Chloroplast

context: Chloroplasts' main role is to conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight and converts it and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water. They then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, much amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell varies from 1 in algae up to 100 in plants like Arabidopsis and wheat.

context: Chloroplasts are highly dynamic—they circulate and are moved around within plant cells, and occasionally pinch in two to reproduce. Their behavior is strongly influenced by environmental factors like light color and intensity. 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. Chloroplasts cannot be made by the plant cell and must be inherited by each daughter cell during cell division.

context: Chloroplasts are one of many types of organelles in the plant cell. They are considered to have originated from cyanobacteria through endosymbiosis—when a eukaryotic cell engulfed a photosynthesizing cyanobacterium that became a permanent resident in the cell. Mitochondria are thought to have come from a similar event, where an aerobic prokaryote was engulfed. This origin of chloroplasts was first suggested by the Russian biologist Konstantin Mereschkowski in 1905 after Andreas Schimper observed in 1883 that chloroplasts closely resemble cyanobacteria. Chloroplasts are only found in plants and algae.

context: Cyanobacteria are considered the ancestors of chloroplasts. They are sometimes called blue-green algae even though they are prokaryotes. They are a diverse phylum of bacteria capable of carrying out photosynthesis, and are gram-negative, meaning that they have two cell membranes. 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. Like chloroplasts, they have thylakoids within. On the thylakoid membranes are photosynthetic pigments, including chlorophyll a. 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).

context: Somewhere around a 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. 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. The new cellular resident quickly became an advantage, providing food for the eukaryotic host, which allowed it to live within it. Over time, the cyanobacterium was assimilated, and many of its genes were lost or transferred to the nucleus of the host. Some of its proteins were then synthesized in the cytoplasm of the host cell, and imported back into the chloroplast (formerly the cyanobacterium).

context: 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). All primary chloroplasts belong to one of three chloroplast lineages—the glaucophyte chloroplast lineage, the rhodophyte, or red algal chloroplast lineage, or the chloroplastidan, or green chloroplast lineage. The second two are the largest, and the green chloroplast lineage is the one that contains the land plants.

context: The alga Cyanophora, a glaucophyte, is thought to be one of the first organisms to contain a chloroplast. 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. Glaucophytes have chloroplasts that retain a peptidoglycan wall between their double membranes, like their cyanobacterial parent. For this reason, glaucophyte chloroplasts are also known as muroplasts. 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. The starch that they synthesize collects outside the chloroplast. Like cyanobacteria, glaucophyte chloroplast thylakoids are studded with light collecting structures called phycobilisomes. For these reasons, glaucophyte chloroplasts are considered a primitive intermediate between cyanobacteria and the more evolved chloroplasts in red algae and plants.

context: Rhodoplasts have a double membrane with an intermembrane space and phycobilin pigments organized into phycobilisomes on the thylakoid membranes, preventing their thylakoids from stacking. Some contain pyrenoids. Rhodoplasts have chlorophyll a and phycobilins for photosynthetic pigments; the phycobilin phycoerytherin is responsible for giving many red algae their distinctive red color. However, since they also contain the blue-green chlorophyll a and other pigments, many are reddish to purple from the combination. 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 phycoerytherin in their rhodoplasts, and can appear more greenish. Rhodoplasts synthesize a form of starch called floridean, which collects into granules outside the rhodoplast, in the cytoplasm of the red alga.

context: The chloroplastidan chloroplasts, or green chloroplasts, are another large, highly diverse primary chloroplast lineage. Their host organisms are commonly known as the green algae and land plants. They differ from glaucophyte and red algal chloroplasts in that they have lost their phycobilisomes, and contain chlorophyll b instead. 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. Chloroplastidan chloroplasts have lost the peptidoglycan wall between their double membrane, and have replaced it with an intermembrane space. 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.

context: 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. 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.

context: Euglenophytes are a group of common flagellated protists that contain chloroplasts derived from a green alga. 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. Euglenophyte chloroplasts have a pyrenoid and thylakoids stacked in groups of three. Starch is stored in the form of paramylon, which is contained in membrane-bound granules in the cytoplasm of the euglenophyte.

context: Cryptophytes, or cryptomonads are a group of algae that contain a red-algal derived chloroplast. Cryptophyte chloroplasts contain a nucleomorph that superficially resembles that of the chlorarachniophytes. Cryptophyte chloroplasts have four membranes, the outermost of which is continuous with the rough endoplasmic reticulum. They synthesize ordinary starch, which is stored in granules found in the periplastid space—outside the original double membrane, in the place that corresponds to the red alga's cytoplasm. Inside cryptophyte chloroplasts is a pyrenoid and thylakoids in stacks of two.

