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| I have transferred all your edits to "Nucleohyaloplasm" page. Current page is the most updated one and contains only your edits. Would you please continue to edit there? Many thanks for your contrubitions. Cafer Zorkun | | I have transferred all your edits to "Nucleohyaloplasm" page. Current page is the most updated one and contains only your edits. Would you please continue to edit there? Many thanks for your contributions. Cafer Zorkun |
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| =Introduction=
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| '''Nucleohyaloplasm''' is the [[cytosol]] within the [[nucleus]], without the [[microfilaments]] and the [[microtubules]]. This liquid part contains [[enzyme]]s and intermediate [[metabolite]]s. Many substances such as [[nucleotide]]s (necessary for purposes such as the [[DNA replication|replication of DNA]] and production of [[Messenger RNA|mRNA]]) and enzymes (which direct activities that take place in the nucleus) are dissolved in the nucleohyaloplasm.
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| As a cytosol, it consists mostly of [[water]], dissolved ions, small molecules, and large water-soluble molecules (such as [[protein]]). It contains about 20% to 30% protein. It has a high concentration of K⁺ ions and a low concentration of Na⁺ ions. Normal human cytosolic [[pH]] ranges between 7.3 - 7.5, depending on the [[cell type]] involved.<ref name=Roos>{{cite journal |author=Roos A, Boron WF |title=Intracellular pH |journal=Physiol. Rev. |volume=61 |issue=2 |pages=296–434 |year=1981 |month=April |pmid=7012859 |url=http://physrev.physiology.org/cgi/pmidlookup?view=long&pmid=7012859}}</ref>
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| =Small particles=
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| Small particles (< 30 kDa) are able to pass through the [[nuclear pore]] complex by [[passive transport]]. The majority of the non-protein molecules have a [[molecular mass]] of less than 300 [[Atomic mass unit|Da]].<ref name=Goodacre>{{cite journal |author=Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB |title=Metabolomics by numbers: acquiring and understanding global metabolite data |journal=Trends Biotechnol. |volume=22 |issue=5 |pages=245–52 |year=2004 |month=May |pmid=15109811 |doi=10.1016/j.tibtech.2004.03.007 |url=http://personalpages.manchester.ac.uk/staff/roy.goodacre/learning/metabprof/Goodacre-TibTech2004.pdf|format=PDF}}</ref> This mixture of small molecules is extraordinarily complex, as the variety of molecules that are involved in metabolism (the [[metabolite]]s) is immense. For example up to 200,000 different small molecules might be made in plants, although not all these will be present in the same species, or in a single cell.<ref name=Weckwerth>{{cite journal |author=Weckwerth W |title=Metabolomics in systems biology |journal=Annu Rev Plant Biol |volume=54 |issue= |pages=669–89 |year=2003 |pmid=14503007 |doi=10.1146/annurev.arplant.54.031902.135014}}</ref> Estimates of the number of metabolites in a single cell of ''[[Escherichia coli|E. coli]]'' or [[Saccharomyces cerevisiae|baker's yeast]] predict that under 1,000 are made.<ref name=Reed>{{cite journal |author=Reed JL, Vo TD, Schilling CH, Palsson BO |title=An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) |journal=Genome Biol. |volume=4 |issue=9 |pages=R54 |year=2003 |pmid=12952533 |pmc=193654 |doi=10.1186/gb-2003-4-9-r54 |url=http://genomebiology.com/1465-6906/4/R54}}</ref><ref name=Förster>{{cite journal |author=Förster J, Famili I, Fu P, Palsson BØ, Nielsen J |title=Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network |journal=Genome Res. |volume=13 |issue=2 |pages=244–53 |year=2003 |month=February |pmid=12566402 |pmc=420374 |doi=10.1101/gr.234503 |url=http://www.genome.org/cgi/pmidlookup?view=long&pmid=12566402}}</ref>
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| ==[[Miscibility|Miscible]] molecules==
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| Miscible molecules such as O<sub>2</sub>, CO<sub>2</sub> and NH<sub>3</sub> occur in any bodily fluid. These molecules are mixed into the liquid, but not turned into ions.
