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Chloroplasts /ˈklɔːrəˌplæsts, -plɑːsts/ are organelles that conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water in plant and algal cells. Chloroplast_sentence_0

They then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplast_sentence_1

Chloroplasts carry out a number of other functions, including fatty acid synthesis, much amino acid synthesis, and the immune response in plants. Chloroplast_sentence_2

The number of chloroplasts per cell varies from one, in unicellular algae, up to 100 in plants like Arabidopsis and wheat. Chloroplast_sentence_3

A chloroplast is a type of organelle known as a plastid, characterized by its two membranes and a high concentration of chlorophyll. Chloroplast_sentence_4

Other plastid types, such as the leucoplast and the chromoplast, contain little chlorophyll and do not carry out photosynthesis. Chloroplast_sentence_5

Chloroplasts are highly dynamic—they circulate and are moved around within plant cells, and occasionally pinch in two to reproduce. Chloroplast_sentence_6

Their behavior is strongly influenced by environmental factors like light color and intensity. Chloroplast_sentence_7

Chloroplasts, like mitochondria, contain their own DNA, which is thought to be inherited from their ancestor—a photosynthetic cyanobacterium that was engulfed by an early eukaryotic cell. Chloroplast_sentence_8

Chloroplasts cannot be made by the plant cell and must be inherited by each daughter cell during cell division. Chloroplast_sentence_9

With one exception (the amoeboid Paulinella chromatophora), all chloroplasts can probably be traced back to a single endosymbiotic event, when a cyanobacterium was engulfed by the eukaryote. Chloroplast_sentence_10

Despite this, chloroplasts can be found in an extremely wide set of organisms, some not even directly related to each other—a consequence of many secondary and even tertiary endosymbiotic events. Chloroplast_sentence_11

The word chloroplast is derived from the Greek words chloros (χλωρός), which means green, and plastes (πλάστης), which means "the one who forms". Chloroplast_sentence_12

Discovery Chloroplast_section_0

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. Chloroplast_sentence_13

In 1883, Andreas Franz Wilhelm Schimper would name these bodies as "chloroplastids" (Chloroplastiden). Chloroplast_sentence_14

In 1884, Eduard Strasburger adopted the term "chloroplasts" (Chloroplasten). Chloroplast_sentence_15

Lineages and evolution Chloroplast_section_1

Chloroplasts are one of many types of organelles in the plant cell. Chloroplast_sentence_16

They are considered to have evolved from endosymbiotic cyanobacteria. Chloroplast_sentence_17

Mitochondria are thought to have come from a similar endosymbiosis event, where an aerobic prokaryote was engulfed. Chloroplast_sentence_18

This origin of chloroplasts was first suggested by the Russian biologist Konstantin Mereschkowski in 1905 after Andreas Franz Wilhelm Schimper observed in 1883 that chloroplasts closely resemble cyanobacteria. Chloroplast_sentence_19

Chloroplasts are only found in plants, algae, and the amoeboid Paulinella chromatophora. Chloroplast_sentence_20

Parent group: Cyanobacteria Chloroplast_section_2

Main article: Cyanobacteria Chloroplast_sentence_21

Chloroplasts are considered endosymbiotic Cyanobacteria. Chloroplast_sentence_22

Cyanobacteria are sometimes called blue-green algae even though they are prokaryotes. Chloroplast_sentence_23

They are a diverse phylum of bacteria capable of carrying out photosynthesis, and are gram-negative, meaning that they have two cell membranes. Chloroplast_sentence_24

Cyanobacteria also contain a peptidoglycan cell wall, which is thicker than in other gram-negative bacteria, and which is located between their two cell membranes. Chloroplast_sentence_25

Like chloroplasts, they have thylakoids within. Chloroplast_sentence_26

On the thylakoid membranes are photosynthetic pigments, including chlorophyll a. Chloroplast_sentence_27

Phycobilins are also common cyanobacterial pigments, usually organized into hemispherical phycobilisomes attached to the outside of the thylakoid membranes (phycobilins are not shared with all chloroplasts though). Chloroplast_sentence_28

Primary endosymbiosis Chloroplast_section_3

Somewhere around 1 to 2 billion years ago, a free-living cyanobacterium entered an early eukaryotic cell, either as food or as an internal parasite, but managed to escape the phagocytic vacuole it was contained in. Chloroplast_sentence_29

The two innermost lipid-bilayer membranes that surround all chloroplasts correspond to the outer and inner membranes of the ancestral cyanobacterium's gram negative cell wall, and not the phagosomal membrane from the host, which was probably lost. Chloroplast_sentence_30

The new cellular resident quickly became an advantage, providing food for the eukaryotic host, which allowed it to live within it. Chloroplast_sentence_31

Over time, the cyanobacterium was assimilated, and many of its genes were lost or transferred to the nucleus of the host. Chloroplast_sentence_32

From genomes that probably originally contained over 3000 genes only about 130 genes remain in the chloroplasts of contemporary plants. Chloroplast_sentence_33

Some of its proteins were then synthesized in the cytoplasm of the host cell, and imported back into the chloroplast (formerly the cyanobacterium). Chloroplast_sentence_34

Separately, somewhere about 90–140 million years ago, it happened again and led to the amoeboid Paulinella chromatophora. Chloroplast_sentence_35

This event is called endosymbiosis, or "cell living inside another cell with a mutual benefit for both". Chloroplast_sentence_36

The external cell is commonly referred to as the host while the internal cell is called the endosymbiont. Chloroplast_sentence_37

Chloroplasts are believed to have arisen after mitochondria, since all eukaryotes contain mitochondria, but not all have chloroplasts. Chloroplast_sentence_38

This is called serial endosymbiosis—an early eukaryote engulfing the mitochondrion ancestor, and some descendants of it then engulfing the chloroplast ancestor, creating a cell with both chloroplasts and mitochondria. Chloroplast_sentence_39

Whether or not primary chloroplasts came from a single endosymbiotic event, or many independent engulfments across various eukaryotic lineages, has long been debated. Chloroplast_sentence_40

It is now generally held that organisms with primary chloroplasts share a single ancestor that took in a cyanobacterium 600–2000 million years ago. Chloroplast_sentence_41

It has been proposed this the closest living relative of this bacterium is Gloeomargarita lithophora. Chloroplast_sentence_42

The exception is the amoeboid Paulinella chromatophora, which descends from an ancestor that took in a Prochlorococcus cyanobacterium 90–500 million years ago. Chloroplast_sentence_43

These chloroplasts, which can be traced back directly to a cyanobacterial ancestor, are known as primary plastids ("plastid" in this context means almost the same thing as chloroplast). Chloroplast_sentence_44

All primary chloroplasts belong to one of four chloroplast lineages—the glaucophyte chloroplast lineage, the amoeboid Paulinella chromatophora lineage, the rhodophyte (red algal) chloroplast lineage, or the chloroplastidan (green) chloroplast lineage. Chloroplast_sentence_45

The rhodophyte and chloroplastidan lineages are the largest, with chloroplastidan (green) being the one that contains the land plants. Chloroplast_sentence_46

Glaucophyta Chloroplast_section_4

See also: Cyanobacteria and Glaucophytes Chloroplast_sentence_47

Usually the endosymbiosis event is considered to have occurred in the Archaeplastida, within which the glaucophyta being the possible earliest diverging lineage. Chloroplast_sentence_48

The glaucophyte chloroplast group is the smallest of the three primary chloroplast lineages, being found in only 13 species, and is thought to be the one that branched off the earliest. Chloroplast_sentence_49

Glaucophytes have chloroplasts that retain a peptidoglycan wall between their double membranes, like their cyanobacterial parent. Chloroplast_sentence_50

For this reason, glaucophyte chloroplasts are also known as 'muroplasts' (besides 'cyanoplasts' or 'cyanelles'). Chloroplast_sentence_51

Glaucophyte chloroplasts also contain concentric unstacked thylakoids, which surround a carboxysome – an icosahedral structure that glaucophyte chloroplasts and cyanobacteria keep their carbon fixation enzyme RuBisCO in. Chloroplast_sentence_52

The starch that they synthesize collects outside the chloroplast. Chloroplast_sentence_53

Like cyanobacteria, glaucophyte and rhodophyte chloroplast thylakoids are studded with light collecting structures called phycobilisomes. Chloroplast_sentence_54

For these reasons, glaucophyte chloroplasts are considered a primitive intermediate between cyanobacteria and the more evolved chloroplasts in red algae and plants. Chloroplast_sentence_55

Rhodophyceae (red algae) Chloroplast_section_5

The rhodophyte, or red algae chloroplast group is another large and diverse chloroplast lineage. Chloroplast_sentence_56

Rhodophyte chloroplasts are also called rhodoplasts, literally "red chloroplasts". Chloroplast_sentence_57

Rhodoplasts have a double membrane with an intermembrane space and phycobilin pigments organized into phycobilisomes on the thylakoid membranes, preventing their thylakoids from stacking. Chloroplast_sentence_58

Some contain pyrenoids. Chloroplast_sentence_59

Rhodoplasts have chlorophyll a and phycobilins for photosynthetic pigments; the phycobilin phycoerythrin is responsible for giving many red algae their distinctive red color. Chloroplast_sentence_60

However, since they also contain the blue-green chlorophyll a and other pigments, many are reddish to purple from the combination. Chloroplast_sentence_61

The red phycoerytherin pigment is an adaptation to help red algae catch more sunlight in deep water—as such, some red algae that live in shallow water have less phycoerythrin in their rhodoplasts, and can appear more greenish. Chloroplast_sentence_62

Rhodoplasts synthesize a form of starch called floridean starch, which collects into granules outside the rhodoplast, in the cytoplasm of the red alga. Chloroplast_sentence_63

Chloroplastida (green algae and plants) Chloroplast_section_6

The chloroplastida chloroplasts, or green chloroplasts, are another large, highly diverse primary chloroplast lineage. Chloroplast_sentence_64

Their host organisms are commonly known as the green algae and land plants. Chloroplast_sentence_65

They differ from glaucophyte and red algal chloroplasts in that they have lost their phycobilisomes, and contain chlorophyll b instead. Chloroplast_sentence_66

Most green chloroplasts are (obviously) green, though some aren't, like some forms of Hæmatococcus pluvialis, due to accessory pigments that override the chlorophylls' green colors. Chloroplast_sentence_67

