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Wednesday, September 9, 2020

Nucleotide

From Wikipedia, the free encyclopedia
 
This nucleotide contains the five-carbon sugar deoxyribose (at center), a nitrogenous base called adenine (upper right), and one phosphate group (left). The deoxyribose sugar joined only to the nitrogenous base forms a Deoxyribonucleoside called deoxyadenosine, whereas the whole structure along with the phosphate group is a nucleotide, a constituent of DNA with the name deoxyadenosine monophosphate.
 
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. 

Nucleotides are composed of three subunit molecules: a nitrogenous base (also known as nucleobase), a five-carbon sugar (ribose or deoxyribose), and a phosphate group consisting of one to three phosphates. The four nitrogenous bases in DNA are guanine, adenine, cytosine and thymine; in RNA, uracil is used in place of thymine. 

Nucleotides also play a central role in metabolism at a fundamental, cellular level. They provide chemical energy—in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP) and uridine triphosphate (UTP)—throughout the cell for the many cellular functions that demand energy, including: amino acid, protein and cell membrane synthesis, moving the cell and cell parts (both internally and intercellularly), cell division, etc. In addition, nucleotides participate in cell signaling (cyclic guanosine monophosphate or cGMP and cyclic adenosine monophosphate or cAMP), and are incorporated into important cofactors of enzymatic reactions (e.g. coenzyme A, FAD, FMN, NAD, and NADP+). 

In experimental biochemistry, nucleotides can be radiolabeled using radionuclides to yield radionucleotides.

Structure

Showing the arrangement of nucleotides within the structure of nucleic acids: At lower left, a monophosphate nucleotide; its nitrogenous base represents one side of a base-pair. At upper right, four nucleotides form two base-pairs: thymine and adenine (connected by double hydrogen bonds) and guanine and cytosine (connected by triple hydrogen bonds). The individual nucleotide monomers are chain-joined at their sugar and phosphate molecules, forming two 'backbones' (a double helix) of a nucleic acid, shown at upper left.
 
A nucleotide is composed of three distinctive chemical sub-units: a five-carbon sugar molecule, a nitrogenous base—which two together are called a nucleoside—and one phosphate group. With all three joined, a nucleotide is also termed a "nucleoside monophosphate", "nucleoside diphosphate" or "nucleoside triphosphate", depending on how many phosphates make up the phosphate group. 

In nucleic acids, nucleotides contain either a purine or a pyrimidine base—i.e., the nitrogenous base molecule, also known as a nucleobase—and are termed ribonucleotides if the sugar is ribose, or deoxyribonucleotides if the sugar is deoxyribose. Individual phosphate molecules repetitively connect the sugar-ring molecules in two adjacent nucleotide monomers, thereby connecting the nucleotide monomers of a nucleic acid end-to-end into a long chain. These chain-joins of sugar and phosphate molecules create a 'backbone' strand for a single- or double helix. In any one strand, the chemical orientation (directionality) of the chain-joins runs from the 5'-end to the 3'-end (read: 5 prime-end to 3 prime-end)—referring to the five carbon sites on sugar molecules in adjacent nucleotides. In a double helix, the two strands are oriented in opposite directions, which permits base pairing and complementarity between the base-pairs, all which is essential for replicating or transcribing the encoded information found in DNA. 

Nucleic acids then are polymeric macromolecules assembled from nucleotides, the monomer-units of nucleic acids. The purine bases adenine and guanine and pyrimidine base cytosine occur in both DNA and RNA, while the pyrimidine bases thymine (in DNA) and uracil (in RNA) occur in just one. Adenine forms a base pair with thymine with two hydrogen bonds, while guanine pairs with cytosine with three hydrogen bonds.