context: Apicomplexans are another group of chromalveolates. Like the helicosproidia, they're parasitic, and have a nonphotosynthetic chloroplast. They were once thought to be related to the helicosproidia, but it is now known that the helicosproida are green algae rather than chromalveolates. The apicomplexans include Plasmodium, the malaria parasite. Many apicomplexans keep a vestigial red algal derived chloroplast called an apicoplast, which they inherited from their ancestors. Other apicomplexans like Cryptosporidium have lost the chloroplast completely. Apicomplexans store their energy in amylopectin starch granules that are located in their cytoplasm, even though they are nonphotosynthetic.

context: Apicoplasts have lost all photosynthetic function, and contain no photosynthetic pigments or true thylakoids. They are bounded by four membranes, but the membranes are not connected to the endoplasmic reticulum. The fact that apicomplexans still keep their nonphotosynthetic chloroplast around demonstrates how the chloroplast carries out important functions other than photosynthesis. Plant chloroplasts provide plant cells with many important things besides sugar, and apicoplasts are no different—they synthesize fatty acids, isopentenyl pyrophosphate, iron-sulfur clusters, and carry out part of the heme pathway. This makes the apicoplast an attractive target for drugs to cure apicomplexan-related diseases. 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.

context: 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. Peridinin is not found in any other group of chloroplasts. The peridinin chloroplast is bounded by three membranes (occasionally two), having lost the red algal endosymbiont's original cell membrane. The outermost membrane is not connected to the endoplasmic reticulum. They contain a pyrenoid, and have triplet-stacked thylakoids. Starch is found outside the chloroplast An important feature of these chloroplasts is that their chloroplast DNA is highly reduced and fragmented into many small circles. Most of the genome has migrated to the nucleus, and only critical photosynthesis-related genes remain in the chloroplast.

context: 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. Karlodinium and Karenia probably took up different heterokontophytes. 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. 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.

context: Members of the genus Dinophysis have a phycobilin-containing chloroplast taken from a cryptophyte. However, the cryptophyte is not an endosymbiont—only the chloroplast seems to have been taken, and the chloroplast has been stripped of its nucleomorph and outermost two membranes, leaving just a two-membraned chloroplast. Cryptophyte chloroplasts require their nucleomorph to maintain themselves, and Dinophysis species grown in cell culture alone cannot survive, so it is possible (but not confirmed) that the Dinophysis chloroplast is a kleptoplast—if so, Dinophysis chloroplasts wear out and Dinophysis species must continually engulf cryptophytes to obtain new chloroplasts to replace the old ones.

context: Some dinophytes, like Kryptoperidinium and Durinskia have a diatom (heterokontophyte) derived chloroplast. These chloroplasts are bounded by up to five membranes, (depending on whether you count the entire diatom endosymbiont as the chloroplast, or just the red algal derived chloroplast inside it). The diatom endosymbiont has been reduced relatively little—it still retains its original 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. However the diatom endosymbiont can't store its own food—its starch is found in granules in the dinophyte host's cytoplasm instead. 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. Diatoms have been engulfed by dinoflagellates at least three times.

context: Lepidodinium viride and its close relatives are dinophytes that lost their original peridinin chloroplast and replaced it with a green algal derived chloroplast (more specifically, a prasinophyte). Lepidodinium is the only dinophyte that has a chloroplast that's not from the rhodoplast lineage. The chloroplast is surrounded by two membranes and has no nucleomorph—all the nucleomorph genes have been transferred to the dinophyte nucleus. 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).

context: While most chloroplasts originate from that first set of endosymbiotic events, Paulinella chromatophora is an exception that acquired a photosynthetic cyanobacterial endosymbiont more recently. It is not clear whether that symbiont is closely related to the ancestral chloroplast of other eukaryotes. Being in the early stages of endosymbiosis, Paulinella chromatophora can offer some insights into how chloroplasts evolved. Paulinella cells contain one or two sausage shaped blue-green photosynthesizing structures called chromatophores, descended from the cyanobacterium Synechococcus. Chromatophores cannot survive outside their host. 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. Chromatophores have transferred much less of their DNA to the nucleus of their host. About 0.3–0.8% of the nuclear DNA in Paulinella is from the chromatophore, compared with 11–14% from the chloroplast in plants.

