red algal chloroplasts in that they have lost their [[phycobilisome]]s, and contain [[chlorophyll b|chlorophyll ''b'']].<ref name="Kim-2009" /> They have also lost the [[peptidoglycan]] wall between their double membrane, leaving an intermembrane space.<ref name="Kim-2009" /> Some [[plant]]s have kept some [[gene]]s required the synthesis of peptidoglycan, but have repurposed them for use in [[#Division|chloroplast division]] instead.<ref name="Machida-2006">{{cite journal | vauthors=Machida M, Takechi K, Sato H, Chung SJ, Kuroiwa H, Takio S, Seki M, Shinozaki K, Fujita T, Hasebe M, Takano H | display-authors=6 | title=Genes for the peptidoglycan synthesis pathway are essential for chloroplast division in moss | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=103 | issue=17 | pages=6753–8 | date=April 2006 | pmid=16618924 | pmc=1458953 | doi=10.1073/pnas.0510693103 | bibcode=2006PNAS..103.6753M | doi-access=free }}</ref> Chloroplastida lineages also keep their [[starch]] ''inside'' their chloroplasts.<ref name="Kim-2009" /><ref name="Keeling-2010" /><ref name="Lewis-2004" /> In plants and some algae, the chloroplast thylakoids are arranged in grana stacks. Some green algal chloroplasts, as well as those of [[hornworts]], contain a structure called a [[pyrenoid]],<ref name="Kim-2009" /> that concentrate [[RuBisCO]] and CO{{sub|2}} in the chloroplast, functionally similar to the glaucophyte [[carboxysome]].<ref name="Moroney-1999">{{cite journal | vauthors=Moroney JV, Somanchi A | title=How Do algae concentrate CO2 to increase the efficiency of photosynthetic carbon fixation? | journal=Plant Physiology | volume=119 | issue=1 | pages=9–16 | date=January 1999 | pmid=9880340 | pmc=1539202 | doi=10.1104/pp.119.1.9 }}</ref><ref>{{cite journal | vauthors=((Robison, T. A.)), ((Oh, Z. G.)), ((Lafferty, D.)), ((Xu, X.)), ((Villarreal, J. C. A.)), ((Gunn, L. H.)), ((Li, F.-W.)) | journal=Nature Plants | title=Hornworts reveal a spatial model for pyrenoid-based CO2-concentrating mechanisms in land plants | pages=63–73 | publisher=Nature Publishing Group | date=3 January 2025 | volume=11 | issue=1 | issn=2055-0278 | doi=10.1038/s41477-024-01871-0| pmid=39753956 }}
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There are some lineages of non-photosynthetic parasitic green algae that have lost their chloroplasts entirely, such as ''[[Prototheca]],''<ref name="Keeling-2010" /> or have no chloroplast while retaining the separate chloroplast genome, as in ''[[Helicosporidium]].''<ref name="Tartar-2004">{{cite journal |vauthors=Tartar A, Boucias DG |date=April 2004 |title=The non-photosynthetic, pathogenic green alga Helicosporidium sp. has retained a modified, functional plastid genome |journal=FEMS Microbiology Letters |volume=233 |issue=1 |pages=153–7 |doi=10.1016/j.femsle.2004.02.006 |pmid=15043882 |doi-access=free}}</ref> Morphological and physiological similarities, as well as [[phylogenetics]], confirm that these are lineages that ancestrally had chloroplasts but have since lost them.<ref name="Tartar-2004" /><ref>{{Cite journal |last1=Ueno |first1=Ryohei |last2=Urano |first2=Naoto |last3=Suzuki |first3=Motofumi |date=2003-06-01 |title=Phylogeny of the non-photosynthetic green micro-algal genus Prototheca (Trebouxiophyceae, Chlorophyta) and related taxa inferred from SSU and LSU ribosomal DNA partial sequence data |url=https://academic.oup.com/femsle/article-abstract/223/2/275/499272?redirectedFrom=fulltext |journal=FEMS Microbiology Letters |volume=223 |issue=2 |pages=275–280 |doi=10.1016/s0378-1097(03)00394-x |pmid=12829298 |issn=0378-1097}}</ref>

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=== ''Paulinella chromatophora'' ===
{{See also|Paulinella|}}
{{Plain image with caption|image=File:Paulinella-chromatophora-fig1ab.jpg|caption=Light micrograph of the amoeboid ''Paulinella chromatophora''|align=left}}

The photosynthetic amoeboids in the genus ''[[Paulinella]]—P. chromatophora, P. micropora,'' and marine ''P. longichromatophora—''have the only known independently evolved chloroplast, often called a '''chromatophore'''.<ref name=":0" group="Note" /> While all other chloroplasts originate from a single ancient endosymbiotic event, ''Paulinella'' independently acquired an endosymbiotic cyanobacterium from the genus ''[[Synechococcus]]'' around 90 – 140 million years ago.<ref name="Macorano-2021" /><ref name="Keeling-2004" /> Each ''Paulinella'' cell contains one or two sausage-shaped chloroplasts;<ref name="Nakayama-2012" /><ref name="Nowack-2011">{{cite journal |vauthors=Nowack EC, Vogel H, Groth M, Grossman AR, Melkonian M, Glöckner G |date=January 2011 |title=Endosymbiotic gene transfer and transcriptional regulation of transferred genes in Paulinella chromatophora |journal=Molecular Biology and Evolution |volume=28 |issue=1 |pages=407–22 |doi=10.1093/molbev/msq209 |pmid=20702568 |doi-access=free}}</ref> they were first described in 1894 by German biologist Robert Lauterborn.<ref>{{Cite journal |last=Archibald |first=John M. |date=25 September 2017 |title=Evolution: Protein Import in a Nascent Photosynthetic Organelle |journal=Current Biology |volume=27 |issue=18 |pages=R1004–R1006 |doi=10.1016/j.cub.2017.08.013 |pmid=28950079 |bibcode=2017CBio...27R1004A |issn=0960-9822|doi-access=free }}</ref> 

The chromatophore is highly reduced compared to its free-living cyanobacterial relatives and has limited functions. For example, it has a genome of about 1 million [[base pair]]s, one third the size of ''Synechococcus'' genomes, and only encodes around 850 proteins.<ref name="Nakayama-2012" /> However, this is still much larger than other chloroplast genomes, which are typically around 150,000 base pairs. Chromatophores have also transferred much less of their DNA to the nucleus of their hosts. About 0.3–0.8% of the nuclear DNA in ''Paulinella'' is from the chromatophore, compared with 11–14% from the chloroplast in plants.<ref name="Nowack-2011" /> Similar to other chloroplasts, ''Paulinella'' provides specific proteins to the chromatophore using a specific targeting sequence.<ref>{{Cite journal |last1=Singer |first1=Anna |last2=Poschmann |first2=Gereon |last3=Mühlich |first3=Cornelia |last4=Valadez-Cano |first4=Cecilio |last5=Hänsch |first5=Sebastian |last6=Hüren |first6=Vanessa |last7=Rensing |first7=Stefan A. |last8=Stühler |first8=Kai |last9=Nowack |first9=Eva C.M. |date=25 September 2017 |title=Massive Protein Import into the Early-Evolutionary-Stage Photosynthetic Organelle of the Amoeba Paulinella chromatophora |journal=Current Biology |volume=27 |issue=18 |pages=2763–2773.e5 |doi=10.1016/j.cub.2017.08.010 |pmid=28889978 |bibcode=2017CBio...27E2763S |issn=0960-9822|doi-access=free }}</ref> Because chromatophores are much younger compared to the canonical chloroplasts, ''Paulinella chromatophora'' is studied to understand how early chloroplasts evolved.<ref name="Nakayama-2012" />

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== Secondary and tertiary chloroplast lineages ==

=== Green algal derived chloroplasts ===
[[Green algae]] have been taken up by many groups in three or four separate events.<ref name="Rogers-2007">{{cite journal | vauthors=Rogers MB, Gilson PR, Su V, McFadden GI, Keeling PJ | title=The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts | journal=Molecular Biology and Evolution | volume=24 | issue=1 | pages=54–62 | date=January 2007 | pmid=16990439 | doi=10.1093/molbev/msl129 | doi-access=free }}</ref> Primarily, secondary chloroplasts derived from green algae are in the [[euglenid|euglenoid]]s and [[chlorarachniophyte]]s. They are also found in one lineage of [[dinoflagellate]]s<ref name="Keeling-2010">{{cite journal | vauthors=Keeling PJ | title=The endosymbiotic origin, diversification and fate of plastids | journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume=365 | issue=1541 | pages=729–48 | date=March 2010 | pmid=20124341 | pmc=2817223 | doi=10.1098/rstb.2009.0103 }}</ref> and possibly the ancestor of the CASH lineage ([[cryptomonad]]s, [[Alveolata|alveolates]], [[stramenopile]]s and [[haptophyte]]s)<ref name="Moustafa-2009">{{cite journal | vauthors=Moustafa A, Beszteri B, Maier UG, Bowler C, Valentin K, Bhattacharya D | title=Genomic footprints of a cryptic plastid endosymbiosis in diatoms | journal=Science | volume=324 | issue=5935 | pages=1724–6 | date=June 2009 | pmid=19556510 | doi=10.1126/science.1172983 | url=https://epic.awi.de/id/eprint/20816/1/Mou2009a.pdf | bibcode=2009Sci...324.1724M | s2cid=11408339 }}</ref> Many green algal derived chloroplasts contain [[pyrenoid]]s, but unlike chloroplasts in their green algal ancestors, storage product collects in granules outside the chloroplast.<ref name="Kim-2009" />

==== Euglenophytes ====
{{See also|Euglenophyceae}}
[[File:Two Euglena.jpg|thumb|''[[Euglena]]'', a [[euglenophyte]], contains secondary chloroplasts from green algae.]]

The euglenophytes are a group of common [[flagellated]] [[protists]] that contain chloroplasts derived from a green alga.<ref name="Keeling-2004" /> Euglenophytes are the only group outside [[Diaphoretickes]] that have chloroplasts without performing [[kleptoplasty]].<ref>{{Cite journal |last1=Burki |first1=Fabien |last2=Roger |first2=Andrew J. |last3=Brown |first3=Matthew W. |last4=Simpson |first4=Alastair G.B. |date=2020-01-01 |title=The New Tree of Eukaryotes |url=https://linkinghub.elsevier.com/retrieve/pii/S0169534719302575 |journal=Trends in Ecology & Evolution |volume=35 |issue=1 |pages=43–55 |doi=10.1016/j.tree.2019.08.008 |pmid=31606140 |bibcode=2020TEcoE..35...43B |issn=0169-5347}}</ref><ref>{{Cite journal |last1=Sibbald |first1=Shannon J. |last2=Archibald |first2=John M. |date=2020-05-20 |title=Genomic Insights into Plastid Evolution |url=https://academic.oup.com/gbe/article/12/7/978/5836826 |journal=Genome Biology and Evolution |volume=12 |issue=7 |pages=978–990 |doi=10.1093/gbe/evaa096|pmid=32402068 |pmc=7348690 }}</ref> Euglenophyte chloroplasts have three membranes. It is thought that the membrane of the primary endosymbiont host was lost (e.g. the green algal membrane), leaving the two cyanobacterial membranes and the secondary host's phagosomal membrane.<ref name="Keeling-2004" /> Euglenophyte chloroplasts have a [[pyrenoid]] and [[thylakoid]]s stacked in groups of three. The carbon fixed through photosynthesis is stored in the form of [[paramylon]], which is contained in membrane-bound granules in the cytoplasm of the euglenophyte.<ref name="Kim-2009" /><ref name="Keeling-2010" />

==== Chlorarachniophytes ====
{{See also|Chlorarachniophyte}}
[[File:Chlorarachnion reptans.jpg|thumb|left|''[[Chlorarachnion reptans]]'' is a chlorarachniophyte. Chlorarachniophytes replaced their original [[red algal]] endosymbiont with a [[green alga]].]]

[[Chlorarachniophytes]] are a rare group of organisms that also contain chloroplasts derived from green algae,<ref name="Keeling-2004" /> though their story is more complicated than that of the euglenophytes. The ancestor of chlorarachniophytes is thought to have been a eukaryote with a ''red'' algal derived chloroplast. It is then thought to have lost its first red algal chloroplast, and later engulfed a green alga, giving it its second, green algal derived chloroplast.<ref name="Keeling-2010" />

Chlorarachniophyte chloroplasts are bounded by four membranes, except near the cell membrane, where the chloroplast membranes fuse into a double membrane.<ref name="Kim-2009" /> Their thylakoids are arranged in loose stacks of three.<ref name="Kim-2009" /> Chlorarachniophytes have a form of polysaccharide called [[chrysolaminarin]], which they store in the cytoplasm,<ref name="Keeling-2010" /> often collected around the chloroplast [[pyrenoid]], which bulges into the cytoplasm.<ref name="Kim-2009" />

Chlorarachniophyte chloroplasts are notable because the green alga they are derived from has not been completely broken down—its nucleus still persists as a [[nucleomorph]]<ref name="Keeling-2004" /> found between the second and third chloroplast membranes<ref name="Kim-2009" />—the [[periplastid space|periplasmic space]], which corresponds to the green alga's cytoplasm.<ref name="Keeling-2010" />

==== Prasinophyte-derived chloroplast ====
{{See also|Lepidodinium}}
[[File:Lepidodinium chlorophorum 68163.jpg|thumb|left|Lepidium chlorophytum green colour is caused by a plastid derived from [[Pedinophyceae]].]]

Dinoflagellates in the genus ''[[Lepidodinium]]'' have lost their original peridinin chloroplast and replaced it with a green algal derived chloroplast (more specifically, a [[prasinophyte]]).<ref name="Kim-2009" /><ref name="Hackett-2004" /> ''Lepidodinium'' is the only dinoflagellate that has a chloroplast that's not from the [[rhodoplast]] lineage. The chloroplast is surrounded by two membranes and has no nucleomorph—all the nucleomorph genes have been transferred to the dinophyte [[cell nucleus|nucleus]].<ref name="Hackett-2004" /> The endosymbiotic event that led to this chloroplast was serial secondary endosymbiosis rather than tertiary endosymbiosis—the endosymbiont was a [[green alga]] containing a primary chloroplast (making a secondary chloroplast).<ref name="Keeling-2010" />

==== Tripartite symbiosis ====
[[File:Abg4102.F1.large.jpg|thumb|left|Pseudoblepharisma tenue with its two photosynthetic symbionts.]]