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| ==Inorganic ions==
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| Relative to the outside of a cell, the concentration of Ca<sup>2+</sup> is low.<ref name=Berridge>{{cite journal |author=Berridge MJ |title=Elementary and global aspects of calcium signalling |journal=J. Physiol. (Lond.) |volume=499 ( Pt 2) |issue= |pages=291–306 |year=1997 |month=March |pmid=9080360 |pmc=1159305 |url=http://www.jphysiol.org/cgi/pmidlookup?view=long&pmid=9080360}}</ref> In addition to sodium and potassium ions the nucleohyaloplasm also contains Mg<sup>2+</sup><ref name=Langelier>{{ cite journal |author=Langelier MF, Baali D, Trinh V, Greenblatt J, Archambault J, Coulombe B |title=The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II |journal=Nucleic Acids Res. |volume=33 |issue=8 |pages=2629-39 |year=2005 |month=May |pmid=15886393 }}</ref>. Some of these magnesium ions are associated with incoming ribonucleoside triphosphate (NTP) as they enter the catalytic center for transcription by RNA polymerase (RNAP) II.<ref name=Langelier/> The remaining typical ions found in any cytosol include chloride and bicarbonate.<ref name=Lodish>{{cite book |author=Lodish, Harvey F. |title=Molecular cell biology |publisher=Scientific American Books |location=New York |year=1999 |pages= |isbn=0-7167-3136-3 |oclc=174431482}}</ref>
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| Intranuclear posttranscriptional modifications such as m[[RNA editing]] convert cytidine to uridine within some mRNA.<ref name=Ashkenas>{{ cite journal |author=Ashkenas J |title=Gene regulation by mRNA editing |journal=Am J Hum Genet. |volume=60 |issue=2 | pages=278-83 |month=Feb |year=1997 |pmid=9012400 }}</ref> This conversion by enzyme EC 3.5.4.5 though infrequent releases ammonia<ref name=3.5.4.5>{{cite web | title = NiceZyme View of ENZYME: EC 3.5.4.5| url = http://www.expasy.org/cgi-bin/nicezyme.pl?3.5.4.5| accessdate = }}</ref> or produces ammonium in solution. This enzyme is Zn<sup>2+</sup> dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion (OH<sup>-</sup>) that performs a nucleophilic attack on the substrate.<ref name=c100269>{{cite web | title = NCBI Conserved Domains: cytidine_deaminase-like Super-family| url = http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=119679| accessdate = }}</ref>
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| Cells also maintain an intracellular iron ion (Fe<sup>2+</sup>) homeostasis.<ref name=Mukhopadhyay>{{ cite journal |author=Mukhopadhyay CK, Attieh ZK, Fox PL |title=Role of ceruloplasmin in cellular iron uptake |journal=Science. |volume=279 |issue=5351 |pages=714-7 |month=Jan |year=1998 |pmid=9445478 }}</ref> Cu<sup>2+</sup> serves as a cofactor.<ref name=1.16.3.1>{{cite web | title = NiceZyme View of ENZYME: EC 1.16.3.1 | url = http://www.expasy.org/cgi-bin/nicezyme.pl? 1.16.3.1 | accessdate = }}</ref>
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| When a nucleotide is incorporated into a growing [[DNA]] or [[RNA]] strand by a [[polymerase]], [[pyrophosphate]] (PP<sub>i</sub>) is released. The pyrophosphate anion has the structure P<sub>2</sub>O<sub>7</sub><sup>4−</sup>, and is an [[acid]] [[anhydride]] of [[phosphate]]. It is unstable in [[aqueous solution]] and rapidly [[hydrolysis|hydrolyze]]s into inorganic phosphate HPO<sub>4</sub><sup>2−</sup> (orthophosphate, P<sub>i</sub>).
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| ==Amino acids==
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| The average mass range for amino acids: 75 - 204 Da. By comparison a water molecule is 18 Da.
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| ==Nucleotides==
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| Nucleotides range in size from 176 Da (OMP) to 523 Da (GTP).
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| ==Cofactors==
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| The lateral speed of biological molecules in passive diffusion in water is on the order of 500 - 50 nm/sec. But in cytosol such as the nucleohyaloplasm: ~120 - 10 nm/sec due to crowding and collisions with large molecules.
