Nucleohyaloplasm
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Nucleohyaloplasm is the cytosol within the nucleus, without the microfilaments and the microtubules. This liquid part contains enzymes and intermediate metabolites. Many substances such as nucleotides (necessary for purposes such as the replication of DNA and production of mRNA) and enzymes (which direct activities that take place in the nucleus) are dissolved in the nucleohyaloplasm.
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.[1]
Small particles
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 Da.[2] This mixture of small molecules is extraordinarily complex, as the variety of molecules that are involved in metabolism (the metabolites) 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.[3] Estimates of the number of metabolites in single cells such as E. coli and baker's yeast predict that under 1,000 are made.[4][5]
Miscible molecules such as O2, CO2 and NH3 occur in any bodily fluid. These molecules are mixed into the liquid, but not turned into ions.
Relative to the outside of a cell, the concentration of Ca2+ is low.[6] In addition to sodium and potassium ions the nucleohyaloplasm also contains Mg2+[7]. 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.[7] The remaining typical ions found in any cytosol include chloride and bicarbonate.[8]
Intranuclear posttranscriptional modifications such as mRNA editing convert cytidine to uridine within some mRNA.[9] This conversion by enzyme EC 3.5.4.5 though infrequent releases ammonia[10] or produces ammonium in solution. This enzyme is Zn2+ 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 that performs a nucleophilic attack on the substrate.[11]
Cells also maintain an intracellular iron ion (Fe2+) homeostasis.[12] Cu2+ serves as a cofactor.[13]
When a nucleotide is incorporated into a growing DNA or RNA strand by a polymerase, pyrophosphate (PPi) is released. The pyrophosphate anion has the structure P2O74−, and is an acid anhydride of phosphate. It is unstable in aqueous solution and rapidly hydrolyzes into inorganic phosphate HPO42− (orthophosphate).
The average mass range for amino acids: 75 - 204 Da. By comparison a water molecule is 18 Da. Nucleotides range in size from 176 Da (OMP) to 523 Da (GTP). 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.
Large particles
Larger particles are also able to pass through the large diameter of a nuclear pore but at almost negligible rates.[14] However, the nucleohyaloplasm does contain large amounts of macromolecules, which can alter how molecules behave, through macromolecular crowding. Since some of these macromolecules have less volume to move in, their effective concentration is increased. This crowding effect can produce large changes in both the rates and chemical equilibrium for reactions in the cytosol.[15] It is particularly important in its ability to alter dissociation constants by favoring the association of macromolecules, such as when multiple proteins come together to form protein complexes, or when DNA-binding proteins bind to their targets in the genome.[16]
The lamins of mammalian nuclei are polypeptides of 60-80 kDa: A (70 kDa), B (68 kDa), and C (60 kDa).[17] A- and B-type lamins, which form separate, but interacting, stable meshworks in the lamina, have different mobilities.[18]
Euchromatin is the less compact DNA form, and contains genes that are frequently expressed by the cell.[19] Active genes, which are generally found in the euchromatic region of the chromosome, tend to be located towards the chromosome's territory boundary.[20]
Heterochromatin is usually localized to the periphery of the nucleus along the nuclear envelope. It mainly consists of genetically inactive satellite sequences,[21] and many genes are repressed to various extents, although some cannot be expressed in euchromatin at all.[22]
Structures
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[23][24] and nuclear lamina are found throughout the inside of the nucleus.
Lamins within the nucleohyaloplasm form another regular structure the nucleoplasmic veil[25]. The veil is excluded from the nucleolus and is present during interphase.[26] The lamin structures that make up the veil bind chromatin and disrupting their structure inhibits transcription of protein-coding genes.[27] Changes also occur in the lamina mesh size.[18]
Besides the nucleolus, the nucleus contains a number of other non-membrane delineated bodies. These include Cajal bodies, Gemini of coiled bodies, polymorphic interphase karyosomal association (PIKA), promyelocytic leukaemia (PML) bodies, paraspeckles 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.[28]
References
- ↑ Roos A, Boron WF (1981). "Intracellular pH". Physiol. Rev. 61 (2): 296–434. PMID 7012859. Unknown parameter
|month=ignored (help) - ↑ Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB (2004). "Metabolomics by numbers: acquiring and understanding global metabolite data" (PDF). Trends Biotechnol. 22 (5): 245–52. doi:10.1016/j.tibtech.2004.03.007. PMID 15109811. Unknown parameter
|month=ignored (help) - ↑ Weckwerth W (2003). "Metabolomics in systems biology". Annu Rev Plant Biol. 54: 669–89. doi:10.1146/annurev.arplant.54.031902.135014. PMID 14503007.
- ↑ Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biol. 4 (9): R54. doi:10.1186/gb-2003-4-9-r54. PMC 193654. PMID 12952533.