The [[ciliate]] ''[[Pseudoblepharisma tenue]]'' has two bacterial symbionts, one pink, one green. In 2021, both symbionts were confirmed to be photosynthetic: Ca. ''[[Thiodictyon]] intracellulare'' ([[Chromatiaceae]]), a [[purple sulfur bacteria|purple sulfur bacterium]] with a genome just half the size of their closest known relatives; and ''[[Chlorella]]'' sp. K10, a green alga.<ref>{{cite journal | pmc=10063809 | date=2023 | last1=Christian | first1=R. | last2=Labbancz | first2=J. | last3=Usadel | first3=B. | last4=Dhingra | first4=A. | title=Understanding protein import in diverse non-green plastids | journal=Frontiers in Genetics | volume=14 | article-number=969931 | doi=10.3389/fgene.2023.969931 | doi-access=free | pmid=37007964 }}</ref> There is also a variant of ''Pseudoblepharisma tenue'' that only contains chloroplasts from green algae and no endosymbiotic purple bacteria.<ref name="Hines">{{cite journal |last1=Hines |first1=Hunter N. |last2=McCarthy |first2=Peter J. |last3=Esteban |first3=Genoveva F. |title=A Case Building Ciliate in the Genus Pseudoblepharisma Found in Subtropical Fresh Water |journal=Diversity |date=27 February 2022 |volume=14 |issue=3 |page=174 |doi=10.3390/d14030174 |doi-access=free|bibcode=2022Diver..14..174H }}</ref>

=== Red algal derived chloroplasts ===
Secondary chloroplasts derived from [[red algae]] appear to have only been taken up only once, which then diversified into a large group called [[chromist]]s or chromalveolates. Today they are found in the [[Haptophyte|haptophytes]], [[Cryptomonad|cryptomonads]], [[Stramenopile|heterokonts]], [[Dinoflagellate|dinoflagellates]] and [[Apicomplexa|apicomplexans]] (the CASH lineage).<ref name="Keeling-2010" /> Red algal secondary chloroplasts usually contain chlorophyll c and are surrounded by four membranes.<ref name="Kim-2009" />

However, chromist [[monophyly]] has been rejected, and it is considered more likely that some chromists acquired their plastids by incorporating another chromist instead of inheriting them from a common ancestor. [[Cryptomonads|Cryptophyte]]s seem to have acquired plastids from red algae, which were then transmitted from them to both the [[Ochrophyte|Heterokontophyte]]s and the [[Haptophyte]]s, and then from these last to the [[Myzozoa]].<ref name="Strassert Irisarri Williams Burki 2021">{{Cite journal |last1=Strassert |first1=Jürgen F. H. |last2=Irisarri |first2=Iker |last3=Williams |first3=Tom A. |last4=Burki |first4=Fabien |date=2021-03-25 |title=A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids |journal=Nature Communications |volume=12 |issue=1 |page=1879 |doi=10.1038/s41467-021-22044-z |pmid=33767194 |pmc=7994803 |bibcode=2021NatCo..12.1879S |issn=2041-1723}}</ref>

==== Cryptophytes ====
{{See also|Cryptomonad}}
[[File:CSIRO ScienceImage 6743 SEM Cryptophyte.jpg|thumb|Cryptophytes under [[Scanning electron microscope|SEM]].]]

[[Cryptomonad|Cryptophytes]], or cryptomonads, are a group of algae that contain a red-algal derived chloroplast. Cryptophyte chloroplasts contain a [[nucleomorph]] that superficially resembles that of the [[chlorarachniophytes]].<ref name="Keeling-2004" /> Cryptophyte chloroplasts have four membranes. The outermost membrane is continuous with the [[rough endoplasmic reticulum]]. They synthesize ordinary [[starch]], which is stored in granules found in the periplastid space—outside the original double membrane, in the place that corresponds to the ancestral red alga's cytoplasm. Inside cryptophyte chloroplasts is a [[pyrenoid]] and [[thylakoid]]s in stacks of two.<ref name="Kim-2009" /> Cryptophyte chloroplasts do not have [[phycobilisome]]s,<ref name="Kim-2009" /> but they do have [[Phycobilin|phycobilin pigments]] which they keep in the thylakoid space, rather than anchored on the outside of their thylakoid membranes.<ref name="Kim-2009" /><ref name="Keeling-2004" />

Cryptophytes may have played a key role in the spreading of red algal based chloroplasts.<ref>{{Cite thesis|last=Toledo|first=Rafael Isaac Ponce| name-list-style=vanc |title=Origins and early evolution of photosynthetic eukaryotes|date=5 March 2018|publisher=Université Paris-Saclay|url=https://tel.archives-ouvertes.fr/tel-01760725|language=en}}</ref><ref>{{cite journal | vauthors=Bodył A | title=Did some red alga-derived plastids evolve via kleptoplastidy? A hypothesis | journal=Biological Reviews of the Cambridge Philosophical Society | volume=93 | issue=1 | pages=201–222 | date=February 2018 | pmid=28544184 | doi=10.1111/brv.12340 | s2cid=24613863 }}</ref>

==== Haptophytes ====
{{See also|Haptophyte}}
[[File:Gephyrocapsa oceanica brighter.jpg|thumb|left|[[Scanning electron micrograph]] of ''[[Gephyrocapsa oceanica]]'', a haptophyte.]]

[[Haptophytes]] are similar and closely related to cryptophytes or heterokontophytes.<ref name="Keeling-2010" /> Their chloroplasts lack a nucleomorph,<ref name="Kim-2009" /><ref name="Keeling-2004" /> their thylakoids are in stacks of three, and they synthesize [[chrysolaminarin]] sugar, which are stored in granules completely outside of the chloroplast, in the cytoplasm of the haptophyte.<ref name="Kim-2009" />

==== Stramenopiles <span style="font-weight: 400;">(heterokontophytes)</span> ====
{{See also|Stramenopile}}[[File:20110123 185042 Diatom.jpg|thumb|upright=0.8|The photosynthetic pigments present in their chloroplasts make [[diatoms]] greenish-brown.]]

The [[stramenopile]]s, also known as heterokontophytes, are a very large and diverse group of eukaryotes. It inlcludes [[Ochrophyta]]—which includes [[diatoms]], [[brown algae]] (seaweeds), and [[golden algae]] (chrysophytes)<ref name="Campbell-2009f" />— and [[Yellow-green algae|Xanthophyceae]] (also called yellow-green algae).<ref name="Keeling-2010" />

Heterokont chloroplasts are very similar to haptophyte chloroplasts. They have a [[pyrenoid]], triplet thylakoids, and, with some exceptions,<ref name="Kim-2009" /> four layer plastidic envelope with the outermost membrane connected to the [[endoplasmic reticulum]]. Like haptophytes, stramenopiles store sugar in [[chrysolaminarin]] granules in the cytoplasm.<ref name="Kim-2009" /> Stramenopile chloroplasts contain [[chlorophyll a|chlorophyll ''a'']] and, with a few exceptions,<ref name="Kim-2009" /> [[Chlorophyll c|chlorophyll ''c'']].<ref name="Keeling-2004" /> They also have [[carotenoid]]s which give them their many colors.<ref name="Campbell-2009f" />

==== Apicomplexans, chromerids, and dinophytes ====
{{See also|Alveolate|Myzozoa}}
The alveolates are a major clade of unicellular eukaryotes of both [[Autotroph|autotrophic]] and [[Heterotroph|heterotrophic]] members. Many members contain a red-algal derived plastid. One notable characteristic of this diverse group is the frequent loss of photosynthesis. However, a majority of these heterotrophs continue to process a non-photosynthetic plastid.<ref name="Janouškovec-2017">{{cite journal | vauthors=Janouškovec J, Gavelis GS, Burki F, Dinh D, Bachvaroff TR, Gornik SG, Bright KJ, Imanian B, Strom SL, Delwiche CF, Waller RF, Fensome RA, Leander BS, Rohwer FL, Saldarriaga JF | display-authors=6 | title=Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=114 | issue=2 | pages=E171–E180 | date=January 2017 | pmid=28028238 | pmc=5240707 | doi=10.1073/pnas.1614842114 | bibcode=2017PNAS..114E.171J | doi-access=free }}</ref>

===== Apicomplexans =====
[[File:Plasmodium.png|thumb|Diagram of Plasmodium, including its apicoplast.]]

[[Apicomplexans]] are a group of alveolates. Like the [[helicosproidia]], they're parasitic, and have a nonphotosynthetic chloroplast.<ref name="Keeling-2010" /> They were once thought to be related to the helicosproidia, but it is now known that the helicosproida are green algae rather than part of the CASH lineage.<ref name="Keeling-2010" /> The apicomplexans include ''[[Plasmodium]]'', the [[malaria]] parasite. Many apicomplexans keep a [[vestigial]] red algal derived chloroplast<ref name="Nair-2011" /><ref name="Keeling-2010" /> called an [[apicoplast]], which they inherited from their ancestors. Apicoplasts have lost all photosynthetic function, and contain no photosynthetic pigments or true thylakoids. They are bounded by four membranes, but the membranes are not connected to the [[endoplasmic reticulum]].<ref name="Kim-2009" /> Other apicomplexans like ''[[Cryptosporidium]]'' have lost the chloroplast completely.<ref name="Nair-2011" /> Apicomplexans store their energy in [[amylopectin]] granules that are located in their cytoplasm, even though they are nonphotosynthetic.<ref name="Kim-2009" />

The fact that apicomplexans still keep their nonphotosynthetic chloroplast around demonstrates how the chloroplast carries out important functions other than [[photosynthesis]]. [[Plant]] chloroplasts provide plant cells with many important things besides sugar, and apicoplasts are no different—they synthesize [[fatty acid]]s, [[isopentenyl pyrophosphate]], [[iron-sulfur clusters]], and carry out part of the [[heme]] pathway.<ref name="Nair-2011" /> The most important apicoplast function is [[isopentenyl pyrophosphate]] synthesis—in fact, apicomplexans die when something interferes with this apicoplast function, and when apicomplexans are grown in an isopentenyl pyrophosphate-rich medium, they dump the organelle.<ref name="Nair-2011" />

===== Chromerids =====
[[File:Vitrella brassicaformis LM Michalek 2020.png|thumb|Typical life cycle stages of [[Vitrella brassicaformis]], a chromerid.]]

The [[chromerid]]s are a group of algae known from Australian corals which comprise some close photosynthetic relatives of the apicomplexans. The first member, ''[[Chromera velia]]'', was discovered and first isolated in 2001. The discovery of ''Chromera velia'' with similar structure to the apicomplexans, provides an important link in the evolutionary history of the apicomplexans and dinophytes. Their plastids have four membranes, lack chlorophyll c and use the type II form of [[RuBisCO]] obtained from a horizontal transfer event.<ref>{{cite journal | vauthors=Quigg A, Kotabová E, Jarešová J, Kaňa R, Setlík J, Sedivá B, Komárek O, Prášil O | display-authors=6 | title=Photosynthesis in Chromera velia represents a simple system with high efficiency | journal=PLOS ONE | volume=7 | issue=10 | article-number=e47036 | date=10 October 2012 | pmid=23071705 | pmc=3468483 | doi=10.1371/journal.pone.0047036 | bibcode=2012PLoSO...747036Q | doi-access=free }}</ref>

===== Dinophytes =====
[[File:Ceratium furca.jpg|thumb|''[[Ceratium furca]]'', a [[peridinin]]-containing dinophyte.<ref>{{cite journal  |vauthors=Meeson BW, Chang SS, Sweeney BM |doi=10.1515/botm.1982.25.8.347 |title=Characterization of Peridinin-Chlorophyll α-Proteins from the Marine Dinoflagellate Ceratium furca |year=1982 |journal=Botanica Marina |volume=25 |issue=8 |pages=347–50|bibcode=1982BoMar..25..347M |s2cid=83867103 }}</ref>]]

The [[dinoflagellates]] are yet another very large and diverse group, around half of which are at least partially photosynthetic (i.e. [[Mixotroph|mixotrophic]]).<ref name="Campbell-2009f" /><ref name="Hackett-2004">{{cite journal | vauthors=Hackett JD, Anderson DM, Erdner DL, Bhattacharya D | title=Dinoflagellates: a remarkable evolutionary experiment | journal=American Journal of Botany | volume=91 | issue=10 | pages=1523–34 | date=October 2004 | pmid=21652307 | doi=10.3732/ajb.91.10.1523 }}</ref> Dinoflagellate chloroplasts have relatively complex history. Most dinoflagellate chloroplasts are secondary [[red algae|red algal]] derived chloroplasts. Many dinoflagellates have lost the chloroplast (becoming nonphotosynthetic), some of these have replaced it though ''tertiary'' endosymbiosis.<ref name="Dorrell-2011">{{cite journal | vauthors=Dorrell RG, Smith AG | title=Do red and green make brown?: perspectives on plastid acquisitions within chromalveolates | journal=Eukaryotic Cell | volume=10 | issue=7 | pages=856–68 | date=July 2011 | pmid=21622904 | pmc=3147421 | doi=10.1128/EC.00326-10 }}</ref> Others replaced their original chloroplast with a [[green algae|green algal]] derived chloroplast.<ref name="Keeling-2004" /><ref name="Keeling-2010" /><ref name="Hackett-2004" /> The peridinin chloroplast is thought to be the dinophytes' "original" chloroplast,<ref name="Hackett-2004" /> which has been lost, reduced, replaced, or has company in several other dinophyte lineages.<ref name="Keeling-2010" />

The most common dinophyte chloroplast is the [[peridinin]]-type chloroplast, characterized by the [[carotenoid]] pigment [[peridinin]] in their chloroplasts, along with [[chlorophyll a|chlorophyll ''a'']] and [[chlorophyll c2|chlorophyll ''c''<sub>2</sub>]].<ref name="Keeling-2004" /><ref name="Hackett-2004" /> Peridinin is not found in any other group of chloroplasts.<ref name="Hackett-2004" /> The peridinin chloroplast is bounded by three membranes (occasionally two),<ref name="Kim-2009" /> having lost the red algal endosymbiont's original cell membrane.<ref name="Keeling-2004" /><ref name="Keeling-2010" /> The outermost membrane is not connected to the endoplasmic reticulum.<ref name="Kim-2009" /><ref name="Hackett-2004" /> They contain a [[pyrenoid]], and have triplet-stacked thylakoids. Starch is found outside the chloroplast.<ref name="Kim-2009" /> Peridinin chloroplasts also have DNA that is highly [[genome reduction|reduced]] and fragmented into many small circles.<ref name="Hackett-2004" /> Most of the genome has migrated to the nucleus, and only critical photosynthesis-related genes remain in the chloroplast. 

