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Ribose

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d-Ribose
Names
IUPAC name
D-Ribose
Systematic IUPAC name
(2R,3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
Other names
d-Ribose
Identifiers
3D model (JSmol)
ChEMBL
ChemSpider
  • 4470639aldehydo form D-(−)-Ribose☒N
DrugBank
EC Number
  • 200-059-4
UNII
  • aldehydo form D-(−)-Ribose: InChI=1/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4+,5-/m0/s1
    Key: PYMYPHUHKUWMLA-LMVFSUKVBD
  • Aldehydo form D-(−)-Ribose: InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4+,5-/m0/s1
    Key: PYMYPHUHKUWMLA-LMVFSUKVSA-N
  • aldehydo form D-(−)-Ribose: C([C@H]([C@H]([C@H](C=O)O)O)O)O
Properties[1][2]
C5H10O5
Molar mass 150.13
Appearance White solid
Melting point 95 °C (203 °F; 368 K)
100g/L (25 °C, 77 °F)
−21.5° (H2O)
Related compounds
Arabinose
Xylose
Lyxose
Related compounds
 Deoxyribose
Except where otherwise noted, data are given for materials in theirstandard state(at 25 °C [77 °F], 100 kPa).
L-RiboseFischer Projection

Riboseis asimple sugarandcarbohydratewithmolecular formulaC5H10O5and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally-occurring form,d-ribose,is a component of theribonucleotidesfrom whichRNAis built, and so this compound is necessary forcoding,decoding,regulationandexpressionofgenes.It has astructural analog,deoxyribose,which is a similarly essential component ofDNA.l-riboseis an unnatural sugar that was first prepared byEmil FischerandOscar Pilotyin 1891.[3]It was not until 1909 thatPhoebus LeveneandWalter Jacobsrecognised thatd-ribosewas anatural product,theenantiomerof Fischer and Piloty's product, and an essential component ofnucleic acids.[4][5][6]Fischer chose the name "ribose" as it is a partial rearrangement of the name of another sugar,arabinose,of which ribose is anepimerat the 2' carbon; both names also relate togum arabic,from which arabinose was first isolated and from which they preparedl-ribose.[6][7]

β-d-ribofuranose
α-d-ribopyranose
d-ribose
l-ribose
Left:Haworth projectionsof one of each of the furanose and pyranose forms ofd-ribose
Right:Fischer projectionof theopen chainforms ofd- andl- ribose

Like most sugars, ribose exists as a mixture ofcyclic formsinequilibriumwith its linear form, and these readily interconvert especially inaqueous solution.[8]The name "ribose" is used in biochemistry and biology to refer to all of these forms, though more specific names for each are used when required. In its linear form, ribose can be recognised as thepentosesugar with all of itshydroxylfunctional groupson the same side in itsFischer projection.d-Ribosehas these hydroxyl groups on the right hand side and is associated with thesystematic name(2R,3R,4R)-2,3,4,5-tetrahydroxypentanal,[9]whilstl-ribosehas its hydroxyl groups appear on the left hand side in a Fischer projection. Cyclisation of ribose occurs viahemiacetalformation due to attack on thealdehydeby the C4' hydroxyl group to produce afuranoseform or by the C5' hydroxyl group to produce apyranoseform. In each case, there are two possible geometric outcomes, named as α- and β- and known asanomers,depending on thestereochemistryat the hemiacetal carbon atom (the "anomeric carbon" ). At room temperature, about 76% ofd-riboseis present in pyranose forms[8]: 228 (α:β = 1:2)[10]and 24% in the furanose forms[8]: 228 (α:β = 1:3),[10]with only about 0.1% of the linear form present.[11][12]

Theribonucleosidesadenosine,cytidine,guanosine,anduridineare allderivativesof β-d-ribofuranose.Metabolically-importantspecies that includephosphorylatedribose includeADP,ATP,coenzyme A,[8]: 228–229 andNADH.cAMPandcGMPserve as secondary messengers in some signaling pathways and are also ribose derivatives. The ribosemoietyappears in some pharmaceutical agents, including the antibioticsneomycinandparomomycin.[10]

Synthesis and sources[edit]

Ribose as its 5-phosphate ester is typically produced from glucose by thepentose phosphate pathway.In at least some archaea, alternative pathways have been identified.[13]

Ribose can be synthesized chemically, but commercial production relies on fermentation of glucose. Using genetically modified strains ofB. subtilis,90 g/liter of ribose can be produced from 200 g of glucose. The conversion entails the intermediacy of gluconate and ribulose.[14]

Ribose has been detected inmeteorites.[15][16]

Structure[edit]

Ribose is analdopentose(a monosaccharide containing fivecarbonatoms that, in itsopen chainform, has analdehydefunctional groupat one end). In the conventional numbering scheme for monosaccharides, the carbon atoms are numbered from C1' (in the aldehyde group) to C5'. Thedeoxyribosederivative found in DNA differs from ribose by having ahydrogenatom in place of thehydroxylgroup at C2'. This hydroxyl group performs a function inRNA splicing.

