Purine

Last updated
Purine
Purin num2.svg
Purine-3D-balls.png
Purine-3D-spacefill.png
Names
IUPAC name
9H-purine
Identifiers
3D model (JSmol)
ChEBI
ChEMBL
ChemSpider
ECHA InfoCard 100.004.020 OOjs UI icon edit-ltr-progressive.svg
KEGG
MeSH Purine
PubChem CID
UNII
  • InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) Yes check.svgY
    Key: KDCGOANMDULRCW-UHFFFAOYSA-N Yes check.svgY
  • InChI=1/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9)
    Key: KDCGOANMDULRCW-UHFFFAOYAO
  • c1c2c(nc[nH]2)ncn1
Properties
C5H4N4
Molar mass 120.115 g·mol−1
Melting point 214 °C (417 °F; 487 K)
500 g/L (RT)
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
Yes check.svgY  verify  (what is  Yes check.svgYX mark.svgN ?)

Purine is a heterocyclic aromatic organic compound that consists of two rings (pyrimidine and imidazole) fused together. It is water-soluble. Purine also gives its name to the wider class of molecules, purines, which include substituted purines and their tautomers. They are the most widely occurring nitrogen-containing heterocycles in nature. [1]

Contents

Dietary sources

Purines are found in high concentration in meat and meat products, especially internal organs such as liver and kidney. In general, plant-based diets are low in purines. [2] High-purine plants and algae include some legumes (lentils, soybeans, and black-eyed peas) and spirulina. Examples of high-purine sources include: sweetbreads, anchovies, sardines, liver, beef kidneys, brains, meat extracts (e.g., Oxo, Bovril), herring, mackerel, scallops, game meats, yeast (beer, yeast extract, nutritional yeast) and gravy. [3]

A moderate amount of purine is also contained in red meat, beef, pork, poultry, fish and seafood, asparagus, cauliflower, spinach, mushrooms, green peas, lentils, dried peas, beans, oatmeal, wheat bran, wheat germ, and haws. [4]

Biochemistry

Purines and pyrimidines make up the two groups of nitrogenous bases, including the two groups of nucleotide bases. The purine bases are guanine (G) and adenine (A) which form corresponding nucleosides-deoxyribonucleosides (deoxyguanosine and deoxyadenosine) with deoxyribose moiety and ribonucleosides (guanosine, adenosine) with ribose moiety. These nucleosides with phosphoric acid form corresponding nucleotides (deoxyguanylate, deoxyadenylate and guanylate, adenylate) which are the building blocks of DNA and RNA, respectively. Purine bases also play an essential role in many metabolic and signalling processes within the compounds guanosine monophosphate (GMP) and adenosine monophosphate (AMP).

In order to perform these essential cellular processes, both purines and pyrimidines are needed by the cell, and in similar quantities. Both purine and pyrimidine are self-inhibiting and activating. When purines are formed, they inhibit the enzymes required for more purine formation. This self-inhibition occurs as they also activate the enzymes needed for pyrimidine formation. Pyrimidine simultaneously self-inhibits and activates purine in a similar manner. Because of this, there is nearly an equal amount of both substances in the cell at all times. [5]

Properties

Purine is both a very weak acid (pKa 8.93) and an even weaker base (pKa 2.39). [6] If dissolved in pure water, the pH is halfway between these two pKa values.

Purine is aromatic, having four tautomers each with a hydrogen bonded to a different one of the four nitrogen atoms. These are identified as 1-H, 3-H, 7-H, and 9-H (see image of numbered ring). The common crystalline form favours the 7-H tautomer, while in polar solvents both the 9-H and 7-H tautomers predominate. [7] Substituents to the rings and interactions with other molecules can shift the equilibrium of these tautomers. [8]

Notable purines

There are many naturally occurring purines. They include the nucleotide bases adenine and guanine. In DNA, these bases form hydrogen bonds with their complementary pyrimidines, thymine and cytosine, respectively. This is called complementary base pairing. In RNA, the complement of adenine is uracil instead of thymine.

Other notable purines are hypoxanthine, xanthine, theophylline, theobromine, caffeine, uric acid and isoguanine.

Purines.svg

Functions

Aside from the crucial roles of purines (adenine and guanine) in DNA and RNA, purines are also significant components in a number of other important biomolecules, such as ATP, GTP, cyclic AMP, NADH, and coenzyme A. Purine (1) itself, has not been found in nature, but it can be produced by organic synthesis.

They may also function directly as neurotransmitters, acting upon purinergic receptors. Adenosine activates adenosine receptors.