Chloroplastida chloroplasts have lost the peptidoglycan wall between their double membrane, leaving an intermembrane space. Chloroplast_sentence_68

Some plants seem to have kept the genes for the synthesis of the peptidoglycan layer, though they've been repurposed for use in chloroplast division instead. Chloroplast_sentence_69

Most of the chloroplasts depicted in this article are green chloroplasts. Chloroplast_sentence_70

Green algae and plants keep their starch inside their chloroplasts, and in plants and some algae, the chloroplast thylakoids are arranged in grana stacks. Chloroplast_sentence_71

Some green algal chloroplasts contain a structure called a pyrenoid, which is functionally similar to the glaucophyte carboxysome in that it is where RuBisCO and CO2 are concentrated in the chloroplast. Chloroplast_sentence_72

Helicosporidium is a genus of nonphotosynthetic parasitic green algae that is thought to contain a vestigial chloroplast. Chloroplast_sentence_73

Genes from a chloroplast and nuclear genes indicating the presence of a chloroplast have been found in Helicosporidium even if nobody's seen the chloroplast itself. Chloroplast_sentence_74

Paulinella chromatophora Chloroplast_section_7

While most chloroplasts originate from that first set of endosymbiotic events, Paulinella chromatophora is an exception that acquired a photosynthetic cyanobacterial endosymbiont more recently. Chloroplast_sentence_75

It is not clear whether that symbiont is closely related to the ancestral chloroplast of other eukaryotes. Chloroplast_sentence_76

Being in the early stages of endosymbiosis, Paulinella chromatophora can offer some insights into how chloroplasts evolved. Chloroplast_sentence_77

Paulinella cells contain one or two sausage shaped blue-green photosynthesizing structures called chromatophores, descended from the cyanobacterium Synechococcus. Chloroplast_sentence_78

Chromatophores cannot survive outside their host. Chloroplast_sentence_79

Chromatophore DNA is about a million base pairs long, containing around 850 protein encoding genes—far less than the three million base pair Synechococcus genome, but much larger than the approximately 150,000 base pair genome of the more assimilated chloroplast. Chloroplast_sentence_80

Chromatophores have transferred much less of their DNA to the nucleus of their host. Chloroplast_sentence_81

About 0.3–0.8% of the nuclear DNA in Paulinella is from the chromatophore, compared with 11–14% from the chloroplast in plants. Chloroplast_sentence_82

Secondary and tertiary endosymbiosis Chloroplast_section_8

Many other organisms obtained chloroplasts from the primary chloroplast lineages through secondary endosymbiosis—engulfing a red or green alga that contained a chloroplast. Chloroplast_sentence_83

These chloroplasts are known as secondary plastids. Chloroplast_sentence_84

While primary chloroplasts have a double membrane from their cyanobacterial ancestor, secondary chloroplasts have additional membranes outside of the original two, as a result of the secondary endosymbiotic event, when a nonphotosynthetic eukaryote engulfed a chloroplast-containing alga but failed to digest it—much like the cyanobacterium at the beginning of this story. Chloroplast_sentence_85

The engulfed alga was broken down, leaving only its chloroplast, and sometimes its cell membrane and nucleus, forming a chloroplast with three or four membranes—the two cyanobacterial membranes, sometimes the eaten alga's cell membrane, and the phagosomal vacuole from the host's cell membrane. Chloroplast_sentence_86

The genes in the phagocytosed eukaryote's nucleus are often transferred to the secondary host's nucleus. Chloroplast_sentence_87

Cryptomonads and chlorarachniophytes retain the phagocytosed eukaryote's nucleus, an object called a nucleomorph, located between the second and third membranes of the chloroplast. Chloroplast_sentence_88

All secondary chloroplasts come from 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. Chloroplast_sentence_89

Green algal derived chloroplasts Chloroplast_section_9

Green algae have been taken up by the euglenids, chlorarachniophytes, a lineage of dinoflagellates, and possibly the ancestor of the CASH lineage (cryptomonads, alveolates, stramenopiles and haptophytes) in three or four separate engulfments. Chloroplast_sentence_90

Many green algal derived chloroplasts contain pyrenoids, but unlike chloroplasts in their green algal ancestors, storage product collects in granules outside the chloroplast. Chloroplast_sentence_91

Euglenophytes Chloroplast_section_10

Euglenophytes are a group of common flagellated protists that contain chloroplasts derived from a green alga. Chloroplast_sentence_92

Euglenophyte chloroplasts have three membranes—it is thought that the membrane of the primary endosymbiont was lost, leaving the cyanobacterial membranes, and the secondary host's phagosomal membrane. Chloroplast_sentence_93

Euglenophyte chloroplasts have a pyrenoid and thylakoids stacked in groups of three. Chloroplast_sentence_94

Photosynthetic product is stored in the form of paramylon, which is contained in membrane-bound granules in the cytoplasm of the euglenophyte. Chloroplast_sentence_95

Chlorarachniophytes Chloroplast_section_11

Chlorarachniophytes /ˌklɔːrəˈræknioʊˌfaɪts/ are a rare group of organisms that also contain chloroplasts derived from green algae, though their story is more complicated than that of the euglenophytes. Chloroplast_sentence_96

The ancestor of chlorarachniophytes is thought to have been a eukaryote with a red algal derived chloroplast. Chloroplast_sentence_97

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. Chloroplast_sentence_98

Chlorarachniophyte chloroplasts are bounded by four membranes, except near the cell membrane, where the chloroplast membranes fuse into a double membrane. Chloroplast_sentence_99

Their thylakoids are arranged in loose stacks of three. Chloroplast_sentence_100

Chlorarachniophytes have a form of polysaccharide called chrysolaminarin, which they store in the cytoplasm, often collected around the chloroplast pyrenoid, which bulges into the cytoplasm. Chloroplast_sentence_101

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 found between the second and third chloroplast membranes—the periplastid space, which corresponds to the green alga's cytoplasm. Chloroplast_sentence_102

Prasinophyte-derived dinophyte chloroplast Chloroplast_section_12

Lepidodinium viride and its close relatives are dinophytes (see below) that lost their original peridinin chloroplast and replaced it with a green algal derived chloroplast (more specifically, a prasinophyte). Chloroplast_sentence_103

Lepidodinium is the only dinophyte that has a chloroplast that's not from the rhodoplast lineage. Chloroplast_sentence_104

The chloroplast is surrounded by two membranes and has no nucleomorph—all the nucleomorph genes have been transferred to the dinophyte nucleus. Chloroplast_sentence_105

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). Chloroplast_sentence_106

Red algal derived chloroplasts Chloroplast_section_13

Cryptophytes Chloroplast_section_14

Cryptophytes, or cryptomonads are a group of algae that contain a red-algal derived chloroplast. Chloroplast_sentence_107

Cryptophyte chloroplasts contain a nucleomorph that superficially resembles that of the chlorarachniophytes. Chloroplast_sentence_108

Cryptophyte chloroplasts have four membranes, the outermost of which is continuous with the rough endoplasmic reticulum. Chloroplast_sentence_109

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 red alga's cytoplasm. Chloroplast_sentence_110

Inside cryptophyte chloroplasts is a pyrenoid and thylakoids in stacks of two. Chloroplast_sentence_111

Their chloroplasts do not have phycobilisomes, but they do have phycobilin pigments which they keep in their thylakoid space, rather than anchored on the outside of their thylakoid membranes. Chloroplast_sentence_112

Cryptophytes may have played a key role in the spreading of red algal based chloroplasts. Chloroplast_sentence_113

Haptophytes Chloroplast_section_15

Haptophytes are similar and closely related to cryptophytes or heterokontophytes. Chloroplast_sentence_114

Their chloroplasts lack a nucleomorph, their thylakoids are in stacks of three, and they synthesize chrysolaminarin sugar, which they store completely outside of the chloroplast, in the cytoplasm of the haptophyte. Chloroplast_sentence_115

Heterokontophytes (stramenopiles) Chloroplast_section_16

The heterokontophytes, also known as the stramenopiles, are a very large and diverse group of eukaryotes. Chloroplast_sentence_116

The photoautotrophic lineage, Ochrophyta, including the diatoms and the brown algae, golden algae, and yellow-green algae, also contains red algal derived chloroplasts. Chloroplast_sentence_117

Heterokont chloroplasts are very similar to haptophyte chloroplasts, containing a pyrenoid, triplet thylakoids, and with some exceptions, having four layer plastidic envelope, the outermost epiplastid membrane connected to the endoplasmic reticulum. Chloroplast_sentence_118

Like haptophytes, heterokontophytes store sugar in chrysolaminarin granules in the cytoplasm. Chloroplast_sentence_119

Heterokontophyte chloroplasts contain chlorophyll a and with a few exceptions chlorophyll c, but also have carotenoids which give them their many colors. Chloroplast_sentence_120

Apicomplexans, chromerids, and dinophytes Chloroplast_section_17

The alveolates are a major clade of unicellular eukaryotes of both autotrophic and heterotrophic members. Chloroplast_sentence_121

The most notable shared characteristic is the presence of cortical (outer-region) alveoli (sacs). Chloroplast_sentence_122

These are flattened vesicles (sacs) packed into a continuous layer just under the membrane and supporting it, typically forming a flexible pellicle (thin skin). Chloroplast_sentence_123

In dinoflagellates they often form armor plates. Chloroplast_sentence_124

Many members contain a red-algal derived plastid. Chloroplast_sentence_125

One notable characteristic of this diverse group is the frequent loss of photosynthesis. Chloroplast_sentence_126

However, a majority of these heterotrophs continue to process a non-photosynthetic plastid. Chloroplast_sentence_127


Apicomplexans are a group of alveolates. Chloroplast_sentence_128

Like the helicosproidia, they're parasitic, and have a nonphotosynthetic chloroplast. Chloroplast_sentence_129

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. Chloroplast_sentence_130

The apicomplexans include Plasmodium, the malaria parasite. Chloroplast_sentence_131

Many apicomplexans keep a vestigial red algal derived chloroplast called an apicoplast, which they inherited from their ancestors. Chloroplast_sentence_132

Other apicomplexans like Cryptosporidium have lost the chloroplast completely. Chloroplast_sentence_133

