Structural phosphate: Difference between revisions

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'''Editor-In-Chief:''' Henry A. Hoff
'''Editor-In-Chief:''' Henry A. Hoff


=Overview=
==Overview==


Inside a cell, phosphate may be structural to a nucleic acid such as [[DNA]] and [[RNA]] or [[phospholipid]]. Outside the cell, phosphate may be dissolved in [[extracellular fluid]] (ECF) or form structures such as bone and teeth. Bringing phosphate in any form into the cell from a phosphate containing structure or for such a structure and when needed transporting phosphate out of the cell perhaps to a structure is a necessary activity of [[phosphate homeostasis]] for that cell.
Inside a cell, phosphate may be structural to a nucleic acid such as [[DNA]] and [[RNA]] or [[phospholipid]]. Outside the cell, phosphate may be dissolved in [[extracellular fluid]] (ECF) or form structures such as bone and teeth. Bringing phosphate in any form into the cell from a phosphate containing structure or for such a structure and when needed transporting phosphate out of the cell perhaps to a structure is a necessary activity of [[phosphate homeostasis]] for that cell.


=Introduction=
==Introduction==


Inorganic phosphate (P<sub>i</sub>) (structural phosphate) behaves as a serine phosphate and is not the same as the enzyme-bound phosphate (catalytic phosphate) derived from ATP during a catalytic reaction.<ref name=Linn>{{ cite journal |author=Linn TC, Srere PA |title=Identification of ATP citrate lyase as a phosphoprotein |journal=J Biol Chem. |volume=254 |issue=5 |month=Mar |year=1979 |pages=1691-8 |pmid= 762167 }}</ref>
Inorganic phosphate ([[Phosphoric acids and phosphates#Orthophosphate|P<sub>i</sub>]]) (structural phosphate) behaves as a serine phosphate and is not the same as the enzyme-bound phosphate (catalytic phosphate) derived from ATP during a catalytic reaction.<ref name=Linn>{{ cite journal |author=Linn TC, Srere PA |title=Identification of ATP citrate lyase as a phosphoprotein |journal=J Biol Chem. |volume=254 |issue=5 |month=Mar |year=1979 |pages=1691-8 |pmid= 762167 }}</ref> The catalytic phosphate in a [[nucleotide]] is usually the phosphate farthest from the [[nucleoside]]. The structural phosphate becomes the hydrolyzed nucleotide after the catalysis that associates with the binding of the [[polymer]]. The structural phosphate is a part of each polymer whether it is a [[microfilament]], [[microtubule]], [[phospholipid]], or [[nucleic acid]]. Inorganic phosphates such as P<sub>i</sub> and [[Pyrophosphate|PP<sub>i</sub>]] can be precipitated with divalent cations like Ca<sup>2+</sup>, Mg<sup>2+</sup>, or others, e.g. Mn<sup>2+</sup>, to form a variety of tissue and mineral composites: [[cartilage]], [[teeth]], and [[bone]]. These in turn eventually become localized to the natural environment and form [[phosphorite]]s.


=Catalytic phosphate=
==Catalytic phosphate==


Inorganic phosphate (P<sub>i</sub>) (structural phosphate) behaves as a serine phosphate and is not the same as the enzyme-bound phosphate (catalytic phosphate) derived from ATP during a lyase reaction of EC 4.1.3.8.<ref name=Linn>{{ cite journal |author=Linn TC, Srere PA |title=Identification of ATP citrate lyase as a phosphoprotein |journal=J Biol Chem. |volume=254 |issue=5 |month=Mar |year=1979 |pages=1691-8 |pmid= 762167 }}</ref> Evidence indicates that EC 4.1.3.8 contains one structural phosphate for each catalytic phosphate, which does not affect its catalytic activity.<ref name=Linn/> The γ phosphate of [[ATP]] is the catalytic phosphate. EC 4.1.3.8 ATP citrate lyase contains acid-labile, catalytic phosphate after the enzyme is reacted with ATP and Mg<sup>2+</sup>, whereas the structural phosphate is acid-stable, base-labile.<ref name=Janski>{{ cite journal |author=Janski AM, Srere PA, Cornell NW, Veech RL |title=Phosphorylation of ATP Citrate Lyase in Response to Glucagon |journal=J Biol Chem. |month=Oct |volume=254 |issue=19 |pages=9365-8 |year=1979 |pmid= 489538 }}</ref> There are 2 mol of acid-labile catalytic phosphate and 2 mol of base-labile structural phosphate per tetramer. The pH 7.5 buffer contained concentrations of ADP, P<sub>i</sub>, and free Mg<sup>2+</sup> similar to those found in vivo.<ref name=Janski/> Glucagon induces an incorporation of acid-stable phosphate into ATP citrate lyase without a concomitant change in enzyme activity.<ref name=Janski/>
Inorganic phosphate (P<sub>i</sub>) (structural phosphate) behaves as a serine phosphate and is not the same as the enzyme-bound phosphate (catalytic phosphate) derived from ATP during a lyase reaction of EC 4.1.3.8.<ref name=Linn>{{ cite journal |author=Linn TC, Srere PA |title=Identification of ATP citrate lyase as a phosphoprotein |journal=J Biol Chem. |volume=254 |issue=5 |month=Mar |year=1979 |pages=1691-8 |pmid= 762167 }}</ref> Evidence indicates that EC 4.1.3.8 contains one structural phosphate for each catalytic phosphate, which does not affect its catalytic activity.<ref name=Linn/> The γ phosphate of [[ATP]] is the catalytic phosphate. EC 4.1.3.8 ATP citrate lyase contains acid-labile, catalytic phosphate after the enzyme is reacted with ATP and Mg<sup>2+</sup>, whereas the structural phosphate is acid-stable, base-labile.<ref name=Janski>{{ cite journal |author=Janski AM, Srere PA, Cornell NW, Veech RL |title=Phosphorylation of ATP Citrate Lyase in Response to Glucagon |journal=J Biol Chem. |month=Oct |volume=254 |issue=19 |pages=9365-8 |year=1979 |pmid= 489538 }}</ref> There are 2 mol of acid-labile catalytic phosphate and 2 mol of base-labile structural phosphate per tetramer. A pH 7.5 buffer associated with EC 4.1.3.8 contains concentrations of ADP, P<sub>i</sub>, and free Mg<sup>2+</sup> similar to those found in vivo.<ref name=Janski/> Glucagon induces an incorporation of acid-stable phosphate into ATP citrate lyase without a concomitant change in enzyme activity.<ref name=Janski/>


=Intracellular structural phosphate=
==Intracellular structural phosphate==


In the mathematical modeling of cell growth and phosphatase biosynthesis it is necessary to determine the intracellular concentration of structural phosphate.<ref name=Toda>{{ cite journal |author=Toda K, Yabe I |title=Mathematical model of cell growth and phosphatase biosynthesis in Saccharomyces carlsbergensis under phosphate limitation |journal=Biotech Bioeng. |year=2004 |month=Feb |volume=21 |issue=3 |pages=487-502 |doi=10.1002/bit.260210310 }}</ref>
In the mathematical modeling of cell growth and phosphatase biosynthesis it is necessary to determine the intracellular concentration of structural phosphate.<ref name=Toda>{{ cite journal |author=Toda K, Yabe I |title=Mathematical model of cell growth and phosphatase biosynthesis in Saccharomyces carlsbergensis under phosphate limitation |journal=Biotech Bioeng. |year=2004 |month=Feb |volume=21 |issue=3 |pages=487-502 |doi=10.1002/bit.260210310 }}</ref>


=[[Nucleotide]]s=
==[[Nucleotide]]s==


Analysis of the phosphate moiety present in mononucleotides (NMP) can allow the identification of structural phosphate binding motifs.<ref name=Babor>{{ cite journal |author= |title=Conserved Positions for Ribose Recognition: Importance of Water Bridging Interactions Among ATP, ADP and FAD-protein Complexes |journal=J Mol Biol. |month=Oct |year=2002 |volume=323 |issue=3 |pages=523-32 |doi=10.1016/S0022-2836(02)00975-0 }}</ref>
Analysis of the phosphate moiety present in mononucleotides (NMP) can allow the identification of structural phosphate binding motifs.<ref name=Babor>{{ cite journal |author=Babor M, Soboleva V, Edelman M |title=Conserved Positions for Ribose Recognition: Importance of Water Bridging Interactions Among ATP, ADP and FAD-protein Complexes |journal=J Mol Biol. |month=Oct |year=2002 |volume=323 |issue=3 |pages=523-32 |doi=10.1016/S0022-2836(02)00975-0 }}</ref>


When nucleotide hydrolysis is coupled to the polymerization process, the two ends of the polymer behave differently, and the critical concentration required for assembly at one end is different from that required for the opposite end. However, NTP hydrolysis is usually associated but not directly coupled with polymerization. When there are NTP-bound subunits at the ends, the polymer is stable and continues to grow slowly. When at the polymer ends there are subunits containing NDP, the polymer is in a shrinking phase, depolymerizes rapidly and completely, and much faster at lower mer concentrations.
When nucleotide hydrolysis is coupled to the polymerization process, the two ends of the polymer behave differently, and the critical concentration required for assembly at one end is different from that required for the opposite end. However, NTP hydrolysis is usually associated but not directly coupled with polymerization. When there are NTP-bound subunits at the ends, the polymer is stable and continues to grow slowly. When at the polymer ends there are subunits containing NDP, the polymer is in a shrinking phase, depolymerizes rapidly and completely, and much faster at lower mer concentrations.