History

The word purine (pure urine) [9] was coined by the German chemist Emil Fischer in 1884. [10] [11] He synthesized it for the first time in 1898. [11] The starting material for the reaction sequence was uric acid (8), which had been isolated from kidney stones by Carl Wilhelm Scheele in 1776. [12] Uric acid was reacted with PCl5 to give 2,6,8-trichloropurine, which was converted with HI and PH4I to give 2,6-diiodopurine. The product was reduced to purine using zinc dust.

Conversion of uric acid (left) to purine (right) via 2,6,8-trichloropurine and 2,6-diiodopurine intermediates FischerPurineSynthesis-crop.svg
Conversion of uric acid (left) to purine (right) via 2,6,8-trichloropurine and 2,6-diiodopurine intermediates

Metabolism

Many organisms have metabolic pathways to synthesize and break down purines.

Purines are biologically synthesized as nucleosides (bases attached to ribose).

Accumulation of modified purine nucleotides is defective to various cellular processes, especially those involving DNA and RNA. To be viable, organisms possess a number of deoxypurine phosphohydrolases, which hydrolyze these purine derivatives removing them from the active NTP and dNTP pools. Deamination of purine bases can result in accumulation of such nucleotides as ITP, dITP, XTP and dXTP. [13]

Defects in enzymes that control purine production and breakdown can severely alter a cell's DNA sequences, which may explain why people who carry certain genetic variants of purine metabolic enzymes have a higher risk for some types of cancer.

Purine biosynthesis in the three domains of life

Organisms in all three domains of life, eukaryotes, bacteria and archaea, are able to carry out de novo biosynthesis of purines. This ability reflects the essentiality of purines for life. The biochemical pathway of synthesis is very similar in eukaryotes and bacterial species, but is more variable among archaeal species. [14] A nearly complete, or complete, set of genes required for purine biosynthesis was determined to be present in 58 of the 65 archaeal species studied. [14] However, also identified were seven archaeal species with entirely, or nearly entirely, absent purine encoding genes. Apparently the archaeal species unable to synthesize purines are able to acquire exogenous purines for growth., [14] and are thus analogous to purine mutants of eukaryotes, e.g. purine mutants of the Ascomycete fungus Neurospora crassa, [15] that also require exogenous purines for growth.

Relationship with gout

Higher levels of meat and seafood consumption are associated with an increased risk of gout, whereas a higher level of consumption of dairy products is associated with a decreased risk. Moderate intake of purine-rich vegetables or protein is not associated with an increased risk of gout. [16] Similar results have been found with the risk of hyperuricemia.

Laboratory synthesis

In addition to in vivo synthesis of purines in purine metabolism, purine can also be synthesized artificially.

Purine is obtained in good yield when formamide is heated in an open vessel at 170 °C for 28 hours. [17]

Purinesynthesis-en.svg

This remarkable reaction and others like it have been discussed in the context of the origin of life. [18]

Patented August 20, 1968, the current recognized method of industrial-scale production of adenine is a modified form of the formamide method. This method heats up formamide under 120 °C conditions within a sealed flask for 5 hours to form adenine. The reaction is heavily increased  in quantity by using a phosphorus oxychloride (phosphoryl chloride) or phosphorus pentachloride as an acid catalyst and sunlight or ultraviolet conditions. After the 5 hours have passed and the formamide-phosphorus oxychloride-adenine solution cools down, water is put into the flask containing the formamide and now-formed adenine. The water-formamide-adenine solution is then poured through a filtering column of activated charcoal. The water and formamide molecules, being small molecules, will pass through the charcoal and into the waste flask; the large adenine molecules, however, will attach or “adsorb” to the charcoal due to the van der waals forces that interact between the adenine and the carbon in the charcoal. Because charcoal has a large surface area, it's able to capture the majority of molecules that pass a certain size (greater than water and formamide) through it. To extract the adenine from the charcoal-adsorbed adenine, ammonia gas dissolved in water (aqua ammonia) is poured onto the activated charcoal-adenine structure to liberate the adenine into the ammonia-water solution. The solution containing water, ammonia, and adenine is then left to air dry, with the adenine losing solubility due to the loss of ammonia gas that previously made the solution basic and capable of dissolving adenine, thus causing it to crystallize into a pure white powder that can be stored. [19]

Oro and Kamat (1961) and Orgel co-workers (1966, 1967) have shown that four molecules of HCN tetramerize to form diaminomaleodinitrile (12), which can be converted into almost all naturally occurring purines. [20] [21] [22] [23] [24] For example, five molecules of HCN condense in an exothermic reaction to make adenine, especially in the presence of ammonia.