Apicomplexans store their energy in amylopectin granules that are located in their cytoplasm, even though they are nonphotosynthetic. Chloroplast_sentence_134

Apicoplasts have lost all photosynthetic function, and contain no photosynthetic pigments or true thylakoids. Chloroplast_sentence_135

They are bounded by four membranes, but the membranes are not connected to the endoplasmic reticulum. Chloroplast_sentence_136

The fact that apicomplexans still keep their nonphotosynthetic chloroplast around demonstrates how the chloroplast carries out important functions other than photosynthesis. Chloroplast_sentence_137

Plant chloroplasts provide plant cells with many important things besides sugar, and apicoplasts are no different—they synthesize fatty acids, isopentenyl pyrophosphate, iron-sulfur clusters, and carry out part of the heme pathway. Chloroplast_sentence_138

This makes the apicoplast an attractive target for drugs to cure apicomplexan-related diseases. Chloroplast_sentence_139

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. Chloroplast_sentence_140


The Chromerida is a newly discovered group of algae from Australian corals which comprises some close photosynthetic relatives of the apicomplexans. Chloroplast_sentence_141

The first member, Chromera velia, was discovered and first isolated in 2001. Chloroplast_sentence_142

The discovery of Chromera velia with similar structure to the apicomplexanss, provides an important link in the evolutionary history of the apicomplexans and dinophytes. Chloroplast_sentence_143

Their plastids have four membranes, lack chlorophyll c and use the type II form of RuBisCO obtained from a horizontal transfer event. Chloroplast_sentence_144


The dinoflagellates are yet another very large and diverse group of protists, around half of which are (at least partially) photosynthetic. Chloroplast_sentence_145

Most dinophyte chloroplasts are secondary red algal derived chloroplasts. Chloroplast_sentence_146

Many other dinophytes have lost the chloroplast (becoming the nonphotosynthetic kind of dinoflagellate), or replaced it though tertiary endosymbiosis—the engulfment of another eukaryotic algae containing a red algal derived chloroplast. Chloroplast_sentence_147

Others replaced their original chloroplast with a green algal derived one. Chloroplast_sentence_148

Most dinophyte chloroplasts contain form II RuBisCO, at least the photosynthetic pigments chlorophyll a, chlorophyll c2, beta-carotene, and at least one dinophyte-unique xanthophyll (peridinin, dinoxanthin, or diadinoxanthin), giving many a golden-brown color. Chloroplast_sentence_149

All dinophytes store starch in their cytoplasm, and most have chloroplasts with thylakoids arranged in stacks of three. Chloroplast_sentence_150

The most common dinophyte chloroplast is the peridinin-type chloroplast, characterized by the carotenoid pigment peridinin in their chloroplasts, along with chlorophyll a and chlorophyll c2. Chloroplast_sentence_151

Peridinin is not found in any other group of chloroplasts. Chloroplast_sentence_152

The peridinin chloroplast is bounded by three membranes (occasionally two), having lost the red algal endosymbiont's original cell membrane. Chloroplast_sentence_153

The outermost membrane is not connected to the endoplasmic reticulum. Chloroplast_sentence_154

They contain a pyrenoid, and have triplet-stacked thylakoids. Chloroplast_sentence_155

Starch is found outside the chloroplast. Chloroplast_sentence_156

An important feature of these chloroplasts is that their chloroplast DNA is highly reduced and fragmented into many small circles. Chloroplast_sentence_157

Most of the genome has migrated to the nucleus, and only critical photosynthesis-related genes remain in the chloroplast. Chloroplast_sentence_158

The peridinin chloroplast is thought to be the dinophytes' "original" chloroplast, which has been lost, reduced, replaced, or has company in several other dinophyte lineages. Chloroplast_sentence_159

Fucoxanthin-containing (haptophyte-derived) dinophyte chloroplasts Chloroplast_section_18

The fucoxanthin dinophyte lineages (including Karlodinium and Karenia) lost their original red algal derived chloroplast, and replaced it with a new chloroplast derived from a haptophyte endosymbiont. Chloroplast_sentence_160

Karlodinium and Karenia probably took up different heterokontophytes. Chloroplast_sentence_161

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. Chloroplast_sentence_162

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. Chloroplast_sentence_163

Fucoxanthin-containing chloroplasts are characterized by having the pigment fucoxanthin (actually 19′-hexanoyloxy-fucoxanthin and/or 19′-butanoyloxy-fucoxanthin) and no peridinin. Chloroplast_sentence_164

Fucoxanthin is also found in haptophyte chloroplasts, providing evidence of ancestry. Chloroplast_sentence_165

Diatom-derived dinophyte chloroplasts Chloroplast_section_19

Some dinophytes, like Kryptoperidinium and Durinskia have a diatom (heterokontophyte) derived chloroplast. Chloroplast_sentence_166

These chloroplasts are bounded by up to five membranes, (depending on whether the entire diatom endosymbiont is counted as the chloroplast, or just the red algal derived chloroplast inside it). Chloroplast_sentence_167

The diatom endosymbiont has been reduced relatively little—it still retains its original mitochondria, and has endoplasmic reticulum, ribosomes, a nucleus, and of course, red algal derived chloroplasts—practically a complete cell, all inside the host's endoplasmic reticulum lumen. Chloroplast_sentence_168

However the diatom endosymbiont can't store its own food—its storage polysaccharide is found in granules in the dinophyte host's cytoplasm instead. Chloroplast_sentence_169

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. Chloroplast_sentence_170

Diatoms have been engulfed by dinoflagellates at least three times. Chloroplast_sentence_171

The diatom endosymbiont is bounded by a single membrane, inside it are chloroplasts with four membranes. Chloroplast_sentence_172

Like the diatom endosymbiont's diatom ancestor, the chloroplasts have triplet thylakoids and pyrenoids. Chloroplast_sentence_173

In some of these genera, the diatom endosymbiont's chloroplasts aren't the only chloroplasts in the dinophyte. Chloroplast_sentence_174

The original three-membraned peridinin chloroplast is still around, converted to an eyespot. Chloroplast_sentence_175

Kleptoplastidy Chloroplast_section_20

Main article: Kleptoplastidy Chloroplast_sentence_176

In some groups of mixotrophic protists, like some dinoflagellates (e.g. Dinophysis), chloroplasts are separated from a captured alga and used temporarily. Chloroplast_sentence_177

These klepto chloroplasts may only have a lifetime of a few days and are then replaced. Chloroplast_sentence_178

Cryptophyte-derived dinophyte chloroplast Chloroplast_section_21

Members of the genus Dinophysis have a phycobilin-containing chloroplast taken from a cryptophyte. Chloroplast_sentence_179

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. Chloroplast_sentence_180

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. Chloroplast_sentence_181

Chloroplast DNA Chloroplast_section_22

Main article: Chloroplast DNA Chloroplast_sentence_182

See also: List of sequenced plastomes Chloroplast_sentence_183

Chloroplasts have their own DNA, often abbreviated as ctDNA, or cpDNA. Chloroplast_sentence_184

It is also known as the plastome. Chloroplast_sentence_185

Its existence was first proved in 1962, and first sequenced in 1986—when two Japanese research teams sequenced the chloroplast DNA of liverwort and tobacco. Chloroplast_sentence_186

Since then, hundreds of chloroplast DNAs from various species have been sequenced, but they are mostly those of land plants and green algaeglaucophytes, red algae, and other algal groups are extremely underrepresented, potentially introducing some bias in views of "typical" chloroplast DNA structure and content. Chloroplast_sentence_187

Molecular structure Chloroplast_section_23

With few exceptions, most chloroplasts have their entire chloroplast genome combined into a single large circular DNA molecule, typically 120,000–170,000 base pairs long. Chloroplast_sentence_188

They can have a contour length of around 30–60 micrometers, and have a mass of about 80–130 million daltons. Chloroplast_sentence_189

While usually thought of as a circular molecule, there is some evidence that chloroplast DNA molecules more often take on a linear shape. Chloroplast_sentence_190

Inverted repeats Chloroplast_section_24

Many chloroplast DNAs contain two inverted repeats, which separate a long single copy section (LSC) from a short single copy section (SSC). Chloroplast_sentence_191

While a given pair of inverted repeats are rarely completely identical, they are always very similar to each other, apparently resulting from concerted evolution. Chloroplast_sentence_192

The inverted repeats vary wildly in length, ranging from 4,000 to 25,000 base pairs long each and containing as few as four or as many as over 150 genes. Chloroplast_sentence_193

Inverted repeats in plants tend to be at the upper end of this range, each being 20,000–25,000 base pairs long. Chloroplast_sentence_194

The inverted repeat regions are highly conserved among land plants, and accumulate few mutations. Chloroplast_sentence_195

Similar inverted repeats exist in the genomes of cyanobacteria and the other two chloroplast lineages (glaucophyta and rhodophyceae), suggesting that they predate the chloroplast, though some chloroplast DNAs have since lost or flipped the inverted repeats (making them direct repeats). Chloroplast_sentence_196

It is possible that the inverted repeats help stabilize the rest of the chloroplast genome, as chloroplast DNAs which have lost some of the inverted repeat segments tend to get rearranged more. Chloroplast_sentence_197

Nucleoids Chloroplast_section_25

New chloroplasts may contain up to 100 copies of their DNA, though the number of chloroplast DNA copies decreases to about 15–20 as the chloroplasts age. Chloroplast_sentence_198

They are usually packed into nucleoids, which can contain several identical chloroplast DNA rings. Chloroplast_sentence_199

Many nucleoids can be found in each chloroplast. Chloroplast_sentence_200

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. Chloroplast_sentence_201

Though chloroplast DNA is not associated with true histones, in red algae, similar proteins that tightly pack each chloroplast DNA ring into a nucleoid have been found. Chloroplast_sentence_202

DNA repair Chloroplast_section_26

In chloroplasts of the moss Physcomitrella patens, the DNA mismatch repair protein Msh1 interacts with the recombinational repair proteins RecA and RecG to maintain chloroplast genome stability. Chloroplast_sentence_203

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. Chloroplast_sentence_204

DNA replication Chloroplast_section_27

The leading model of cpDNA replication Chloroplast_section_28

The mechanism for chloroplast DNA (cpDNA) replication has not been conclusively determined, but two main models have been proposed. Chloroplast_sentence_205