=[[Microfilament]]s=
==[[Microfilament]]s==


During the assembly of actin into microfilaments, actin-ATP becomes actin ADP upon polymerization.
During the assembly of actin into microfilaments, actin-ATP becomes actin ADP upon polymerization.


=[[Microtubule]]s=
==[[Microtubule]]s==


P<sub>i</sub>, BeF<sub>3</sub> or AIF<sub>4</sub>, structural phosphate analogs, have a stabilizing effect on microtubules containing GDP tubulin.<ref name=Avila>{{ cite journal |author=Avila J |title=Microtubule dynamics |journal=FASEB J. |year=1990 |month=Dec |volume=4 |issue=15 |pages=3284-90 |pmid= 2253844 }}</ref> The structural phosphate of microtubules is the GDP in the interior of the polymer.
P<sub>i</sub>, BeF<sub>3</sub> or AIF<sub>4</sub>, structural phosphate analogs, have a stabilizing effect on microtubules containing GDP tubulin.<ref name=Avila>{{ cite journal |author=Avila J |title=Microtubule dynamics |journal=FASEB J. |year=1990 |month=Dec |volume=4 |issue=15 |pages=3284-90 |pmid= 2253844 }}</ref> The structural phosphate of microtubules is the GDP in the interior of the polymer.


=[[Phospholipid]]=
==[[Phospholipid]]==


=[[Nucleic acid]]=
Phospholipids are a major component of the plasma membrane and organelle membranes. In normal cell plasma membranes, phospholipids are asymmetrically distributed: [[phosphatidylcholine]] (PC) and [[sphingomyelin]] (SM) predominantly in the exoplasmic leaflet and [[phosphatidylserine]] (PS) and [[phosphatidylethanolamine]] (PE) in the cytoplasmic leaflet. All phospholipids in eukaryotic plasma membranes undergo a slow passive transbilayer movement.<ref name=Pomorski>{{ cite journal |author=Pomorski T, Muller P, Zimmermann B, Burger K, Devaux PF, Herrmann A |title=Transbilayer movement of fluorescent and spin-labeled phospholipids in the plasma membrane of human fibroblasts: a quantitative approach |journal=J Cell Sci. |volume=109 |issue=Pt 3 |year=1996 |month=Mar |pages=687-98 |pmid= 8907713 }}</ref> Half-times of redistribution are 3.6 min for PS.<ref name=Pomorski/> Both PC and SM have higher diffusion rates probably indicative of [[endocytosis]].


=[[Cartilage]]=
A typical molecule of PC, SM, PS, or PE contains one monophosphate group. The entire PC molecule contains glycerol, P<sub>i</sub>, choline and fatty acids for 760 Da<ref name=phosphacholine>{{ cite web |title=1-palmitoyl-2-oleoylphosphatidylcholine - PubChem Public Chemical Database |url=http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5497103&ncount=38#Synonyms }}</ref> with an average diameter of ~2.16 nm. However, the fatty acids extend between the bilayers of the [[cell membrane]]. The head of a PC molecule is 314 Da<ref name=tidylcholine>{{ cite web |title=Phosphatidylcholines - PubChem Public Chemical Database |url=http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=10425706&loc=ec_rcs }}</ref>, with an average diameter of ~1.62 nm. The head contains the structural monophosphate. For an cell of 10 µm diameter, there may be up to ~7.6 x 10<sup>7</sup> molecules of PC in the exoplasmic leaflet, if the leaflet were entirely composed of PC.


=[[Teeth]]=
The sphingomyelins (SMs) are found largely in the brain and other nervous tissue. They contain phosphocholine or phosphoethanolamine as their polar head group. The head group containing phosphocholine is 285 Da<ref name=phosphosphingo>{{ cite web |title=Sphingomyelins - PubChem Public Chemical Database |url=http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=23657817&loc=ec_rcs }}</ref>, with an average diameter of ~1.56 nm. SMs can have fatty acid tails, such as in sphingosine phosphorylcholine 465 Da<ref name=phosphorylcholine>{{ cite web |title=sphingosine phosphorylcholine - PubChem Public Chemical Database |url=http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=9847290&loc=ec_rcs }}</ref> (one tail) or TNPAL-sphingomyelin 874 Da<ref name=TNPAL>{{ cite web |title=TNPAL-Sphingomyelin - PubChem Public Chemical Database |url=http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5789378&loc=ec_rcs }}</ref> (two tails). Although the head size of the SMs is comparable to that of PC, the number of phosphates in the exoplasmic leaflet would be at ~8.2 x 10<sup>7</sup>, if composed entirely of SM.
 
In the cytoplasmic leaflet are PS and PE. The head of PS is 385 Da<ref name=tidylserine>{{ cite web |title=Phosphatidylserine - PubChem Public Chemical Database |url=http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=6323481&loc=ec_rcs }}</ref>, with an average diameter of ~1.72 nm. As the cell membrane averages about 7 nm in thickness, the cytoplasmic leaflet can have ~6.7 x 10<sup>7</sup> molecules of PS, if totally composed of PS. The head of PE is 271 Da<ref name=tidylethanolamine>{{ cite web |title=Phosphatidylethanolamines - PubChem Public Chemical Database |url=http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=24771772&loc=ec_rcs }}</ref>, with an average diameter of ~1.54 nm. The cytoplasmic leaflet would have ~8.4 x 10<sup>7</sup> molecules of PE, if totally composed of PE.
 
If half and half, the number of phosphates in the cytoplasmic leaflet would be ~7.6 x 10<sup>7</sup>. Half and half in the exoplasmic leaflet would yield ~7.9 x 10<sup>7</sup> molecules of phosphate. The entire cell membrane could have up to ~1.6 x 10<sup>8</sup> molecules of phosphate.
 
==[[Nucleic acid]]==
 
Phosphate is a component of [[DNA]] and [[RNA]]. Most of the structural phosphate in nucleic acids is in the phospho-diester linkage.<ref name=Battley>{{ cite journal |author=Battley EH |title=On the enthalpy of formation of Escherichia coli K-12 cells |journal=Biotech Bioeng. |month=Jan |year=1992 |volume=39 |issue=1 |pages=5-12 |doi=10.1002/bit.260390103 }}</ref>
 
===Ribonucleic acid ([[RNA]])===
[[Image:RNA chemical structure.GIF|thumb|left|Chemical structure of RNA.]]
 
The variety and type of RNA is extensive. Each has to be [[Transcription (genetics)|transcribed]] from the applicable portion of [[DNA]] in the [[euchromatin]]. The unfolded structure of euchromatin allows gene regulatory proteins and [[RNA polymerase]] (RNAP) complexes to bind to the DNA sequence, which can then initiate the transcription process. Control of the process of gene transcription affects patterns of gene expression and thereby allows a cell to adapt to a changing environment, perform specialized roles within an organism, and maintain basic metabolic processes necessary for survival. RNAP can initiate [[transcription]] at specific DNA sequences known as [[promoter]]s. It then produces an RNA chain which is [[Complementarity (molecular biology)|complementary]] to the template DNA strand. The process of adding [[nucleotide]]s to the RNA strand is known as [[Transcription (genetics)#Elongation|elongation]].
 
