Editing Cytosol (section)

==Organization==
Although the components of the cytosol are not separated into regions by cell membranes, these components do not always mix randomly and several levels of organization can localize specific molecules to defined sites within the cytosol.<ref>{{cite journal |vauthors=Norris V, den Blaauwen T, Cabin-Flaman A |title=Functional Taxonomy of Bacterial Hyperstructures |journal=Microbiol. Mol. Biol. Rev. |volume=71 |issue=1 |pages=230–53 |date=March 2007 |pmid=17347523 |pmc=1847379 |doi=10.1128/MMBR.00035-06 }}</ref>

===Concentration gradients===
Although small molecules [[diffusion|diffuse]] rapidly in the cytosol, concentration gradients can still be produced within this compartment. A well-studied example of these are the "calcium sparks" that are produced for a short period in the region around an open [[calcium channel]].<ref>{{cite journal |vauthors=Wang SQ, Wei C, Zhao G |title=Imaging microdomain Ca2+ in muscle cells |journal=Circ. Res. |volume=94 |issue=8 |pages=1011–22 |date=April 2004 |pmid=15117829 |doi=10.1161/01.RES.0000125883.68447.A1 |doi-access=free }}</ref> These are about 2&nbsp;[[micrometre]]s in diameter and last for only a few [[millisecond]]s, although several sparks can merge to form larger gradients, called "calcium waves".<ref>{{cite journal |author=Jaffe LF |title=Classes and mechanisms of calcium waves |journal=[[Cell Calcium]] |volume=14 |issue=10 |pages=736–45 |date=November 1993 |pmid=8131190 |doi=10.1016/0143-4160(93)90099-R}}</ref> Concentration gradients of other small molecules, such as [[oxygen]] and [[adenosine triphosphate]] may be produced in cells around clusters of [[mitochondrion|mitochondria]], although these are less well understood.<ref>{{cite journal | author=Aw, T.Y. |year=2000 |title=Intracellular compartmentation of organelles and gradients of low molecular weight species |journal=Int Rev Cytol |volume=192 |pages=223–53 |doi=10.1016/S0074-7696(08)60528-8 |pmid=10553281 | series=International Review of Cytology | isbn=978-0-12-364596-8}}</ref><ref>{{cite journal |vauthors=Weiss JN, Korge P |title=The cytoplasm: no longer a well-mixed bag |journal=Circ. Res. |volume=89 |issue=2 |pages=108–10 |date=20 July 2001|pmid=11463714 |doi=10.1161/res.89.2.108 |doi-access=free }}</ref>

===Protein complexes===
Proteins can associate to form [[protein complex]]es, these often contain a set of proteins with similar functions, such as enzymes that carry out several steps in the same metabolic pathway.<ref>{{cite journal |author=Srere PA |title=Complexes of sequential metabolic enzymes |journal=[[Annu. Rev. Biochem.]] |volume=56 |pages=89–124 |year=1987 |pmid=2441660 |doi=10.1146/annurev.bi.56.070187.000513}}</ref> This organization can allow [[substrate channeling]], which is when the product of one enzyme is passed directly to the next enzyme in a pathway without being released into solution.<ref>{{cite journal |author=Perham RN |title=Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions |journal=[[Annu. Rev. Biochem.]] |volume=69 |pages=961–1004 |year=2000 |pmid=10966480 |doi=10.1146/annurev.biochem.69.1.961}}</ref> Channeling can make a pathway more rapid and efficient than it would be if the enzymes were randomly distributed in the cytosol, and can also prevent the release of unstable reaction intermediates.<ref>{{cite journal |vauthors=Huang X, Holden HM, Raushel FM |s2cid=16722363 |title=Channeling of substrates and intermediates in enzyme-catalyzed reactions |journal=[[Annu. Rev. Biochem.]] |volume=70 |pages=149–80 |year=2001 |pmid=11395405 |doi=10.1146/annurev.biochem.70.1.149}}</ref> Although a wide variety of metabolic pathways involve enzymes that are tightly bound to each other, others may involve more loosely associated complexes that are very difficult to study outside the cell.<ref>{{cite journal |vauthors=Mowbray J, Moses V |title=The tentative identification in Escherichia coli of a multienzyme complex with glycolytic activity |journal=Eur. J. Biochem. |volume=66 |issue=1 |pages=25–36 |date=June 1976 |pmid=133800 |doi=10.1111/j.1432-1033.1976.tb10421.x}}</ref><ref>{{cite journal |vauthors=Srivastava DK, Bernhard SA |title=Metabolite transfer via enzyme-enzyme complexes |journal=Science |volume=234 |issue=4780 |pages=1081–6 |date=November 1986 |pmid=3775377 |doi=10.1126/science.3775377|bibcode=1986Sci...234.1081S }}</ref> Consequently, the importance of these complexes for metabolism in general remains unclear.

[[Image:Carboxysome.png|thumb|right|400px|[[Carboxysome]]s are protein-enclosed [[bacterial microcompartment]]s within the cytosol. On the left is an [[electron microscope]] image of carboxysomes, and on the right a model of their structure.]]