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| =Large particles=
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| Larger particles are also able to pass through the large diameter of a nuclear pore but at almost negligible rates.<ref name=Campbell>{{cite book |last=Campbell |first=Neil A. |title=Biology |year=1987 |isbn=0-8053-1840-2 |pages=795}}</ref> However, the nucleohyaloplasm does contain large amounts of [[macromolecule]]s, which can alter how molecules behave, through [[macromolecular crowding]]. Since some of these macromolecules have less volume to move in, their [[activity (chemistry)|effective concentration]] is increased. This crowding effect can produce large changes in both the [[reaction rate|rates]] and [[chemical equilibrium]] for reactions in the nucleohyaloplasm.<ref name=Ellis>{{cite journal |author=Ellis RJ |title=Macromolecular crowding: obvious but underappreciated |journal=Trends Biochem. Sci. |volume=26 |issue=10 |pages=597–604 |year=2001 |month=October |pmid=11590012 |doi=10.1016/S0968-0004(01)01938-7}}</ref> It is particularly important in its ability to alter [[dissociation constant]]s by favoring the association of macromolecules, such as when multiple proteins come together to form [[protein complex]]es, or when [[DNA-binding protein]]s bind to their targets in the [[genome]].<ref name=Zhou>{{cite journal |author=Zhou HX, Rivas G, Minton AP |title=Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences |journal=Annu Rev Biophys |volume=37 |issue= |pages=375–97 |year=2008 |pmid=18573087 |doi=10.1146/annurev.biophys.37.032807.125817}}</ref>
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| The lamins of mammalian nuclei are polypeptides of 60-80 kDa: A (70 kDa), B (68 kDa), and C (60 kDa).<ref name=Urich>{{ cite book | author=Klaus Urich |title=Comparative Animal Biochemistry |publisher=Springer |year=1994 |page=359 |isbn=3540574204, 9783540574200 }}</ref> A- and B-type lamins, which form separate, but interacting, stable meshworks in the lamina, have different mobilities.<ref name=Shimi>{{ cite journal |author=Shimi T, Pfleghaar K, Kojima S, Pack CG, Solovei I, Goldman AE, Adam SA, Shumaker DK, Kinjo M, Cremer T, Goldman RD |title=The A- and B-type nuclear lamin networks: microdomains involved in chromatin organization and transcription |journal=Genes Dev. |volume=22 |issue=24 |pages=3409-21 |month=Dec |year=2008 |pmid=19141474 }}</ref>
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| ==Chromatin==
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| [[Euchromatin]] is the less compact DNA form, and contains genes that are frequently [[gene expression|expressed]] by the cell.<ref name=Ehrenhofer-Murray>{{cite journal | author = Ehrenhofer-Murray A | title = Chromatin dynamics at DNA replication, transcription and repair | journal = Eur J Biochem | volume = 271 | issue = 12 | pages = 2335–2349 | year = 2004 | pmid = 15182349 | doi = 10.1111/j.1432-1033.2004.04162.x }}</ref> Active genes, which are generally found in the euchromatic region of the chromosome, tend to be located towards the chromosome's territory boundary.<ref name=Kurz>{{cite journal |author= Kurz A , Lampel S, Nickolenko JE, Bradl J, Benner A, Zirbel RM, Cremer T, Lichter P |title = Active and inactive genes localize preferentially in the periphery of chromosome territories |doi = 10.1083/jcb.135.5.1195 | journal = J of Cell Biol. |volume=135 |issue = | pages =1195–1205 | publisher = The Rockefeller University Press | year = 1996 | url = http://intl.jcb.org/cgi/content/abstract/135/5/1195 | pmid =8947544 }}</ref>
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| [[Heterochromatin]] is usually localized to the periphery of the nucleus along the nuclear envelope. It mainly consists of genetically inactive [[satellite DNA|satellite sequences]],<ref name=Lohe>{{cite journal| author = Lohe, A.R., ''et al.''| title = Mapping simple repeated DNA sequences in heterochromatin of ''Drosophila melanogaster''| year = 1993| journal = [[Genetics (journal)|Genetics]]| volume = 134| issue = 4| pages = 1149–1174| issn = 0016-6731| url = http://www.genetics.org/cgi/content/full/134/4/1149| pmid = 8375654}}</ref> and many genes are repressed to various extents, although some cannot be expressed in euchromatin at all.<ref name=Lu>{{cite journal| author = Lu, B.Y., ''et al.''| year = 2000| title = Heterochromatin protein 1 is required for the normal expression of two heterochromatin genes in Drosophila| journal = [[Genetics (journal)|Genetics]]| volume = 155| issue = 2| pages = 699–708| url = http://www.genetics.org/cgi/content/full/155/2/699| issn = 0016-6731| pmid = 10835392}}</ref>
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| ==Nucleolus==
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| The nucleolus is roughly spherical, and is surrounded by the euchromatin. No membrane separates the nucleolus from the nucleohyaloplasm. Nucleoli carry out the production and maturation of ribosomes. Large numbers of ribosomes are found inside.