{| class="wikitable sortable"
|+ RNAs involved in protein synthesis
|-
! Type !! Abbr. !! Function !! Distribution !! Ref.
|-
| [[Messenger RNA]] || mRNA || [[Genetic code|Codes]] for protein  || All cells
|-
| [[Ribosomal RNA]] || rRNA || [[Translation (genetics)|Translation]] || All cells
|-
| [[7SL RNA|Signal recognition particle RNA]] || 7SL RNA or SRP RNA|| Membrane integration / mRNA tagging for export|| All organisms ||<ref name= Gribaldo >{{cite journal | author=Gribaldo S, Brochier-Armanet C| title=The origin and evolution of Archaea: a state of the art| journal=Philos Trans R Soc Lond B Biol Sci.| year=2006| volume=361 | issue=1470| pages=1007–22| pmid=16754611| doi=10.1098/rstb.2006.1841}}</ref>
|-
| [[Transfer RNA]] || tRNA || Translation || All cells
|-
| [[tmRNA|Transfer-messenger RNA]] || tmRNA || Rescuing stalled ribosomes Terminating translation || Bacteria ||<ref name=Gillet>{{cite journal | author=Gillet R, Felden B| title=Emerging views on tmRNA-mediated protein tagging and ribosome rescue | journal = Molecular Microbiology| volume=42| issue=4 | pages=879–85| year=2001| doi=10.1046/j.1365-2958.2001.02701.x }}</ref>
|-
|}
 
{| class="wikitable sortable"
|+ RNAs involved in post-transcriptional modification or DNA replication
|-
! Type !! Abbr. !! Function !! Distribution !! Ref.
|-
| [[Small nuclear RNA]] || snRNA || Splicing and other functions || [[Eukaryote]]s and [[archaea]] ||<ref name= Thore >{{cite journal | author=Thore S, Mayer C, Sauter C, Weeks S, Suck D| title=Crystal Structures of the ''Pyrococcus abyssi'' Sm Core and Its Complex with RNA | journal=J. Biol. Chem.| year=2003| volume=278| issue=2| pages=1239–47| doi=10.1074/jbc.M207685200 |url=http://www.jbc.org/cgi/content/full/278/2/1239 }}</ref>
|-
| [[Small nucleolar RNA]] || snoRNA || Nucleotide modification of RNAs [[RNA editing]] || Eukaryotes and archaea ||<ref name=Kiss>{{cite journal | author=Kiss T| title=Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs| journal=The EMBO Journal| year=2001| volume=20| pages=3617–22| doi=10.1093/emboj/20.14.3617 |url=http://www.nature.com/emboj/journal/v20/n14/full/7593858a.html}}</ref>
|-
| [[SmY RNA]] || SmY || mRNA trans-splicing || Nematodes || <ref name=Jones>{{cite journal |author=Jones TA, Otto W, Marz M, Eddy SR, Stadler PF |title=A survey of nematode SmY RNAs |journal=RNA Biol |volume=6 |issue=1 |pages=5–8 |year=2009 |pmid=19106623 |doi= |url=http://www.landesbioscience.com/journals/rna/abstract.php?id=7634}}</ref>
|-
| [[Small Cajal body-specific RNA]] || scaRNA || Type of snoRNA; Nucleotide modification of RNAs || ||
|-
| [[Guide RNA]] || gRNA || mRNA nucleotide modification / [[RNA editing]] || [[Kinetoplastid]] [[mitochondria]] ||<ref name=Alfonzo>{{cite journal | author=Alfonzo JD, Thiemann O, Simpson L | title=The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria| journal=Nucleic Acids Research| year=1997| volume=25| issue=19| pages=3751–59| pmid=9380494 | doi=10.1093/nar/25.19.3751 |url=http://nar.oxfordjournals.org/cgi/content/abstract/25/19/3751}}</ref>
|-
| [[RNase P|Ribonuclease P]] || RNase P || tRNA maturation || All organisms ||<ref>{{cite journal | author=Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW| title=RNase P RNAs from some Archaea are catalytically active | journal=Proc Natl Acad Sci USA| year=1999| volume=96 | issue=14| pages=7803–08| pmid=10393902| doi=10.1073/pnas.96.14.7803}}</ref>
|-
| [[RNase MRP|Ribonuclease MRP]] || RNase MRP || rRNA maturation, [[DNA replication]] || Eukaryotes ||<ref>{{cite journal | author=Woodhams MD, Stadler PF, Penny D, Collins LJ| title=RNase MRP and the RNA processing cascade in the eukaryotic ancestor| journal=BMC Evolutionary Biology| year=2007| volume=7| pages=S13| doi=10.1186/1471-2148-7-S1-S13}}</ref>
|-
| [[Y RNA]] || || RNA processing, DNA replication || Animals ||<ref>{{cite journal | author=Perreault J, Perreault J-P, Boire G| title=Ro-associated Y RNAs in metazoans: evolution and diversification| journal=Molecular Biology and Evolution | year=2007 | volume=24| issue=8| pages=1678–89 | doi=10.1093/molbev/msm084}}</ref>
|-
| [[Telomerase RNA]] || || [[Telomere]] synthesis || Most eukaryotes ||<ref>{{cite journal | author=Lustig AJ| title=Crisis intervention: The role of telomerase| journal=Proc Natl Acad Sci USA | year=1999| volume=96| issue=7| pages=3339–41| pmid=10097039| doi=10.1073/pnas.96.7.3339}}</ref>
|-
| [[Ribozyme]] || || [[Catalysis]] || All cells
|-
| [[Transposon]] || || Self-propagating || All cells
|-
|}
 
{| class="wikitable sortable"
|+ Regulatory RNAs
|-
! Type !! Abbr. !! Function !! Distribution !! Ref.
|-
| [[Antisense RNA]] || aRNA || Transcriptional attenuation / mRNA degradation / mRNA stabilisation / Translation block Gene regulation || All organisms ||<ref name=Brantl1>{{cite journal | author=Brantl S| title=Antisense-RNA regulation and RNA interference| journal=Biochimica et Biophysica Acta| year=2002| volume=1575| issue=1–3| pages=15–25| pmid=12020814}}</ref><ref name=Brantl2>{{cite journal |author=Brantl S |title=Regulatory mechanisms employed by cis-encoded antisense RNAs |journal=Curr Opin Microbiol. |volume=10 |issue=2 |pages=102–9 |year=2007 |pmid=17387036 |doi=10.1016/j.mib.2007.03.012}}</ref>
|-
| Cis-natural antisense transcript || || Gene regulation || ||
|-
| [[CRISPR]] RNA || crRNA || Resistance to parasites, probably by targeting their DNA || Bacteria and archaea ||<ref>{{cite journal |author=Brouns SJ, Jore MM, Lundgren M, ''et al'' |title=Small CRISPR RNAs guide antiviral defense in prokaryotes |journal=Science (New York, N.Y.) |volume=321 |issue=5891 |pages=960–4 |year=2008 |month=August |pmid=18703739 |doi=10.1126/science.1159689}}</ref>
|-
| [[Long noncoding RNA]] || Long&nbsp;ncRNA || Various || Eukaryotes ||
|-
| [[MicroRNA]] || miRNA || Gene regulation || Most eukaryotes ||<ref name=Lin>{{cite journal | author=Lin S-L, Miller JD, Ying S-Y| title=Intronic microRNA (miRNA)| journal=Journal of Biomedicine and Biotechnology| year=2006 |pages=1–13| pmid=17057362| doi=10.1155/JBB/2006/26818| volume=2006}}</ref>
|-
| [[Piwi-interacting RNA]] || piRNA || Transposon defense Gene regulation|| Animal [[germline]] cells ||<ref name=Horwich>{{cite journal | author=Horwich MD, Li C Matranga C, Vagin V, Farley G, Wang P, Zamore PD| title=The ''Drosophila'' RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC| journal=Current Biology| year=2007| volume=17| pages=1265–72| doi=10.1016/j.cub.2007.06.030}}</ref><ref name=Ghildiyal>{{cite journal |author=Ghildiyal M, Zamore PD |title=Small silencing RNAs: an expanding universe |journal=Nat. Rev. Genet. |volume=10 |issue=2 |pages=94–108 |year=2009 |month=February |pmid=19148191 |doi=10.1038/nrg2504}}</ref>
|-
| [[Small interfering RNA]] || siRNA || Gene regulation || Most [[eukaryote]]s ||<ref name=Ahmad>{{cite journal | author=Ahmad K, Henikoff S | title=Epigenetic consequences of nucleosome dynamics | journal=Cell| year=2002| volume=111 | issue=3| pages=281–84| doi=10.1016/S0092-8674(02)01081-4}}</ref>
|-
| [[Trans-acting siRNA]] || tasiRNA || Gene regulation || Land plants||<ref>{{cite journal | author=Vazquez F, Vaucheret H| title=Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs| journal=Mol. Cell| issue=16 | year=2004 |pages=1–13| pmid=17057362}}</ref>
|-
| [[rasiRNA|Repeat associated siRNA]] || rasiRNA || Type of piRNA; transposon defense|| Drosophila || <ref>{{cite journal |author=Desset S, Buchon N, Meignin C, Coiffet M, Vaury C |title=In Drosophila melanogaster the COM locus directs the somatic silencing of two retrotransposons through both Piwi-dependent and -independent pathways |journal=PLoS ONE |volume=3 |issue=2 |pages=e1526 |year=2008 |pmid=18253480 |pmc=2211404 |doi=10.1371/journal.pone.0001526}}</ref>
|-
|}
 
Enstructuring P<sub>i</sub> into any RNA is usually not accomplished by reacting directly with [[ribose]] for RNA, [[deoxyribose]] present in DNA, [[purine]]s, or [[pyrimidine]]s. Although DNA records the sequence of [[nucleobase]]s that are connected by ribose to P<sub>i</sub>, the transcription process chosen by probably all life on Earth requires triphosphate nucleotides ([[Nucleoside triphosphate|NTP]]s).
 