The "d- "in the named-ribose refers to thestereochemistryof thechiralcarbon atom farthest away from the aldehyde group (C4'). Ind-ribose, as in alld-sugars, this carbon atom has the same configuration as ind-glyceraldehyde.

  • α-d-Ribopyranose
    α-d-Ribopyranose
  • β-d-Ribopyranose
    β-d-Ribopyranose
  • α-d-Ribofuranose
    α-d-Ribofuranose
  • β-d-Ribofuranose
    β-d-Ribofuranose

Relative abundance of forms of ribose in solution: β-d-ribopyranose (59%), α-d-ribopyranose (20%), β-d-ribofuranose (13%), α-d-ribofuranose (7%) and open chain (0.1%).[11]

For ribose residues innucleosidesandnucleotide,the torsion angles for the rotation encompassing the bonds influence the configuration of the respective nucleoside and nucleotide. Thesecondary structureof a nucleic acid is determined by the rotation of its 7torsion angles.[17]Having a large amount of torsion angles allows for greater flexibility.

In closed ring riboses, the observed flexibility mentioned above is not observed because the ring cycle imposes a limit on the number of torsion angles possible in the structure.[17]Conformers of closed form riboses differ in regards to how the loneoxygenin the molecule is positioned respective to thenitrogenous base(also known as anucleobaseor just a base) attached to the ribose. If a carbon is facing towards the base, then the ribose is labeled as endo. If a carbon is facing away from the base, then the ribose is labeled as exo. If there is an oxygen molecule attached to the 2' carbon of a closed cycle ribose, then the exo confirmation is more stable because it decreases the interactions of the oxygen with the base.[17]The difference itself is quite small, but when looking at an entire chain of RNA the slight difference amounts to a sizable impact.

  • Some pucker configurations of Ribose
  • 2' endo
    2' endo
  • 2' endo 3' exo
    2' endo 3' exo
  • 3' endo 2' exo
    3' endo 2' exo
  • 3' endo
    3' endo

A ribose molecule is typically represented as a planar molecule on paper. Despite this, it is typically non-planar in nature. Even between hydrogen atoms, the many constituents on a ribose molecule causesteric hindranceand strain between them. To relieve this crowding andring strain,the ring puckers, i.e. becomes non-planar.[18]This puckering is achieved by displacing an atom from the plane, relieving the strain and yielding a more stable configuration.[17]Puckering, otherwise known as the sugar ring conformation (specifically ribose sugar), can be described by the amplitude of pucker as well as thepseudorotationangle. The pseudo-rotation angle can be described as either "north (N)" or "south (S)" range. While both ranges are found in double helices, the north range is commonly associated with RNA and theA form of DNA.In contrast, the south range is associated withB form DNA.Z-DNAcontains sugars in both the north and south ranges.[19]When only a single atom is displaced, it is referred to as an "envelope" pucker. When two atoms are displaced, it is referred to as a "twist" pucker, in reference to the zigzag orientation.[20]In an "endo" pucker, the major displacement of atoms is on the β-face, the same side as the C4'-C5' bond and the base. In an "exo" pucker, the major displacement of atoms is on the α-face, on the opposite side of the ring. The major forms of ribose are the 3'-endo pucker (commonly adopted by RNA and A-form DNA) and 2'-endo pucker (commonly adopted by B-form DNA).[21]These ring puckers are developed from changes in ring torsion angles; there are infinite combinations of angles so therefore, there is an infinite number of transposable pucker conformations, each separated by disparate activation energies.

Functions[edit]

ATP is derived from ribose; it contains one ribose, threephosphategroups, and anadeninebase. ATP is created duringcellular respirationfromadenosine diphosphate(ATP with one less phosphate group).

Signaling pathways[edit]

Ribose is a building block in secondary signaling molecules such ascyclic adenosine monophosphate(cAMP) which is derived from ATP. One specific case in which cAMP is used is incAMP-dependent signaling pathways.In cAMP signaling pathways, either a stimulative or inhibitory hormone receptor is activated by asignal molecule.These receptors are linked to a stimulative or inhibitory regulativeG-protein.When a stimulative G-protein is activated,adenylyl cyclasecatalyzesATP into cAMP by using Mg2+or Mn2+.cAMP, a secondary messenger, then goes on to activateprotein kinase A,which is anenzymethat regulates cellmetabolism.Protein kinase A regulates metabolic enzymes byphosphorylationwhich causes a change in the cell depending on the original signal molecule. The opposite occurs when an inhibitory G-protein is activated; the G-protein inhibits adenylyl cyclase and ATP is not converted to cAMP.