context: Chloroplasts have their own DNA, often abbreviated as ctDNA, or cpDNA. It is also known as the plastome. 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. Since then, hundreds of chloroplast DNAs from various species have been sequenced, but they're mostly those of land plants and green algae—glaucophytes, red algae, and other algal groups are extremely underrepresented, potentially introducing some bias in views of "typical" chloroplast DNA structure and content.

context: The inverted repeat regions are highly conserved among land plants, and accumulate few mutations. Similar inverted repeats exist in the genomes of cyanobacteria and the other two chloroplast lineages (glaucophyta and rhodophyceæ), suggesting that they predate the chloroplast, though some chloroplast DNAs have since lost or flipped the inverted repeats (making them direct repeats). 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.

context: The mechanism for chloroplast DNA (cpDNA) replication has not been conclusively determined, but two main models have been proposed. Scientists have attempted to observe chloroplast replication via electron microscopy since the 1970s. The results of the microscopy experiments led to the idea that chloroplast DNA replicates using a double displacement loop (D-loop). As the D-loop moves through the circular DNA, it adopts a theta intermediary form, also known as a Cairns replication intermediate, and completes replication with a rolling circle mechanism. Transcription starts at specific points of origin. Multiple replication forks open up, allowing replication machinery to transcribe the DNA. As replication continues, the forks grow and eventually converge. The new cpDNA structures separate, creating daughter cpDNA chromosomes.

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

context: One of competing model for cpDNA replication asserts that most cpDNA is linear and participates in homologous recombination and replication structures similar to bacteriophage T4. 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. When the original experiments on cpDNA were performed, scientists did notice linear structures; however, they attributed these linear forms to broken circles. 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. At the same time, homologous recombination does not expand the multiple A --> G gradients seen in plastomes. 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.

context: Endosymbiotic gene transfer is how we know about the lost chloroplasts in many chromalveolate lineages. Even if a chloroplast is eventually lost, the genes it donated to the former host's nucleus persist, providing evidence for the lost chloroplast's existence. For example, while diatoms (a heterokontophyte) now have a red algal derived chloroplast, the presence of many green algal genes in the diatom nucleus provide evidence that the diatom ancestor (probably the ancestor of all chromalveolates too) had a green algal derived chloroplast at some point, which was subsequently replaced by the red chloroplast.

context: Curiously, around half of the protein products of transferred genes aren't even targeted back to the chloroplast. Many became exaptations, taking on new functions like participating in cell division, protein routing, and even disease resistance. A few chloroplast genes found new homes in the mitochondrial genome—most became nonfunctional pseudogenes, though a few tRNA genes still work in the mitochondrion. Some transferred chloroplast DNA protein products get directed to the secretory pathway (though it should be noted that 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, you have to cross the cell membrane, just like if you were headed for the extracellular space. In those cases, chloroplast-targeted proteins do initially travel along the secretory pathway).

context: 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. Phosphorylation helps many proteins bind the polypeptide, keeping it from folding prematurely. 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. At the same time, they have to keep just enough shape so that they can be recognized by the chloroplast. These proteins also help the polypeptide get imported into the chloroplast.

context: In land plants, chloroplasts are generally lens-shaped, 5–8 μm in diameter and 1–3 μm thick. 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). 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. 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).

context: There are some common misconceptions about the outer and inner chloroplast membranes. The fact that chloroplasts are surrounded by a double membrane is often cited as evidence that they are the descendants of endosymbiotic cyanobacteria. This is often interpreted as meaning the outer chloroplast membrane is the product of the host's cell membrane infolding to form a vesicle to surround the ancestral cyanobacterium—which is not true—both chloroplast membranes are homologous to the cyanobacterium's original double membranes.

context: The chloroplast double membrane is also often compared to the mitochondrial double membrane. This is not a valid comparison—the inner mitochondria membrane is used to run proton pumps and carry out oxidative phosphorylation across to generate ATP energy. The only chloroplast structure that can considered analogous to it is the internal thylakoid system. 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. In addition, in terms of function, the inner chloroplast membrane, which regulates metabolite passage and synthesizes some materials, has no counterpart in the mitochondrion.

context: The chloroplast membranes sometimes protrude out into the cytoplasm, forming a stromule, or stroma-containing tubule. Stromules are very rare in chloroplasts, and are much more common in other plastids like chromoplasts and amyloplasts in petals and roots, respectively. 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. 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. However, there is a growing body of evidence that stromules are functional, integral features of plant cell plastids, not merely artifacts.