For example, consider making a mRNA for a particular protein from the point of view of phosphate enstructuring. As of 2008 [[dystrophin]] has the longest gene known, at [[Locus_(genetics)|locus]] Xp21.2. The [[primary transcript]] measures 2.4 megabases (thus the gene comprises 0.008% of the  human genome), and takes 16 hours to transcribe. The 79 [[exons]]<ref name=Strachan>{{ cite book |author=Strachan T, Read AP |year=1999 |title=Human molecular genetics 2 |edition=2nd |publisher=John Wiley & Sons, Inc. |location=New York, USA |isbn=0471133736 }}</ref> code for a protein of over 3500 amino acid (aa) residues. It is human GeneID: 1756.<ref name=dystrophin>{{ cite web |title=Entrez Gene: DMD dystrophin |url=http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=1756| accessdate = }}</ref> [[Protein isoform|Isoform]] Dp427c has 3677 aa<ref name=Dp427c>{{ cite web |title=Entrez Protein - dystrophin Dp427c isoform [Homo spiens] |url=http://www.ncbi.nlm.nih.gov:80/protein/5032281?report=genpept }}</ref> which are specified by 3677 codons of 3 nucleotides each. That's 11,031 [[Nucleotide#Nucleotides|NMP]]s with one P<sub>i</sub> each.
 
But the gene portion that is transcribed also contains a [[5' cap]] requiring one [[GTP]], a [[Five prime untranslated region|5' UTR]], 78 [[intron]]s, and a [[Three prime untranslated region|3' UTR]] or as mentioned 2.4 Mb of one P<sub>i</sub> each. In this excess generation of RNA dystrophin is not unique. More than 95% of the enstructured phosphate for RNA synthesized by [[RNA polymerase II]] never reaches the [[cytoplasm]]. The main reason for this is due to the removal of [[intron]]s which account for 80% of the total bases.<ref name=Jacjson>{{cite journal | author = Jackson DA, Pombo A, Iborra F | title = The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells | journal = FASEB J. | volume = 14 | issue = 2 | pages = 242-54 | year = 2000 | pmid = 10657981 | doi = | issn = | url = http://www.fasebj.org/cgi/content/abstract/14/2/242  }}</ref>
 
Per the apparently available [[Phosphate homeostasis#Phosphate reserves|phosphate reserve]] in a cell or [[Phosphate homeostasis#Intracellular phosphate|intracellular phosphate]] of about 10<sup>-3</sup> P<sub>i</sub> (1 molecule of P<sub>i</sub> per 1000 other molecules, such as water) at any particular location and a rate of about 42 NTPs per second to transcribe this mRNA, some form of [[Nucleohyaloplasm#Intra-nuclear transport|intranuclear transport]] other than [[Passive transport|diffusion]] is needed. While the number of transcription units varies at any given moment, should per [[Nucleohyaloplasm#Transcription factories|transcription factories]] there be ~64,000 polymerase II active transcription units operating at about 42 NTPs per second, there would need to be a way to supply a total phosphate of ~2,700,000 NTPs per second to all transcription units in parallel.
 
With respect to [[Phosphate homeostasis#Phosphate reserves|phosphate reserves]] each ATP is recycled about once every minute on average. This may also be true for [[Cytidine triphosphate|CTP]], [[Guanosine triphosphate|GTP]], and [[Uridine triphosphate|UTP]]. That is ~0.07 recycled NTPs per second are available to transcribe on average.
 
Using the information derived regarding [[Transduction (biophysics)#Signal Transduction|signal transduction]] for a water molecule of speed 15 µms<sup>-1</sup>, if a nucleus of 5 µm diameter contains ~64,000 transcription units uniformly distributed throughout (a volume with ~120 nm diameter for each unit), it would take about 40 seconds for a GTP molecule to interact with one unit with ten molecules in each unit volume. The GTP molecule would have a speed of ~2800 nms<sup>-1</sup>. But to get to 24 ms between interactions would take ~17,000 NTP molecules in a volume of ~120 nm diameter. That is ~68 µg/ml GTP. As the total number of normally available [[Phosphate homeostasis#Intracellular phosphate|intracellular phosphate]] molecules, if uniformly distributed throughout the cell, would be ~33,000 molecules of all phosphate compunds within each ~120 nm diameter volume, diffusion may be sufficient. Pulling in additional phosphate from extracellular fluid would help to increase the amount of available phosphate, probably enough to make 42 NTPs per second reasonable.
 
Subtracting the estimated number of phosphates in the genome DNA yields ~21,000 phosphate molecules for all other purposes. The amount of phosphate in the cell membrane would reduce the available phosphate to ~20,000 molecules. But, if half the available phosphate is already tied up in RNA or other structures, then transport across the cell membrane and diffusion throughout the cell is mandatory.
 
Alternatively, if the actual translational speed of a water molecule is closer to 75 µms<sup>-1</sup>, the needed phosphate is in ~3,400 NTPs. However, for transcription of a mRNA roughly equal amounts of ATP, CTP, GTP, and UTP need to be present in each ~120 nm diameter volume. That's ~13,600 NTPs with 3 phosphates each for ~41,000 phosphates. To have the needed concentration in the nucleus, the entire cell needs to be at the same level of phosphate in the cytosol. The total phosphate uniformly distributed by diffusion throughout the cytosol is ~24 x 10<sup>9</sup>: ~6.0 x 10<sup>9</sup> each of ATP, CTP, GTP, and UTP.
 