The difference between ribose and deoxyribose is the presence of a 2'OH

Metabolism[edit]

Ribose is referred to as the "molecular currency" because of its involvement in intracellular energy transfers.[citation needed]For example,nicotinamide adenine dinucleotide(NAD),flavin adenine dinucleotide(FAD), andnicotinamide adenine dinucleotide phosphate(NADP) all contain thed-ribofuranosemoiety.They can each bederived fromd-ribose after it is converted tod-ribose 5-phosphateby the enzymeribokinase.[22][23]NAD, FAD, and NADP act as electron acceptors in biochemicalredoxreactions in major metabolic pathways includingglycolysis,thecitric acid cycle,fermentation,and theelectron transport chain.

Pentose Phosphate Pathway: begins withd-glucose and includesd-ribose 5-phosphate as an intermediate

Nucleotide biosynthesis[edit]

Nucleotides are synthesized through salvage orde novo synthesis.[24]Nucleotide salvageuses pieces of previously made nucleotides and re-synthesizes them for future use. In de novo, amino acids, carbon dioxide, folate derivatives, andphosphoribosyl pyrophosphate(PRPP) are used to synthesize nucleotides.[24]Both de novo and salvage require PRPP which is synthesized from ATP and ribose 5-phosphate by an enzyme calledPRPP synthetase.[24]

Modifications[edit]

Modifications in nature[edit]

Ribokinasecatalyzes the conversion ofd-ribose tod-ribose 5-phosphate.Once converted,d-ribose-5-phosphate is available for the manufacturing of theamino acidstryptophanandhistidine,or for use in thepentose phosphate pathway.The absorption ofd-ribose is 88–100% in the small intestines (up to 200 mg/kg·h).[25]

One important modification occurs at the C2' position of the ribose molecule. By adding anO-alkylgroup, the nuclear resistance of the RNA is increased because of additional stabilizing forces. These forces are stabilizing because of the increase ofintramolecular hydrogen bondingand an increase in theglycosidic bondstability.[26]The resulting increase of resistance leads to increases in thehalf-lifeofsiRNAand the potential therapeutic potential in cells and animals.[27]Themethylationof ribose at particular sites is correlated with a decrease in immune stimulation.[28]

Synthetic modifications[edit]

Along with phosphorylation, ribofuranose molecules can exchange their oxygen withseleniumandsulfurto produce similar sugars that only vary at the 4' position. These derivatives are morelipophilicthan the original molecule. Increased lipophilicity makes these species more suitable for use in techniques such asPCR,RNA aptamerpost-modification,antisense technology,and for phasingX-ray crystallographicdata.[27]

Similar to the 2' modifications in nature, a synthetic modification of ribose includes the addition offluorineat the 2' position. Thisfluorinatedribose acts similar to the methylated ribose because it is capable of suppressing immune stimulation depending on the location of the ribose in the DNA strand.[26]The big difference between methylation and fluorination, is the latter only occurs through synthetic modifications. The addition of fluorine leads to an increase in the stabilization of the glycosidic bond and an increase of intramolecular hydrogen bonds.[26]

Medical uses[edit]

d-ribose has been suggested for use in management ofcongestive heart failure[29](as well as other forms of heart disease) and forchronic fatigue syndrome(CFS), also called myalgic encephalomyelitis (ME) in an open-label non-blinded, non-randomized, and non-crossover subjective study.[30]

Supplementald-ribose can bypass part of thepentose phosphate pathway,an energy-producing pathway, to produced-ribose-5-phosphate. The enzymeglucose-6-phosphate-dehydrogenase(G-6-PDH) is often in short supply in cells, but more so in diseased tissue, such as inmyocardialcells in patients with cardiac disease. The supply ofd-ribose in themitochondriais directly correlated with ATP production; decreasedd-ribose supply reduces the amount of ATP being produced. Studies suggest that supplementingd-ribose following tissue ischemia (e.g. myocardial ischemia) increases myocardial ATP production, and therefore mitochondrial function. Essentially, administering supplementald-ribose bypasses an enzymatic step in the pentose phosphate pathway by providing an alternate source of 5-phospho-d-ribose 1-pyrophosphatefor ATP production. Supplementald-ribose enhances recovery of ATP levels while also reducing cellular injury in humans and other animals. One study suggested that the use of supplementald-ribose reduces the instance ofanginain men with diagnosedcoronary artery disease.[31]d-Ribose has been used to treat manypathologicalconditions, such as chronic fatigue syndrome,fibromyalgia,and myocardial dysfunction. It is also used to reduce symptoms of cramping, pain, stiffness, etc. after exercise and to improve athletic performance[citation needed].

References[edit]

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  29. ^Omran, Heyder; McCarter, Dean; St Cyr, John; Lüderitz, Berndt (2004)."ᴅ-Ribose aids congestive heart failure patients".Experimental & Clinical Cardiology.Summer (9(2)): 117–118.PMC2716264.PMID19641697.
  30. ^Teitelbaum, Jacob E.; Johnson, Clarence; St Cyr, John (26 November 2006). "The use of ᴅ-ribose in chronic fatigue syndrome and fibromyalgia: a pilot study".The Journal of Alternative and Complementary Medicine.12(9): 857–862.CiteSeerX10.1.1.582.4800.doi:10.1089/acm.2006.12.857.PMID17109576.
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