Most dinophyte chloroplasts contain form II RuBisCO, at least the [[photosynthetic pigments]] [[chlorophyll a|chlorophyll ''a'']], [[chlorophyll c2|chlorophyll ''c<sub>2</sub>'']], [[beta-carotene|''beta''-carotene]], and at least one dinophyte-unique [[xanthophyll]] ([[peridinin]], [[dinoxanthin]], or [[diadinoxanthin]]), giving many a golden-brown color.<ref name="Janouškovec-2017" /><ref name="Hackett-2004" /> All dinophytes store starch in their cytoplasm, and most have chloroplasts with thylakoids arranged in stacks of three.<ref name="Kim-2009" />

=== Haptophyte-derived chloroplasts ===
[[File:Karenia brevis.jpg|thumb|upright|''[[Karenia brevis]]'' is a [[fucoxanthin]]-containing dynophyte responsible for [[algal bloom]]s called "[[red tide]]s".<ref name="Hackett-2004" />]]

The [[fucoxanthin]] dinophyte lineages (including ''[[Karlodinium]]'' and ''[[Karenia (dinoflagellate)|Karenia]]'')<ref name="Keeling-2010" /> lost their original red algal derived chloroplast, and replaced it with a new chloroplast derived from a [[haptophyte]] endosymbiont, making these tertiary plastids. ''[[Karlodinium]]'' and ''[[Karenia (dinoflagellate)|Karenia]]'' probably took up different endosymbionts.<ref name="Keeling-2010" /> Because the haptophyte chloroplast has four membranes, tertiary endosymbiosis would be expected to create a six membraned chloroplast, adding the haptophyte's [[cell membrane]] and the dinophyte's [[phagosomal vacuole]].<ref name="Tengs-2000" /> However, the haptophyte was heavily reduced, stripped of a few membranes and its nucleus, leaving only its chloroplast (with its original double membrane), and possibly one or two additional membranes around it.<ref name="Keeling-2010" /><ref name="Tengs-2000">{{cite journal | vauthors=Tengs T, Dahlberg OJ, Shalchian-Tabrizi K, Klaveness D, Rudi K, Delwiche CF, Jakobsen KS | title=Phylogenetic analyses indicate that the 19'Hexanoyloxy-fucoxanthin-containing dinoflagellates have tertiary plastids of haptophyte origin | journal=Molecular Biology and Evolution | volume=17 | issue=5 | pages=718–29 | date=May 2000 | pmid=10779532 | doi=10.1093/oxfordjournals.molbev.a026350 | author-link4=Dag Klaveness (limnologist) | doi-access=free }}</ref>

Fucoxanthin-containing chloroplasts are characterized by having the pigment [[fucoxanthin]] (actually [[19′-hexanoyloxy-fucoxanthin]] and/or [[19′-butanoyloxy-fucoxanthin]]) and no peridinin. Fucoxanthin is also found in haptophyte chloroplasts, providing evidence of ancestry.<ref name="Hackett-2004" />

=== Diatom-derived chloroplasts ===
[[File:Durinskia baltica.jpg|thumb|Durinskia is a genus significant to the study of endosymbiotic events and organelle integration.<ref name="Zerdoner2017">{{cite journal | vauthors = Žerdoner Čalasan A, Kretschmann J, Gottschling M | title = Absence of co-phylogeny indicates repeated diatom capture in dinophytes hosting a tertiary endosymbiont. | journal = Organisms Diversity & Evolution | date = March 2018 | volume = 18 | issue = 1 | pages = 29–38 | doi = 10.1007/s13127-017-0348-0 | bibcode = 2018ODivE..18...29Z | s2cid = 3830963 }}</ref>]]

Some dinophytes, like ''[[Kryptoperidinium]]'' and ''[[Durinskia]]'',<ref name="Keeling-2010" /> have a [[diatom]] ([[heterokontophyte]])-derived chloroplast.<ref name="Keeling-2004" /> These chloroplasts are bounded by up to ''five'' membranes,<ref name="Keeling-2004" /> (depending on whether the entire diatom endosymbiont is counted as the chloroplast, or just the red algal derived chloroplast inside it). The diatom endosymbiont has been reduced relatively little—it still retains its original [[Mitochondrion|mitochondria]],<ref name="Keeling-2010" /> and has [[endoplasmic reticulum]], [[ribosome]]s, a [[cell nucleus|nucleus]], and of course, red algal derived chloroplasts—practically a complete [[cell (biology)|cell]],<ref name="Schnepf-1999">{{cite journal | vauthors=Schnepf E, Elbrächter M |doi=10.1080/00173139908559217 |title=Dinophyte chloroplasts and phylogeny – A review |year=1999 |journal=Grana |volume=38 |issue=2–3 |pages=81–97|doi-access=free |bibcode=1999Grana..38...81S }}</ref> all inside the host's [[endoplasmic reticulum lumen]].<ref name="Keeling-2010" /> However the diatom endosymbiont can't store its own food—its storage polysaccharide is found in granules in the dinophyte host's cytoplasm instead.<ref name="Kim-2009" /><ref name="Schnepf-1999" /> The diatom endosymbiont's nucleus is present, but it probably can't be called a [[nucleomorph]] because it shows no sign of [[genome reduction]], and might have even been ''expanded''.<ref name="Keeling-2010" /> Diatoms have been engulfed by dinoflagellates at least three times.<ref name="Keeling-2010" />

The diatom endosymbiont is bounded by a single membrane,<ref name="Hackett-2004" /> inside it are chloroplasts with four membranes. Like the diatom endosymbiont's diatom ancestor, the chloroplasts have triplet thylakoids and [[pyrenoid]]s.<ref name="Schnepf-1999" />

In some of these [[genera]], the diatom endosymbiont's chloroplasts aren't the only chloroplasts in the dinophyte. The original three-membraned peridinin chloroplast is still around, converted to an [[Eyespot apparatus|eyespot]].<ref name="Keeling-2004" /><ref name="Keeling-2010" />

=== Kleptoplasty ===
{{Main|Kleptoplasty}}


In some groups of [[mixotrophic]] [[protist]]s, like some [[dinoflagellate]]s (e.g. ''[[Dinophysis]]''), chloroplasts are separated from a captured alga and used temporarily. These [[kleptoplasty|klepto chloroplasts]] may only have a lifetime of a few days and are then replaced.<ref name="Skovgaard-1998">{{cite journal |doi=10.3354/ame015293 |title=Role of chloroplast retention in a marine dinoflagellate |year=1998 |last1=Skovgaard |first1=Alf | name-list-style=vanc |journal=Aquatic Microbial Ecology |volume=15 |pages=293–301|doi-access=free }}</ref><ref>{{cite journal | vauthors=Dorrell RG, Howe CJ | title=Integration of plastids with their hosts: Lessons learned from dinoflagellates | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=112 | issue=33 | pages=10247–54 | date=August 2015 | pmid=25995366 | pmc=4547248 | doi=10.1073/pnas.1421380112 | bibcode=2015PNAS..11210247D | doi-access=free }}</ref>

==== Cryptophyte-derived dinophyte chloroplast ====
[[File:Dinophysis acuminata.jpg|thumb|left|upright|''[[Dinophysis acuminata]]'' has chloroplasts taken from a [[cryptomonad|cryptophyte]].<ref name="Keeling-2004" />]]

Members of the genus ''[[Dinophysis]]'' have a [[phycobilin]]-containing<ref name="Tengs-2000" /> chloroplast taken from a [[cryptomonad|cryptophyte]].<ref name="Keeling-2004" /> However, the cryptophyte is not an endosymbiont—only the chloroplast seems to have been taken, and the chloroplast has been stripped of its [[nucleomorph]] and outermost two membranes, leaving just a two-membraned chloroplast. Cryptophyte chloroplasts require their nucleomorph to maintain themselves, and ''Dinophysis'' species grown in [[cell culture]] alone cannot survive, so it is possible (but not confirmed) that the ''Dinophysis'' chloroplast is a [[kleptoplast]]—if so, ''Dinophysis'' chloroplasts wear out and ''Dinophysis'' species must continually engulf cryptophytes to obtain new chloroplasts to replace the old ones.<ref name="Hackett-2004" />

== Chloroplast DNA ==

{{Main|Chloroplast DNA}}
{{See also|List of sequenced plastomes}}

Chloroplasts, like other endosymbiotic organelles, contain a [[genome]] separate from that in the cell [[Cell nucleus|nucleus]]. The existence of [[chloroplast DNA]] (cpDNA) was identified biochemically in 1959,<ref name="Stocking-1959" /> and confirmed by electron microscopy in 1962.<ref name="Plaut-1962" /> The discoveries that the chloroplast contains ribosomes<ref name="Lyttleton-1962" /> and performs protein synthesis<ref name="Heber, U.-1962" /> revealed that the chloroplast is genetically semi-autonomous. Chloroplast DNA was first sequenced in 1986.<ref name="UniHamburg">{{cite web|title=Chloroplasts and Other Plastids|url=http://www.biologie.uni-hamburg.de/b-online/e23/23a.htm|publisher=University of Hamburg|access-date=27 December 2012|archive-url=https://web.archive.org/web/20120925191743/http://www.biologie.uni-hamburg.de/b-online/e23/23a.htm|archive-date=25 September 2012}}</ref> Since then, hundreds of chloroplast genomes from various species have been [[DNA sequencing|sequenced]], but they are mostly those of [[land plants]] and [[green algae]]—[[glaucophytes]], [[red algae]], and other algal groups are extremely underrepresented, potentially introducing some [[Selection bias|bias]] in views of "typical" chloroplast DNA structure and content.<ref name="Sandelius-2009">{{cite book |last=Sandelius |first=Anna Stina | name-list-style=vanc |title=The Chloroplast: Interactions with the Environment |year=2009 |publisher=Springer |isbn=978-3-540-68696-5 |page=18 |url=https://books.google.com/books?id=aQR__H2XBnUC&pg=PA18}}</ref>

{{Chloroplast DNA|caption='''Chloroplast DNA''' Interactive gene map of chloroplast DNA from ''[[Nicotiana tabacum]]''. Segments with labels on the inside are on the B strand of [[DNA]], segments with labels on the outside are on the A strand. Notches indicate [[introns]].}}

=== Molecular structure ===

With few exceptions, most chloroplasts have their entire chloroplast genome combined into a single large circular DNA molecule,<ref name="Sandelius-2009" /> typically 120,000–170,000 [[base pair]]s long<ref name="Dann-2002">{{cite book |last=Dann |first=Leighton |url=http://www.bioscience-explained.org/ENvol1_2/pdf/ctDNAEN.pdf |title=Bioscience—Explained |publisher=BIOSCIENCE EXPLAINED |year=2002 |location=Green DNA |archive-url=https://web.archive.org/web/20101214102105/http://www.bioscience-explained.org/ENvol1_2/pdf/ctDNAEN.pdf |archive-date=14 December 2010 |url-status=live |name-list-style=vanc}}</ref><ref name="Clegg-1994" /><ref name="Shaw-2007" /><ref name="Milo">{{cite web | vauthors=Milo R, Phillips R |url=http://book.bionumbers.org/how-large-are-chloroplasts/|title=Cell Biology by the Numbers: How large are chloroplasts?|website =book.bionumbers.org |access-date=7 February 2017}}</ref> and a mass of about 80–130&nbsp;million [[dalton (unit)|daltons]].<ref name="Burgess-1989b">{{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=62 |url=https://books.google.com/books?id=r808AAAAIAAJ&pg=PA62}}</ref> While chloroplast genomes can almost always be assembled into a circular map, the physical DNA molecules inside cells take on a variety of linear and branching forms.<ref name="Sandelius-2009" /><ref>{{Cite journal |last=Green |first=Beverley R. |date=28 April 2011 |title=Chloroplast genomes of photosynthetic eukaryotes |url=https://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04541.x |journal=The Plant Journal |language=en |volume=66 |issue=1 |pages=34–44 |doi=10.1111/j.1365-313X.2011.04541.x |pmid=21443621 |issn=0960-7412|url-access=subscription }}</ref> New chloroplasts may contain up to 100 copies of their genome,<ref name="Dann-2002" /> though the number of copies decreases to about 15–20 as the chloroplasts age.<ref name="PlantBiochem-2005">{{cite book|title=Plant Biochemistry |edition=3rd |year=2005|publisher=Academic Press|page=[https://archive.org/details/isbn_9788131200032/page/517 517]|url=https://archive.org/details/isbn_9788131200032|url-access=registration |quote=number of copies of ctDNA per chloroplast. |isbn=978-0-12-088391-2}}</ref>

Chloroplast DNA is usually condensed into [[nucleoid]]s, which can contain multiple copies of the chloroplast genome. Many nucleoids can be found in each chloroplast.<ref name="Burgess-1989b" /> In primitive [[red algae]], the chloroplast DNA nucleoids are clustered in the center of the chloroplast, while in green plants and [[green algae]], the nucleoids are dispersed throughout the [[stroma (fluid)|stroma]].<ref name="Kobayashi-2002" /> Chloroplast DNA is not associated with true [[histone]]s, proteins that are used to pack DNA molecules tightly in eukaryote nuclei.<ref name="Campbell-2009c" /> Though in [[red algae]], similar proteins tightly pack each chloroplast DNA ring in a [[nucleoid]].<ref name="Kobayashi-2002">{{cite journal | vauthors=Kobayashi T, Takahara M, Miyagishima SY, Kuroiwa H, Sasaki N, Ohta N, Matsuzaki M, Kuroiwa T | display-authors=6 | title=Detection and localization of a chloroplast-encoded HU-like protein that organizes chloroplast nucleoids | journal=The Plant Cell | volume=14 | issue=7 | pages=1579–89 | date=July 2002 | pmid=12119376 | pmc=150708 | doi=10.1105/tpc.002717 | bibcode=2002PlanC..14.1579K }}</ref>

Many chloroplast genomes contain two [[inverted repeat]]s, which separate a long single copy section (LSC) from a short single copy section (SSC).<ref name="Shaw-2007">{{cite journal | vauthors=Shaw J, Lickey EB, Schilling EE, Small RL | s2cid=30501148 | title=Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III | journal=American Journal of Botany | volume=94 | issue=3 | pages=275–88 | date=March 2007 | pmid=21636401 | doi=10.3732/ajb.94.3.275 }}</ref> A given pair of inverted repeats are rarely identical, but they are always very similar to each other, apparently resulting from [[concerted evolution]].<ref name="Sandelius-2009" /> The inverted repeats vary wildly in length, ranging from 4,000 to 25,000 [[base pair]]s long each and containing as few as four or as many as over 150 genes.<ref name="Sandelius-2009" /> The inverted repeat regions are highly [[Conserved sequence|conserved]] in land plants, and accumulate few mutations.<ref name="Shaw-2007" /><ref name="Kolodner-1979">{{cite journal |vauthors=Kolodner R, Tewari KK |date=January 1979 |title=Inverted repeats in chloroplast DNA from higher plants |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=76 |issue=1 |pages=41–5 |bibcode=1979PNAS...76...41K |doi=10.1073/pnas.76.1.41 |pmc=382872 |pmid=16592612 |doi-access=free}}</ref>