{| class="wikitable sortable"
|+ Average phosphate content of human RNAs
|-
! Abbr. !! GeneID !! Number of basepairs !! Accumulative average phosphates
|-
| mRNA || 1  || 1488 || 1488
|-
| mRNA || 2 || 4425 || 2956.5
|-
| mRNA || 9 || 873 || 2262
|-
| mRNA || 10 || 873 || 1914.8
|-
| mRNA || 12 || 1272 || 1786.2
|-
| ncRNA || 245 || 2768 || 2768
|-
| ncRNA || 303 || 1343 || 2055.5
|-
| ncRNA || 305 || 1350 || 1820.3
|-
| ncRNA || 1057 || 985 || 1611.5
|-
| ncRNA || 1197 || 1812 || 1651.6
|-
| ncRNA || 1587 variant 1 || 2642 || 1816.7
|-
| ncRNA || 1587 variant 2 || 2396 || 1988.4
|-
| ncRNA || 1587 variant 3 || 2491 || 1973.4
|-
| miscRNA (ncRNA) || 711 || 2264 || 2264
|-
| miscRNA (ncRNA) || 3262 || 1198 || 1731
|-
| miscRNA (ncRNA) || 5820 || 1918 || 1793.3
|-
| miscRNA (Long? ncRNA) || 7503 || 19271 || 6162.8
|-
| miscRNA (ncRNA) || 8123 || 3373 || 5604.8
|-
| miscRNA (ncRNA) || 8420 || 939 || 4827.2
|-
| rRNA || 4549 || 953 || 953
|-
| rRNA || 4550 || 1558 || 1255.5
|-
| rRNA (ribosome component) || 6052 || --- || ---
|-
| rRNA (ribosome component) || 6053 || --- || ---
|-
| rRNA (ribosome component) || 6054 || --- || ---
|-
| rRNA (ribosome component) || 6055 || --- || ---
|-
| rRNA (ribosome component) || 6056 || --- || ---
|-
| rRNA || 100008587 || 156 || 889
|-
| rRNA || 100008588 || 1869 || 1134
|-
| rRNA || 100008589 || 5070 || 1921.2
|-
| SRP RNA (miscRNA) || 6029 || 299 || 299
|-
| SRP RNA (scRNA) || 378706 || 299 || 299
|-
| tRNA || 4511 (mitochondrial) || 65 || 65
|-
| tRNA || 4553 (mitochondrial) || 68 || 66.5
|-
| tRNA || 4555 (mitochondrial) || 67 || 66.7
|-
| tRNA || 4556 (mitochondrial) || 68 || 67
|-
| tRNA || 4558 (mitochondrial) || 70 || 67.6
|-
| snRNA (spliceosome) || 6060 || 164 || 164
|-
| snRNA (spliceosome) || 6066 || 188 || 176
|-
| snRNA (ncRNA) || 125050 || 332 || 228
|-
| snRNA (spliceosome) || 100151683 || 130 || 203.5
|-
| snRNA (spliceosome) || 100151684 || 125 || 187.8
|-
| snoRNA (ncRNA) || 6043 || 135 || 135
|-
| snoRNA (ncRNA) || 6044 || 154 || 144.5
|-
| snoRNA (ncRNA) || 6079 || 148 || 145.7
|-
| snoRNA (ncRNA) || 6080 || 207 || 161
|-
| snoRNA (ncRNA) || 6081 || 205 || 169.8
|-
| RNase P (miscRNA) || 85495 || 341 || 341
|-
| RNase MRP (miscRNA) || 6023 || 265 || 265
|-
| Y RNA (scRNA) || 6084 || 113 || 113
|-
| Y RNA (scRNA) || 6085 || 102 || 107.5
|-
| Y RNA (scRNA) || 6086 || 96 || 103.7
|-
| Y RNA (scRNA) || 6090 || 84 || 98.8
|-
| Telomerase RNA (miscRNA) || 7012 || 451 || 451
|-
| Ribozyme (ncRNA || 54677 || 1264 || 1264
|-
| [[Alu sequence]] (Transposon) || ? || ~300 || ~300
|-
| aRNA (miscRNA) || 6315 || 1472 || 1472
|-
| aRNA (miscRNA) || 8475 || 1286 || 1379
|-
| aRNA (miscRNA) || 9383 || 37027 || 13261.7
|-
| aRNA (miscRNA) || 10108 || --- || 13261.7
|-
| aRNA (miscRNA) || 10737 variant 1 || 1357 || 13261.7
|-
| aRNA (miscRNA) || 10737 variant 2 || 1115 || 8451.4
|-
| aRNA (miscRNA) || 10740 || 5125 || 7897
|-
| Long ncRNA || 7503 || 19271 || 19271
|-
| Long ncRNA || 9383 || 37027 || 28149
|-
| Long ncRNA || 10984 || 59461 || 38586.3
|-
| miRNA || 406991 || 71 || 71
|-
| miRNA || 406952 || 83 || 77
|-
| miRNA || 406902 || 109 || 87.7
|-
| miRNA || 407043 || 109 || 93
|-
| miRNA || 407006 || 109 || 96.2
|-
| [[Piwi-interacting RNA|piRNA]] || ? || 29-30 || 29-30
|-
| [[Small interfering RNA|siRNA]] || ? || 20-25 || 20-25
|-
|}
 
In the table above those RNAs with a GeneID less than 30000 are found by searching among the human GeneIDs up to 30000. A total of 230 RNA genes, including variants, occur prior to GeneID 30000. There are as of July 22, 2009, 15827 human genes of all types, including variants and pseudogenes, at and before GeneID: 30000. Of the pseudogenes, 521 are inactive. Many of the active pseudogenes are RNA transcribing genes. Some 611 of these GeneIDs are also not transcribed genes. Some 14,695 are active and transcribed.
 
Using a [[Phosphate homeostasis#Phosphate budget|likely cellular phosphate budget in a human adult]] as a guide, an average cell could be operating ~28,800 transcription units. For a lateral speed of 37 µms<sup>-1</sup> of a water molecule, an average cell could operate ~14,400 transcription units by diffusion.
 
For an average cell of "default" cell type running the 14,695 active and transcribeable genes including variants, 14,464 mRNAs and 230 other assorted RNAs are being transcribed. As the above table lists the number of phosphates per RNA on average, an RNA transcription budget can be estimated, assuming each is halfway through transcription.
 
{| class="wikitable sortable"
|+ Estimated phosphate budget for RNAs
|-
! Abbr. !! Number of RNAs !! Number of structural phosphates !! Accumulative phosphates
|-
| mRNA || 14,464  || ~12.9 x 10<sup>6</sup> || ~12.9 x 10<sup>6</sup>
|-
| snoRNA || 77 || ~6500 || ~12.9 x 10<sup>6</sup>
|-
| tRNA || 59 || ~2000 || ~12.9 x 10<sup>6</sup>
|-
| miscRNA || 39 || ~94,000 || ~13.0 x 10<sup>6</sup>
|-
| ncRNA || 21 || ~21,000 || ~13.0 x 10<sup>6</sup>
|-
| RNA || 11 || ~10,000 || ~13.1 x 10<sup>6</sup>
|-
| aRNA || 7 || ~28,000 || ~13.1 x 10<sup>6</sup>
|-
| rRNA || 6 || ~5800 || ~13.1 x 10<sup>6</sup>
|-
| Y RNA || 4 || ~200 || ~13.1 x 10<sup>6</sup>
|-
| SRP || 2 || ~300 || ~13.1 x 10<sup>6</sup>
|-
| snRNA || 2 || ~200 || ~13.1 x 10<sup>6</sup>
|-
| Long ncRNA || 2 || ~39,000 || ~13.1 x 10<sup>6</sup>
|-
|}
 
===Deoxyribonucleic acid ([[DNA]])===
 
The entire human genome has ~3.4 Gb in its DNA, with one P<sub>i</sub> each. That is ~3.4 x 10<sup>9</sup> P<sub>i</sub> tied up in DNA per strand, ~6.8 x 10<sup>9</sup> P<sub>i</sub> total structural phosphate in each nucleus. With ~19 x 10<sup>9</sup> P<sub>i</sub> per cell in some form, that leaves ~12 x 10<sup>9</sup> P<sub>i</sub> per cell for all other functions and forms.
 
Mitochondria have their own genetic material, and the machinery to manufacture their own [[RNA]]s and [[protein]]s. A published human mitochondrial DNA sequence revealed 16,569&nbsp;[[base pair]]s encoding 37 total genes, 24&nbsp;[[tRNA]] and [[rRNA]] genes and 13&nbsp;[[peptide]] genes.<ref name=Anderson>{{cite journal |author=Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, et al. | title=Sequence and organization of the human mitochondrial genome | journal=Nature. | year=1981 |month=Apr |volume=290 |issue=5806 |pages=4&ndash;65  | volume = 410 | pages = 141 | doi = 10.1038/290457a0 }}</ref> The mitochondrial matrix contains several (2-10) copies of the [[mitochondrial DNA]] [[genome]]. Up to ~2000 mitochondria can occur per cell. This can enstructure up to ~3.3 x 10<sup>8</sup> phosphates.
 
==[[Cartilage]]==
 
Mineralization in the extracellular matrix starting with hydroxyapatite deposition into a collagenous scaffolding of cartilage, cementum, dentin and bone is initially regulated locally by calcium, orthophosphate, and pyrophosphate ion concentrations.
 
Although cuboid calcium phosphate crystals are absent in young articular cartilage, they are sometimes present in old normal articular cartilage occasionally adjacent to larger areas of pyrophosphate crystals.<ref name=Ali>{{ cite journal |author=Ali SY, Griffiths S |title=Formation of calcium phosphate crystals in normal and osteoarthritic cartilage |journal=Ann Rheum Dis. |month=Aug |year=1983 |volume=42 |issue=Suppl 1 |pages=45-8 |pmid= 6615026 }}</ref>
 
Endochondrial ossification of cartilage development ultimately leads to mineralization of the extracellular matrix.<ref name=Wuthier>{{ cite journal |author=Wuthier RE |title=Involvement of cellular metabolism of calcium and phosphate in calcification of avian growth plate cartilage |journal=J Nutr. |year=1993 |month=Feb |volume=123 |issue=2 Suppl |pages=301-9 |pmid= 8429379 }}</ref> Metabolism of Ca<sup>2+</sup> and P<sub>i</sub> by cartilage growth plate chondrocytes, involved in matrix vesicle formation, clearly are integral features of endochondrial calcification.<ref name=Wuthier/> This calcification is apparently due to the diffusion barrier and avascularity progressing from the zone of proliferation to the zone of hypertrophy of the cartilage growth plate chondrocytes environment.<ref name=Wuthier/>
 
==[[Teeth]]==


[[Hydroxyapatite]], which is a [[crystal]]line [[calcium phosphate]] is the primary mineral of enamel.<ref name=Johnson>{{ cite web |title=Biology of the Human Dentition |author=Johnson, Clarke |url=http://www.uic.edu/classes/orla/orla312/BHDTwo.htm |year=1998 }}</ref>
[[Hydroxyapatite]], which is a [[crystal]]line [[calcium phosphate]] is the primary mineral of enamel.<ref name=Johnson>{{ cite web |title=Biology of the Human Dentition |author=Johnson, Clarke |url=http://www.uic.edu/classes/orla/orla312/BHDTwo.htm |year=1998 }}</ref>
Line 47: Line 351:
Cementum is a specialized bony substance covering the root of a tooth, composed of approximately 45% inorganic material (mainly hydroxyapatite), 33% organic material (mainly collagen) and 22% water.
Cementum is a specialized bony substance covering the root of a tooth, composed of approximately 45% inorganic material (mainly hydroxyapatite), 33% organic material (mainly collagen) and 22% water.