===Protein compartments===
Some protein complexes contain a large central cavity that is isolated from the remainder of the cytosol. One example of such an enclosed compartment is the [[proteasome]].<ref>{{cite journal |vauthors=Groll M, Clausen T |title=Molecular shredders: how proteasomes fulfill their role |journal=Curr. Opin. Struct. Biol. |volume=13 |issue=6 |pages=665–73 |date=December 2003 |pmid=14675543 |doi=10.1016/j.sbi.2003.10.005}}</ref> Here, a set of subunits form a hollow barrel containing [[protease]]s that degrade cytosolic proteins. Since these would be damaging if they mixed freely with the remainder of the cytosol, the barrel is capped by a set of regulatory proteins that recognize proteins with a signal directing them for degradation (a [[ubiquitin]] tag) and feed them into the proteolytic cavity.<ref>{{cite journal |vauthors=Nandi D, Tahiliani P, Kumar A, Chandu D |title=The ubiquitin-proteasome system |journal=J. Biosci. |volume=31 |issue=1 |pages=137–55 |date=March 2006 |pmid=16595883 |url=http://www.ias.ac.in/jbiosci/mar2006/137.pdf |archive-url=https://web.archive.org/web/20060702012628/http://www.ias.ac.in/jbiosci/mar2006/137.pdf |archive-date=2006-07-02 |url-status=live |doi=10.1007/BF02705243|s2cid=21603835 }}</ref>

Another large class of protein compartments are [[bacterial microcompartments]], which are made of a protein shell that encapsulates various enzymes.<ref name="Bobik-2007">{{cite journal|author=Bobik, T. A. |title=Bacterial Microcompartments |year=2007 |journal=Microbe |volume=2 |pages=25–31 |url=http://www.asm.org/ASM/files/ccLibraryFiles/Filename/000000002765/znw00107000025.pdf |publisher=Am Soc Microbiol |url-status=dead |archive-url=https://web.archive.org/web/20080802025916/http://www.asm.org/ASM/files/ccLibraryFiles/Filename/000000002765/znw00107000025.pdf |archive-date=2008-08-02 }}</ref> These compartments are typically about 100–200 [[nanometre]]s across and made of interlocking proteins.<ref>{{cite journal |vauthors=Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM |title=Protein-based organelles in bacteria: carboxysomes and related microcompartments |journal=Nat. Rev. Microbiol. |volume=6 |pages=681–691 |date=August 2008 |pmid=18679172 |doi=10.1038/nrmicro1913 |issue=9|s2cid=22666203 }}</ref> A well-understood example is the [[carboxysome]], which contains enzymes involved in [[carbon fixation]] such as [[RuBisCO]].<ref>{{cite journal |vauthors=Badger MR, Price GD |title=CO<sub>2</sub> concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution |journal=J. Exp. Bot. |volume=54 |issue=383 |pages=609–22 |date=February 2003 |pmid=12554704 |doi=10.1093/jxb/erg076 |doi-access=free }}</ref>

===Biomolecular condensates===
Non-membrane bound organelles can form as [[biomolecular condensate]]s, which arise by clustering, [[oligomerisation]], or [[polymerisation]] of [[macromolecules]] to drive [[colloid]]al phase separation of the cytoplasm or nucleus.

===Cytoskeletal sieving===
Although the [[cytoskeleton]] is not part of the cytosol, the presence of this network of filaments restricts the diffusion of large particles in the cell. For example, in several studies tracer particles larger than about 25&nbsp;[[nanometre]]s (about the size of a [[ribosome]])<ref>{{cite journal |author=Cate JH |title=Construction of low-resolution x-ray crystallographic electron density maps of the ribosome |journal=Methods |volume=25 |issue=3 |pages=303–8 |date=November 2001 |pmid=11860284 |doi=10.1006/meth.2001.1242|url=https://zenodo.org/record/1229926 }}</ref>  were excluded from parts of the cytosol around the edges of the cell and next to the nucleus.<ref>{{cite journal |vauthors=Provance DW, McDowall A, Marko M, Luby-Phelps K |title=Cytoarchitecture of size-excluding compartments in living cells |journal=J. Cell Sci. |volume=106 |issue=2 |pages=565–77 |date=1 October 1993|doi=10.1242/jcs.106.2.565 |pmid=7980739 |url=http://jcs.biologists.org/cgi/pmidlookup?view=long&pmid=7980739 }}</ref><ref>{{cite journal |vauthors=Luby-Phelps K, Castle PE, Taylor DL, Lanni F |title=Hindered diffusion of inert tracer particles in the cytoplasm of mouse 3T3 cells |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=84 |issue=14 |pages=4910–3 |date=July 1987 |pmid=3474634 |pmc=305216 |doi=10.1073/pnas.84.14.4910|bibcode=1987PNAS...84.4910L |doi-access=free }}</ref> These "excluding compartments" may contain a much denser meshwork of [[actin]] fibres than the remainder of the cytosol. These microdomains could influence the distribution of large structures such as [[ribosome]]s and organelles within the cytosol by excluding them from some areas and concentrating them in others.<ref>{{cite journal |author=Luby-Phelps K |title=Effect of cytoarchitecture on the transport and localization of protein synthetic machinery |journal=J. Cell. Biochem. |volume=52 |issue=2 |pages=140–7 |date=June 1993 |pmid=8366131 |doi=10.1002/jcb.240520205|s2cid=12063324 }}</ref>