Scientists have attempted to observe chloroplast replication via electron microscopy since the 1970s. Chloroplast_sentence_206

The results of the microscopy experiments led to the idea that chloroplast DNA replicates using a double displacement loop (D-loop). Chloroplast_sentence_207

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. Chloroplast_sentence_208

Transcription starts at specific points of origin. Chloroplast_sentence_209

Multiple replication forks open up, allowing replication machinery to transcribe the DNA. Chloroplast_sentence_210

As replication continues, the forks grow and eventually converge. Chloroplast_sentence_211

The new cpDNA structures separate, creating daughter cpDNA chromosomes. Chloroplast_sentence_212

In addition to the early microscopy experiments, this model is also supported by the amounts of deamination seen in cpDNA. Chloroplast_sentence_213

Deamination occurs when an amino group is lost and is a mutation that often results in base changes. Chloroplast_sentence_214

When adenine is deaminated, it becomes hypoxanthine. Chloroplast_sentence_215

Hypoxanthine can bind to cytosine, and when the XC base pair is replicated, it becomes a GC (thus, an A → G base change). Chloroplast_sentence_216

Deamination Chloroplast_section_29

In cpDNA, there are several A → G deamination gradients. Chloroplast_sentence_217

DNA becomes susceptible to deamination events when it is single stranded. Chloroplast_sentence_218

When replication forks form, the strand not being copied is single stranded, and thus at risk for A → G deamination. Chloroplast_sentence_219

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). Chloroplast_sentence_220

This mechanism is still the leading theory today; however, a second theory suggests that most cpDNA is actually linear and replicates through homologous recombination. Chloroplast_sentence_221

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. Chloroplast_sentence_222

Alternative model of replication Chloroplast_section_30

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. Chloroplast_sentence_223

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. Chloroplast_sentence_224

When the original experiments on cpDNA were performed, scientists did notice linear structures; however, they attributed these linear forms to broken circles. Chloroplast_sentence_225

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. Chloroplast_sentence_226

At the same time, homologous recombination does not expand the multiple A --> G gradients seen in plastomes. Chloroplast_sentence_227

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. Chloroplast_sentence_228

Gene content and protein synthesis Chloroplast_section_31

The chloroplast genome most commonly includes around 100 genes that code for a variety of things, mostly to do with the protein pipeline and photosynthesis. Chloroplast_sentence_229

As in prokaryotes, genes in chloroplast DNA are organized into operons. Chloroplast_sentence_230

Unlike prokaryotic DNA molecules, chloroplast DNA molecules contain introns (plant mitochondrial DNAs do too, but not human mtDNAs). Chloroplast_sentence_231

Among land plants, the contents of the chloroplast genome are fairly similar. Chloroplast_sentence_232

Chloroplast genome reduction and gene transfer Chloroplast_section_32

Over time, many parts of the chloroplast genome were transferred to the nuclear genome of the host, a process called endosymbiotic gene transfer. Chloroplast_sentence_233

As a result, the chloroplast genome is heavily reduced compared to that of free-living cyanobacteria. Chloroplast_sentence_234

Chloroplasts may contain 60–100 genes whereas cyanobacteria often have more than 1500 genes in their genome. Chloroplast_sentence_235

Recently, a plastid without a genome was found, demonstrating chloroplasts can lose their genome during endosymbiotic the gene transfer process. Chloroplast_sentence_236

Endosymbiotic gene transfer is how we know about the lost chloroplasts in many CASH lineages. Chloroplast_sentence_237

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. Chloroplast_sentence_238

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. Chloroplast_sentence_239

In land plants, some 11–14% of the DNA in their nuclei can be traced back to the chloroplast, up to 18% in Arabidopsis, corresponding to about 4,500 protein-coding genes. Chloroplast_sentence_240

There have been a few recent transfers of genes from the chloroplast DNA to the nuclear genome in land plants. Chloroplast_sentence_241

Of the approximately 3000 proteins found in chloroplasts, some 95% of them are encoded by nuclear genes. Chloroplast_sentence_242

Many of the chloroplast's protein complexes consist of subunits from both the chloroplast genome and the host's nuclear genome. Chloroplast_sentence_243

As a result, protein synthesis must be coordinated between the chloroplast and the nucleus. Chloroplast_sentence_244

The chloroplast is mostly under nuclear control, though chloroplasts can also give out signals regulating gene expression in the nucleus, called retrograde signaling. Chloroplast_sentence_245

Protein synthesis Chloroplast_section_33

See also: Transcription and translation Chloroplast_sentence_246

Protein synthesis within chloroplasts relies on two RNA polymerases. Chloroplast_sentence_247

One is coded by the chloroplast DNA, the other is of nuclear origin. Chloroplast_sentence_248

The two RNA polymerases may recognize and bind to different kinds of promoters within the chloroplast genome. Chloroplast_sentence_249

The ribosomes in chloroplasts are similar to bacterial ribosomes. Chloroplast_sentence_250

Protein targeting and import Chloroplast_section_34

See also: Translation Chloroplast_sentence_251

Because so many chloroplast genes have been moved to the nucleus, many proteins that would originally have been translated in the chloroplast are now synthesized in the cytoplasm of the plant cell. Chloroplast_sentence_252

These proteins must be directed back to the chloroplast, and imported through at least two chloroplast membranes. Chloroplast_sentence_253

Curiously, around half of the protein products of transferred genes aren't even targeted back to the chloroplast. Chloroplast_sentence_254

Many became exaptations, taking on new functions like participating in cell division, protein routing, and even disease resistance. Chloroplast_sentence_255

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. Chloroplast_sentence_256

Some transferred chloroplast DNA protein products get directed to the secretory pathway, though many 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. Chloroplast_sentence_257

In those cases, chloroplast-targeted proteins do initially travel along the secretory pathway. Chloroplast_sentence_258

Because the cell acquiring a chloroplast already had 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. Chloroplast_sentence_259

In most, but not all cases, nuclear-encoded chloroplast proteins are translated with a cleavable transit peptide that's added to the N-terminus of the protein precursor. Chloroplast_sentence_260

Sometimes the transit sequence is found on the C-terminus of the protein, or within the functional part of the protein. Chloroplast_sentence_261

Transport proteins and membrane translocons Chloroplast_section_35

After a chloroplast polypeptide is synthesized on a ribosome in the cytosol, an enzyme specific to chloroplast proteins phosphorylates, or adds a phosphate group to many (but not all) of them in their transit sequences. Chloroplast_sentence_262

Phosphorylation helps many proteins bind the polypeptide, keeping it from folding prematurely. Chloroplast_sentence_263

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. Chloroplast_sentence_264

At the same time, they have to keep just enough shape so that they can be recognized by the chloroplast. Chloroplast_sentence_265

These proteins also help the polypeptide get imported into the chloroplast. Chloroplast_sentence_266

From here, chloroplast proteins bound for the stroma must pass through two protein complexes—the TOC complex, or translocon on the outer chloroplast membrane, and the TIC translocon, or translocon on the inner chloroplast membrane translocon. Chloroplast_sentence_267

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 intermembrane space. Chloroplast_sentence_268

Structure Chloroplast_section_36

In land plants, chloroplasts are generally lens-shaped, 3–10 μm in diameter and 1–3 μm thick. Chloroplast_sentence_269

Corn seedling chloroplasts are ≈20 µm in volume. Chloroplast_sentence_270

Greater diversity in chloroplast shapes exists among the algae, which often contain a single chloroplast that can be shaped like a net (e.g., Oedogonium), a cup (e.g., Chlamydomonas), a ribbon-like spiral around the edges of the cell (e.g., Spirogyra), or slightly twisted bands at the cell edges (e.g., Sirogonium). Chloroplast_sentence_271

Some algae have two chloroplasts in each cell; they are star-shaped in Zygnema, or may follow the shape of half the cell in order Desmidiales. Chloroplast_sentence_272

In some algae, the chloroplast takes up most of the cell, with pockets for the nucleus and other organelles, for example, some species of Chlorella have a cup-shaped chloroplast that occupies much of the cell. Chloroplast_sentence_273

All chloroplasts have at least three membrane systems—the outer chloroplast membrane, the inner chloroplast membrane, and the thylakoid system. Chloroplast_sentence_274

Chloroplasts that are the product of secondary endosymbiosis may have additional membranes surrounding these three. Chloroplast_sentence_275

Inside the outer and inner chloroplast membranes is the chloroplast stroma, a semi-gel-like fluid that makes up much of a chloroplast's volume, and in which the thylakoid system floats. Chloroplast_sentence_276

See also: Chloroplast membrane Chloroplast_sentence_277

There are some common misconceptions about the outer and inner chloroplast membranes. Chloroplast_sentence_278

The fact that chloroplasts are surrounded by a double membrane is often cited as evidence that they are the descendants of endosymbiotic cyanobacteria. Chloroplast_sentence_279

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 homologous to the cyanobacterium's original double membranes. Chloroplast_sentence_280

The chloroplast double membrane is also often compared to the mitochondrial double membrane. Chloroplast_sentence_281

This is not a valid comparison—the inner mitochondria membrane is used to run proton pumps and carry out oxidative phosphorylation across to generate ATP energy. Chloroplast_sentence_282

The only chloroplast structure that can considered analogous to it is the internal thylakoid system. Chloroplast_sentence_283

Even so, in terms of "in-out", the direction of chloroplast H ion flow is in the opposite direction compared to oxidative phosphorylation in mitochondria. Chloroplast_sentence_284

In addition, in terms of function, the inner chloroplast membrane, which regulates metabolite passage and synthesizes some materials, has no counterpart in the mitochondrion. Chloroplast_sentence_285

Outer chloroplast membrane Chloroplast_section_37

Main article: Chloroplast membrane Chloroplast_sentence_286

The outer chloroplast membrane is a semi-porous membrane that small molecules and ions can easily diffuse across. Chloroplast_sentence_287

However, it is not permeable to larger proteins, so chloroplast polypeptides being synthesized in the cell cytoplasm must be transported across the outer chloroplast membrane by the TOC complex, or translocon on the outer chloroplast membrane. Chloroplast_sentence_288