=[[Bone]]=
==[[Bone]]==


During [[bone resorption]] high levels of phosphate are released into the ECF as [[osteoclast]]s tunnel into mineralized bone, breaking it down and releasing phosphate, that results in a transfer of phosphate from bone fluid to the blood. During [[Child development|childhood]], bone formation exceeds resorption, but as the [[Ageing|aging process]] occurs, resorption exceeds formation.
During [[bone resorption]] high levels of phosphate are released into the ECF as [[osteoclast]]s tunnel into mineralized bone, breaking it down and releasing phosphate, that results in a transfer of phosphate from bone fluid to the blood. During [[Child development|childhood]], bone formation exceeds resorption, but as the [[Ageing|aging process]] occurs, resorption exceeds formation.
Line 53: Line 357:
Transphosphorylation between nucleotides and hydroxyapatite (HA) results in a pyrophosphate on HA that is distinctive from pyrophosphate absorbed onto HA from solution. This may be due to a different orientation of the pyrophosphate on the surface depending on the origin of the pyrophosphate.<ref name=Taves>{{ cite journal |author=Taves DR, Reedy RC |title=A structural basis for the transphosphorylation of nucleotides with hydroxyapatite |journal=Calcified Tissue International |month=Dec |year=1969 |volume=3 |issue=1 |pages=284-92 |doi=10.1007/BF02058670 }}</ref>
Transphosphorylation between nucleotides and hydroxyapatite (HA) results in a pyrophosphate on HA that is distinctive from pyrophosphate absorbed onto HA from solution. This may be due to a different orientation of the pyrophosphate on the surface depending on the origin of the pyrophosphate.<ref name=Taves>{{ cite journal |author=Taves DR, Reedy RC |title=A structural basis for the transphosphorylation of nucleotides with hydroxyapatite |journal=Calcified Tissue International |month=Dec |year=1969 |volume=3 |issue=1 |pages=284-92 |doi=10.1007/BF02058670 }}</ref>


=Sedimentary [[phosphorite]]s=
==Sedimentary [[phosphorite]]s==
 
Phosphogenesis under palaeoceanographic conditions that were different from modern phosphorite depositional systems occurred across a broad range of palaeoenvironments in the shallow and broad epicontinental Phosphoria Sea.<ref name=Hiatt>{{ cite journal |author=Hiatt EE, Budd DA |title=Sedimentary phosphate formation in warm shallow waters: new insights into the palaeoceanography of the Permian Phosphoria Sea from analysis of phosphate oxygen isotopes |journal=Sedimentary Geol. |month=Dec |year=2001 |volume=145 |issue=1-2 |pages=119-33 |doi=10.1016/S0037-0738(01)00127-0  }}</ref> These conditions were revealed by oxygen isotope analyses of the structural phosphate in sedimentary phosphorites of the Upper Permian Phosphoria Formation.<ref name=Hiatt/>
 
==Acknowledgements==
 
The content on this page was first contributed by: Henry A. Hoff.
 
Initial content for this page in some instances came from [http://www.wikipedia.org Wikipedia].


Phosphogenesis under palaeoceanographic conditions that were different from modern phosphorite depositional systems occurred across a broad range of palaeoenvironments in the shallow and broad epicontinental Phosphoria Sea as revealed by oxygen isotope analyses of the structural phosphate in sedimentary phosphorites of the Upper Permian Phosphoria Formation.<ref name=Hiatt>{{ cite journal |author=Hiatt EE, Budd DA |title=Sedimentary phosphate formation in warm shallow waters: new insights into the palaeoceanography of the Permian Phosphoria Sea from analysis of phosphate oxygen isotopes |journal=Sedimentary Geol. |month=Dec |year=2001 |volume=145 |issue=1-2 |pages=119-33 |doi=10.1016/S0037-0738(01)00127-0  }}</ref>
==References==
{{reflist|2}}


=References=
{{Phosphate biochemistry}}
{{reflist}}


[[Category:Inorganic compounds]]
[[Category:Inorganic compounds]]
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[[Category:Anatomy]]
[[Category:Anatomy]]


{{SIB}}
 


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Editor-In-Chief: Henry A. Hoff

Overview

Inside a cell, phosphate may be structural to a nucleic acid such as DNA and RNA or phospholipid. Outside the cell, phosphate may be dissolved in extracellular fluid (ECF) or form structures such as bone and teeth. Bringing phosphate in any form into the cell from a phosphate containing structure or for such a structure and when needed transporting phosphate out of the cell perhaps to a structure is a necessary activity of phosphate homeostasis for that cell.

Introduction

Inorganic phosphate (Pi) (structural phosphate) behaves as a serine phosphate and is not the same as the enzyme-bound phosphate (catalytic phosphate) derived from ATP during a catalytic reaction.[1] The catalytic phosphate in a nucleotide is usually the phosphate farthest from the nucleoside. The structural phosphate becomes the hydrolyzed nucleotide after the catalysis that associates with the binding of the polymer. The structural phosphate is a part of each polymer whether it is a microfilament, microtubule, phospholipid, or nucleic acid. Inorganic phosphates such as Pi and PPi can be precipitated with divalent cations like Ca2+, Mg2+, or others, e.g. Mn2+, to form a variety of tissue and mineral composites: cartilage, teeth, and bone. These in turn eventually become localized to the natural environment and form phosphorites.

Catalytic phosphate

Inorganic phosphate (Pi) (structural phosphate) behaves as a serine phosphate and is not the same as the enzyme-bound phosphate (catalytic phosphate) derived from ATP during a lyase reaction of EC 4.1.3.8.[1] Evidence indicates that EC 4.1.3.8 contains one structural phosphate for each catalytic phosphate, which does not affect its catalytic activity.[1] The γ phosphate of ATP is the catalytic phosphate. EC 4.1.3.8 ATP citrate lyase contains acid-labile, catalytic phosphate after the enzyme is reacted with ATP and Mg2+, whereas the structural phosphate is acid-stable, base-labile.[2] There are 2 mol of acid-labile catalytic phosphate and 2 mol of base-labile structural phosphate per tetramer. A pH 7.5 buffer associated with EC 4.1.3.8 contains concentrations of ADP, Pi, and free Mg2+ similar to those found in vivo.[2] Glucagon induces an incorporation of acid-stable phosphate into ATP citrate lyase without a concomitant change in enzyme activity.[2]

Intracellular structural phosphate

In the mathematical modeling of cell growth and phosphatase biosynthesis it is necessary to determine the intracellular concentration of structural phosphate.[3]

Nucleotides

Analysis of the phosphate moiety present in mononucleotides (NMP) can allow the identification of structural phosphate binding motifs.[4]

When nucleotide hydrolysis is coupled to the polymerization process, the two ends of the polymer behave differently, and the critical concentration required for assembly at one end is different from that required for the opposite end. However, NTP hydrolysis is usually associated but not directly coupled with polymerization. When there are NTP-bound subunits at the ends, the polymer is stable and continues to grow slowly. When at the polymer ends there are subunits containing NDP, the polymer is in a shrinking phase, depolymerizes rapidly and completely, and much faster at lower mer concentrations.

Microfilaments

During the assembly of actin into microfilaments, actin-ATP becomes actin ADP upon polymerization.

Microtubules

Pi, BeF3 or AIF4, structural phosphate analogs, have a stabilizing effect on microtubules containing GDP tubulin.[5] The structural phosphate of microtubules is the GDP in the interior of the polymer.

Phospholipid

Phospholipids are a major component of the plasma membrane and organelle membranes. In normal cell plasma membranes, phospholipids are asymmetrically distributed: phosphatidylcholine (PC) and sphingomyelin (SM) predominantly in the exoplasmic leaflet and phosphatidylserine (PS) and phosphatidylethanolamine (PE) in the cytoplasmic leaflet. All phospholipids in eukaryotic plasma membranes undergo a slow passive transbilayer movement.[6] Half-times of redistribution are 3.6 min for PS.[6] Both PC and SM have higher diffusion rates probably indicative of endocytosis.