In addition to being building blocks for construction of nucleic acid polymers, singular nucleotides play roles in cellular energy storage and provision, cellular signaling, as a source of phosphate groups used to modulate the activity of proteins and other signaling molecules, and as enzymatic cofactors, often carrying out redox reactions. Signaling cyclic nucleotides are formed by binding the phosphate group twice to the same sugar molecule, bridging the 5'- and 3'- hydroxyl groups of the sugar. Some signaling nucleotides differ from the standard single-phosphate group configuration, in having multiple phosphate groups attached to different positions on the sugar. Nucleotide cofactors include a wider range of chemical groups attached to the sugar via the glycosidic bond, including nicotinamide and flavin, and in the latter case, the ribose sugar is linear rather than forming the ring seen in other nucleotides.

 
Structural elements of three nucleotides—where one-, two- or three-phosphates are attached to the nucleoside (in yellow, blue, green) at center: 1st, the nucleotide termed as a nucleoside monophosphate is formed by adding a phosphate (in red); 2nd, adding a second phosphate forms a nucleoside diphosphate; 3rd, adding a third phosphate results in a nucleoside triphosphate. + The nitrogenous base (nucleobase) is indicated by "Base" and "glycosidic bond" (sugar bond). All five primary, or canonical, bases—the purines and pyrimidines—are sketched at right (in blue).

Synthesis

Nucleotides can be synthesized by a variety of means both in vitro and in vivo.

In vitro, protecting groups may be used during laboratory production of nucleotides. A purified nucleoside is protected to create a phosphoramidite, which can then be used to obtain analogues not found in nature and/or to synthesize an oligonucleotide.




In vivo, nucleotides can be synthesized de novo or recycled through salvage pathways. The components used in de novo nucleotide synthesis are derived from biosynthetic precursors of carbohydrate and amino acid metabolism, and from ammonia and carbon dioxide. The liver is the major organ of de novo synthesis of all four nucleotides. De novo synthesis of pyrimidines and purines follows two different pathways. Pyrimidines are synthesized first from aspartate and carbamoyl-phosphate in the cytoplasm to the common precursor ring structure orotic acid, onto which a phosphorylated ribosyl unit is covalently linked. Purines, however, are first synthesized from the sugar template onto which the ring synthesis occurs. For reference, the syntheses of the purine and pyrimidine nucleotides are carried out by several enzymes in the cytoplasm of the cell, not within a specific organelle. Nucleotides undergo breakdown such that useful parts can be reused in synthesis reactions to create new nucleotides.

Pyrimidine ribonucleotide synthesis

The synthesis of UMP.
The color scheme is as follows: enzymes, coenzymes, substrate names, inorganic molecules
The synthesis of the pyrimidines CTP and UTP occurs in the cytoplasm and starts with the formation of carbamoyl phosphate from glutamine and CO2. Next, aspartate carbamoyltransferase catalyzes a condensation reaction between aspartate and carbamoyl phosphate to form carbamoyl aspartic acid, which is cyclized into 4,5-dihydroorotic acid by dihydroorotase. The latter is converted to orotate by dihydroorotate oxidase. The net reaction is:
(S)-Dihydroorotate + O2 → Orotate + H2O2
Orotate is covalently linked with a phosphorylated ribosyl unit. The covalent linkage between the ribose and pyrimidine occurs at position C1 of the ribose unit, which contains a pyrophosphate, and N1 of the pyrimidine ring. Orotate phosphoribosyltransferase (PRPP transferase) catalyzes the net reaction yielding orotidine monophosphate (OMP):
Orotate + 5-Phospho-α-D-ribose 1-diphosphate (PRPP) → Orotidine 5'-phosphate + Pyrophosphate
Orotidine 5'-monophosphate is decarboxylated by orotidine-5'-phosphate decarboxylase to form uridine monophosphate (UMP). PRPP transferase catalyzes both the ribosylation and decarboxylation reactions, forming UMP from orotic acid in the presence of PRPP. It is from UMP that other pyrimidine nucleotides are derived. UMP is phosphorylated by two kinases to uridine triphosphate (UTP) via two sequential reactions with ATP. First the diphosphate form UDP is produced, which in turn is phosphorylated to UTP. Both steps are fueled by ATP hydrolysis:
ATP + UMP → ADP + UDP
UDP + ATP → UTP + ADP
CTP is subsequently formed by amination of UTP by the catalytic activity of CTP synthetase. Glutamine is the NH3 donor and the reaction is fueled by ATP hydrolysis, too:
UTP + Glutamine + ATP + H2O → CTP + ADP + Pi
Cytidine monophosphate (CMP) is derived from cytidine triphosphate (CTP) with subsequent loss of two phosphates.

