Editing Chloroplast (section)

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

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

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

==== Thylakoid structure ====

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

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

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

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

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

====Thylakoid composition====

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

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

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

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