Similar inverted repeats exist in the genomes of cyanobacteria and the other two chloroplast lineages ([[glaucophyta]] and [[rhodophyceae]]), suggesting that they predate the chloroplast.<ref name="Sandelius-2009" /> Some chloroplast genomes have since lost<ref name="Kolodner-1979" /><ref name="Palmer-1982" /> or flipped the inverted repeats (making them [[direct repeat]]s).<ref name="Sandelius-2009" /> It is possible that the inverted repeats help stabilize the rest of the chloroplast genome, as chloroplast genomes which have lost some of the inverted repeat segments tend to get rearranged more.<ref name="Palmer-1982">{{cite journal | vauthors=Palmer JD, Thompson WF | title=Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost | journal=Cell | volume=29 | issue=2 | pages=537–50 | date=June 1982 | pmid=6288261 | doi=10.1016/0092-8674(82)90170-2 | s2cid=11571695 }}</ref>

===DNA repair and replication===

In chloroplasts of the moss ''[[Physcomitrella patens]]'', the [[DNA mismatch repair]] protein Msh1 interacts with the [[homologous recombination|recombination]]al [[DNA repair|repair]] proteins [[RecA]] and RecG to maintain chloroplast [[genome]] stability.<ref name="Odahara-2017">{{cite journal | vauthors=Odahara M, Kishita Y, Sekine Y | title=MSH1 maintains organelle genome stability and genetically interacts with RECA and RECG in the moss Physcomitrella patens | journal=The Plant Journal | volume=91 | issue=3 | pages=455–465 | date=August 2017 | pmid=28407383 | doi=10.1111/tpj.13573 | bibcode=2017PlJ....91..455O | doi-access=free }}</ref> In chloroplasts of the plant ''[[Arabidopsis thaliana]]'' the [[RecA]] protein maintains the integrity of the chloroplast's DNA by a process that likely involves the recombinational repair of [[DNA damage (naturally occurring)|DNA damage]].<ref name="Rowan-2010">{{cite journal | vauthors=Rowan BA, Oldenburg DJ, Bendich AJ | title=RecA maintains the integrity of chloroplast DNA molecules in Arabidopsis | journal=Journal of Experimental Botany | volume=61 | issue=10 | pages=2575–88 | date=June 2010 | pmid=20406785 | pmc=2882256 | doi=10.1093/jxb/erq088 }}</ref>

[[File:CpDNA Replication.png|thumb|upright=1.65|Chloroplast DNA replication via multiple [[D-loop]] mechanisms. Adapted from Krishnan NM, Rao BJ's paper "A comparative approach to elucidate chloroplast genome replication."]]
The mechanism for chloroplast DNA (cpDNA) replication has not been conclusively determined, but two main models have been proposed. Scientists have attempted to observe chloroplast replication via [[electron microscopy]] since the 1970s.<ref name="Krishnan-2009">{{cite journal | vauthors=Krishnan NM, Rao BJ | title=A comparative approach to elucidate chloroplast genome replication | journal=BMC Genomics | volume=10 | issue=237 | page=237 | date=May 2009 | pmid=19457260 | pmc=2695485 | doi=10.1186/1471-2164-10-237 | doi-access=free }}</ref><ref name="Heinhorst-1993">{{cite journal | vauthors=Heinhorst S, Cannon GC |title=DNA replication in chloroplasts|journal=Journal of Cell Science|date=1993|volume=104|pages=1–9|doi=10.1242/jcs.104.1.1|url=https://aquila.usm.edu/cgi/viewcontent.cgi?article=7560&context=fac_pubs|url-access=subscription}}</ref> The results of the microscopy experiments led to the idea that chloroplast DNA replicates using a double displacement loop (D-loop). As the D-loop moves through the circular DNA, it adopts a theta intermediary form, also known as a Cairns replication intermediate, and completes replication with a rolling circle mechanism.<ref name="Krishnan-2009"/><ref name="Bendich-2004">{{cite journal |vauthors=Bendich AJ |date=July 2004 |title=Circular chloroplast chromosomes: the grand illusion |journal=The Plant Cell |volume=16 |issue=7 |pages=1661–6 |doi=10.1105/tpc.160771 |pmc=514151 |pmid=15235123|bibcode=2004PlanC..16.1661B }}</ref> Transcription starts at specific points of origin. Multiple replication forks open up, allowing replication machinery to transcribe the DNA. As replication continues, the forks grow and eventually converge. The new cpDNA structures separate, creating daughter cpDNA chromosomes.

In addition to the early microscopy experiments, this model is also supported by the amounts of [[deamination]] seen in cpDNA.<ref name="Krishnan-2009"/> Deamination occurs when an amino group is lost and is a mutation that often results in base changes. When adenine is deaminated, it becomes [[hypoxanthine]]. Hypoxanthine can bind to cytosine, and when the XC base pair is replicated, it becomes a GC (thus, an A → G base change).<ref name=Biocyclopedia>{{cite web|title=Effect of chemical mutagens on nucleotide sequence|url=http://www.biocyclopedia.com/index/genetics/mutations_molecular_level_mechanism/effect_of_chemical_mutagens_on_nucleotide_sequence.php|website=Biocyclopedia|access-date=24 October 2015}}</ref>
[[File:Adenine Deaminates to Guanine.png|thumb|left|upright=1.35|Over time, base changes in the DNA sequence can arise from deamination mutations. When adenine is deaminated, it becomes hypoxanthine, which can pair with cytosine. During replication, the cytosine will pair with guanine, causing an A --> G base change.]]

In cpDNA, there are several A → G deamination gradients. DNA becomes susceptible to deamination events when it is single stranded. When replication forks form, the strand not being copied is single stranded, and thus at risk for A → G deamination. Therefore, gradients in deamination indicate that replication forks were most likely present and the direction that they initially opened (the highest gradient is most likely nearest the start site because it was single stranded for the longest amount of time).<ref name="Krishnan-2009"/> This mechanism is still the leading theory today; however, a second theory suggests that most cpDNA is actually linear and replicates through homologous recombination. It further contends that only a minority of the genetic material is kept in circular chromosomes while the rest is in branched, linear, or other complex structures.<ref name="Krishnan-2009"/><ref name="Bendich-2004"/>

One of competing model for cpDNA replication asserts that most cpDNA is linear and participates in [[homologous recombination]] and replication structures similar to the linear and circular DNA structures of [[bacteriophage T4]].<ref name="Bendich-2004"/><ref name="Bernstein-1973">{{cite journal | vauthors=Bernstein H, Bernstein C | title=Circular and branched circular concatenates as possible intermediates in bacteriophage T4 DNA replication | journal=Journal of Molecular Biology | volume=77 | issue=3 | pages=355–61 | date=July 1973 | pmid=4580243 | doi=10.1016/0022-2836(73)90443-9 }}</ref> It has been established that some plants have linear cpDNA, such as maize, and that more species still contain complex structures that scientists do not yet understand.<ref name="Bendich-2004"/> When the original experiments on cpDNA were performed, scientists did notice linear structures; however, they attributed these linear forms to broken circles.<ref name="Bendich-2004"/> If the branched and complex structures seen in cpDNA experiments are real and not artifacts of concatenated circular DNA or broken circles, then a D-loop mechanism of replication is insufficient to explain how those structures would replicate.<ref name="Bendich-2004"/> At the same time, homologous recombination does not expand the multiple A --> G gradients seen in plastomes.<ref name="Krishnan-2009"/> Because of the failure to explain the deamination gradient as well as the numerous plant species that have been shown to have circular cpDNA, the predominant theory continues to hold that most cpDNA is circular and most likely replicates via a D loop mechanism.

=== Gene content and protein synthesis ===

The ancestral cyanobacteria that led to chloroplasts probably had a genome that contained over 3000 genes, but only approximately 100 genes remain in contemporary chloroplast genomes.<ref name="Milo" /><ref name="McFadden-2001">{{cite journal | vauthors=McFadden GI | title=Chloroplast origin and integration | journal=Plant Physiology | volume=125 | issue=1 | pages=50–3 | date=January 2001 | pmid=11154294 | pmc=1539323 | doi=10.1104/pp.125.1.50 }}</ref><ref name="Clegg-1994">{{cite journal | vauthors=Clegg MT, Gaut BS, Learn GH, Morton BR | title=Rates and patterns of chloroplast DNA evolution | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=91 | issue=15 | pages=6795–801 | date=July 1994 | pmid=8041699 | pmc=44285 | doi=10.1073/pnas.91.15.6795 | bibcode=1994PNAS...91.6795C | doi-access=free }}</ref> These genes code for a variety of things, mostly to do with the [[protein synthesis|protein pipeline]] and [[photosynthesis]]. As in [[prokaryotes]], genes in chloroplast DNA are organized into [[operons]].<ref name="McFadden-2001" /> Unlike [[prokaryotic]] DNA molecules, chloroplast DNA molecules contain [[introns]] (plant [[mitochondrial DNA]]s do too, but not human mtDNAs).<ref name="Alberts-2002b" />

Among land plants, the contents of the chloroplast genome are fairly similar.<ref name="Shaw-2007" />

==== Chloroplast genome reduction and gene transfer ====

Over time, many parts of the chloroplast genome were transferred to the [[nuclear genome]] of the host,<ref name="Dann-2002" /><ref name="Clegg-1994" /><ref>{{cite journal | vauthors=Huang CY, Ayliffe MA, Timmis JN | title=Direct measurement of the transfer rate of chloroplast DNA into the nucleus | journal=Nature | volume=422 | issue=6927 | pages=72–6 | date=March 2003 | pmid=12594458 | doi=10.1038/nature01435 | bibcode=2003Natur.422...72H | s2cid=4319507 }}</ref> a process called ''[[endosymbiotic gene transfer]]''. As a result, the chloroplast genome is heavily [[genome reduction|reduced]] compared to that of free-living cyanobacteria. Chloroplasts may contain 60–100 genes whereas cyanobacteria often have more than 1500 genes in their genome.<ref name="Martin-2002">{{cite journal | vauthors=Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D | display-authors=6 | title=Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=99 | issue=19 | pages=12246–51 | date=September 2002 | pmid=12218172 | pmc=129430 | doi=10.1073/pnas.182432999 | bibcode=2002PNAS...9912246M | doi-access=free }}</ref> Recently, a plastid without a genome was found, demonstrating chloroplasts can lose their genome during endosymbiotic the gene transfer process.<ref>{{cite journal | vauthors=Smith DR, Lee RW | title=A plastid without a genome: evidence from the nonphotosynthetic green algal genus Polytomella | journal=Plant Physiology | volume=164 | issue=4 | pages=1812–9 | date=April 2014 | pmid=24563281 | pmc=3982744 | doi=10.1104/pp.113.233718 }}</ref>

Endosymbiotic gene transfer is how we know about the [[#Secondary and tertiary endosymbiosis|lost chloroplasts]] in many CASH lineages. Even if a chloroplast is eventually lost, the genes it donated to the former host's nucleus persist, providing evidence for the lost chloroplast's existence. For example, while [[diatoms]] (a [[heterokontophyte]]) now have a [[red algal derived chloroplast]], the presence of many [[green algal]] genes in the diatom nucleus provide evidence that the diatom ancestor had a [[green algal derived chloroplast]] at some point, which was subsequently replaced by the red chloroplast.<ref name="Moustafa-2009" />

In land plants, some 11–14% of the DNA in their nuclei can be traced back to the chloroplast,<ref name="Nowack-2011" /> up to 18% in ''[[Arabidopsis]]'', corresponding to about 4,500 protein-coding genes.<ref name="Archibald-2006">{{cite journal | vauthors=Archibald JM | title=Algal genomics: exploring the imprint of endosymbiosis | journal=Current Biology | volume=16 | issue=24 | pages=R1033-5 | date=December 2006 | pmid=17174910 | doi=10.1016/j.cub.2006.11.008 | doi-access=free | bibcode=2006CBio...16R1033A }}</ref> There have been a few recent transfers of genes from the chloroplast DNA to the nuclear genome in land plants.<ref name="Clegg-1994" />

Of the approximately 3000 proteins found in chloroplasts, some 95% of them are encoded by nuclear genes. Many of the chloroplast's protein complexes consist of subunits from both the chloroplast genome and the host's nuclear genome. As a result, [[protein synthesis]] must be coordinated between the chloroplast and the nucleus. The chloroplast is mostly under nuclear control, though chloroplasts can also give out signals regulating [[gene expression]] in the nucleus, called ''[[retrograde signaling]]''.<ref name="Koussevitzky-2007">{{cite journal|vauthors= Koussevitzky S, Nott A, Mockler TC, Hong F, Sachetto-Martins G, Surpin M, Lim J, Mittler R, Chory J|display-authors=6|title=Signals from chloroplasts converge to regulate nuclear gene expression|journal=Science|volume=316|issue=5825|pages=715–9|date=May 2007|pmid= 17395793|doi= 10.1126/science.1140516|bibcode= 2007Sci...316..715K|s2cid=245901639}}
* {{cite magazine |author=Bob Grant |date=1 April 2009 |title=Communicating with chloroplasts |magazine=The Scientist |url=https://www.the-scientist.com/hot-paper/communicating-with-chloroplasts-44253}}</ref> Recent research indicates that parts of the retrograde signaling network once considered characteristic for land plants emerged already in an algal progenitor,<ref>{{Cite journal |last1=de Vries |first1=Jan |last2=Curtis |first2=Bruce A. |last3=Gould |first3=Sven B. |last4=Archibald |first4=John M. |date=10 April 2018 |title=Embryophyte stress signaling evolved in the algal progenitors of land plants |journal=Proceedings of the National Academy of Sciences |language=en |volume=115 |issue=15 |pages=E3471–E3480 |doi=10.1073/pnas.1719230115 |issn=0027-8424 |pmc=5899452 |pmid=29581286 |bibcode=2018PNAS..115E3471D |doi-access=free }}</ref><ref>{{Cite journal |last1=Nishiyama |first1=Tomoaki |last2=Sakayama |first2=Hidetoshi |last3=de Vries |first3=Jan |last4=Buschmann |first4=Henrik |last5=Saint-Marcoux |first5=Denis |last6=Ullrich |first6=Kristian K. |last7=Haas |first7=Fabian B. |last8=Vanderstraeten |first8=Lisa |last9=Becker |first9=Dirk |last10=Lang |first10=Daniel |last11=Vosolsobě |first11=Stanislav |last12=Rombauts |first12=Stephane |last13=Wilhelmsson |first13=Per K.I. |last14=Janitza |first14=Philipp |last15=Kern |first15=Ramona |date=July 2018 |title=The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization |journal=Cell |language=en |volume=174 |issue=2 |pages=448–464.e24 |doi=10.1016/j.cell.2018.06.033|pmid=30007417 |s2cid=206569169 |doi-access=free }}</ref><ref>{{Cite journal |last1=Zhao |first1=Chenchen |last2=Wang |first2=Yuanyuan |last3=Chan |first3=Kai Xun |last4=Marchant |first4=D. Blaine |last5=Franks |first5=Peter J. |last6=Randall |first6=David |last7=Tee |first7=Estee E. |last8=Chen |first8=Guang |last9=Ramesh |first9=Sunita |last10=Phua |first10=Su Yin |last11=Zhang |first11=Ben |last12=Hills |first12=Adrian |last13=Dai |first13=Fei |last14=Xue |first14=Dawei |last15=Gilliham |first15=Matthew |date=12 March 2019 |title=Evolution of chloroplast retrograde signaling facilitates green plant adaptation to land |journal=Proceedings of the National Academy of Sciences |language=en |volume=116 |issue=11 |pages=5015–5020 |doi=10.1073/pnas.1812092116 |issn=0027-8424 |pmc=6421419 |pmid=30804180 |bibcode=2019PNAS..116.5015Z |doi-access=free }}</ref> integrating into co-expressed cohorts of genes in the closest algal relatives of land plants.<ref>{{Cite journal |last1=Dadras |first1=Armin |last2=Fürst-Jansen |first2=Janine M. R. |last3=Darienko |first3=Tatyana |last4=Krone |first4=Denis |last5=Scholz |first5=Patricia |last6=Sun |first6=Siqi |last7=Herrfurth |first7=Cornelia |last8=Rieseberg |first8=Tim P. |last9=Irisarri |first9=Iker |last10=Steinkamp |first10=Rasmus |last11=Hansen |first11=Maike |last12=Buschmann |first12=Henrik |last13=Valerius |first13=Oliver |last14=Braus |first14=Gerhard H. |last15=Hoecker |first15=Ute |date=28 August 2023 |title=Environmental gradients reveal stress hubs pre-dating plant terrestrialization |journal=Nature Plants |volume=9 |issue=9 |pages=1419–1438 |language=en |doi=10.1038/s41477-023-01491-0 |pmid=37640935 |pmc=10505561 |bibcode=2023NatPl...9.1419D |issn=2055-0278}}</ref>

