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
  • 4470639 aldehydo 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)
100 g/L (25 °C, 77 °F)
−21.5° (H2O)
Related compounds
Related aldopentoses
 Arabinose
Xylose
Lyxose
Related compounds
 Deoxyribose
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
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L-Ribose Fischer Projection

Ribose is a

Oscar Piloty in 1891.[3] It was not until 1909 that Phoebus Levene and Walter Jacobs recognised that d-ribose was a natural product, the enantiomer of Fischer and Piloty's product, and an essential component of nucleic 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 an epimer at the 2' carbon; both names also relate to gum arabic, from which arabinose was first isolated and from which they prepared l-ribose.[6][7]

open chain
forms of d- and l- ribose

Like most sugars, ribose exists as a mixture of

hydroxyl functional groups on the same side in its Fischer projection. d-Ribose has these hydroxyl groups on the right hand side and is associated with the systematic name (2R,3R,4R)-2,3,4,5-tetrahydroxypentanal,[9] whilst l-ribose has its hydroxyl groups appear on the left hand side in a Fischer projection. Cyclisation of ribose occurs via hemiacetal formation due to attack on the aldehyde by the C4' hydroxyl group to produce a furanose form or by the C5' hydroxyl group to produce a pyranose form. In each case, there are two possible geometric outcomes, named as α- and β- and known as anomers, depending on the stereochemistry at the hemiacetal carbon atom (the "anomeric carbon"). At room temperature, about 76% of d-ribose is 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]

The

phosphorylated ribose include ADP, ATP, coenzyme A,[8]: 228–229  and NADH. cAMP and cGMP serve as secondary messengers in some signaling pathways and are also ribose derivatives. The ribose moiety appears in some pharmaceutical agents, including the antibiotics neomycin and paromomycin.[10]

Synthesis and sources

Ribose as its 5-phosphate ester is typically produced from glucose by the pentose 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 of

B. 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 in meteorites.[15][16]

Structure

Ribose is an

hydroxyl group at C2'. This hydroxyl group performs a function in RNA splicing
.

The "d-" in the name d-ribose refers to the

d-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 in

torsion 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.

nitrogenous base (also known as a nucleobase or 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.

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 cause

B form DNA. Z-DNA contains 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

ATP is derived from ribose; it contains one ribose, three phosphate groups, and an adenine base. ATP is created during cellular respiration from adenosine diphosphate (ATP with one less phosphate group).

Signaling pathways

Ribose is a building block in secondary signaling molecules such as

signal molecule. These receptors are linked to a stimulative or inhibitory regulative G-protein. When a stimulative G-protein is activated, adenylyl cyclase catalyzes ATP into cAMP by using Mg2+ or Mn2+. cAMP, a secondary messenger, then goes on to activate protein kinase A, which is an enzyme that regulates cell metabolism. Protein kinase A regulates metabolic enzymes by phosphorylation which 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

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), and nicotinamide adenine dinucleotide phosphate (NADP) all contain the d-ribofuranose moiety. They can each be derived from d-ribose after it is converted to d-ribose 5-phosphate by the enzyme ribokinase.[22][23] NAD, FAD, and NADP act as electron acceptors in biochemical redox reactions in major metabolic pathways including glycolysis, the citric acid cycle, fermentation, and the electron transport chain.

Pentose Phosphate Pathway: begins with d-glucose and includes d-ribose 5-phosphate as an intermediate

Nucleotide biosynthesis

Nucleotides are synthesized through salvage or

PRPP synthetase.[24]

Modifications

Modifications in nature

amino acids tryptophan and histidine, or for use in the pentose phosphate pathway. The absorption of d-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 an

intramolecular hydrogen bonding and an increase in the glycosidic bond stability.[26] The resulting increase of resistance leads to increases in the half-life of siRNA and the potential therapeutic potential in cells and animals.[27] The methylation of ribose at particular sites is correlated with a decrease in immune stimulation.[28]

Synthetic modifications

Along with phosphorylation, ribofuranose molecules can exchange their oxygen with selenium and sulfur to produce similar sugars that only vary at the 4' position. These derivatives are more lipophilic than the original molecule. Increased lipophilicity makes these species more suitable for use in techniques such as PCR, RNA aptamer post-modification, antisense technology, and for phasing X-ray crystallographic data.[27]

Similar to the 2' modifications in nature, a synthetic modification of ribose includes the addition of

fluorinated ribose 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

d-ribose has been suggested for use in management of

chronic fatigue syndrome (CFS), also called myalgic encephalomyelitis (ME) in an open-label non-blinded, non-randomized, and non-crossover subjective study.[30]

Supplemental d-ribose can bypass part of the

pathological conditions, 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

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  9. ^ Leigh, Jeffery (July–August 2012). "Non-IUPAC Nomenclature Systems". Chemistry International. 34 (4). International Union of Pure and Applied Chemistry. Archived from the original on 5 December 2019. Retrieved 15 December 2019.
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  15. ^ Steigerwald, Bill; Jones, Nancy; Furukawa, Yoshihiro (18 November 2019). "First Detection of Sugars in Meteorites Gives Clues to Origin of Life". NASA. Archived from the original on 15 January 2021. Retrieved 18 November 2019.
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  25. ^ "Herbal Remedies, Supplements A-Z Index". PDRHealth.com. PDR, LLC. Archived from the original on 11 October 2008.
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  31. ^ "Ribose". wa.kaiserpermanente.org. Archived from the original on 3 March 2021. Retrieved 7 October 2019.
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