context: Some chloroplasts contain a structure called the chloroplast peripheral reticulum. It is often found in the chloroplasts of C4 plants, though it has also been found in some C3 angiosperms, and even some gymnosperms. 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. Its purpose is thought to be to increase the chloroplast's surface area for cross-membrane transport between its stroma and the cell cytoplasm. The small vesicles sometimes observed may serve as transport vesicles to shuttle stuff between the thylakoids and intermembrane space.

context: Chloroplasts have their own ribosomes, which they use to synthesize a small fraction of their proteins. Chloroplast ribosomes are about two-thirds the size of cytoplasmic ribosomes (around 17 nm vs 25 nm). They take mRNAs transcribed from the chloroplast DNA and translate them into protein. While similar to bacterial ribosomes, chloroplast translation is more complex than in bacteria, so chloroplast ribosomes include some chloroplast-unique features. 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. Such loss is also rarely observed in other plastids and prokaryotes.

context: Plastoglobuli (singular plastoglobulus, sometimes spelled plastoglobule(s)), are spherical bubbles of lipids and proteins about 45–60 nanometers across. They are surrounded by a lipid monolayer. 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. Plastoglobuli also exhibit a greater size variation under these conditions. They are also common in etioplasts, but decrease in number as the etioplasts mature into chloroplasts.

context: 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. In normal green chloroplasts, the vast majority of plastoglobuli occur singularly, attached directly to their parent thylakoid. In old or stressed chloroplasts, plastoglobuli tend to occur in linked groups or chains, still always anchored to a thylakoid.

context: The chloroplasts of some hornworts and algae contain structures called pyrenoids. They are not found in higher plants. Pyrenoids are roughly spherical and highly refractive bodies which are a site of starch accumulation in plants that contain them. They consist of a matrix opaque to electrons, surrounded by two hemispherical starch plates. The starch is accumulated as the pyrenoids mature. In algae with carbon concentrating mechanisms, the enzyme rubisco is found in the pyrenoids. Starch can also accumulate around the pyrenoids when CO2 is scarce. Pyrenoids can divide to form new pyrenoids, or be produced "de novo".

context: In the helical thylakoid model, grana consist of a stack of flattened circular granal thylakoids that resemble pancakes. Each granum can contain anywhere from two to a hundred thylakoids, though grana with 10–20 thylakoids are most common. Wrapped around the grana are helicoid stromal thylakoids, also known as frets or lamellar thylakoids. The helices ascend at an angle of 20–25°, connecting to each granal thylakoid at a bridge-like slit junction. The helicoids may extend as large sheets that link multiple grana, or narrow to tube-like bridges between grana. 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.

context: Embedded in the thylakoid membranes are important protein complexes which carry out the light reactions of photosynthesis. Photosystem II and photosystem I contain light-harvesting complexes with chlorophyll and carotenoids that absorb light energy and use it to energize electrons. Molecules in the thylakoid membrane use the energized electrons to pump hydrogen ions into the thylakoid space, decreasing the pH and turning it acidic. ATP synthase is a large protein complex that harnesses the concentration gradient of the hydrogen ions in the thylakoid space to generate ATP energy as the hydrogen ions flow back out into the stroma—much like a dam turbine.

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

context: In addition to chlorophylls, another group of yellow–orange pigments called carotenoids are also found in the photosystems. There are about thirty photosynthetic carotenoids. 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. β-carotene is a bright red-orange carotenoid found in nearly all chloroplasts, like chlorophyll a. Xanthophylls, especially the orange-red zeaxanthin, are also common. Many other forms of carotenoids exist that are only found in certain groups of chloroplasts.

context: Phycobilins are a third group of pigments found in cyanobacteria, and glaucophyte, red algal, and cryptophyte chloroplasts. Phycobilins come in all colors, though phycoerytherin is one of the pigments that makes many red algae red. Phycobilins often organize into relatively large protein complexes about 40 nanometers across called phycobilisomes. Like photosystem I and ATP synthase, phycobilisomes jut into the stroma, preventing thylakoid stacking in red algal chloroplasts. Cryptophyte chloroplasts and some cyanobacteria don't have their phycobilin pigments organized into phycobilisomes, and keep them in their thylakoid space instead.

context: To fix carbon dioxide into sugar molecules in the process of photosynthesis, chloroplasts use an enzyme called rubisco. 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. This has the end result of ATP energy being wasted and CO2 being released, all with no sugar being produced. 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.