The chloroplast membranes sometimes protrude out into the cytoplasm, forming a stromule, or stroma-containing tubule. Chloroplast_sentence_289

Stromules are very rare in chloroplasts, and are much more common in other plastids like chromoplasts and amyloplasts in petals and roots, respectively. Chloroplast_sentence_290

They may exist to increase the chloroplast's surface area for cross-membrane transport, because they are often branched and tangled with the endoplasmic reticulum. Chloroplast_sentence_291

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. Chloroplast_sentence_292

However, there is a growing body of evidence that stromules are functional, integral features of plant cell plastids, not merely artifacts. Chloroplast_sentence_293

Intermembrane space and peptidoglycan wall Chloroplast_section_38

Usually, a thin intermembrane space about 10–20 nanometers thick exists between the outer and inner chloroplast membranes. Chloroplast_sentence_294

Glaucophyte algal chloroplasts have a peptidoglycan layer between the chloroplast membranes. Chloroplast_sentence_295

It corresponds to the peptidoglycan cell wall of their cyanobacterial ancestors, which is located between their two cell membranes. Chloroplast_sentence_296

These chloroplasts are called muroplasts (from Latin "mura", meaning "wall"). Chloroplast_sentence_297

Other chloroplasts have lost the cyanobacterial wall, leaving an intermembrane space between the two chloroplast envelope membranes. Chloroplast_sentence_298

Inner chloroplast membrane Chloroplast_section_39

Main article: Chloroplast membrane Chloroplast_sentence_299

The inner chloroplast membrane borders the stroma and regulates passage of materials in and out of the chloroplast. Chloroplast_sentence_300

After passing through the TOC complex in the outer chloroplast membrane, polypeptides must pass through the TIC complex (translocon on the inner chloroplast membrane) which is located in the inner chloroplast membrane. Chloroplast_sentence_301

In addition to regulating the passage of materials, the inner chloroplast membrane is where fatty acids, lipids, and carotenoids are synthesized. Chloroplast_sentence_302

Peripheral reticulum Chloroplast_section_40

Some chloroplasts contain a structure called the chloroplast peripheral reticulum. Chloroplast_sentence_303

It is often found in the chloroplasts of C4 plants, though it has also been found in some C3 angiosperms, and even some gymnosperms. Chloroplast_sentence_304

The chloroplast peripheral reticulum consists of a maze of membranous tubes and vesicles continuous with the inner chloroplast membrane that extends into the internal stromal fluid of the chloroplast. Chloroplast_sentence_305

Its purpose is thought to be to increase the chloroplast's surface area for cross-membrane transport between its stroma and the cell cytoplasm. Chloroplast_sentence_306

The small vesicles sometimes observed may serve as transport vesicles to shuttle stuff between the thylakoids and intermembrane space. Chloroplast_sentence_307

Stroma Chloroplast_section_41

Main article: Stroma Chloroplast_sentence_308

The protein-rich, alkaline, aqueous fluid within the inner chloroplast membrane and outside of the thylakoid space is called the stroma, which corresponds to the cytosol of the original cyanobacterium. Chloroplast_sentence_309

Nucleoids of chloroplast DNA, chloroplast ribosomes, the thylakoid system with plastoglobuli, starch granules, and many proteins can be found floating around in it. Chloroplast_sentence_310

The Calvin cycle, which fixes CO2 into G3P takes place in the stroma. Chloroplast_sentence_311

Chloroplast ribosomes Chloroplast_section_42

Chloroplasts have their own ribosomes, which they use to synthesize a small fraction of their proteins. Chloroplast_sentence_312

Chloroplast ribosomes are about two-thirds the size of cytoplasmic ribosomes (around 17 nm vs 25 nm). Chloroplast_sentence_313

They take mRNAs transcribed from the chloroplast DNA and translate them into protein. Chloroplast_sentence_314

While similar to bacterial ribosomes, chloroplast translation is more complex than in bacteria, so chloroplast ribosomes include some chloroplast-unique features. Chloroplast_sentence_315

Small subunit ribosomal RNAs in several Chlorophyta and euglenid chloroplasts lack motifs for shine-dalgarno sequence recognition, which is considered essential for translation initiation in most chloroplasts and prokaryotes. Chloroplast_sentence_316

Such loss is also rarely observed in other plastids and prokaryotes. Chloroplast_sentence_317

Plastoglobuli Chloroplast_section_43

Plastoglobuli (singular plastoglobulus, sometimes spelled plastoglobule(s)), are spherical bubbles of lipids and proteins about 45–60 nanometers across. Chloroplast_sentence_318

They are surrounded by a lipid monolayer. Chloroplast_sentence_319

Plastoglobuli are found in all chloroplasts, but become more common when the chloroplast is under oxidative stress, or when it ages and transitions into a gerontoplast. Chloroplast_sentence_320

Plastoglobuli also exhibit a greater size variation under these conditions. Chloroplast_sentence_321

They are also common in etioplasts, but decrease in number as the etioplasts mature into chloroplasts. Chloroplast_sentence_322

Plastoglubuli contain both structural proteins and enzymes involved in lipid synthesis and metabolism. Chloroplast_sentence_323

They contain many types of lipids including plastoquinone, vitamin E, carotenoids and chlorophylls. Chloroplast_sentence_324

Plastoglobuli were once thought to be free-floating in the 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. Chloroplast_sentence_325

In normal green chloroplasts, the vast majority of plastoglobuli occur singularly, attached directly to their parent thylakoid. Chloroplast_sentence_326

In old or stressed chloroplasts, plastoglobuli tend to occur in linked groups or chains, still always anchored to a thylakoid. Chloroplast_sentence_327

Plastoglobuli form when a bubble appears between the layers of the lipid bilayer of the thylakoid membrane, or bud from existing plastoglubuli—though they never detach and float off into the stroma. Chloroplast_sentence_328

Practically all plastoglobuli form on or near the highly curved edges of the thylakoid disks or sheets. Chloroplast_sentence_329

They are also more common on stromal thylakoids than on granal ones. Chloroplast_sentence_330

Starch granules Chloroplast_section_44

Starch granules are very common in chloroplasts, typically taking up 15% of the organelle's volume, though in some other plastids like amyloplasts, they can be big enough to distort the shape of the organelle. Chloroplast_sentence_331

Starch granules are simply accumulations of starch in the stroma, and are not bounded by a membrane. Chloroplast_sentence_332

Starch granules appear and grow throughout the day, as the chloroplast synthesizes sugars, and are consumed at night to fuel respiration and continue sugar export into the phloem, though in mature chloroplasts, it is rare for a starch granule to be completely consumed or for a new granule to accumulate. Chloroplast_sentence_333

Starch granules vary in composition and location across different chloroplast lineages. Chloroplast_sentence_334

In red algae, starch granules are found in the cytoplasm rather than in the chloroplast. Chloroplast_sentence_335

In C4 plants, mesophyll chloroplasts, which do not synthesize sugars, lack starch granules. Chloroplast_sentence_336

RuBisCO Chloroplast_section_45

Main article: RuBisCO Chloroplast_sentence_337

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. Chloroplast_sentence_338

RuBisCO is the enzyme that fixes CO2 into sugar molecules. Chloroplast_sentence_339

In C3 plants, RuBisCO is abundant in all chloroplasts, though in C4 plants, it is confined to the bundle sheath chloroplasts, where the Calvin cycle is carried out in C4 plants. Chloroplast_sentence_340

Pyrenoids Chloroplast_section_46

Main article: Pyrenoid Chloroplast_sentence_341

The chloroplasts of some hornworts and algae contain structures called pyrenoids. Chloroplast_sentence_342

They are not found in higher plants. Chloroplast_sentence_343

Pyrenoids are roughly spherical and highly refractive bodies which are a site of starch accumulation in plants that contain them. Chloroplast_sentence_344

They consist of a matrix opaque to electrons, surrounded by two hemispherical starch plates. Chloroplast_sentence_345

The starch is accumulated as the pyrenoids mature. Chloroplast_sentence_346

In algae with carbon concentrating mechanisms, the enzyme RuBisCO is found in the pyrenoids. Chloroplast_sentence_347

Starch can also accumulate around the pyrenoids when CO2 is scarce. Chloroplast_sentence_348

Pyrenoids can divide to form new pyrenoids, or be produced "de novo". Chloroplast_sentence_349

Thylakoid system Chloroplast_section_47

Main article: Thylakoid Chloroplast_sentence_350

Thylakoids (sometimes spelled thylakoïds), are small interconnected sacks which contain the membranes that the light reactions of photosynthesis take place on. Chloroplast_sentence_351

The word thylakoid comes from the Greek word thylakos which means "sack". Chloroplast_sentence_352

Suspended within the chloroplast stroma is the thylakoid system, a highly dynamic collection of membranous sacks called thylakoids where chlorophyll is found and the light reactions of photosynthesis happen. Chloroplast_sentence_353

In most vascular plant chloroplasts, the thylakoids are arranged in stacks called grana, though in certain C4 plant chloroplasts and some algal chloroplasts, the thylakoids are free floating. Chloroplast_sentence_354

Thylakoid structure Chloroplast_section_48

Using a light microscope, it is just barely possible to see tiny green granules—which were named grana. Chloroplast_sentence_355

With electron microscopy, it became possible to see the thylakoid system in more detail, revealing it to consist of stacks of flat thylakoids which made up the grana, and long interconnecting stromal thylakoids which linked different grana. Chloroplast_sentence_356

In the transmission electron microscope, thylakoid membranes appear as alternating light-and-dark bands, 8.5 nanometers thick. Chloroplast_sentence_357

For a long time, the three-dimensional structure of the thylakoid membrane system had been unknown or disputed. Chloroplast_sentence_358

Many models have been proposed, the most prevalent being the helical model, in which granum stacks of thylakoids are wrapped by helical stromal thylakoids. Chloroplast_sentence_359

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. Chloroplast_sentence_360

The helical model was supported by several additional works, 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. Chloroplast_sentence_361

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. Chloroplast_sentence_362

Grana consist of a stacks of flattened circular granal thylakoids that resemble pancakes. Chloroplast_sentence_363

Each granum can contain anywhere from two to a hundred thylakoids, though grana with 10–20 thylakoids are most common. Chloroplast_sentence_364