==== Protein synthesis ====

{{See also|transcription (genetics)|Translation (biology)|label 1=Transcription|label 2=translation}}
Protein synthesis within chloroplasts relies on two [[RNA polymerase]]s. One is coded by the chloroplast DNA, the other is of [[cell nucleus|nuclear]] origin. The two RNA polymerases may recognize and bind to different kinds of [[promoter (genetics)|promoters]] within the chloroplast genome.<ref name="Hedtke-1997">{{cite journal | vauthors=Hedtke B, Börner T, Weihe A | title=Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis | journal=Science | volume=277 | issue=5327 | pages=809–11 | date=August 1997 | pmid=9242608 | doi=10.1126/science.277.5327.809 }}</ref> The [[ribosome]]s in chloroplasts are similar to bacterial ribosomes.<ref name="Harris-1994">{{cite journal | vauthors=Harris EH, Boynton JE, Gillham NW | title=Chloroplast ribosomes and protein synthesis | journal=Microbiological Reviews | volume=58 | issue=4 | pages=700–54 | date=December 1994 | pmid=7854253 | pmc=372988 | doi=10.1128/MMBR.58.4.700-754.1994 }}</ref>

{{Expand section|Genome size differences between algae and land plants, chloroplast stuff coded by the nucleus|date=January 2013}}

=== Protein targeting and import ===

{{See also|Translation (biology)|label 1=Translation}}

Because so many chloroplast genes have been moved to the nucleus, many [[protein]]s that would originally have been [[Translation (biology)|translated]] in the chloroplast are now synthesized in the cytoplasm of the plant cell. These proteins must be directed back to the chloroplast, and imported through at least two chloroplast membranes.<ref name="Soll-2004">{{cite journal | vauthors=Soll J, Schleiff E | title=Protein import into chloroplasts | journal=Nature Reviews Molecular Cell Biology | volume=5 | issue=3 | pages=198–208 | date=March 2004 | pmid=14991000 | doi=10.1038/nrm1333 | s2cid=32453554 | url=http://nbn-resolving.de/urn:nbn:de:bvb:19-epub-3587-4 }}</ref>

Curiously, around half of the protein products of transferred genes aren't even targeted back to the chloroplast. Many became [[exaptations]], taking on new functions like participating in [[cell division]], [[protein routing]], and even [[disease resistance]]. A few chloroplast genes found new homes in the [[mitochondrial genome]]—most became nonfunctional [[pseudogenes]], though a few [[tRNA]] genes still work in the [[mitochondrion]].<ref name="Martin-2002" /> Some transferred chloroplast DNA protein products get directed to the [[secretory pathway]],<ref name="Martin-2002" /> though many [[#Secondary and tertiary endosymbiosis|secondary plastids]] are bounded by an outermost membrane derived from the host's [[cell membrane]], and therefore [[topologically]] outside of the cell because to reach the chloroplast from the [[cytosol]], the [[cell membrane]] must be crossed, which signifies entrance into the [[extracellular space]]. In those cases, chloroplast-targeted proteins do initially travel along the secretory pathway.<ref name="Keeling-2010" />

Because the cell acquiring a chloroplast [[#Primary endosymbiosis|already]] had [[Mitochondrion|mitochondria]] (and [[peroxisomes]], and a [[cell membrane]] for secretion), the new chloroplast host had to develop a unique [[protein targeting system]] to avoid having chloroplast proteins being sent to the wrong [[organelle]].<ref name="Soll-2004" />

{{plain image with caption|File:Tetrapeptide structural formulae.svg| The two ends of a polypeptide are called the [[N-terminus]], or ''amino end'', and the [[C-terminus]], or ''carboxyl end''.<ref name="Campbell-2009a">{{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) | page=340 | isbn=978-0-8053-6844-4 }}</ref> This [[polypeptide]] has four [[amino acids]] linked together. At the left is the [[N-terminus]], with its [[amino group|amino]] (H<sub>2</sub>'''N''') group in green. The blue [[C-terminus]], with its [[carboxyl group]] ('''C'''O<sub>2</sub>H) is at the right.|370px|right|bottom|triangle|#00aa15}}

In most, but not all cases, nuclear-encoded chloroplast proteins are [[Translation (biology)|translated]] with a ''[[cleavable transit peptide]]'' that's added to the N-terminus of the protein precursor. Sometimes the transit sequence is found on the C-terminus of the protein,<ref name="Lung-2012">{{cite journal | vauthors=Lung SC, Chuong SD | title=A transit peptide-like sorting signal at the C terminus directs the Bienertia sinuspersici preprotein receptor Toc159 to the chloroplast outer membrane | journal=The Plant Cell | volume=24 | issue=4 | pages=1560–78 | date=April 2012 | pmid=22517318 | pmc=3398564 | doi=10.1105/tpc.112.096248 | bibcode=2012PlanC..24.1560L }}</ref> or within the functional part of the protein.<ref name="Soll-2004" />

==== Transport proteins and membrane translocons ====

After a chloroplast [[polypeptide]] is synthesized on a [[ribosome]] in the [[cytosol]], an enzyme [[enzyme specificity|specific]] to chloroplast proteins<ref name="Waegemann-1996">{{cite journal | vauthors=Waegemann K, Soll J | title=Phosphorylation of the transit sequence of chloroplast precursor proteins | journal=The Journal of Biological Chemistry | volume=271 | issue=11 | pages=6545–54 | date=March 1996 | pmid=8626459 | doi=10.1074/jbc.271.11.6545 | doi-access=free }}</ref> [[phosphorylates]], or adds a [[phosphate group]] to many (but not all) of them in their transit sequences.<ref name="Soll-2004" />
Phosphorylation helps many proteins bind the polypeptide, keeping it from [[protein folding|folding]] prematurely.<ref name="Soll-2004" /> This is important because it prevents chloroplast proteins from assuming their active form and carrying out their chloroplast functions in the wrong place—the [[cytosol]].<ref name="May-2000" /><ref name="Jarvis-2001">{{cite journal | vauthors=Jarvis P, Soll J | title=Toc, Tic, and chloroplast protein import | journal=Biochimica et Biophysica Acta (BBA) - Molecular Cell Research | volume=1541 | issue=1–2 | pages=64–79 | date=December 2001 | pmid=11750663 | doi=10.1016/S0167-4889(01)00147-1 | doi-access=free }}</ref> At the same time, they have to keep just enough shape so that they can be recognized by the chloroplast.<ref name="May-2000">{{cite journal | vauthors=May T, Soll J | title=14-3-3 proteins form a guidance complex with chloroplast precursor proteins in plants | journal=The Plant Cell | volume=12 | issue=1 | pages=53–64 | date=January 2000 | pmid=10634907 | pmc=140214 | doi=10.1105/tpc.12.1.53 | bibcode=2000PlanC..12...53M }}</ref> These proteins also help the polypeptide get imported into the chloroplast.<ref name="Soll-2004" />

From here, chloroplast proteins bound for the stroma must pass through two protein complexes—the [[TOC complex]], or ''[[translocon|'''t'''ranslocon]] on the '''o'''uter '''c'''hloroplast membrane'', and the [[TIC translocon]], or '''''t'''ranslocon on the '''i'''nner '''c'''hloroplast membrane [[translocon]]''.<!--Yes, that's what the source says--><ref name="Soll-2004" /> Chloroplast polypeptide chains probably often travel through the two complexes at the same time, but the TIC complex can also retrieve preproteins lost in the [[chloroplast intermembrane space|intermembrane space]].<ref name="Soll-2004" />

== 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}}</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" />
{{clear}}

=== 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 | url-access=subscription }}</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 | article-number=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|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'''
-->
|-
| style="text-align: right; padding-right: 10px; border-right: 4px solid #24d12b;"| '''[[Land plants|<span style="color:#24d12b;">Land plants</span>]]'''
| style="background:#00bb90; color:#fff;"|
| style="background:#00bb34; color:#fff;"|
|
|
| style="background:#e2c000; color:#fff;"|
| style="background:#ff9e00; color:#fff; opacity:0.5;"|
| style="background:#ff6000; color:#fff; border-right:2px solid white;"|

|-
| style="text-align: right; padding-right: 10px; border-right: 4px solid #24d14e;"| '''[[Green algae|<span style="color:#24d14e;">Green algae</span>]]'''
| style="background:#00bb90; color:#fff;"|
| style="background:#00bb34; color:#fff;"|
| style="background:#d3cf00; color:#fff; opacity:0.3;"|
|
| style="background:#e2c000; color:#fff;"|
| style="background:#ff9e00; color:#fff; opacity:0.5;"|
| style="background:#ff6000; color:#fff; border-right:2px solid white;"|
|
|-
| 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>]]'''
| style="background:#00bb90; color:#fff;"|
| style="background:#00bb34; color:#fff;"|
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| style="background:#e2c000; color:#fff;"|
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| style="background:#ff6000; color:#fff; border-right:2px solid white;"|

|-
| style="background:#00bb90; color:#fff;"|
| style="background:#00bb34; color:#fff;"|
|
|
| style="background:#e2c000; color:#fff;"|
|
| style="background:#ff6000; color:#fff; border-right:2px solid white;"|

|-
| style="text-align: right; padding-right: 10px; border-right: 4px solid #dc003e;"| '''[[Red algae|<span style="color:#dc003e;">Multicellular red algae</span>]]'''
| style="background:#00bb90; color:#fff;"|
|
|
|
| style="background:#e2c000; color:#fff;"|
| style="background:#ff9e00; color:#fff; opacity:0.5;"|
| style="background:#ff6000; color:#fff; opacity:0.5; border-right:2px solid white;"|
| style="background:#ff0040; color:#fff;"|

|-
| style="text-align: right; padding-right: 10px; border-right: 4px solid #dc0052;"| '''[[Red algae|<span style="color:#dc0052;">Unicellular red algae</span>]]'''
| style="background:#00bb90; color:#fff;"|
|
|
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| style="background:#e2c000; color:#fff; opacity:0.8;"|
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| style="background:#ff6000; color:#fff; opacity:0.5; border-right:2px solid white;"|
| style="background:#ff0040; color:#fff;"|

|-
| 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;"|
|
| style="background:#d3cf00; color:#fff;"|
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| style="background:#e2c000; color:#fff;"|
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| style="background:#ff6000; color:#fff; opacity:1; border-right:2px solid white;"|
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|-
| style="background:#00bb90; color:#fff;"|
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| style="background:#d3cf00; color:#fff;"|
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| style="background:#e2c000; color:#fff;"|
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| style="background:#ff6000; color:#fff; opacity:0.5; border-right:2px solid white;"|
|
|-
| style="text-align: right; padding-right: 10px; border-right: 4px solid #ca4300;"| '''[[Cryptomonad|<span style="color:#ca4300;">Cryptophytes</span>]]'''
| style="background:#00bb90; color:#fff;"|
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| style="background:#d3cf00; color:#fff;"|
|
| style="background:#e2c000; color:#fff; opacity:0.5;"|
| style="background:#ff9e00; color:#fff;"|
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| style="background:#ff0040; color:#fff;"|

|-
| style="text-align: right; padding-right: 10px; border-right: 4px solid #00ca9b;"| '''[[Glaucophytes|<span style="color:#00ca9b;">Glaucophytes</span>]]'''
| style="background:#00bb90; color:#fff;"|
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| style="background:#e2c000; color:#fff; opacity:0.8;"|
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| style="background:#ff6000; color:#fff; opacity:1; border-right:2px solid white;"|
| style="background:#ff0040; color:#fff;"|

|-
| style="text-align: right; padding-right: 10px; border-right: 4px solid #00c9be;"| '''[[Cyanobacteria|<span style="color:#00c9be;">Cyanobacteria</span>]]'''
| style="background:#00bb90; color:#fff;"|
| 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;"|
| style="background:#ff9e00; color:#fff; opacity:0.5;"|
| style="background:#ff6000; color:#fff; opacity:1; border-right:2px solid white;"|
| style="background:#ff0040; color:#fff;"|
|}

=== 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>

== Function and chemistry ==

=== Guard cell chloroplasts ===

{{expand section|determined functions, controversial functions, characteristics and population|date=August 2013}}

Unlike most epidermal cells, the [[guard cells]] of plant [[stomata]] contain relatively well-developed chloroplasts.<ref name="Lawson">Lawson T. and J. I. L. Morison. Essay 10.1 Guard Cell Photosynthesis. Plant Physiology and Development, Sixth Edition [http://6e.plantphys.net/essay10.01.html]</ref> However, exactly what they do is controversial.<ref>{{Cite journal | vauthors=Zeiger E, Talbott LD, Frechilla S, Srivastava A, Zhu J | title=The guard cell chloroplast: A perspective for the twenty-first century | doi=10.1046/j.0028-646X.2001.NPH328.doc.x | journal=New Phytologist | volume=153 | issue=3 | pages=415–424 | year=2002 | pmid=33863211 | bibcode=2002NewPh.153..415Z }}</ref>