Basicpurines.png

The Traube purine synthesis (1900) is a classic reaction (named after Wilhelm Traube) between an amine-substituted pyrimidine and formic acid. [25]

TraubePurineSynthesis.svg

Prebiotic synthesis of purine ribonucleosides

In order to understand how life arose, knowledge is required of the chemical pathways that permit formation of the key building blocks of life under plausible prebiotic conditions. Nam et al. (2018) [26] demonstrated the direct condensation of purine and pyrimidine nucleobases with ribose to give ribonucleosides in aqueous microdroplets, a key step leading to RNA formation. Also, a plausible prebiotic process for synthesizing purine ribonucleosides was presented by Becker et al. in 2016. [27]

See also

Related Research Articles

<span class="mw-page-title-main">Guanine</span> Chemical compound of DNA and RNA

Guanine is one of the four main nucleotide bases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine. In DNA, guanine is paired with cytosine. The guanine nucleoside is called guanosine.

<span class="mw-page-title-main">Nucleotide</span> Biological molecules constituting nucleic acids

Nucleotides are organic molecules composed of a nitrogenous base, a pentose sugar 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 obtained in the diet and are also synthesized from common nutrients by the liver.

Pyrimidine is an aromatic, heterocyclic, organic compound similar to pyridine. One of the three diazines, it has nitrogen atoms at positions 1 and 3 in the ring. The other diazines are pyrazine and pyridazine.

Uric acid is a heterocyclic compound of carbon, nitrogen, oxygen, and hydrogen with the formula C5H4N4O3. It forms ions and salts known as urates and acid urates, such as ammonium acid urate. Uric acid is a product of the metabolic breakdown of purine nucleotides, and it is a normal component of urine. High blood concentrations of uric acid can lead to gout and are associated with other medical conditions, including diabetes and the formation of ammonium acid urate kidney stones.

<span class="mw-page-title-main">Adenine</span> Chemical compound in DNA and RNA

Adenine is a purine nucleotide base. It is one of the four nucleobases in the nucleic acids of DNA, the other three being guanine (G), cytosine (C), and thymine (T). Adenine derivatives have various roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate (ATP) and the cofactors nicotinamide adenine dinucleotide (NAD), flavin adenine dinucleotide (FAD) and Coenzyme A. It also has functions in protein synthesis and as a chemical component of DNA and RNA. The shape of adenine is complementary to either thymine in DNA or uracil in RNA.

<span class="mw-page-title-main">Uracil</span> Chemical compound of RNA

Uracil is one of the four nucleotide bases in the nucleic acid RNA. The others are adenine (A), cytosine (C), and guanine (G). In RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced by thymine (T). Uracil is a demethylated form of thymine.

<span class="mw-page-title-main">Nucleotide base</span> Nitrogen-containing biological compounds that form nucleosides

Nucleotide bases are nitrogen-containing biological compounds that form nucleosides, which, in turn, are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Five nucleobases—adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)—are called primary or canonical. They function as the fundamental units of the genetic code, with the bases A, G, C, and T being found in DNA while A, G, C, and U are found in RNA. Thymine and uracil are distinguished by merely the presence or absence of a methyl group on the fifth carbon (C5) of these heterocyclic six-membered rings. In addition, some viruses have aminoadenine (Z) instead of adenine. It differs in having an extra amine group, creating a more stable bond to thymine.

<span class="mw-page-title-main">Nucleoside</span> Any of several glycosylamines comprising a nucleobase and a sugar molecule

Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase and a five-carbon sugar whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups. In a nucleoside, the anomeric carbon is linked through a glycosidic bond to the N9 of a purine or the N1 of a pyrimidine. Nucleotides are the molecular building blocks of DNA and RNA.

<span class="mw-page-title-main">Ribonucleotide</span> Nucleotide containing ribose as its pentose component

In biochemistry, a ribonucleotide is a nucleotide containing ribose as its pentose component. It is considered a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. Ribonucleotides themselves are basic monomeric building blocks for RNA. Deoxyribonucleotides, formed by reducing ribonucleotides with the enzyme ribonucleotide reductase (RNR), are essential building blocks for DNA. There are several differences between DNA deoxyribonucleotides and RNA ribonucleotides. Successive nucleotides are linked together via phosphodiester bonds.

A salvage pathway is a pathway in which a biological product is produced from intermediates in the degradative pathway of its own or a similar substance. The term often refers to nucleotide salvage in particular, in which nucleotides are synthesized from intermediates in their degradative pathway.