Wrapped around the grana are multiple parallel right-handed helical stromal thylakoids, also known as frets or lamellar thylakoids. Chloroplast_sentence_365

The helices ascend at an angle of ~20°, connecting to each granal thylakoid at a bridge-like slit junction. Chloroplast_sentence_366

The stroma lamellae extend as large sheets perpendicular to the grana columns. Chloroplast_sentence_367

These sheets are connected to the right-handed helices either directly or through bifurcations that form left-handed helical membrane surfaces. Chloroplast_sentence_368

The left-handed helical surfaces have a similar tilt angle to the right-handed helices (~20°), but ¼ the pitch. Chloroplast_sentence_369

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. Chloroplast_sentence_370

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. Chloroplast_sentence_371

Thylakoid composition Chloroplast_section_49

Embedded in the thylakoid membranes are important protein complexes which carry out the light reactions of photosynthesis. Chloroplast_sentence_372

Photosystem II and photosystem I contain light-harvesting complexes with chlorophyll and carotenoids that absorb light energy and use it to energize electrons. Chloroplast_sentence_373

Molecules in the thylakoid membrane use the energized electrons to pump hydrogen ions into the thylakoid space, decreasing the pH and turning it acidic. Chloroplast_sentence_374

ATP synthase is a large protein complex that harnesses the concentration gradient of the hydrogen ions in the thylakoid space to generate ATP energy as the hydrogen ions flow back out into the stroma—much like a dam turbine. Chloroplast_sentence_375

There are two types of thylakoids—granal thylakoids, which are arranged in grana, and stromal thylakoids, which are in contact with the stroma. Chloroplast_sentence_376

Granal thylakoids are pancake-shaped circular disks about 300–600 nanometers in diameter. Chloroplast_sentence_377

Stromal thylakoids are helicoid sheets that spiral around grana. Chloroplast_sentence_378

The flat tops and bottoms of granal thylakoids contain only the relatively flat photosystem II protein complex. Chloroplast_sentence_379

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. Chloroplast_sentence_380

In contrast, photosystem I and ATP synthase are large protein complexes which jut out into the stroma. Chloroplast_sentence_381

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. Chloroplast_sentence_382

These large protein complexes may act as spacers between the sheets of stromal thylakoids. Chloroplast_sentence_383

The number of thylakoids and the total thylakoid area of a chloroplast is influenced by light exposure. Chloroplast_sentence_384

Shaded chloroplasts contain larger and more grana with more thylakoid membrane area than chloroplasts exposed to bright light, which have smaller and fewer grana and less thylakoid area. Chloroplast_sentence_385

Thylakoid extent can change within minutes of light exposure or removal. Chloroplast_sentence_386

Pigments and chloroplast colors Chloroplast_section_50

Inside the photosystems embedded in chloroplast thylakoid membranes are various photosynthetic pigments, which absorb and transfer light energy. Chloroplast_sentence_387

The types of pigments found are different in various groups of chloroplasts, and are responsible for a wide variety of chloroplast colorations. Chloroplast_sentence_388

Chlorophylls Chloroplast_section_51

Chlorophyll a is found in all chloroplasts, as well as their cyanobacterial ancestors. Chloroplast_sentence_389

Chlorophyll a is a blue-green pigment partially responsible for giving most cyanobacteria and chloroplasts their color. Chloroplast_sentence_390

Other forms of chlorophyll exist, such as the accessory pigments chlorophyll b, chlorophyll c, chlorophyll d, and chlorophyll f. Chloroplast_sentence_391

Chlorophyll b is an olive green pigment found only in the chloroplasts of plants, green algae, any secondary chloroplasts obtained through the secondary endosymbiosis of a green alga, and a few cyanobacteria. Chloroplast_sentence_392

It is the chlorophylls a and b together that make most plant and green algal chloroplasts green. Chloroplast_sentence_393

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. Chloroplast_sentence_394

Chlorophyll c is also found in some green algae and cyanobacteria. Chloroplast_sentence_395

Chlorophylls d and f are pigments found only in some cyanobacteria. Chloroplast_sentence_396

Carotenoids Chloroplast_section_52

In addition to chlorophylls, another group of yelloworange pigments called carotenoids are also found in the photosystems. Chloroplast_sentence_397

There are about thirty photosynthetic carotenoids. Chloroplast_sentence_398

They help transfer and dissipate excess energy, and their bright colors sometimes override the chlorophyll green, like during the fall, when the leaves of some land plants change color. Chloroplast_sentence_399

β-carotene is a bright red-orange carotenoid found in nearly all chloroplasts, like chlorophyll a. Chloroplast_sentence_400

Xanthophylls, especially the orange-red zeaxanthin, are also common. Chloroplast_sentence_401

Many other forms of carotenoids exist that are only found in certain groups of chloroplasts. Chloroplast_sentence_402

Phycobilins Chloroplast_section_53

Phycobilins are a third group of pigments found in cyanobacteria, and glaucophyte, red algal, and cryptophyte chloroplasts. Chloroplast_sentence_403

Phycobilins come in all colors, though phycoerytherin is one of the pigments that makes many red algae red. Chloroplast_sentence_404

Phycobilins often organize into relatively large protein complexes about 40 nanometers across called phycobilisomes. Chloroplast_sentence_405

Like photosystem I and ATP synthase, phycobilisomes jut into the stroma, preventing thylakoid stacking in red algal chloroplasts. Chloroplast_sentence_406

Cryptophyte chloroplasts and some cyanobacteria don't have their phycobilin pigments organized into phycobilisomes, and keep them in their thylakoid space instead. Chloroplast_sentence_407

Specialized chloroplasts in C4 plants Chloroplast_section_54

See also: Photosynthesis and C4 photosynthesis Chloroplast_sentence_408

To fix carbon dioxide into sugar molecules in the process of photosynthesis, chloroplasts use an enzyme called RuBisCO. Chloroplast_sentence_409

RuBisCO has a problem—it has trouble distinguishing between carbon dioxide and oxygen, so at high oxygen concentrations, RuBisCO starts accidentally adding oxygen to sugar precursors. Chloroplast_sentence_410

This has the end result of ATP energy being wasted and CO 2 being released, all with no sugar being produced. Chloroplast_sentence_411

This is a big problem, since O2 is produced by the initial light reactions of photosynthesis, causing issues down the line in the Calvin cycle which uses RuBisCO. Chloroplast_sentence_412

C4 plants evolved a way to solve this—by spatially separating the light reactions and the Calvin cycle. Chloroplast_sentence_413

The light reactions, which store light energy in ATP and NADPH, are done in the mesophyll cells of a C4 leaf. Chloroplast_sentence_414

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 in a leaf. Chloroplast_sentence_415

As a result, chloroplasts in C4 mesophyll cells and bundle sheath cells are specialized for each stage of photosynthesis. Chloroplast_sentence_416

In mesophyll cells, chloroplasts are specialized for the light reactions, so they lack RuBisCO, and have normal grana and thylakoids, which they use to make ATP and NADPH, as well as oxygen. Chloroplast_sentence_417

They store CO 2 in a four-carbon compound, which is why the process is called C4 photosynthesis. Chloroplast_sentence_418

The four-carbon compound is then transported to the bundle sheath chloroplasts, where it drops off CO 2 and returns to the mesophyll. Chloroplast_sentence_419

Bundle sheath chloroplasts do not carry out the light reactions, preventing oxygen from building up in them and disrupting RuBisCO activity. Chloroplast_sentence_420

Because of this, they lack thylakoids organized into 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 ATP to power the Calvin cycle without generating oxygen. Chloroplast_sentence_421

They lack photosystem II, and only have photosystem I—the only protein complex needed for cyclic electron flow. Chloroplast_sentence_422

Because the job of bundle sheath chloroplasts is to carry out the Calvin cycle and make sugar, they often contain large starch grains. Chloroplast_sentence_423

Both types of chloroplast contain large amounts of chloroplast peripheral reticulum, which they use to get more surface area to transport stuff in and out of them. Chloroplast_sentence_424

Mesophyll chloroplasts have a little more peripheral reticulum than bundle sheath chloroplasts. Chloroplast_sentence_425

Location Chloroplast_section_55

Distribution in a plant Chloroplast_section_56

Not all cells in a multicellular plant contain chloroplasts. Chloroplast_sentence_426

All green parts of a plant contain chloroplasts—the chloroplasts, or more specifically, the chlorophyll in them are what make the photosynthetic parts of a plant green. Chloroplast_sentence_427

The plant cells which contain chloroplasts are usually parenchyma cells, though chloroplasts can also be found in collenchyma tissue. Chloroplast_sentence_428

A plant cell which contains chloroplasts is known as a chlorenchyma cell. Chloroplast_sentence_429

A typical chlorenchyma cell of a land plant contains about 10 to 100 chloroplasts. Chloroplast_sentence_430

In some plants such as cacti, chloroplasts are found in the stems, though in most plants, chloroplasts are concentrated in the leaves. Chloroplast_sentence_431

One square millimeter of leaf tissue can contain half a million chloroplasts. Chloroplast_sentence_432

Within a leaf, chloroplasts are mainly found in the mesophyll layers of a leaf, and the guard cells of stomata. Chloroplast_sentence_433

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. Chloroplast_sentence_434

Chloroplasts can also be found in the bundle sheath cells of a leaf, especially in C4 plants, which carry out the Calvin cycle in their bundle sheath cells. Chloroplast_sentence_435

They are often absent from the epidermis of a leaf. Chloroplast_sentence_436

Cellular location Chloroplast_section_57

Chloroplast movement Chloroplast_section_58

See also: Cytoplasmic streaming Chloroplast_sentence_437

The chloroplasts of plant and algal cells can orient themselves to best suit the available light. Chloroplast_sentence_438

In low-light conditions, they will spread out in a sheet—maximizing the surface area to absorb light. Chloroplast_sentence_439

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. Chloroplast_sentence_440

This reduces exposure and protects them from photooxidative damage. Chloroplast_sentence_441

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. Chloroplast_sentence_442

Chloroplast movement is considered one of the most closely regulated stimulus-response systems that can be found in plants. Chloroplast_sentence_443

Mitochondria have also been observed to follow chloroplasts as they move. Chloroplast_sentence_444

In higher plants, chloroplast movement is run by phototropins, blue light photoreceptors also responsible for plant phototropism. Chloroplast_sentence_445