=== Plant innate immunity ===

[[Plant]]s lack specialized [[immune cells]]—all plant cells participate in the plant [[plant innate immunity|immune response]]. Chloroplasts, along with the [[Cell nucleus|nucleus]], [[cell membrane]], and [[endoplasmic reticulum]],<ref name="Padmanabhan-2010">{{cite journal | vauthors=Padmanabhan MS, Dinesh-Kumar SP | title=All hands on deck—the role of chloroplasts, endoplasmic reticulum, and the nucleus in driving plant innate immunity | journal=Molecular Plant-Microbe Interactions | volume=23 | issue=11 | pages=1368–80 | date=November 2010 | pmid=20923348 | doi=10.1094/MPMI-05-10-0113 | bibcode=2010MPMI...23.1368P | doi-access=free }}</ref> are key players in [[pathogen]] defense. Due to its role in a plant cell's immune response, pathogens frequently target the chloroplast.<ref name="Padmanabhan-2010" />

Plants have two main immune responses—the [[hypersensitive response]], in which infected cells seal themselves off and undergo [[programmed cell death]], and [[systemic acquired resistance]], where infected cells release signals warning the rest of the plant of a pathogen's presence.
Chloroplasts stimulate both responses by purposely damaging their photosynthetic system, producing [[reactive oxygen species]]. High levels of reactive oxygen species will cause the [[hypersensitive response]]. The reactive oxygen species also directly kill any pathogens within the cell. Lower levels of reactive oxygen species initiate [[systemic acquired resistance]], triggering defense-molecule production in the rest of the plant.<ref name="Padmanabhan-2010" />

In some plants, chloroplasts are known to move closer to the infection site and the [[Cell nucleus|nucleus]] during an infection.<ref name="Padmanabhan-2010" />

Chloroplasts can serve as cellular sensors. After detecting stress in a cell, which might be due to a pathogen, chloroplasts begin producing molecules like [[salicylic acid]], [[jasmonic acid]], [[nitric oxide]] and [[reactive oxygen species]] which can serve as defense-signals. As cellular signals, reactive oxygen species are unstable molecules, so they probably don't leave the chloroplast, but instead pass on their signal to an unknown second messenger molecule. All these molecules initiate [[retrograde signaling (cell biology)|retrograde signaling]]—signals from the chloroplast that regulate [[gene expression]] in the nucleus.<ref name="Padmanabhan-2010" />

In addition to defense signaling, chloroplasts, with the help of the [[peroxisome]]s,<ref name="Katsir-2008">{{cite journal | vauthors=Katsir L, Chung HS, Koo AJ, Howe GA | title=Jasmonate signaling: a conserved mechanism of hormone sensing | journal=Current Opinion in Plant Biology | volume=11 | issue=4 | pages=428–35 | date=August 2008 | pmid=18583180 | pmc=2560989 | doi=10.1016/j.pbi.2008.05.004 | bibcode=2008COPB...11..428K }}</ref> help synthesize an important defense molecule, [[jasmonate]]. Chloroplasts synthesize all the [[fatty acid]]s in a plant cell<ref name="Padmanabhan-2010" /><ref name="Schnurr-2002">{{cite journal | vauthors=Schnurr JA, Shockey JM, de Boer GJ, Browse JA | title=Fatty acid export from the chloroplast. Molecular characterization of a major plastidial acyl-coenzyme A synthetase from Arabidopsis | journal=Plant Physiology | volume=129 | issue=4 | pages=1700–9 | date=August 2002 | pmid=12177483 | pmc=166758 | doi=10.1104/pp.003251 }}</ref>—[[linoleic acid]], a fatty acid, is a precursor to jasmonate.<ref name="Padmanabhan-2010" />

=== Photosynthesis ===

{{main|Photosynthesis}}

One of the main functions of the chloroplast is its role in [[photosynthesis]], the process by which light is transformed into chemical energy, to subsequently produce food in the form of [[sugars]]. [[Water]] (H<sub>2</sub>O) and [[carbon dioxide]] (CO<sub>2</sub>) are used in photosynthesis, and sugar and [[oxygen]] (O<sub>2</sub>) are made, using [[light energy]]. Photosynthesis is divided into two stages—the [[light reactions]], where water is split to produce oxygen, and the [[dark reactions]], or [[Calvin cycle]], which builds sugar molecules from carbon dioxide. The two phases are linked by the energy carriers [[adenosine triphosphate]] (ATP) and [[nicotinamide adenine dinucleotide phosphate]] (NADP<sup>+</sup>).<ref name="Pearson-2009" /><ref name="Campbell-2006">{{cite book |last1=Campbell |first1=Neil A. |first2=Brad |last2=Williamson |first3=Robin J. |last3=Heyden | name-list-style=vanc |title=Biology: Exploring Life |publisher=Pearson Prentice Hall |year=2006 |location=Boston, Massachusetts |url=http://www.phschool.com/el_marketing.html |isbn=978-0-13-250882-7}}{{page needed|date=August 2013}}</ref>

==== Light reactions ====
{{main|Light reactions}}

{{Plain image with caption|File:Thylakoid membrane 3.svg|The [[light reactions]] of photosynthesis take place across the [[thylakoid]] membranes.<!-- [[Photosystem&nbsp;II]] is usually found in the appressed thylakoid membranes between stacked granal thylakoids, while [[photosystem&nbsp;I]] and [[ATP synthase]] is found in portions of the thylakoid membrane in contact with the stroma.-->|450px|right|top|triangle|#ccc}}

The light reactions take place on the thylakoid membranes. They take [[light energy]] and store it in [[NADPH]], a form of NADP<sup>+</sup>, and [[Adenosine triphosphate|ATP]] to fuel the [[dark reactions]].

===== Energy carriers =====

{{Main|Adenosine triphosphate|NADPH}}

ATP is the phosphorylated version of [[adenosine diphosphate]] (ADP), which stores energy in a cell and powers most cellular activities. ATP is the energized form, while ADP is the (partially) depleted form. NADP<sup>+</sup> is an electron carrier which ferries high energy electrons. In the light reactions, it gets [[redox reaction|reduced]], meaning it picks up electrons, becoming [[NADPH]].

===== Photophosphorylation =====

{{main|Photophosphorylation}}

Like mitochondria, chloroplasts use the [[potential energy]] stored in an [[Hydron (chemistry)|H<sup>+</sup>]], or hydrogen ion, gradient to generate ATP energy. The two [[photosystems]] capture light energy to energize [[electrons]] taken from [[water]], and release them down an [[electron transport chain]]. The [[Plastoquinone|molecules]] between the photosystems harness the electrons' energy to pump hydrogen ions into the thylakoid space, creating a [[concentration gradient]], with more hydrogen ions (up to a thousand times as many)<ref name="Campbell-2009b" /> inside the thylakoid system than in the stroma. The hydrogen ions in the thylakoid space then [[diffuse]] back down their concentration gradient, flowing back out into the stroma through [[ATP synthase]]. ATP synthase uses the energy from the flowing hydrogen ions to [[phosphorylate]] [[adenosine diphosphate]] into [[adenosine triphosphate]], or ATP.<ref name="Campbell-2009b" /><ref>{{cite journal | vauthors=Jagendorf AT, Uribe E | title=ATP formation caused by acid-base transition of spinach chloroplasts | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=55 | issue=1 | pages=170–7 | date=January 1966 | pmid=5220864 | pmc=285771 | doi=10.1073/pnas.55.1.170 | bibcode=1966PNAS...55..170J | doi-access=free }}</ref> Because chloroplast ATP synthase projects out into the stroma, the ATP is synthesized there, in position to be used in the dark reactions.<ref name="Berg-2002b">{{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 19.4|edition=5. ed., 4. print.|url=https://archive.org/details/biochemistrychap00jere| url-access=registration }}</ref>

===== NADP<sup>+</sup> reduction =====

{{See also|Redox reaction}}

[[Electrons]] are often removed from the [[electron transport chains]] to charge [[NADP+|NADP<sup>+</sup>]] with electrons, [[reduction reaction|reducing]] it to [[NADPH]]. Like ATP synthase, [[ferredoxin—NADP+ reductase|ferredoxin-NADP<sup>+</sup> reductase]], the enzyme that reduces NADP<sup>+</sup>, releases the NADPH it makes into the stroma, right where it is needed for the dark reactions.<ref name="Berg-2002b" />

Because NADP<sup>+</sup> reduction removes electrons from the electron transport chains, they must be replaced—the job of [[photosystem II]], which splits [[water]] molecules (H<sub>2</sub>O) to obtain the electrons from its [[hydrogen atoms]].<ref name="Campbell-2009b" /><ref name="Pearson-2009">{{cite book|title=Biology—Concepts and Connections|year=2009|publisher=Pearson|pages=108–118}}</ref>

===== Cyclic photophosphorylation =====

{{Main|Cyclic photophosphorylation}}

While [[photosystem II]] [[photolyzes]] water to obtain and energize new electrons, [[photosystem I]] simply reenergizes depleted electrons at the end of an electron transport chain. Normally, the reenergized electrons are taken by NADP<sup>+</sup>, though sometimes they can flow back down more H<sup>+</sup>-pumping electron transport chains to transport more hydrogen ions into the thylakoid space to generate more ATP. This is termed [[cyclic photophosphorylation]] because the electrons are recycled. Cyclic photophosphorylation is common in [[C4 plants|{{C4}} plants]], which need more [[Adenosine triphosphate|ATP]] than [[NADPH]].<ref name="Campbell-2009d" />

==== 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]].

=== pH ===

Because of the [[Hydron (chemistry)|H<sup>+</sup>]] gradient across the thylakoid membrane, the interior of the thylakoid is [[acidic]], with a [[pH]] around 4,<ref>{{cite book|title=Biochemistry.|year=2002|publisher=W H Freeman|pages=Section 19.4|url=https://www.ncbi.nlm.nih.gov/books/NBK22519/|archive-url=https://web.archive.org/web/20210116195232/https://www.ncbi.nlm.nih.gov/books/NBK22519/|archive-date=16 January 2021| vauthors=Berg JM, Tymoczko JL, Stryer L |edition=5th |access-date=30 October 2012}}</ref> while the stroma is slightly basic, with a pH of around 8.<ref name="Hauser-1995">{{cite journal | vauthors=Hauser M, Eichelmann H, Oja V, Heber U, Laisk A | title=Stimulation by Light of Rapid pH Regulation in the Chloroplast Stroma in Vivo as Indicated by CO2 Solubilization in Leaves | journal=Plant Physiology | volume=108 | issue=3 | pages=1059–1066 | date=July 1995 | pmid=12228527 | pmc=157457 | doi=10.1104/pp.108.3.1059 }}</ref>
The optimal stroma pH for the Calvin cycle is 8.1, with the reaction nearly stopping when the pH falls below 7.3.<ref name="Werdan-1975" />

[[CO2|CO<sub>2</sub>]] in water can form [[carbonic acid]], which can disturb the pH of isolated chloroplasts, interfering with photosynthesis, even though CO<sub>2</sub> is [[Enzyme substrate (biology)|used]] in photosynthesis. However, chloroplasts in living [[plant cells]] are not affected by this as much.<ref name="Hauser-1995" />

Chloroplasts can pump [[Potassium|K<sup>+</sup>]] and H<sup>+</sup> ions in and out of themselves using a poorly understood light-driven transport system.<ref name="Hauser-1995" />

In the presence of light, the pH of the thylakoid lumen can drop up to 1.5 pH units, while the pH of the stroma can rise by nearly one pH unit.<ref name="Werdan-1975">{{cite journal | vauthors=Werdan K, Heldt HW, Milovancev M | title=The role of pH in the regulation of carbon fixation in the chloroplast stroma. Studies on CO2 fixation in the light and dark | journal=Biochimica et Biophysica Acta (BBA) - Bioenergetics | volume=396 | issue=2 | pages=276–92 | date=August 1975 | pmid=239746 | doi=10.1016/0005-2728(75)90041-9 }}</ref>

=== Amino acid synthesis ===

Chloroplasts alone make almost all of a plant cell's [[amino acids]] in their [[stroma (fluid)|stroma]]<ref name="Burgess-1989e" /> except the [[sulfur-containing amino acids|sulfur-containing]] ones like [[cysteine]] and [[methionine]].<ref name="Ferro-2002">{{cite journal | vauthors=Ferro M, Salvi D, Riviere-Rolland H, Vermat T, Seigneurin-Berny D, Grunwald D, Garin J, Joyard J, Rolland N | display-authors=6 | title=Integral membrane proteins of the chloroplast envelope: identification and subcellular localization of new transporters | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=99 | issue=17 | pages=11487–92 | date=August 2002 | pmid=12177442 | pmc=123283 | doi=10.1073/pnas.172390399 | bibcode=2002PNAS...9911487F | doi-access=free }}</ref><ref name="Rolland-1992" /> Cysteine is made in the chloroplast (the [[proplastid]] too) but it is also synthesized in the [[cytosol]] and [[Mitochondrion|mitochondria]], probably because it has trouble crossing membranes to get to where it is needed.<ref name="Rolland-1992">{{cite journal | vauthors=Rolland N, Droux M, Douce R | title=Subcellular Distribution of O-Acetylserine(thiol)lyase in Cauliflower (Brassica oleracea L.) Inflorescence | journal=Plant Physiology | volume=98 | issue=3 | pages=927–35 | date=March 1992 | pmid=16668766 | pmc=1080289 | doi=10.1104/pp.98.3.927 }}</ref> The chloroplast is known to make the precursors to methionine but it is unclear whether the organelle carries out the last leg of the pathway or if it happens in the [[cytosol]].<ref name="Ravanel-1998">{{cite journal | vauthors=Ravanel S, Gakière B, Job D, Douce R | title=The specific features of methionine biosynthesis and metabolism in plants | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=95 | issue=13 | pages=7805–12 | date=June 1998 | pmid=9636232 | pmc=22764 | doi=10.1073/pnas.95.13.7805 | bibcode=1998PNAS...95.7805R | doi-access=free }}</ref>

=== Other nitrogen compounds ===

Chloroplasts make all of a cell's [[purine]]s and [[pyrimidine]]s—the [[nitrogenous base]]s found in [[DNA]] and [[RNA]].<ref name="Burgess-1989e" /> They also convert [[nitrite]] (NO<sub>2</sub><sup>−</sup>) into [[ammonia]] (NH<sub>3</sub>) which supplies the plant with [[nitrogen]] to make its [[amino acid]]s and [[nucleotide]]s.<ref name="Burgess-1989e" />