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| =Structures=
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| Of the structures local to the nucleohyaloplasm, some serve to confine it such as the inner membrane of the [[nuclear envelope]]. While others are completely suspended within it, for example, the [[nucleolus]]. Still others such as the [[nuclear matrix]]<ref name=Nickerson>{{cite journal |author=Nickerson J |title=Experimental observations of a nuclear matrix |journal=J. Cell. Sci. |volume=114 |issue=Pt 3 |pages=463–74 |year=2001 |month=February |pmid=11171316 |url=http://jcs.biologists.org/cgi/content/abstract/114/3/463}}</ref><ref name=Tetko>{{cite journal |author=Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KF |title=Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana |journal=PLoS Comput. Biol. |volume=2 |issue=3 |pages=e21 |year=2006 |month=March |pmid=16604187 |pmc=1420657 |doi=10.1371/journal.pcbi.0020021 }}</ref> and [[nuclear lamina]] are found throughout the inside of the nucleus.
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| Lamins within the nucleohyaloplasm form another regular structure the nucleoplasmic veil<ref name=Goldman>{{cite journal | author = Goldman R, Gruenbaum Y, Moir R, Shumaker D, Spann T | title = Nuclear lamins: building blocks of nuclear architecture | doi = 10.1101/gad.960502 | url=http://www.genesdev.org/cgi/content/full/16/5/533 | journal = Genes Dev | volume = 16 | issue = 5 | pages = 533–547 | year = 2002 | pmid = 11877373}}</ref>. The veil is excluded from the [[nucleolus]] and is present during [[interphase]].<ref name="Moir">{{cite journal | author = Moir RD, Yoona M, Khuona S, Goldman RD. | title = Nuclear Lamins A and B1: Different Pathways of Assembly during Nuclear Envelope Formation in Living Cells | journal = Journal of Cell Biology | year = 2000 | volume = 151 | issue = 6 | pages = 1155–1168 | pmid = 11121432 | doi = 10.1083/jcb.151.6.1155 }}</ref> The lamin structures that make up the veil bind [[chromatin]] and disrupting their structure inhibits transcription of protein-coding genes.<ref name=Spann>{{cite journal | author= Spann TP, Goldman AE, Wang C, Huang S, Goldman RD | journal = J of Cell Biol. | title = Alteration of nuclear lamin organization inhibits RNA polymerase II–dependent transcription | year = 2002 | volume = 156 | issue = 4 | pages = 603–608 | pmid = 11854306 | doi = 10.1083/jcb.200112047 }}</ref> Changes also occur in the lamina mesh size.<ref name=Shimi/>
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| Besides the nucleolus, the [[Cell nucleus|nucleus]] contains a number of other non-membrane delineated bodies. These include [[Cajal body|Cajal bodies]], Gemini of coiled bodies, polymorphic interphase karyosomal association (PIKA), promyelocytic leukaemia (PML) bodies, [[paraspeckle]]s and splicing speckles. Although little is known about a number of these domains, they are significant in that they show that the nucleohyaloplasm is not a uniform mixture, but rather contains organized functional subdomains.<ref name=Dundr>{{cite journal |author= Dundr M, Misteli T |title = Functional architecture in the cell nucleus | journal = Biochem J. | issue = 356 | pages = 297–310 | year = 2001 | pmid = 11368755 | doi = 10.1146/annurev.cellbio.20.010403.103738}}</ref>
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| =Human nucleohyaloplasm=
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| =References=
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| {{reflist}}
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