In some algae, mosses, ferns, and flowering plants, chloroplast movement is influenced by red light in addition to blue light, though very long red wavelengths inhibit movement rather than speeding it up. Chloroplast_sentence_446

Blue light generally causes chloroplasts to seek shelter, while red light draws them out to maximize light absorption. Chloroplast_sentence_447

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. Chloroplast_sentence_448

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. Chloroplast_sentence_449

Function and chemistry Chloroplast_section_59

Guard cell chloroplasts Chloroplast_section_60

Unlike most epidermal cells, the guard cells of plant stomata contain relatively well-developed chloroplasts. Chloroplast_sentence_450

However, exactly what they do is controversial. Chloroplast_sentence_451

Plant innate immunity Chloroplast_section_61

Plants lack specialized immune cells—all plant cells participate in the plant immune response. Chloroplast_sentence_452

Chloroplasts, along with the nucleus, cell membrane, and endoplasmic reticulum, are key players in pathogen defense. Chloroplast_sentence_453

Due to its role in a plant cell's immune response, pathogens frequently target the chloroplast. Chloroplast_sentence_454

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. Chloroplast_sentence_455

Chloroplasts stimulate both responses by purposely damaging their photosynthetic system, producing reactive oxygen species. Chloroplast_sentence_456

High levels of reactive oxygen species will cause the hypersensitive response. Chloroplast_sentence_457

The reactive oxygen species also directly kill any pathogens within the cell. Chloroplast_sentence_458

Lower levels of reactive oxygen species initiate systemic acquired resistance, triggering defense-molecule production in the rest of the plant. Chloroplast_sentence_459

In some plants, chloroplasts are known to move closer to the infection site and the nucleus during an infection. Chloroplast_sentence_460

Chloroplasts can serve as cellular sensors. Chloroplast_sentence_461

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. Chloroplast_sentence_462

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. Chloroplast_sentence_463

All these molecules initiate retrograde signaling—signals from the chloroplast that regulate gene expression in the nucleus. Chloroplast_sentence_464

In addition to defense signaling, chloroplasts, with the help of the peroxisomes, help synthesize an important defense molecule, jasmonate. Chloroplast_sentence_465

Chloroplasts synthesize all the fatty acids in a plant cell—linoleic acid, a fatty acid, is a precursor to jasmonate. Chloroplast_sentence_466

Photosynthesis Chloroplast_section_62

Main article: Photosynthesis Chloroplast_sentence_467

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. Chloroplast_sentence_468

Water (H2O) and carbon dioxide (CO2) are used in photosynthesis, and sugar and oxygen (O2) is made, using light energy. Chloroplast_sentence_469

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. Chloroplast_sentence_470

The two phases are linked by the energy carriers adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADP). Chloroplast_sentence_471

Light reactions Chloroplast_section_63

Main article: Light reactions Chloroplast_sentence_472

The light reactions take place on the thylakoid membranes. Chloroplast_sentence_473

They take light energy and store it in NADPH, a form of NADP, and ATP to fuel the dark reactions. Chloroplast_sentence_474

Energy carriers Chloroplast_section_64

Main articles: Adenosine triphosphate and NADPH Chloroplast_sentence_475

ATP is the phosphorylated version of adenosine diphosphate (ADP), which stores energy in a cell and powers most cellular activities. Chloroplast_sentence_476

ATP is the energized form, while ADP is the (partially) depleted form. Chloroplast_sentence_477

NADP is an electron carrier which ferries high energy electrons. Chloroplast_sentence_478

In the light reactions, it gets reduced, meaning it picks up electrons, becoming NADPH. Chloroplast_sentence_479

Photophosphorylation Chloroplast_section_65

Main article: Photophosphorylation Chloroplast_sentence_480

Like mitochondria, chloroplasts use the potential energy stored in an H, or hydrogen ion gradient to generate ATP energy. Chloroplast_sentence_481

The two photosystems capture light energy to energize electrons taken from water, and release them down an electron transport chain. Chloroplast_sentence_482

The 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) inside the thylakoid system than in the stroma. Chloroplast_sentence_483

The hydrogen ions in the thylakoid space then diffuse back down their concentration gradient, flowing back out into the stroma through ATP synthase. Chloroplast_sentence_484

ATP synthase uses the energy from the flowing hydrogen ions to phosphorylate adenosine diphosphate into adenosine triphosphate, or ATP. Chloroplast_sentence_485

Because chloroplast ATP synthase projects out into the stroma, the ATP is synthesized there, in position to be used in the dark reactions. Chloroplast_sentence_486

NADP+ reduction Chloroplast_section_66

See also: Redox reaction Chloroplast_sentence_487

Electrons are often removed from the electron transport chains to charge NADP with electrons, reducing it to NADPH. Chloroplast_sentence_488

Like ATP synthase, ferredoxin-NADP reductase, the enzyme that reduces NADP, releases the NADPH it makes into the stroma, right where it is needed for the dark reactions. Chloroplast_sentence_489

Because NADP reduction removes electrons from the electron transport chains, they must be replaced—the job of photosystem II, which splits water molecules (H2O) to obtain the electrons from its hydrogen atoms. Chloroplast_sentence_490

Cyclic photophosphorylation Chloroplast_section_67

Main article: Cyclic photophosphorylation Chloroplast_sentence_491

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. Chloroplast_sentence_492

Normally, the reenergized electrons are taken by NADP, though sometimes they can flow back down more H-pumping electron transport chains to transport more hydrogen ions into the thylakoid space to generate more ATP. Chloroplast_sentence_493

This is termed cyclic photophosphorylation because the electrons are recycled. Chloroplast_sentence_494

Cyclic photophosphorylation is common in C4 plants, which need more ATP than NADPH. Chloroplast_sentence_495

Dark reactions Chloroplast_section_68

Main article: Dark reactions Chloroplast_sentence_496

The Calvin cycle, also known as the dark reactions, is a series of biochemical reactions that fixes CO2 into G3P sugar molecules and uses the energy and electrons from the ATP and NADPH made in the light reactions. Chloroplast_sentence_497

The Calvin cycle takes place in the stroma of the chloroplast. Chloroplast_sentence_498

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. Chloroplast_sentence_499

Carbon fixation and G3P synthesis Chloroplast_section_69

The Calvin cycle starts by using the enzyme RuBisCO to fix CO2 into five-carbon Ribulose bisphosphate (RuBP) molecules. Chloroplast_sentence_500

The result is unstable six-carbon molecules that immediately break down into three-carbon molecules called 3-phosphoglyceric acid, or 3-PGA. Chloroplast_sentence_501

The ATP and NADPH made in the light reactions is used to convert the 3-PGA into glyceraldehyde-3-phosphate, or G3P sugar molecules. Chloroplast_sentence_502

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. Chloroplast_sentence_503

Sugars and starches Chloroplast_section_70

Glyceraldehyde-3-phosphate can double up to form larger sugar molecules like glucose and fructose. Chloroplast_sentence_504

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. Chloroplast_sentence_505

Alternatively, glucose monomers in the chloroplast can be linked together to make starch, which accumulates into the starch grains found in the chloroplast. Chloroplast_sentence_506

Under conditions such as high atmospheric CO2 concentrations, these starch grains may grow very large, distorting the grana and thylakoids. Chloroplast_sentence_507

The starch granules displace the thylakoids, but leave them intact. Chloroplast_sentence_508

Waterlogged roots 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). Chloroplast_sentence_509

This depletes a plant's free phosphate supply, which indirectly stimulates chloroplast starch synthesis. Chloroplast_sentence_510

While linked to low photosynthesis rates, the starch grains themselves may not necessarily interfere significantly with the efficiency of photosynthesis, and might simply be a side effect of another photosynthesis-depressing factor. Chloroplast_sentence_511

Photorespiration Chloroplast_section_71

Photorespiration can occur when the oxygen concentration is too high. Chloroplast_sentence_512

RuBisCO cannot distinguish between oxygen and carbon dioxide very well, so it can accidentally add O2 instead of CO2 to RuBP. Chloroplast_sentence_513

This process reduces the efficiency of photosynthesis—it consumes ATP and oxygen, releases CO2, and produces no sugar. Chloroplast_sentence_514

It can waste up to half the carbon fixed by the Calvin cycle. Chloroplast_sentence_515

Several mechanisms have evolved in different lineages that raise the carbon dioxide concentration relative to oxygen within the chloroplast, increasing the efficiency of photosynthesis. Chloroplast_sentence_516

These mechanisms are called carbon dioxide concentrating mechanisms, or CCMs. Chloroplast_sentence_517

These include Crassulacean acid metabolism, C4 carbon fixation, and pyrenoids. Chloroplast_sentence_518

Chloroplasts in C4 plants are notable as they exhibit a distinct chloroplast dimorphism. Chloroplast_sentence_519

pH Chloroplast_section_72

Because of the H gradient across the thylakoid membrane, the interior of the thylakoid is acidic, with a pH around 4, while the stroma is slightly basic, with a pH of around 8. Chloroplast_sentence_520

The optimal stroma pH for the Calvin cycle is 8.1, with the reaction nearly stopping when the pH falls below 7.3. Chloroplast_sentence_521

CO2 in water can form carbonic acid, which can disturb the pH of isolated chloroplasts, interfering with photosynthesis, even though CO2 is used in photosynthesis. Chloroplast_sentence_522

However, chloroplasts in living plant cells are not affected by this as much. Chloroplast_sentence_523

Chloroplasts can pump K and H ions in and out of themselves using a poorly understood light-driven transport system. Chloroplast_sentence_524

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. Chloroplast_sentence_525

Amino acid synthesis Chloroplast_section_73

Chloroplasts alone make almost all of a plant cell's amino acids in their stroma except the sulfur-containing ones like cysteine and methionine. Chloroplast_sentence_526

Cysteine is made in the chloroplast (the proplastid too) but it is also synthesized in the cytosol and mitochondria, probably because it has trouble crossing membranes to get to where it is needed. Chloroplast_sentence_527

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. Chloroplast_sentence_528

Other nitrogen compounds Chloroplast_section_74

Chloroplasts make all of a cell's purines and pyrimidines—the nitrogenous bases found in DNA and RNA. Chloroplast_sentence_529