=== Other chemical products ===

{{expand section|needs more about lipids, also paramylon|date=March 2013}}

The plastid is the site of diverse and complex [[lipid]] synthesis in plants.<ref name="Buchanan BB">Buchanan BB, Gruissem W, Jones RL (Eds.). 2015. Biochemistry & Molecular Biology of Plants. Wiley Blackwell.</ref><ref name="Joyard-2010">{{cite journal | vauthors=Joyard J, Ferro M, Masselon C, Seigneurin-Berny D, Salvi D, Garin J, Rolland N | title=Chloroplast proteomics highlights the subcellular compartmentation of lipid metabolism | journal=Progress in Lipid Research | volume=49 | issue=2 | pages=128–58 | date=April 2010 | pmid=19879895 | doi=10.1016/j.plipres.2009.10.003 }}</ref> The carbon used to form the majority of the lipid is from [[acetyl-CoA]], which is the decarboxylation product of [[pyruvate]].<ref name="Buchanan BB" /> Pyruvate may enter the plastid from the cytosol by passive diffusion through the membrane after production in [[glycolysis]].<ref name="Proudlove-1981">{{cite journal | vauthors=Proudlove MO, Thurman DA | year=1981 | title=The uptake of 2-oxoglutarate and pyruvate by isolated pea chloroplasts | journal=New Phytologist | volume=88 | issue=2| pages=255–264 | doi=10.1111/j.1469-8137.1981.tb01722.x | doi-access=free | bibcode=1981NewPh..88..255P }}</ref> Pyruvate is also made in the plastid from phosphoenolpyruvate, a metabolite made in the cytosol from pyruvate or [[3-Phosphoglyceric acid|PGA]].<ref name="Buchanan BB" /> Acetate in the cytosol is unavailable for lipid biosynthesis in the plastid.<ref name="Bao-2000">Bao X, Focke M, Pollard M, Ohlrogge J. 2000. Understanding in vivo carbon precursor supply for fatty acid synthesis in leaf tissue. Plant Journal 22, 39–50.</ref> The typical length of fatty acids produced in the plastid are 16 or 18 carbons, with 0-3 [[Cis–trans isomerism|cis]] double bonds.<ref name="Ohlrogge-1995">{{cite journal | vauthors=Ohlrogge J, Browse J | year=1995 | title=Lipid Biosynthesis | journal=The Plant Cell | volume=7 | issue=7| pages=957–970 | doi=10.1105/tpc.7.7.957 | pmid=7640528 | pmc=160893 | doi-access=free }}</ref>

The biosynthesis of fatty acids from acetyl-CoA primarily requires two enzymes. Acetyl-CoA carboxylase creates malonyl-CoA, used in both the first step and the extension steps of synthesis. Fatty acid synthase (FAS) is a large complex of enzymes and cofactors including acyl carrier protein (ACP) which holds the acyl chain as it is synthesized. The initiation of synthesis begins with the condensation of malonyl-ACP with acetyl-CoA to produce ketobutyryl-ACP. 2 reductions involving the use of [[NADPH]] and one dehydration creates butyryl-ACP. Extension of the fatty acid comes from repeated cycles of malonyl-ACP condensation, reduction, and dehydration.<ref name="Buchanan BB" />

Other lipids are derived from the [[Non-mevalonate pathway|methyl-erythritol phosphate (MEP) pathway]] and consist of [[Gibberellin|gibberelins]], [[sterols]], [[abscisic acid]], [[phytol]], and innumerable [[secondary metabolite]]s.<ref name="Buchanan BB" />

== Location ==

{{Plain image with caption|File:Leaf tissue structure flat.svg|A cross section of a leaf, showing chloroplasts in its [[mesophyll tissue|mesophyll]] cells. Stomal guard cells also have chloroplasts, though much fewer than mesophyll cells.|500px|right|bottom|triangle|#5ca255}}

=== Distribution in a plant ===

Not all cells in a multicellular plant contain chloroplasts. All green parts of a plant contain chloroplasts as the color comes from the [[chlorophyll]].<ref name="Campbell-2009g" /> The [[plant cells]] which contain chloroplasts are usually [[parenchyma]] cells, though chloroplasts can also be found in [[collenchyma]] tissue.<ref>{{cite book |last=Roberts |first=Keith |url=https://books.google.com/books?id=ucilIjrex5cC&pg=PA16 |title=Handbook of plant science |publisher=Wiley |year=2007 |isbn=978-0-470-05723-0 |location=Chichester, West Sussex, England |page=16 |name-list-style=vanc}}</ref> A plant cell which contains chloroplasts is known as a [[chlorenchyma]] cell. A typical [[chlorenchyma]] cell of a land plant contains about 10 to 100 chloroplasts.

In some plants such as [[cacti]], chloroplasts are found in the [[Plant stem|stems]],<ref>{{cite book |title=Biology |vauthors=Campbell NA, Reece JB, Urry LA, Cain ML, Wasserman, Minorsky PV, Jackson RB |publisher=Benjamin Cummings (Pearson) |year=2009 |isbn=978-0-8053-6844-4 |edition=8th |page=742}}</ref> though in most plants, chloroplasts are concentrated in the [[leaves]]. One square [[millimeter]] of leaf tissue can contain half a million chloroplasts.<ref name="Campbell-2009g" /> Within a leaf, chloroplasts are mainly found in the [[Mesophyll cell|mesophyll]] layers of a [[leaf]], and the [[guard cells]] of [[stomata]]. [[Palisade mesophyll]] cells can contain 30–70 chloroplasts per cell, while stomatal guard cells contain only around 8–15 per cell, as well as much less [[chlorophyll]]. Chloroplasts can also be found in the [[bundle sheath]] cells of a leaf, especially in [[C4 plants|C{{sub|4}} plants]], which carry out the [[Calvin cycle]] in their bundle sheath cells. They are often absent from the [[Epidermis (botany)|epidermis]] of a leaf.<ref name="Lawson" />

=== Cellular location ===
{{plain image with caption|File:Chloroplast movement.svg|When chloroplasts are exposed to direct sunlight, they stack along the [[wikt:anticlinal|anticlinal cell walls]] to minimize exposure. In the dark they spread out in sheets along the [[wikt:periclinal|periclinal walls]] to maximize light absorption.|460px|right|bottom|triangle|#3fbceb}}

==== Chloroplast movement ====
{{See also|Cytoplasmic streaming}}

The chloroplasts of plant and algal cells can orient themselves to best suit the available light. In low-light conditions, they will spread out in a sheet—maximizing the surface area to absorb light. Under intense light, they will seek shelter by aligning in vertical columns along the plant cell's [[cell wall]] or turning sideways so that light strikes them edge-on. This reduces exposure and protects them from [[photooxidative damage]].<ref name="Wells-1979">{{Cite journal |last1=Wells |first1=C. |last2=Balish |first2=E. |year=1979 |title=The mitogenic activity of lipopolysaccharide for spleen cells from germfree, conventional, and gnotobiotic rats |journal=Canadian Journal of Microbiology |volume=25 |issue=9 |pages=1087–93 |doi=10.1139/m79-166 |pmid=540263}}</ref> This ability to distribute chloroplasts so that they can take shelter behind each other or spread out may be the reason why land plants evolved to have many small chloroplasts instead of a few big ones.<ref name="Glynn-2007" />
Chloroplast movement is considered one of the most closely regulated stimulus-response systems that can be found in plants.<ref name="Dong-1998">{{cite journal |vauthors=Dong XJ, Nagai R, Takagi S |year=1998 |title=Microfilaments Anchor Chloroplasts along the Outer Periclinal Wall in Vallisneria Epidermal Cells through Cooperation of PFR and Photosynthesis |journal=Plant and Cell Physiology |volume=39 |issue=12 |pages=1299–306 |doi=10.1093/oxfordjournals.pcp.a029334 |doi-access=free}}</ref> [[Mitochondrion|Mitochondria]] have also been observed to follow chloroplasts as they move.<ref name="Takagi-2003">{{cite journal |vauthors=Takagi S |date=June 2003 |title=Actin-based photo-orientation movement of chloroplasts in plant cells |journal=The Journal of Experimental Biology |volume=206 |issue=Pt 12 |pages=1963–9 |doi=10.1242/jeb.00215 |pmid=12756277 |doi-access=free|bibcode=2003JExpB.206.1963T }}</ref>

In higher plants, chloroplast movement is run by [[phototropins]], blue light [[Photoreceptor protein|photoreceptors]] also responsible for plant [[phototropism]]. In some algae, [[moss]]es, [[fern]]s, and [[flowering plant]]s, chloroplast movement is influenced by red light in addition to blue light,<ref name="Wells-1979" /> though very long red wavelengths inhibit movement rather than speeding it up. Blue light generally causes chloroplasts to seek shelter, while red light draws them out to maximize light absorption.<ref name="Takagi-2003" />

Studies of ''[[Vallisneria gigantea]]'', an aquatic [[flowering plant]], have shown that chloroplasts can get moving within five minutes of light exposure, though they don't initially show any net directionality. They may move along [[microfilament]] tracks, and the fact that the microfilament mesh changes shape to form a honeycomb structure surrounding the chloroplasts after they have moved suggests that microfilaments may help to anchor chloroplasts in place.<ref name="Dong-1998" /><ref name="Takagi-2003" />

== Differentiation, replication, and inheritance ==

{{Main|Plastid}}

{{plain image with caption|Plastids types flat.svg|'''Plastid types''' ''(Interactive diagram)'' Plants contain many different kinds of plastids in their cells.|300px|right|bottom|triangle|#bbb|image override=<imagemap>
File:Plastids types flat.svg|300px

circle 315 89 36 [[Proplastid]]
circle 161 147 36 [[Etioplast]]
circle 407 241 36 [[Leucoplast]]
circle 83 281 36 [[Chromoplast]]
circle 202 426 36 [[Amyloplast]]
circle 350 425 36 [[Elaioplast]]
circle 512 428 36 [[Proteinoplast]]
rect 357 65 468 88 [[Proplastid]]
rect 430 182 544 210 [[Leucoplast]]
rect 113 82 208 104 [[Etioplast]]
rect 12 320 148 345 [[Chromoplast]]
rect 141 466 259 490 [[Amyloplast]]
rect 300 465 405 488 [[Elaioplast]]
rect 447 466 594 491 [[Proteinoplast]]
poly 207 257 199 252 197 241 202 227 213 213 226 205 240 201 253 201 266 203 279 208 287 218 288 229 285 236 270 241 256 241 243 241 230 246 220 255 212 257 [[#Differentiation, replication, and inheritance|Chloroplast]]
rect 179 265 301 289 [[#Differentiation, replication, and inheritance|Chloroplast]]
rect 0 0 600 500 [[:File:Plastids types flat.svg]]

desc none
</imagemap>}}

Chloroplasts are a special type of a plant cell organelle called a '''plastid''', though the two terms are sometimes used interchangeably. There are many other types of plastids, which carry out various functions. All chloroplasts in a plant are descended from undifferentiated proplastids found in the [[zygote]],<ref name="Burgess-1989e">{{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=56|url=https://books.google.com/books?id=r808AAAAIAAJ&pg=PA56}}</ref> or fertilized egg. Proplastids are commonly found in an adult plant's [[apical meristem]]s. Chloroplasts do not normally develop from proplastids in [[root tip meristems]]<ref name="Gunning-1996b">{{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/n135 20]|url=https://archive.org/details/plantcellbiology00gunn_0| url-access=registration }}</ref>—instead, the formation of starch-storing [[amyloplasts]] is more common.<ref name="Burgess-1989e" />

In [[Shoot (botany)|shoots]], proplastids from [[shoot apical meristems]] can gradually develop into chloroplasts in [[photosynthetic]] leaf tissues as the leaf matures, if exposed to the required light.<ref name="Alberts-2002a" /> This process involves invaginations of the inner plastid membrane, forming sheets of membrane that project into the internal [[Stroma (fluid)|stroma]]. These membrane sheets then fold to form [[thylakoid]]s and [[Thylakoid|grana]].<ref name="Burgess-1989d">{{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|pages=54–55|url=https://books.google.com/books?id=r808AAAAIAAJ&pg=PA54|edition=Pbk.}}</ref>

If [[angiosperm]] shoots are not exposed to the required light for chloroplast formation, proplastids may develop into an [[etioplast]] stage before becoming chloroplasts. An etioplast is a plastid that lacks [[chlorophyll]], and has inner membrane invaginations that form a lattice of tubes in their stroma, called a [[prolamellar body]]. While etioplasts lack chlorophyll, they have a yellow chlorophyll [[precursor (chemistry)|precursor]] stocked.<ref name="Alberts-2002a" /> Within a few minutes of light exposure, the prolamellar body begins to reorganize into stacks of thylakoids, and chlorophyll starts to be produced. This process, where the etioplast becomes a chloroplast, takes several hours.<ref name="Burgess-1989d" /> [[Gymnosperms]] do not require light to form chloroplasts.<ref name="Burgess-1989d" />

Light, however, does not guarantee that a proplastid will develop into a chloroplast. Whether a proplastid develops into a chloroplast some other kind of plastid is mostly controlled by the [[Cell nucleus|nucleus]]<ref name="Alberts-2002a" /> and is largely influenced by the kind of cell it resides in.<ref name="Burgess-1989e" />

{{plain image with caption|Plastids conversions-en.svg|Many plastid interconversions are possible.|300px|right|bottom|triangle|#bbb}}

=== Plastid interconversion ===

Plastid differentiation is not permanent, in fact many interconversions are possible. Chloroplasts may be converted to [[chromoplast]]s, which are [[pigment]]-filled plastids responsible for the bright colors seen in [[flowers]] and ripe [[fruit]]. Starch storing [[amyloplast]]s can also be converted to chromoplasts, and it is possible for proplastids to develop straight into chromoplasts. Chromoplasts and amyloplasts can also become chloroplasts, like what happens when a [[carrot]] or a [[potato]] is illuminated. If a plant is injured, or something else causes a plant cell to revert to a [[meristematic]] state, chloroplasts and other plastids can turn back into proplastids. Chloroplast, amyloplast, chromoplast, proplastid are not absolute; state—intermediate forms are common.<ref name="Burgess-1989e" />

=== Division ===

{{expand section|functions, Z-ring dynamic assembly, regulators such as Giant Chloroplast 1 <!--- Sorry, just had to mention it.--->|date=February 2013}}

Most chloroplasts in a photosynthetic cell do not develop directly from proplastids or etioplasts. In fact, a typical [[shoot meristematic]] plant cell contains only 7–20 [[proplastids]]. These proplastids differentiate into chloroplasts, which divide to create the 30–70 chloroplasts found in a mature photosynthetic plant cell. If the cell [[Mitosis|divides]], chloroplast division provides the additional chloroplasts to partition between the two daughter cells.<ref name="Burgess-1989c">{{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=57|url=https://books.google.com/books?id=r808AAAAIAAJ&pg=PA57|edition=Pbk.}}</ref>