A typical molecule of PC, SM, PS, or PE contains one monophosphate group. The entire PC molecule contains glycerol, Pi, choline and fatty acids for 760 Da[7] with an average diameter of ~2.16 nm. However, the fatty acids extend between the bilayers of the cell membrane. The head of a PC molecule is 314 Da[8], with an average diameter of ~1.62 nm. The head contains the structural monophosphate. For an cell of 10 µm diameter, there may be up to ~7.6 x 107 molecules of PC in the exoplasmic leaflet, if the leaflet were entirely composed of PC.

The sphingomyelins (SMs) are found largely in the brain and other nervous tissue. They contain phosphocholine or phosphoethanolamine as their polar head group. The head group containing phosphocholine is 285 Da[9], with an average diameter of ~1.56 nm. SMs can have fatty acid tails, such as in sphingosine phosphorylcholine 465 Da[10] (one tail) or TNPAL-sphingomyelin 874 Da[11] (two tails). Although the head size of the SMs is comparable to that of PC, the number of phosphates in the exoplasmic leaflet would be at ~8.2 x 107, if composed entirely of SM.

In the cytoplasmic leaflet are PS and PE. The head of PS is 385 Da[12], with an average diameter of ~1.72 nm. As the cell membrane averages about 7 nm in thickness, the cytoplasmic leaflet can have ~6.7 x 107 molecules of PS, if totally composed of PS. The head of PE is 271 Da[13], with an average diameter of ~1.54 nm. The cytoplasmic leaflet would have ~8.4 x 107 molecules of PE, if totally composed of PE.

If half and half, the number of phosphates in the cytoplasmic leaflet would be ~7.6 x 107. Half and half in the exoplasmic leaflet would yield ~7.9 x 107 molecules of phosphate. The entire cell membrane could have up to ~1.6 x 108 molecules of phosphate.

Nucleic acid

Phosphate is a component of DNA and RNA. Most of the structural phosphate in nucleic acids is in the phospho-diester linkage.[14]

Ribonucleic acid (RNA)

Chemical structure of RNA.

The variety and type of RNA is extensive. Each has to be transcribed from the applicable portion of DNA in the euchromatin. The unfolded structure of euchromatin allows gene regulatory proteins and RNA polymerase (RNAP) complexes to bind to the DNA sequence, which can then initiate the transcription process. Control of the process of gene transcription affects patterns of gene expression and thereby allows a cell to adapt to a changing environment, perform specialized roles within an organism, and maintain basic metabolic processes necessary for survival. RNAP can initiate transcription at specific DNA sequences known as promoters. It then produces an RNA chain which is complementary to the template DNA strand. The process of adding nucleotides to the RNA strand is known as elongation.

RNAs involved in protein synthesis
Type Abbr. Function Distribution Ref.
Messenger RNA mRNA Codes for protein All cells
Ribosomal RNA rRNA Translation All cells
Signal recognition particle RNA 7SL RNA or SRP RNA Membrane integration / mRNA tagging for export All organisms [15]
Transfer RNA tRNA Translation All cells
Transfer-messenger RNA tmRNA Rescuing stalled ribosomes Terminating translation Bacteria [16]
RNAs involved in post-transcriptional modification or DNA replication
Type Abbr. Function Distribution Ref.
Small nuclear RNA snRNA Splicing and other functions Eukaryotes and archaea [17]
Small nucleolar RNA snoRNA Nucleotide modification of RNAs RNA editing Eukaryotes and archaea [18]
SmY RNA SmY mRNA trans-splicing Nematodes [19]
Small Cajal body-specific RNA scaRNA Type of snoRNA; Nucleotide modification of RNAs
Guide RNA gRNA mRNA nucleotide modification / RNA editing Kinetoplastid mitochondria [20]
Ribonuclease P RNase P tRNA maturation All organisms [21]
Ribonuclease MRP RNase MRP rRNA maturation, DNA replication Eukaryotes [22]
Y RNA RNA processing, DNA replication Animals [23]
Telomerase RNA Telomere synthesis Most eukaryotes [24]
Ribozyme Catalysis All cells
Transposon Self-propagating All cells
Regulatory RNAs
Type Abbr. Function Distribution Ref.
Antisense RNA aRNA Transcriptional attenuation / mRNA degradation / mRNA stabilisation / Translation block Gene regulation All organisms [25][26]
Cis-natural antisense transcript Gene regulation
CRISPR RNA crRNA Resistance to parasites, probably by targeting their DNA Bacteria and archaea [27]
Long noncoding RNA Long ncRNA Various Eukaryotes
MicroRNA miRNA Gene regulation Most eukaryotes [28]
Piwi-interacting RNA piRNA Transposon defense Gene regulation Animal germline cells [29][30]
Small interfering RNA siRNA Gene regulation Most eukaryotes [31]
Trans-acting siRNA tasiRNA Gene regulation Land plants [32]
Repeat associated siRNA rasiRNA Type of piRNA; transposon defense Drosophila [33]

Enstructuring Pi into any RNA is usually not accomplished by reacting directly with ribose for RNA, deoxyribose present in DNA, purines, or pyrimidines. Although DNA records the sequence of nucleobases that are connected by ribose to Pi, the transcription process chosen by probably all life on Earth requires triphosphate nucleotides (NTPs).

For example, consider making a mRNA for a particular protein from the point of view of phosphate enstructuring. As of 2008 dystrophin has the longest gene known, at locus Xp21.2. The primary transcript measures 2.4 megabases (thus the gene comprises 0.008% of the human genome), and takes 16 hours to transcribe. The 79 exons[34] code for a protein of over 3500 amino acid (aa) residues. It is human GeneID: 1756.[35] Isoform Dp427c has 3677 aa[36] which are specified by 3677 codons of 3 nucleotides each. That's 11,031 NMPs with one Pi each.

But the gene portion that is transcribed also contains a 5' cap requiring one GTP, a 5' UTR, 78 introns, and a 3' UTR or as mentioned 2.4 Mb of one Pi each. In this excess generation of RNA dystrophin is not unique. More than 95% of the enstructured phosphate for RNA synthesized by RNA polymerase II never reaches the cytoplasm. The main reason for this is due to the removal of introns which account for 80% of the total bases.[37]

Per the apparently available phosphate reserve in a cell or intracellular phosphate of about 10-3 Pi (1 molecule of Pi per 1000 other molecules, such as water) at any particular location and a rate of about 42 NTPs per second to transcribe this mRNA, some form of intranuclear transport other than diffusion is needed. While the number of transcription units varies at any given moment, should per transcription factories there be ~64,000 polymerase II active transcription units operating at about 42 NTPs per second, there would need to be a way to supply a total phosphate of ~2,700,000 NTPs per second to all transcription units in parallel.

With respect to phosphate reserves each ATP is recycled about once every minute on average. This may also be true for CTP, GTP, and UTP. That is ~0.07 recycled NTPs per second are available to transcribe on average.

Using the information derived regarding signal transduction for a water molecule of speed 15 µms-1, if a nucleus of 5 µm diameter contains ~64,000 transcription units uniformly distributed throughout (a volume with ~120 nm diameter for each unit), it would take about 40 seconds for a GTP molecule to interact with one unit with ten molecules in each unit volume. The GTP molecule would have a speed of ~2800 nms-1. But to get to 24 ms between interactions would take ~17,000 NTP molecules in a volume of ~120 nm diameter. That is ~68 µg/ml GTP. As the total number of normally available intracellular phosphate molecules, if uniformly distributed throughout the cell, would be ~33,000 molecules of all phosphate compunds within each ~120 nm diameter volume, diffusion may be sufficient. Pulling in additional phosphate from extracellular fluid would help to increase the amount of available phosphate, probably enough to make 42 NTPs per second reasonable.

Subtracting the estimated number of phosphates in the genome DNA yields ~21,000 phosphate molecules for all other purposes. The amount of phosphate in the cell membrane would reduce the available phosphate to ~20,000 molecules. But, if half the available phosphate is already tied up in RNA or other structures, then transport across the cell membrane and diffusion throughout the cell is mandatory.

Alternatively, if the actual translational speed of a water molecule is closer to 75 µms-1, the needed phosphate is in ~3,400 NTPs. However, for transcription of a mRNA roughly equal amounts of ATP, CTP, GTP, and UTP need to be present in each ~120 nm diameter volume. That's ~13,600 NTPs with 3 phosphates each for ~41,000 phosphates. To have the needed concentration in the nucleus, the entire cell needs to be at the same level of phosphate in the cytosol. The total phosphate uniformly distributed by diffusion throughout the cytosol is ~24 x 109: ~6.0 x 109 each of ATP, CTP, GTP, and UTP.