They also convert nitrite (NO2) into ammonia (NH3) which supplies the plant with nitrogen to make its amino acids and nucleotides. Chloroplast_sentence_530

Other chemical products Chloroplast_section_75

The plastid is the site of diverse and complex lipid synthesis in plants. Chloroplast_sentence_531

The carbon used to form the majority of the lipid is from acetyl-CoA, which is the decarboxylation product of pyruvate. Chloroplast_sentence_532

Pyruvate may enter the plastid from the cytosol by passive diffusion through the membrane after production in glycolysis. Chloroplast_sentence_533

Pyruvate is also made in the plastid from phosphoenolpyruvate, a metabolite made in the cytosol from pyruvate or PGA. Chloroplast_sentence_534

Acetate in the cytosol is unavailable for lipid biosynthesis in the plastid. Chloroplast_sentence_535

The typical length of fatty acids produced in the plastid are 16 or 18 carbons, with 0-3 cis double bonds. Chloroplast_sentence_536

The biosynthesis of fatty acids from acetyl-CoA primarily requires two enzymes. Chloroplast_sentence_537

Acetyl-CoA carboxylase creates malonyl-CoA, used in both the first step and the extension steps of synthesis. Chloroplast_sentence_538

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. Chloroplast_sentence_539

The initiation of synthesis begins with the condensation of malonyl-ACP with acetyl-CoA to produce ketobutyryl-ACP. Chloroplast_sentence_540

2 reductions involving the use of NADPH and one dehydration creates butyryl-ACP. Chloroplast_sentence_541

Extension of the fatty acid comes from repeated cycles of malonyl-ACP condensation, reduction, and dehydration. Chloroplast_sentence_542

Other lipids are derived from the methyl-erythritol phosphate (MEP) pathway and consist of gibberelins, sterols, abscisic acid, phytol, and innumerable secondary metabolites. Chloroplast_sentence_543

Differentiation, replication, and inheritance Chloroplast_section_76

Main article: Plastid Chloroplast_sentence_544

Chloroplasts are a special type of a plant cell organelle called a plastid, though the two terms are sometimes used interchangeably. Chloroplast_sentence_545

There are many other types of plastids, which carry out various functions. Chloroplast_sentence_546

All chloroplasts in a plant are descended from undifferentiated proplastids found in the zygote, or fertilized egg. Chloroplast_sentence_547

Proplastids are commonly found in an adult plant's apical meristems. Chloroplast_sentence_548

Chloroplasts do not normally develop from proplastids in root tip meristems—instead, the formation of starch-storing amyloplasts is more common. Chloroplast_sentence_549

In 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. Chloroplast_sentence_550

This process involves invaginations of the inner plastid membrane, forming sheets of membrane that project into the internal stroma. Chloroplast_sentence_551

These membrane sheets then fold to form thylakoids and grana. Chloroplast_sentence_552

If angiosperm shoots are not exposed to the required light for chloroplast formation, proplastids may develop into an etioplast stage before becoming chloroplasts. Chloroplast_sentence_553

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. Chloroplast_sentence_554

While etioplasts lack chlorophyll, they have a yellow chlorophyll precursor stocked. Chloroplast_sentence_555

Within a few minutes of light exposure, the prolamellar body begins to reorganize into stacks of thylakoids, and chlorophyll starts to be produced. Chloroplast_sentence_556

This process, where the etioplast becomes a chloroplast, takes several hours. Chloroplast_sentence_557

Gymnosperms do not require light to form chloroplasts. Chloroplast_sentence_558

Light, however, does not guarantee that a proplastid will develop into a chloroplast. Chloroplast_sentence_559

Whether a proplastid develops into a chloroplast some other kind of plastid is mostly controlled by the nucleus and is largely influenced by the kind of cell it resides in. Chloroplast_sentence_560

Plastid interconversion Chloroplast_section_77

Plastid differentiation is not permanent, in fact many interconversions are possible. Chloroplast_sentence_561

Chloroplasts may be converted to chromoplasts, which are pigment-filled plastids responsible for the bright colors seen in flowers and ripe fruit. Chloroplast_sentence_562

Starch storing amyloplasts can also be converted to chromoplasts, and it is possible for proplastids to develop straight into chromoplasts. Chloroplast_sentence_563

Chromoplasts and amyloplasts can also become chloroplasts, like what happens when a carrot or a potato is illuminated. Chloroplast_sentence_564

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_sentence_565

Chloroplast, amyloplast, chromoplast, proplast, etc., are not absolute states—intermediate forms are common. Chloroplast_sentence_566

Division Chloroplast_section_78

Most chloroplasts in a photosynthetic cell do not develop directly from proplastids or etioplasts. Chloroplast_sentence_567

In fact, a typical shoot meristematic plant cell contains only 7–20 proplastids. Chloroplast_sentence_568

These proplastids differentiate into chloroplasts, which divide to create the 30–70 chloroplasts found in a mature photosynthetic plant cell. Chloroplast_sentence_569

If the cell divides, chloroplast division provides the additional chloroplasts to partition between the two daughter cells. Chloroplast_sentence_570

In single-celled algae, chloroplast division is the only way new chloroplasts are formed. Chloroplast_sentence_571

There is no proplastid differentiation—when an algal cell divides, its chloroplast divides along with it, and each daughter cell receives a mature chloroplast. Chloroplast_sentence_572

Almost all chloroplasts in a cell divide, rather than a small group of rapidly dividing chloroplasts. Chloroplast_sentence_573

Chloroplasts have no definite S-phase—their DNA replication is not synchronized or limited to that of their host cells. Chloroplast_sentence_574

Much of what we know about chloroplast division comes from studying organisms like Arabidopsis and the red alga Cyanidioschyzon merolæ. Chloroplast_sentence_575

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. Chloroplast_sentence_576

The Min system manages the placement of the Z-ring, ensuring that the chloroplast is cleaved more or less evenly. Chloroplast_sentence_577

The protein MinD prevents FtsZ from linking up and forming filaments. Chloroplast_sentence_578

Another protein ARC3 may also be involved, but it is not very well understood. Chloroplast_sentence_579

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. Chloroplast_sentence_580

Next, the two plastid-dividing rings, or PD rings form. Chloroplast_sentence_581

The inner plastid-dividing ring is located in the inner side of the chloroplast's inner membrane, and is formed first. Chloroplast_sentence_582

The outer plastid-dividing ring is found wrapped around the outer chloroplast membrane. Chloroplast_sentence_583

It consists of filaments about 5 nanometers across, arranged in rows 6.4 nanometers apart, and shrinks to squeeze the chloroplast. Chloroplast_sentence_584

This is when chloroplast constriction begins. Chloroplast_sentence_585

In a few species like Cyanidioschyzon merolæ, chloroplasts have a third plastid-dividing ring located in the chloroplast's intermembrane space. Chloroplast_sentence_586

Late into the constriction phase, dynamin proteins assemble around the outer plastid-dividing ring, helping provide force to squeeze the chloroplast. Chloroplast_sentence_587

Meanwhile, the Z-ring and the inner plastid-dividing ring break down. Chloroplast_sentence_588

During this stage, the many chloroplast DNA plasmids floating around in the stroma are partitioned and distributed to the two forming daughter chloroplasts. Chloroplast_sentence_589

Later, the dynamins migrate under the outer plastid dividing ring, into direct contact with the chloroplast's outer membrane, to cleave the chloroplast in two daughter chloroplasts. Chloroplast_sentence_590

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. Chloroplast_sentence_591

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. Chloroplast_sentence_592

Regulation Chloroplast_section_79

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. Chloroplast_sentence_593

In organisms like plants, whose cells contain multiple chloroplasts, coordination is looser and less important. Chloroplast_sentence_594

It is likely that chloroplast and cell division are somewhat synchronized, though the mechanisms for it are mostly unknown. Chloroplast_sentence_595

Light has been shown to be a requirement for chloroplast division. Chloroplast_sentence_596

Chloroplasts can grow and progress through some of the constriction stages under poor quality green light, but are slow to complete division—they require exposure to bright white light to complete division. Chloroplast_sentence_597

Spinach leaves grown under green light have been observed to contain many large dumbbell-shaped chloroplasts. Chloroplast_sentence_598

Exposure to white light can stimulate these chloroplasts to divide and reduce the population of dumbbell-shaped chloroplasts. Chloroplast_sentence_599

Chloroplast inheritance Chloroplast_section_80

Like mitochondria, chloroplasts are usually inherited from a single parent. Chloroplast_sentence_600

Biparental chloroplast inheritance—where plastid genes are inherited from both parent plants—occurs in very low levels in some flowering plants. Chloroplast_sentence_601

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. Chloroplast_sentence_602

Parental chloroplasts can be sorted so that only one type is present in each offspring. Chloroplast_sentence_603

Gymnosperms, such as pine trees, mostly pass on chloroplasts paternally, while flowering plants often inherit chloroplasts maternally. Chloroplast_sentence_604

Flowering plants were once thought to only inherit chloroplasts maternally. Chloroplast_sentence_605

However, there are now many documented cases of angiosperms inheriting chloroplasts paternally. Chloroplast_sentence_606

Angiosperms, which pass on chloroplasts maternally, have many ways to prevent paternal inheritance. Chloroplast_sentence_607

Most of them produce sperm cells that do not contain any plastids. Chloroplast_sentence_608

There are many other documented mechanisms that prevent paternal inheritance in these flowering plants, such as different rates of chloroplast replication within the embryo. Chloroplast_sentence_609

Among angiosperms, paternal chloroplast inheritance is observed more often in hybrids than in offspring from parents of the same species. Chloroplast_sentence_610

This suggests that incompatible hybrid genes might interfere with the mechanisms that prevent paternal inheritance. Chloroplast_sentence_611

Transplastomic plants Chloroplast_section_81

Recently, chloroplasts have caught attention by developers of genetically modified crops. Chloroplast_sentence_612

Since, in most flowering plants, chloroplasts are not inherited from the male parent, transgenes in these plastids cannot be disseminated by pollen. Chloroplast_sentence_613

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. Chloroplast_sentence_614

This biological containment strategy is therefore suitable for establishing the coexistence of conventional and organic agriculture. Chloroplast_sentence_615

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. Chloroplast_sentence_616

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