- ↑ Förster J, Famili I, Fu P, Palsson BØ, Nielsen J (2003). "Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network". Genome Res. 13 (2): 244–53. doi:10.1101/gr.234503. PMC 420374. PMID 12566402. Unknown parameter
|month=ignored (help) - ↑ Berridge MJ (1997). "Elementary and global aspects of calcium signalling". J. Physiol. (Lond.). 499 ( Pt 2): 291–306. PMC 1159305. PMID 9080360. Unknown parameter
|month=ignored (help) - ↑ 7.0 7.1 Langelier MF, Baali D, Trinh V, Greenblatt J, Archambault J, Coulombe B (2005). "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". Nucleic Acids Res. 33 (8): 2629–39. PMID 15886393. Unknown parameter
|month=ignored (help) - ↑ Lodish, Harvey F. (1999). Molecular cell biology. New York: Scientific American Books. ISBN 0-7167-3136-3. OCLC 174431482.
- ↑ Ashkenas J (1997). "Gene regulation by mRNA editing". Am J Hum Genet. 60 (2): 278–83. PMID 9012400. Unknown parameter
|month=ignored (help) - ↑ "NiceZyme View of ENZYME: EC 3.5.4.5".
- ↑ "NCBI Conserved Domains: cytidine_deaminase-like Super-family".
- ↑ Mukhopadhyay CK, Attieh ZK, Fox PL (1998). "Role of ceruloplasmin in cellular iron uptake". Science. 279 (5351): 714–7. PMID 9445478. Unknown parameter
|month=ignored (help) - ↑ 1.16.3.1 "NiceZyme View of ENZYME: EC 1.16.3.1" Check
|url=value (help). - ↑ Campbell, Neil A. (1987). Biology. p. 795. ISBN 0-8053-1840-2.
- ↑ Ellis RJ (2001). "Macromolecular crowding: obvious but underappreciated". Trends Biochem. Sci. 26 (10): 597–604. doi:10.1016/S0968-0004(01)01938-7. PMID 11590012. Unknown parameter
|month=ignored (help) - ↑ Zhou HX, Rivas G, Minton AP (2008). "Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences". Annu Rev Biophys. 37: 375–97. doi:10.1146/annurev.biophys.37.032807.125817. PMID 18573087.
- ↑ Klaus Urich (1994). Comparative Animal Biochemistry. Springer. p. 359. ISBN 3540574204, 9783540574200 Check
|isbn=value: invalid character (help). - ↑ 18.0 18.1 Shimi T, Pfleghaar K, Kojima S, Pack CG, Solovei I, Goldman AE, Adam SA, Shumaker DK, Kinjo M, Cremer T, Goldman RD (2008). "The A- and B-type nuclear lamin networks: microdomains involved in chromatin organization and transcription". Genes Dev. 22 (24): 3409–21. PMID 19141474. Unknown parameter
|month=ignored (help) - ↑ Ehrenhofer-Murray A (2004). "Chromatin dynamics at DNA replication, transcription and repair". Eur J Biochem. 271 (12): 2335–2349. doi:10.1111/j.1432-1033.2004.04162.x. PMID 15182349.
- ↑ Kurz A , Lampel S, Nickolenko JE, Bradl J, Benner A, Zirbel RM, Cremer T, Lichter P (1996). "Active and inactive genes localize preferentially in the periphery of chromosome territories". J of Cell Biol. The Rockefeller University Press. 135: 1195–1205. doi:10.1083/jcb.135.5.1195. PMID 8947544.
- ↑ Lohe, A.R.; et al. (1993). "Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster". Genetics. 134 (4): 1149–1174. ISSN 0016-6731. PMID 8375654.
- ↑ Lu, B.Y.; et al. (2000). "Heterochromatin protein 1 is required for the normal expression of two heterochromatin genes in Drosophila". Genetics. 155 (2): 699–708. ISSN 0016-6731. PMID 10835392.
- ↑ Nickerson J (2001). "Experimental observations of a nuclear matrix". J. Cell. Sci. 114 (Pt 3): 463–74. PMID 11171316. Unknown parameter
|month=ignored (help) - ↑ Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KF (2006). "Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana". PLoS Comput. Biol. 2 (3): e21. doi:10.1371/journal.pcbi.0020021. PMC 1420657. PMID 16604187. Unknown parameter
|month=ignored (help) - ↑ Goldman R, Gruenbaum Y, Moir R, Shumaker D, Spann T (2002). "Nuclear lamins: building blocks of nuclear architecture". Genes Dev. 16 (5): 533–547. doi:10.1101/gad.960502. PMID 11877373.
- ↑ Moir RD, Yoona M, Khuona S, Goldman RD. (2000). "Nuclear Lamins A and B1: Different Pathways of Assembly during Nuclear Envelope Formation in Living Cells". Journal of Cell Biology. 151 (6): 1155–1168. doi:10.1083/jcb.151.6.1155. PMID 11121432.
- ↑ Spann TP, Goldman AE, Wang C, Huang S, Goldman RD (2002). "Alteration of nuclear lamin organization inhibits RNA polymerase II–dependent transcription". J of Cell Biol. 156 (4): 603–608. doi:10.1083/jcb.200112047. PMID 11854306.
- ↑ Dundr M, Misteli T (2001). "Functional architecture in the cell nucleus". Biochem J. (356): 297–310. doi:10.1146/annurev.cellbio.20.010403.103738. PMID 11368755.