Average phosphate content of human RNAs
Abbr. GeneID Number of basepairs Accumulative average phosphates
mRNA 1 1488 1488
mRNA 2 4425 2956.5
mRNA 9 873 2262
mRNA 10 873 1914.8
mRNA 12 1272 1786.2
ncRNA 245 2768 2768
ncRNA 303 1343 2055.5
ncRNA 305 1350 1820.3
ncRNA 1057 985 1611.5
ncRNA 1197 1812 1651.6
ncRNA 1587 variant 1 2642 1816.7
ncRNA 1587 variant 2 2396 1988.4
ncRNA 1587 variant 3 2491 1973.4
miscRNA (ncRNA) 711 2264 2264
miscRNA (ncRNA) 3262 1198 1731
miscRNA (ncRNA) 5820 1918 1793.3
miscRNA (Long? ncRNA) 7503 19271 6162.8
miscRNA (ncRNA) 8123 3373 5604.8
miscRNA (ncRNA) 8420 939 4827.2
rRNA 4549 953 953
rRNA 4550 1558 1255.5
rRNA (ribosome component) 6052 --- ---
rRNA (ribosome component) 6053 --- ---
rRNA (ribosome component) 6054 --- ---
rRNA (ribosome component) 6055 --- ---
rRNA (ribosome component) 6056 --- ---
rRNA 100008587 156 889
rRNA 100008588 1869 1134
rRNA 100008589 5070 1921.2
SRP RNA (miscRNA) 6029 299 299
SRP RNA (scRNA) 378706 299 299
tRNA 4511 (mitochondrial) 65 65
tRNA 4553 (mitochondrial) 68 66.5
tRNA 4555 (mitochondrial) 67 66.7
tRNA 4556 (mitochondrial) 68 67
tRNA 4558 (mitochondrial) 70 67.6
snRNA (spliceosome) 6060 164 164
snRNA (spliceosome) 6066 188 176
snRNA (ncRNA) 125050 332 228
snRNA (spliceosome) 100151683 130 203.5
snRNA (spliceosome) 100151684 125 187.8
snoRNA (ncRNA) 6043 135 135
snoRNA (ncRNA) 6044 154 144.5
snoRNA (ncRNA) 6079 148 145.7
snoRNA (ncRNA) 6080 207 161
snoRNA (ncRNA) 6081 205 169.8
RNase P (miscRNA) 85495 341 341
RNase MRP (miscRNA) 6023 265 265
Y RNA (scRNA) 6084 113 113
Y RNA (scRNA) 6085 102 107.5
Y RNA (scRNA) 6086 96 103.7
Y RNA (scRNA) 6090 84 98.8
Telomerase RNA (miscRNA) 7012 451 451
Ribozyme (ncRNA 54677 1264 1264
Alu sequence (Transposon) ? ~300 ~300
aRNA (miscRNA) 6315 1472 1472
aRNA (miscRNA) 8475 1286 1379
aRNA (miscRNA) 9383 37027 13261.7
aRNA (miscRNA) 10108 --- 13261.7
aRNA (miscRNA) 10737 variant 1 1357 13261.7
aRNA (miscRNA) 10737 variant 2 1115 8451.4
aRNA (miscRNA) 10740 5125 7897
Long ncRNA 7503 19271 19271
Long ncRNA 9383 37027 28149
Long ncRNA 10984 59461 38586.3
miRNA 406991 71 71
miRNA 406952 83 77
miRNA 406902 109 87.7
miRNA 407043 109 93
miRNA 407006 109 96.2
piRNA ? 29-30 29-30
siRNA ? 20-25 20-25

In the table above those RNAs with a GeneID less than 30000 are found by searching among the human GeneIDs up to 30000. A total of 230 RNA genes, including variants, occur prior to GeneID 30000. There are as of July 22, 2009, 15827 human genes of all types, including variants and pseudogenes, at and before GeneID: 30000. Of the pseudogenes, 521 are inactive. Many of the active pseudogenes are RNA transcribing genes. Some 611 of these GeneIDs are also not transcribed genes. Some 14,695 are active and transcribed.

Using a likely cellular phosphate budget in a human adult as a guide, an average cell could be operating ~28,800 transcription units. For a lateral speed of 37 µms-1 of a water molecule, an average cell could operate ~14,400 transcription units by diffusion.

For an average cell of "default" cell type running the 14,695 active and transcribeable genes including variants, 14,464 mRNAs and 230 other assorted RNAs are being transcribed. As the above table lists the number of phosphates per RNA on average, an RNA transcription budget can be estimated, assuming each is halfway through transcription.

Estimated phosphate budget for RNAs
Abbr. Number of RNAs Number of structural phosphates Accumulative phosphates
mRNA 14,464 ~12.9 x 106 ~12.9 x 106
snoRNA 77 ~6500 ~12.9 x 106
tRNA 59 ~2000 ~12.9 x 106
miscRNA 39 ~94,000 ~13.0 x 106
ncRNA 21 ~21,000 ~13.0 x 106
RNA 11 ~10,000 ~13.1 x 106
aRNA 7 ~28,000 ~13.1 x 106
rRNA 6 ~5800 ~13.1 x 106
Y RNA 4 ~200 ~13.1 x 106
SRP 2 ~300 ~13.1 x 106
snRNA 2 ~200 ~13.1 x 106
Long ncRNA 2 ~39,000 ~13.1 x 106

Deoxyribonucleic acid (DNA)

The entire human genome has ~3.4 Gb in its DNA, with one Pi each. That is ~3.4 x 109 Pi tied up in DNA per strand, ~6.8 x 109 Pi total structural phosphate in each nucleus. With ~19 x 109 Pi per cell in some form, that leaves ~12 x 109 Pi per cell for all other functions and forms.

Mitochondria have their own genetic material, and the machinery to manufacture their own RNAs and proteins. A published human mitochondrial DNA sequence revealed 16,569 base pairs encoding 37 total genes, 24 tRNA and rRNA genes and 13 peptide genes.[38] The mitochondrial matrix contains several (2-10) copies of the mitochondrial DNA genome. Up to ~2000 mitochondria can occur per cell. This can enstructure up to ~3.3 x 108 phosphates.

Cartilage

Mineralization in the extracellular matrix starting with hydroxyapatite deposition into a collagenous scaffolding of cartilage, cementum, dentin and bone is initially regulated locally by calcium, orthophosphate, and pyrophosphate ion concentrations.

Although cuboid calcium phosphate crystals are absent in young articular cartilage, they are sometimes present in old normal articular cartilage occasionally adjacent to larger areas of pyrophosphate crystals.[39]

Endochondrial ossification of cartilage development ultimately leads to mineralization of the extracellular matrix.[40] Metabolism of Ca2+ and Pi by cartilage growth plate chondrocytes, involved in matrix vesicle formation, clearly are integral features of endochondrial calcification.[40] This calcification is apparently due to the diffusion barrier and avascularity progressing from the zone of proliferation to the zone of hypertrophy of the cartilage growth plate chondrocytes environment.[40]

Teeth

Hydroxyapatite, which is a crystalline calcium phosphate is the primary mineral of enamel.[41]

By weight, seventy percent of dentin consists of the mineral, hydroxylapatite, twenty percent is organic material, and ten percent is water.[42]

Cementum is a specialized bony substance covering the root of a tooth, composed of approximately 45% inorganic material (mainly hydroxyapatite), 33% organic material (mainly collagen) and 22% water.

Bone

During bone resorption high levels of phosphate are released into the ECF as osteoclasts tunnel into mineralized bone, breaking it down and releasing phosphate, that results in a transfer of phosphate from bone fluid to the blood. During childhood, bone formation exceeds resorption, but as the aging process occurs, resorption exceeds formation.

Transphosphorylation between nucleotides and hydroxyapatite (HA) results in a pyrophosphate on HA that is distinctive from pyrophosphate absorbed onto HA from solution. This may be due to a different orientation of the pyrophosphate on the surface depending on the origin of the pyrophosphate.[43]

Sedimentary phosphorites

Phosphogenesis under palaeoceanographic conditions that were different from modern phosphorite depositional systems occurred across a broad range of palaeoenvironments in the shallow and broad epicontinental Phosphoria Sea.[44] These conditions were revealed by oxygen isotope analyses of the structural phosphate in sedimentary phosphorites of the Upper Permian Phosphoria Formation.[44]

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from Wikipedia.

References

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