Purine ribonucleotide synthesis

The atoms that are used to build the purine nucleotides come from a variety of sources:
The synthesis of IMP. The color scheme is as follows: enzymes, coenzymes, substrate names, metal ions, inorganic molecules
Nucleotide synthesis.svg The biosynthetic origins of purine ring atoms

N1 arises from the amine group of Asp
C2 and C8 originate from formate
N3 and N9 are contributed by the amide group of Gln
C4, C5 and N7 are derived from Gly
C6 comes from HCO3 (CO2)
The de novo synthesis of purine nucleotides by which these precursors are incorporated into the purine ring proceeds by a 10-step pathway to the branch-point intermediate IMP, the nucleotide of the base hypoxanthine. AMP and GMP are subsequently synthesized from this intermediate via separate, two-step pathways. Thus, purine moieties are initially formed as part of the ribonucleotides rather than as free bases.




Six enzymes take part in IMP synthesis. Three of them are multifunctional:

  • GART (reactions 2, 3, and 5)
  • PAICS (reactions 6, and 7)
  • ATIC (reactions 9, and 10)
The pathway starts with the formation of PRPP. PRPS1 is the enzyme that activates R5P, which is formed primarily by the pentose phosphate pathway, to PRPP by reacting it with ATP. The reaction is unusual in that a pyrophosphoryl group is directly transferred from ATP to C1 of R5P and that the product has the α configuration about C1. This reaction is also shared with the pathways for the synthesis of Trp, His, and the pyrimidine nucleotides. Being on a major metabolic crossroad and requiring much energy, this reaction is highly regulated.

In the first reaction unique to purine nucleotide biosynthesis, PPAT catalyzes the displacement of PRPP's pyrophosphate group (PPi) by an amide nitrogen donated from either glutamine (N), glycine (N&C), aspartate (N), folic acid (C1), or CO2. This is the committed step in purine synthesis. The reaction occurs with the inversion of configuration about ribose C1, thereby forming β-5-phosphorybosylamine (5-PRA) and establishing the anomeric form of the future nucleotide.

Next, a glycine is incorporated fueled by ATP hydrolysis and the carboxyl group forms an amine bond to the NH2 previously introduced. A one-carbon unit from folic acid coenzyme N10-formyl-THF is then added to the amino group of the substituted glycine followed by the closure of the imidazole ring. Next, a second NH2 group is transferred from a glutamine to the first carbon of the glycine unit. A carboxylation of the second carbon of the glycin unit is concomitantly added. This new carbon is modified by the additional of a third NH2 unit, this time transferred from an aspartate residue. Finally, a second one-carbon unit from formyl-THF is added to the nitrogen group and the ring covalently closed to form the common purine precursor inosine monophosphate (IMP).

Inosine monophosphate is converted to adenosine monophosphate in two steps. First, GTP hydrolysis fuels the addition of aspartate to IMP by adenylosuccinate synthase, substituting the carbonyl oxygen for a nitrogen and forming the intermediate adenylosuccinate. Fumarate is then cleaved off forming adenosine monophosphate. This step is catalyzed by adenylosuccinate lyase.

Inosine monophosphate is converted to guanosine monophosphate by the oxidation of IMP forming xanthylate, followed by the insertion of an amino group at C2. NAD+ is the electron acceptor in the oxidation reaction. The amide group transfer from glutamine is fueled by ATP hydrolysis.