context: As a result, chloroplasts in C4 mesophyll cells and bundle sheath cells are specialized for each stage of photosynthesis. In mesophyll cells, chloroplasts are specialized for the light reactions, so they lack rubisco, and have normal grana and thylakoids, which they use to make ATP and NADPH, as well as oxygen. They store CO2 in a four-carbon compound, which is why the process is called C4 photosynthesis. The four-carbon compound is then transported to the bundle sheath chloroplasts, where it drops off CO2 and returns to the mesophyll. Bundle sheath chloroplasts do not carry out the light reactions, preventing oxygen from building up in them and disrupting rubisco activity. 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. They lack photosystem II, and only have photosystem I—the only protein complex needed for cyclic electron flow. Because the job of bundle sheath chloroplasts is to carry out the Calvin cycle and make sugar, they often contain large starch grains.

context: Not all cells in a multicellular plant contain chloroplasts. 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. The plant cells which contain chloroplasts are usually parenchyma cells, though chloroplasts can also be found in collenchyma tissue. A plant cell which contains chloroplasts is known as a chlorenchyma cell. A typical chlorenchyma cell of a land plant contains about 10 to 100 chloroplasts.

context: In some plants such as cacti, chloroplasts are found in the stems, though in most plants, chloroplasts are concentrated in the leaves. One square millimeter of leaf tissue can contain half a million chloroplasts. Within a leaf, chloroplasts are mainly found in the mesophyll layers of a leaf, and the guard cells of stomata. Palisade mesophyll cells can contain 30–70 chloroplasts per cell, while stomatal guard cells contain only around 8–15 per cell, as well as much less chlorophyll. Chloroplasts can also be found in the bundle sheath cells of a leaf, especially in C4 plants, which carry out the Calvin cycle in their bundle sheath cells. They are often absent from the epidermis of a leaf.

context: The chloroplasts of plant and algal cells can orient themselves to best suit the available light. In low-light conditions, they will spread out in a sheet—maximizing the surface area to absorb light. Under intense light, they will seek shelter by aligning in vertical columns along the plant cell's cell wall or turning sideways so that light strikes them edge-on. This reduces exposure and protects them from photooxidative damage. 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 movement is considered one of the most closely regulated stimulus-response systems that can be found in plants. Mitochondria have also been observed to follow chloroplasts as they move.

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

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

context: One of the main functions of the chloroplast is its role in photosynthesis, the process by which light is transformed into chemical energy, to subsequently produce food in the form of sugars. Water (H2O) and carbon dioxide (CO2) are used in photosynthesis, and sugar and oxygen (O2) is made, using light energy. Photosynthesis is divided into two stages—the light reactions, where water is split to produce oxygen, and the dark reactions, or Calvin cycle, which builds sugar molecules from carbon dioxide. The two phases are linked by the energy carriers adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADP+).

context: Like mitochondria, chloroplasts use the potential energy stored in an H+, or hydrogen ion gradient to generate ATP energy. The two photosystems capture light energy to energize electrons taken from water, and release them down an electron transport chain. The 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. The hydrogen ions in the thylakoid space then diffuse back down their concentration gradient, flowing back out into the stroma through ATP synthase. ATP synthase uses the energy from the flowing hydrogen ions to phosphorylate adenosine diphosphate into adenosine triphosphate, or ATP. Because chloroplast ATP synthase projects out into the stroma, the ATP is synthesized there, in position to be used in the dark reactions.

context: While photosystem II photolyzes water to obtain and energize new electrons, photosystem I simply reenergizes depleted electrons at the end of an electron transport chain. Normally, the reenergized electrons are taken by NADP+, 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. This is termed cyclic photophosphorylation because the electrons are recycled. Cyclic photophosphorylation is common in C4 plants, which need more ATP than NADPH.

context: The Calvin cycle starts by using the enzyme Rubisco to fix CO2 into five-carbon Ribulose bisphosphate (RuBP) molecules. The result is unstable six-carbon molecules that immediately break down into three-carbon molecules called 3-phosphoglyceric acid, or 3-PGA. The ATP and NADPH made in the light reactions is used to convert the 3-PGA into glyceraldehyde-3-phosphate, or G3P sugar molecules. Most of the G3P molecules are recycled back into RuBP using energy from more ATP, but one out of every six produced leaves the cycle—the end product of the dark reactions.

context: Alternatively, glucose monomers in the chloroplast can be linked together to make starch, which accumulates into the starch grains found in the chloroplast. Under conditions such as high atmospheric CO2 concentrations, these starch grains may grow very large, distorting the grana and thylakoids. The starch granules displace the thylakoids, but leave them intact. 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). This depletes a plant's free phosphate supply, which indirectly stimulates chloroplast starch synthesis. 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.

