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Introduction

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 a single cell of E. coli or 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

Structures

Human nucleohyaloplasm

  1. ↑ Roos A, Boron WF (1981). "Intracellular pH". Physiol. Rev. 61 (2): 296–434. PMID 7012859. Unknown parameter |month= ignored (help)
  2. ↑ 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)
  3. ↑ Weckwerth W (2003). "Metabolomics in systems biology". Annu Rev Plant Biol. 54: 669–89. doi:10.1146/annurev.arplant.54.031902.135014. PMID 14503007.
  4. ↑ 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.
  5. ↑ 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)
  6. ↑ 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. ↑ 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)
  8. ↑ Lodish, Harvey F. (1999). Molecular cell biology. New York: Scientific American Books. ISBN 0-7167-3136-3. OCLC 174431482.
  9. ↑ Ashkenas J (1997). "Gene regulation by mRNA editing". Am J Hum Genet. 60 (2): 278–83. PMID 9012400. Unknown parameter |month= ignored (help)
  10. ↑ "NiceZyme View of ENZYME: EC 3.5.4.5".
  11. ↑ "NCBI Conserved Domains: cytidine_deaminase-like Super-family".
  12. ↑ 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)
  13. ↑ 1.16.3.1 "NiceZyme View of ENZYME: EC 1.16.3.1" Check |url= value (help).
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