Pyrimidine and purine degradation

In humans, pyrimidine rings (C, T, U) can be degraded completely to CO2 and NH3 (urea excretion). That having been said, purine rings (G, A) cannot. Instead they are degraded to the metabolically inert uric acid which is then excreted from the body. Uric acid is formed when GMP is split into the base guanine and ribose. Guanine is deaminated to xanthine which in turn is oxidized to uric acid. This last reaction is irreversible. Similarly, uric acid can be formed when AMP is deaminated to IMP from which the ribose unit is removed to form hypoxanthine. Hypoxanthine is oxidized to xanthine and finally to uric acid. Instead of uric acid secretion, guanine and IMP can be used for recycling purposes and nucleic acid synthesis in the presence of PRPP and aspartate (NH3 donor).

Unnatural base pair (UBP)

An unnatural base pair (UBP) is a designed subunit (or nucleobase) of DNA which is created in a laboratory and does not occur in nature. In 2012, a group of American scientists led by Floyd Romesberg, a chemical biologist at the Scripps Research Institute in San Diego, California, published that his team designed an unnatural base pair (UBP). The two new artificial nucleotides or Unnatural Base Pair (UBP) were named d5SICS and dNaM. More technically, these artificial nucleotides bearing hydrophobic nucleobases, feature two fused aromatic rings that form a (d5SICS–dNaM) complex or base pair in DNA. In 2014 the same team from the Scripps Research Institute reported that they synthesized a stretch of circular DNA known as a plasmid containing natural T-A and C-G base pairs along with the best-performing UBP Romesberg's laboratory had designed, and inserted it into cells of the common bacterium E. coli that successfully replicated the unnatural base pairs through multiple generations. This is the first known example of a living organism passing along an expanded genetic code to subsequent generations. This was in part achieved by the addition of a supportive algal gene that expresses a nucleotide triphosphate transporter which efficiently imports the triphosphates of both d5SICSTP and dNaMTP into E. coli bacteria. Then, the natural bacterial replication pathways use them to accurately replicate the plasmid containing d5SICS–dNaM.




The successful incorporation of a third base pair is a significant breakthrough toward the goal of greatly expanding the number of amino acids which can be encoded by DNA, from the existing 21 amino acids to a theoretically possible 172, thereby expanding the potential for living organisms to produce novel proteins. The artificial strings of DNA do not encode for anything yet, but scientists speculate they could be designed to manufacture new proteins which could have industrial or pharmaceutical uses.

Length unit

Nucleotide (abbreviated "nt") is a common unit of length for single-stranded nucleic acids, similar to how base pair is a unit of length for double-stranded nucleic acids.

Nucleotide supplements

A study done by the Department of Sports Science at the University of Hull in Hull, UK has shown that nucleotides have significant impact on cortisol levels in saliva. Post exercise, the experimental nucleotide group had lower cortisol levels in their blood than the control or the placebo. Additionally, post supplement values of Immunoglobulin A were significantly higher than either the placebo or the control. The study concluded, "nucleotide supplementation blunts the response of the hormones associated with physiological stress."

Another study conducted in 2013 looked at the impact nucleotide supplementation had on the immune system in athletes. In the study, all athletes were male and were highly skilled in taekwondo. Out of the twenty athletes tested, half received a placebo and half received 480 mg per day of nucleotide supplement. After thirty days, the study concluded that nucleotide supplementation may counteract the impairment of the body's immune function after heavy exercise.

Abbreviation codes for degenerate bases

The IUPAC has designated the symbols for nucleotides. Apart from the five (A, G, C, T/U) bases, often degenerate bases are used especially for designing PCR primers. These nucleotide codes are listed here. Some primer sequences may also include the character "I", which codes for the non-standard nucleotide inosine. Inosine occurs in tRNAs, and will pair with adenine, cytosine, or thymine. This character does not appear in the following table however, because it does not represent a degeneracy. While inosine can serve a similar function as the degeneracy "D", it is an actual nucleotide, rather than a representation of a mix of nucleotides that covers each possible pairing needed.