context: Photorespiration can occur when the oxygen concentration is too high. Rubisco cannot distinguish between oxygen and carbon dioxide very well, so it can accidentally add O2 instead of CO2 to RuBP. This process reduces the efficiency of photosynthesis—it consumes ATP and oxygen, releases CO2, and produces no sugar. It can waste up to half the carbon fixed by the Calvin cycle. Several mechanisms have evolved in different lineages that raise the carbon dioxide concentration relative to oxygen within the chloroplast, increasing the efficiency of photosynthesis. These mechanisms are called carbon dioxide concentrating mechanisms, or CCMs. These include Crassulacean acid metabolism, C4 carbon fixation, and pyrenoids. Chloroplasts in C4 plants are notable as they exhibit a distinct chloroplast dimorphism.

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

context: Chloroplasts are a special type of a plant cell organelle called a plastid, though the two terms are sometimes used interchangeably. There are many other types of plastids, which carry out various functions. All chloroplasts in a plant are descended from undifferentiated proplastids found in the zygote, or fertilized egg. Proplastids are commonly found in an adult plant's apical meristems. Chloroplasts do not normally develop from proplastids in root tip meristems—instead, the formation of starch-storing amyloplasts is more common.

context: If angiosperm shoots are not exposed to the required light for chloroplast formation, proplastids may develop into an etioplast stage before becoming chloroplasts. An etioplast is a plastid that lacks chlorophyll, and has inner membrane invaginations that form a lattice of tubes in their stroma, called a prolamellar body. While etioplasts lack chlorophyll, they have a yellow chlorophyll precursor stocked. Within a few minutes of light exposure, the prolamellar body begins to reorganize into stacks of thylakoids, and chlorophyll starts to be produced. This process, where the etioplast becomes a chloroplast, takes several hours. Gymnosperms do not require light to form chloroplasts.

context: Plastid differentiation is not permanent, in fact many interconversions are possible. Chloroplasts may be converted to chromoplasts, which are pigment-filled plastids responsible for the bright colors seen in flowers and ripe fruit. Starch storing amyloplasts can also be converted to chromoplasts, and it is possible for proplastids to develop straight into chromoplasts. Chromoplasts and amyloplasts can also become chloroplasts, like what happens when a carrot or a potato is illuminated. If a plant is injured, or something else causes a plant cell to revert to a meristematic state, chloroplasts and other plastids can turn back into proplastids. Chloroplast, amyloplast, chromoplast, proplast, etc., are not absolute states—intermediate forms are common.

context: 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. The Min system manages the placement of the Z-ring, ensuring that the chloroplast is cleaved more or less evenly. The protein MinD prevents FtsZ from linking up and forming filaments. Another protein ARC3 may also be involved, but it is not very well understood. These proteins are active at the poles of the chloroplast, preventing Z-ring formation there, but near the center of the chloroplast, MinE inhibits them, allowing the Z-ring to form.

context: Next, the two plastid-dividing rings, or PD rings form. The inner plastid-dividing ring is located in the inner side of the chloroplast's inner membrane, and is formed first. The outer plastid-dividing ring is found wrapped around the outer chloroplast membrane. It consists of filaments about 5 nanometers across, arranged in rows 6.4 nanometers apart, and shrinks to squeeze the chloroplast. This is when chloroplast constriction begins.
In a few species like Cyanidioschyzon merolæ, chloroplasts have a third plastid-dividing ring located in the chloroplast's intermembrane space.

context: Light has been shown to be a requirement for chloroplast division. 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. Spinach leaves grown under green light have been observed to contain many large dumbbell-shaped chloroplasts. Exposure to white light can stimulate these chloroplasts to divide and reduce the population of dumbbell-shaped chloroplasts.

context: Recently, chloroplasts have caught attention by developers of genetically modified crops. Since, in most flowering plants, chloroplasts are not inherited from the male parent, transgenes in these plastids cannot be disseminated by pollen. This makes plastid transformation a valuable tool for the creation and cultivation of genetically modified plants that are biologically contained, thus posing significantly lower environmental risks. This biological containment strategy is therefore suitable for establishing the coexistence of conventional and organic agriculture. While the reliability of this mechanism has not yet been studied for all relevant crop species, recent results in tobacco plants are promising, showing a failed containment rate of transplastomic plants at 3 in 1,000,000.