In single-celled [[algae]], chloroplast division is the only way new chloroplasts are formed. There is no proplastid differentiation—when an algal cell divides, its chloroplast divides along with it, and each [[daughter cell]] receives a mature chloroplast.<ref name="Burgess-1989d" />

Almost all chloroplasts in a cell divide, rather than a small group of rapidly dividing chloroplasts.<ref name="Possingham-1976">{{cite journal |doi=10.1098/rspb.1976.0047 |title=Chloroplast Replication and Chloroplast DNA Synthesis in Spinach Leaves |year=1976 | vauthors=Possingham JV, Rose RJ |journal=Proceedings of the Royal Society B: Biological Sciences |volume=193 |issue=1112 |pages=295–305 |bibcode=1976RSPSB.193..295P|s2cid=2691108 }}</ref> Chloroplasts have no definite [[S-phase]]—their DNA replication is not synchronized or limited to that of their host cells.<ref name="Cannon-1993">{{cite journal | vauthors=Cannon GC, Heinhorst S |title=DNA replication in chloroplasts |journal=Journal of Cell Science |date=1 January 1993 |volume=104 |issue=1 |pages=1–9 |doi=10.1242/jcs.104.1.1 |url=http://jcs.biologists.org/content/104/1/1 |citeseerx=10.1.1.1026.3732 }}</ref>
Much of what we know about chloroplast division comes from studying organisms like ''[[Arabidopsis]]'' and the red alga ''[[Cyanidioschyzon merolæ]]''.<ref name="Glynn-2007" />

{{plain image with caption|Chloroplast division.svg|Most chloroplasts in plant cells, and all chloroplasts in [[algae]] arise from chloroplast division.<ref name="Burgess-1989d" /> ''Picture references,<ref name="Glynn-2007" /><ref name="Miyagishima-2003" />''|800px|center|bottom|triangle|#00cd4c}}

The division process starts when the proteins [[FtsZ1]] and [[FtsZ2]] assemble into filaments, and with the help of a protein [[ARC6]], form a structure called a Z-ring within the chloroplast's stroma.<ref name="Glynn-2007">{{cite journal | vauthors=Glynn JM, Miyagishima SY, Yoder DW, Osteryoung KW, Vitha S | title=Chloroplast division | journal=Traffic | volume=8 | issue=5 | pages=451–61 | date=May 2007 | pmid=17451550 | doi=10.1111/j.1600-0854.2007.00545.x | s2cid=2808844 | doi-access=free }}</ref><ref name="Miyagishima-2003">{{cite journal | vauthors=Miyagishima SY, Nishida K, Mori T, Matsuzaki M, Higashiyama T, Kuroiwa H, Kuroiwa T | title=A plant-specific dynamin-related protein forms a ring at the chloroplast division site | journal=The Plant Cell | volume=15 | issue=3 | pages=655–65 | date=March 2003 | pmid=12615939 | pmc=150020 | doi=10.1105/tpc.009373 | bibcode=2003PlanC..15..655M }}</ref> The [[Min system]] manages the placement of the Z-ring, ensuring that the chloroplast is cleaved more or less evenly. The protein [[MinD]] prevents FtsZ from linking up and forming filaments. Another protein [[ARC3]] may also be involved, but it is not very well understood. These proteins are active at the poles of the chloroplast, preventing Z-ring formation there, but near the center of the chloroplast, [[MinE]] inhibits them, allowing the Z-ring to form.<ref name="Glynn-2007" />

Next, the two [[plastid-dividing rings]], or PD rings form. The inner plastid-dividing ring is located in the inner side of the chloroplast's inner membrane, and is formed first.<ref name="Glynn-2007" /> The outer plastid-dividing ring is found wrapped around the outer chloroplast membrane. It consists of filaments about 5 nanometers across,<ref name="Glynn-2007" /> arranged in rows 6.4 nanometers apart, and shrinks to squeeze the chloroplast. This is when chloroplast constriction begins.<ref name="Miyagishima-2003" /> <br />In a few species like ''[[Cyanidioschyzon merolæ]]'', chloroplasts have a third plastid-dividing ring located in the chloroplast's intermembrane space.<ref name="Glynn-2007" /><ref name="Miyagishima-2003" />

Late into the constriction phase, [[dynamin]] proteins assemble around the outer plastid-dividing ring,<ref name="Miyagishima-2003" /> helping provide force to squeeze the chloroplast.<ref name="Glynn-2007" /> Meanwhile, the Z-ring and the inner plastid-dividing ring break down.<ref name="Miyagishima-2003" /> During this stage, the many chloroplast DNA plasmids floating around in the stroma are partitioned and distributed to the two forming daughter chloroplasts.<ref name="Hashimoto-1989">{{cite journal | vauthors=Hashimoto H, Possingham JV | title=Effect of light on the chloroplast division cycle and DNA synthesis in cultured leaf discs of spinach | journal=Plant Physiology | volume=89 | issue=4 | pages=1178–83 | date=April 1989 | pmid=16666681 | pmc=1055993 | doi=10.1104/pp.89.4.1178 }}</ref>

Later, the dynamins migrate under the outer plastid dividing ring, into direct contact with the chloroplast's outer membrane,<ref name="Miyagishima-2003" /> to cleave the chloroplast in two daughter chloroplasts.<ref name="Glynn-2007" />

A remnant of the outer plastid dividing ring remains floating between the two daughter chloroplasts, and a remnant of the dynamin ring remains attached to one of the daughter chloroplasts.<ref name="Miyagishima-2003" />

Of the five or six rings involved in chloroplast division, only the outer plastid-dividing ring is present for the entire constriction and division phase—while the Z-ring forms first, constriction does not begin until the outer plastid-dividing ring forms.<ref name="Miyagishima-2003" />

{{plain image with caption|File:Moss chloroplasts 100× objective oblique.jpg|'''Chloroplast division''' In this [[light micrograph]] of some [[moss]] chloroplasts, many dumbbell-shaped chloroplasts can be seen dividing. Grana are also just barely visible as small granules.|330px|right|bottom|triangle|#7ee232|image override={{Stacked image|File:Moss chloroplasts 100× objective oblique.jpg|File:Moss chloroplasts 100× objective oblique text.svg|330px|In this light micrograph of some [[moss]] chloroplasts, some dumbbell-shaped chloroplasts can be seen dividing. Grana are also just barely visible as small granules.|top=155px|left=8px}}}}

==== Regulation ====

In species of [[algae]] that contain a single chloroplast, regulation of chloroplast division is extremely important to ensure that each daughter cell receives a chloroplast—chloroplasts can't be made from scratch.<ref name="Alberts-2002b">{{cite book |last=Alberts |first=Bruce | name-list-style=vanc |title=Molecular biology of the cell|year=2002|publisher=Garland|location=New York [u.a.]|isbn=0-8153-4072-9|url=https://www.ncbi.nlm.nih.gov/books/NBK26924/|edition=4.}}</ref><ref name="Glynn-2007" /> In organisms like plants, whose cells contain multiple chloroplasts, coordination is looser and less important. It is likely that chloroplast and cell division are somewhat synchronized, though the mechanisms for it are mostly unknown.<ref name="Glynn-2007" />

Light has been shown to be a requirement for chloroplast division. Chloroplasts can grow and progress through some of the constriction stages under [[Chlorophyll#Spectrophotometry|poor quality green light]], but are slow to complete division—they require exposure to bright white light to complete division. Spinach leaves grown under green light have been observed to contain many large dumbbell-shaped chloroplasts. Exposure to white light can stimulate these chloroplasts to divide and reduce the population of dumbbell-shaped chloroplasts.<ref name="Possingham-1976" /><ref name="Hashimoto-1989" />

=== Chloroplast inheritance ===

Like [[Mitochondrion#Replication and inheritance|mitochondria]], chloroplasts are usually inherited from a single parent. Biparental chloroplast inheritance—where plastid genes are inherited from both parent plants—occurs in very low levels in some flowering plants.<ref name="Hansen-2007" />

Many mechanisms prevent biparental chloroplast DNA inheritance, including selective destruction of chloroplasts or their genes within the [[gamete]] or [[zygote]], and chloroplasts from one parent being excluded from the embryo. Parental chloroplasts can be sorted so that only one type is present in each offspring.<ref name="Birky-1995">{{cite journal | vauthors=Birky CW | title=Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=92 | issue=25 | pages=11331–8 | date=December 1995 | pmid=8524780 | pmc=40394 | doi=10.1073/pnas.92.25.11331 | bibcode=1995PNAS...9211331B | doi-access=free }}</ref>

[[Gymnosperm]]s, such as [[pine tree]]s, mostly pass on chloroplasts paternally,<ref>{{cite journal | vauthors=Powell W, Morgante M, McDevitt R, Vendramin GG, Rafalski JA | title=Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=92 | issue=17 | pages=7759–63 | date=August 1995 | pmid=7644491 | pmc=41225 | doi=10.1073/pnas.92.17.7759 | quote=In the pines, the chloroplast genome is transmitted through pollen | bibcode=1995PNAS...92.7759P | doi-access=free }}</ref> while [[flowering plant]]s often inherit chloroplasts maternally.<ref>{{cite journal | vauthors=Stegemann S, Hartmann S, Ruf S, Bock R | title=High-frequency gene transfer from the chloroplast genome to the nucleus | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=100 | issue=15 | pages=8828–33 | date=July 2003 | pmid=12817081 | pmc=166398 | doi=10.1073/pnas.1430924100 | bibcode=2003PNAS..100.8828S | doi-access=free }}</ref><ref name="Ruf-2007" /> Flowering plants were once thought to only inherit chloroplasts maternally. However, there are now many documented cases of [[angiosperms]] inheriting chloroplasts paternally.<ref name="Hansen-2007">{{cite journal | vauthors=Hansen AK, Escobar LK, Gilbert LE, Jansen RK | title=Paternal, maternal, and biparental inheritance of the chloroplast genome in Passiflora (Passifloraceae): implications for phylogenetic studies | journal=American Journal of Botany | volume=94 | issue=1 | pages=42–6 | date=January 2007 | pmid=21642206 | doi=10.3732/ajb.94.1.42 | bibcode=2007AmJB...94...42H }}</ref>

[[Flowering plant|Angiosperms]], which pass on chloroplasts maternally, have many ways to prevent paternal inheritance. Most of them produce [[sperm cells]] that do not contain any plastids. There are many other documented mechanisms that prevent paternal inheritance in these flowering plants, such as different rates of chloroplast replication within the embryo.<ref name="Hansen-2007" />

Among angiosperms, paternal chloroplast inheritance is observed more often in [[Hybrid (biology)|hybrids]] than in offspring from parents of the same species. This suggests that incompatible hybrid genes might interfere with the mechanisms that prevent paternal inheritance.<ref name="Hansen-2007" />

==== Transplastomic plants ====

Recently, chloroplasts have caught attention by developers of [[genetically modified crops]]. Since, in most flowering plants, chloroplasts are not inherited from the male parent, [[transgene]]s in these plastids cannot be disseminated by [[pollen]]. This makes [[plastid transformation]] a valuable tool for the creation and cultivation of genetically modified plants that are biologically contained, thus posing significantly lower environmental risks. This [[biological containment]] strategy is therefore suitable for establishing the [[Co-existence of genetically modified and conventional crops and derived food and feed|coexistence of conventional and organic agriculture]]. While the reliability of this mechanism has not yet been studied for all relevant crop species, recent results in tobacco plants are promising, showing a failed containment rate of transplastomic plants at 3 in 1,000,000.<ref name="Ruf-2007">{{cite journal | vauthors=Ruf S, Karcher D, Bock R | title=Determining the transgene containment level provided by chloroplast transformation | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=104 | issue=17 | pages=6998–7002 | date=April 2007 | pmid=17420459 | pmc=1849964 | doi=10.1073/pnas.0700008104 | bibcode=2007PNAS..104.6998R | doi-access=free }}</ref>

== Footnotes ==
<references group="Note" />

== References ==

{{Reflist|refs=
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<ref name="Nair-2011">{{cite journal | vauthors=Nair SC, Striepen B | title=What do human parasites do with a chloroplast anyway? | journal=PLOS Biology | volume=9 | issue=8 | article-number=e1001137 | date=August 2011 | pmid=21912515 | pmc=3166169 | doi=10.1371/journal.pbio.1001137 | doi-access=free }}</ref>
<ref name="Stocking-1959">{{cite journal | author1=Stocking, C. R. |author2=Gifford, E. M. |name-list-style=amp | title=Incorporation of thymidine into chloroplasts of Spirogyra | journal=Biochemical and Biophysical Research Communications | year=1959 | volume=1 | issue=3 | pages=159–164 | doi=10.1016/0006-291X(59)90010-5 |bibcode=1959BBRC....1..159S }}</ref>
<ref name="Plaut-1962">{{cite journal | author1=Ris, H. |author2=Plaut, W. | title=Ultrastructure of DNA-containing areas in the chloroplast of Chlamydomonas | journal=J. Cell Biol. | year=1962 | volume=13 | issue=3 | pages=383–91 | doi=10.1083/jcb.13.3.383|pmid=14492436 |pmc=2106071 }}</ref>
<ref name="Heber, U.-1962">{{cite journal | author1=Heber, U. | title=Protein synthesis in chloroplasts during photosynthesis | journal=Nature | year=1962 | volume=195 | issue=1 | pages=91–92 | doi=10.1038/195091a0| pmid=13905812 | bibcode=1962Natur.195...91H | s2cid=4265095 }}</ref>
<ref name="Lyttleton-1962">{{cite journal | author1=Lyttleton, J. W. | title=Isolation of ribosomes from spinach chloroplasts | journal=Exp. Cell Res. | year=1962 | volume=26 | issue=1 | pages=312–317 | doi=10.1016/0014-4827(62)90183-0| pmid=14467684 }}</ref>
}}

== External links ==

{{Commons category|Chloroplasts}}

* [http://ccdb.ucsd.edu/sand/main?stype=lite&keyword=chloroplast&Submit=Go&event=display&start=1 Chloroplast – Cell Centered Database]
* {{cite journal | vauthors=Clegg MT, Gaut BS, Learn GH, Morton BR | title=Rates and patterns of chloroplast DNA evolution | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=91 | issue=15 | pages=6795–801 | date=July 1994 | pmid=8041699 | pmc=44285 | doi=10.1073/pnas.91.15.6795 | bibcode=1994PNAS...91.6795C | doi-access=free }}
* [https://web.archive.org/web/20110720155136/http://www.coextra.eu/projects/project199.html Co-Extra research on chloroplast transformation]
* [https://www.ncbi.nlm.nih.gov/nuccore/7525012?report=graph NCBI full chloroplast genome]

{{organelles}}
{{Botany}}
{{Self-replicating organic structures}}

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[[Category:Photosynthesis]]
[[Category:Plastids]]
[[Category:Endosymbiotic events]]