Symbol Description Bases represented
A adenine A


1
C cytosine
C
G guanine

G
T thymine


T
U uracil


U
W weak A

T 2
S strong
C G
M amino A C
K keto

G T
R purine A
G
Y pyrimidine
C
T
B not A (B comes after A)
C G T 3
D not C (D comes after C) A
G T
H not G (H comes after G) A C
T
V not T (V comes after T and U) A C G
N any base (not a gap) A C G T 4

Ribose

From Wikipedia, the free encyclopedia
 
d-Ribose
D-Ribose.png
DRibose Fischer.svg
Beta-D-Ribofuranose.svg
Beta-D-Ribopyranose.svg
Names
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 ☒
DrugBank
EC Number
  • 200-059-4
PubChem CID
UNII
Properties
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).
L-Ribose Fischer Projection
 
Ribose is a simple sugar and carbohydrate with molecular formula C5H10O5 and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally-occurring form, d-ribose, is a component of the ribonucleotides from which RNA is built, and so this compound is necessary for coding, decoding, regulation and expression of genes. It has a structural analog, deoxyribose, which is a similarly essential component of DNA. l-Ribose is an unnatural sugar that was first prepared by Emil Fischer and Oscar Piloty in 1891. 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. 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.

β-d-ribofuranose
 
α-d-ribopyranose
 
d-ribose
 
l-ribose
 
Top: Haworth projections of one of each of the furanose and pyranose forms of d-ribose
Bottom: Fischer projection of the open chain forms of d- and l-ribose
 
 

Like most sugars, ribose exists as a mixture of cyclic forms in equilibrium with its linear form, and these readily interconvert especially in aqueous solution. 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 the pentose sugar with all of its 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, 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 (α:β = 1:2)[10] and 24% in the furanose forms (α:β = 1:3), with only about 0.1% of the linear form present.

The ribonucleosides adenosine, cytidine, guanosine, and uridine are all derivatives of β-d-ribofuranose. Metabolically-important species that include phosphorylated ribose include ADP, ATP, coenzyme A, 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.

Sources

In November 2019, scientists reported detecting, for the first time, sugar molecules, including ribose, in meteorites, suggesting that chemical processes on asteroids can produce some fundamentally essential bio-ingredients important to life, and supporting the notion of an RNA world prior to a DNA-based origin of life on Earth, and possibly, as well, the notion of panspermia.

Structure

Ribose is an aldopentose (a monosaccharide containing five carbon atoms) that, in its open chain form, has an aldehyde functional group at one end. In the conventional numbering scheme for monosaccharides, the carbon atoms are numbered from C1' (in the aldehyde group) to C5'. The deoxyribose derivative found in DNA differs from ribose by having a hydrogen atom in place of the hydroxyl group at C2'. This hydroxyl group performs a function in RNA splicing

Like many monosaccharides, ribose exists in an equilibrium among 5 forms—the linear form H−(C=O)−(CHOH)4–H and either of the two ring forms: α- or β-ribofuranose ("C3'-endo"), with a five-membered tetrahydrofuran ring, and α- or β-ribopyranose ("C2'-endo"), with a six-membered tetrahydropyran ring. 

The “d-” in the name d-ribose refers to the stereochemistry of the chiral carbon atom farthest away from the aldehyde group (C4'). In d-ribose, as in all d-sugars, this carbon atom has the same configuration as in d-glyceraldehyde.
Relative abundance of different 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%).

When ribose sugars are in nucleosides and nucleotide, the torsion angles for the rotation encompassing the bonds influence the configuration of the respective nucleoside and nucleotide. The secondary structure of a nucleic acid is determined by the rotation of its 7 torsion angles. Having a large amount of torsion angles allows for greater flexibility of a molecule. However, because these sugars have a higher degree of flexibility, it leads to many issues when simulating conditions for RNA molecules because there are so many different conformations of ribose.

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. There are different conformations of closed form riboses. These differ in regards to how the lone oxygen in the molecule is positioned respective to the 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. 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 steric hindrance and strain between them. To relieve this crowding and ring strain, the ring puckers, i.e. becomes non-planar. This puckering is achieved by displacing an atom from the plane, relieving the strain and yielding a more stable configuration. Puckering, otherwise known as the sugar ring conformation (specifically ribose sugar), can be described by the amplitude of pucker as well as the pseudorotation angle. 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 the A form of DNA. In contrast, the south range is associated with B form DNA. Z-DNA contains sugars in both the north and south ranges. 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. 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). 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 different activation energies.

Functions in Biochemistry

Ribose plays many important roles in metabolism, which means that it is involved in a lot of biochemistry. Ribose is used as a building block for a lot of the signals and products throughout the metabolic pathway. One of the most important products of the metabolic pathway is adenosine triphosphate (ATP), which provides energy that drives processes in cells. 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 also plays a major role in signaling pathways because it is a building block in secondary signaling molecules such as cyclic adenosine monophosphate (cAMP) which is derived from ATP. One specific case in which cAMP is used is in cAMP-dependent signaling pathways. In cAMP signaling pathways, either a stimulative or inhibitory hormone receptor is activated by a 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

DNA vs RNA

DNA contains a deoxygenated form of ribose called deoxyribose. The difference between ribose and deoxyribose is the presence of an OH group on the 2' carbon of the ring in ribose, making ribose less stable than deoxyribose and more susceptible to hydrolysis.

RNA hydrolysis mechanism: The 2' OH in RNA can be hydrolyzed causing RNA to be less stable than DNA. Hydrolysis of RNA leads to a break in the backbone of RNA.

Metabolism

Ribose is referred to as the "molecular currency" because of its involvement in intracellular energy transfers. 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. 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

Pentose phosphate pathway

d-Ribose 5-phosphate is also produced from d-glucose via the pentose phosphate pathway and is then used to make nucleotides for RNA and DNA. 

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

Modifications

Modifications in nature

In biology, d-ribose must be phosphorylated by the cell before it can be used. Ribokinase catalyzes this reaction by converting d-ribose to d-ribose 5-phosphate. Once converted, d-ribose-5-phosphate is available for the manufacturing of the 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).

In addition to phosphorylation, there are other modifications. One important modification occurs at the C2' position of the ribose molecule. By adding an O-alkyl group, the nuclear resistance of the RNA is increased because of additional stabilizing forces. These forces are stabilizing because of the increase of intramolecular hydrogen bonding and an increase in the glycosidic bond stability. The resulting increase of resistance leads to increases in the half-life of siRNA and the potential therapeutic potential in cells and animals. The methylation of ribose at particular sites is correlated with a decrease in immune stimulation.

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 substitutions are very notable, because the molecules produced are more lipophilic than the original molecule. The increase in lipophilicity makes the new molecules more suitable subjects for use in techniques such as PCR, RNA aptamer post-modifcation, antisense technology, and for phasing X-ray crystallographic data.

Similar to the 2' modifications in nature, a synthetic modification of ribose includes the addition of fluorine at the 2' position. This 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. 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.

Medical uses

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

Supplemental d-ribose can bypass part of the pentose phosphate pathway, an energy-producing pathway, to produce d-ribose-5-phosphate. The enzyme glucose-6-phosphate-dehydrogenase (G-6-PDH) is often in short supply in cells, but more so in diseased tissue, such as in myocardial cells in patients with cardiac disease. The supply of d-ribose in the mitochondria is directly correlated with ATP production; decreased d-ribose supply reduces the amount of ATP being produced. Studies suggest that supplementing d-ribose following tissue ischemia (e.g. myocardial ischemia) increases myocardial ATP production, and therefore mitochondrial function. Essentially, administering supplemental d-ribose bypasses an enzymatic step in the pentose phosphate pathway by providing an alternate source of 5-phospho-d-ribose 1-pyrophosphate for ATP production. Supplemental d-ribose enhances recovery of ATP levels while also reducing cellular injury in humans and other animals. One study suggested that the use of supplemental d-ribose reduces the instance of angina in men with diagnosed coronary artery disease. d-Ribose has been used to treat many 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.

Risks

Oral D-Ribose intake is linked to memory loss, anxiety, & Aβ-like deposits associated with Alzheimer’s in mice.

Political psychology

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