A nucleoside triphosphate is a nucleoside containing a nitrogenous base bound to a 5-carbon sugar, with three phosphate groups bound to the sugar. They are the molecular precursors of both DNA and RNA, which are chains of nucleotides made through the processes of DNA replication and transcription. Nucleoside triphosphates also serve as a source of energy for cellular reactions and are involved in signalling pathways.

<span class="mw-page-title-main">Depurination</span>

Depurination is a chemical reaction of purine deoxyribonucleosides, deoxyadenosine and deoxyguanosine, and ribonucleosides, adenosine or guanosine, in which the β-N-glycosidic bond is hydrolytically cleaved releasing a nucleic base, adenine or guanine, respectively. The second product of depurination of deoxyribonucleosides and ribonucleosides is sugar, 2'-deoxyribose and ribose, respectively. More complex compounds containing nucleoside residues, nucleotides and nucleic acids, also suffer from depurination. Deoxyribonucleosides and their derivatives are substantially more prone to depurination than their corresponding ribonucleoside counterparts. Loss of pyrimidine bases occurs by a similar mechanism, but at a substantially lower rate.

<span class="mw-page-title-main">Nucleic acid metabolism</span> Process

Nucleic acid metabolism is a collective term that refers to the variety of chemical reactions by which nucleic acids are either synthesized or degraded. Nucleic acids are polymers made up of a variety of monomers called nucleotides. Nucleotide synthesis is an anabolic mechanism generally involving the chemical reaction of phosphate, pentose sugar, and a nitrogenous base. Degradation of nucleic acids is a catabolic reaction and the resulting parts of the nucleotides or nucleobases can be salvaged to recreate new nucleotides. Both synthesis and degradation reactions require multiple enzymes to facilitate the event. Defects or deficiencies in these enzymes can lead to a variety of diseases.

Pyrimidine biosynthesis occurs both in the body and through organic synthesis.

<span class="mw-page-title-main">Ribose 5-phosphate</span> Chemical compound

Ribose 5-phosphate (R5P) is both a product and an intermediate of the pentose phosphate pathway. The last step of the oxidative reactions in the pentose phosphate pathway is the production of ribulose 5-phosphate. Depending on the body's state, ribulose 5-phosphate can reversibly isomerize to ribose 5-phosphate. Ribulose 5-phosphate can alternatively undergo a series of isomerizations as well as transaldolations and transketolations that result in the production of other pentose phosphates as well as fructose 6-phosphate and glyceraldehyde 3-phosphate.

Purine metabolism refers to the metabolic pathways to synthesize and break down purines that are present in many organisms.

<span class="mw-page-title-main">Nucleic acid analogue</span> Compound analogous to naturally occurring RNA and DNA

Nucleic acid analogues are compounds which are analogous to naturally occurring RNA and DNA, used in medicine and in molecular biology research. Nucleic acids are chains of nucleotides, which are composed of three parts: a phosphate backbone, a pentose sugar, either ribose or deoxyribose, and one of four nucleobases. An analogue may have any of these altered. Typically the analogue nucleobases confer, among other things, different base pairing and base stacking properties. Examples include universal bases, which can pair with all four canonical bases, and phosphate-sugar backbone analogues such as PNA, which affect the properties of the chain . Nucleic acid analogues are also called xeno nucleic acids and represent one of the main pillars of xenobiology, the design of new-to-nature forms of life based on alternative biochemistries.

Synthesis of nucleosides involves the coupling of a nucleophilic, heterocyclic base with an electrophilic sugar. The silyl-Hilbert-Johnson reaction, which employs silylated heterocyclic bases and electrophilic sugar derivatives in the presence of a Lewis acid, is the most common method for forming nucleosides in this manner.

<span class="mw-page-title-main">Purine nucleotide cycle</span> Protein metabolic pathway

The Purine Nucleotide Cycle is a metabolic pathway in protein metabolism requiring the amino acids aspartate and glutamate. The cycle is used to regulate the levels of adenine nucleotides, in which ammonia and fumarate are generated. AMP converts into IMP and the byproduct ammonia. IMP converts to S-AMP (adenylosuccinate), which then converts to AMP and the byproduct fumarate. The fumarate goes on to produce ATP (energy) via oxidative phosphorylation as it enters the Krebs cycle and then the electron transport chain. Lowenstein first described this pathway and outlined its importance in processes including amino acid catabolism and regulation of flux through glycolysis and the Krebs cycle.

Formamide-based prebiotic chemistry is a reconstruction of the beginnings of life on Earth, assuming that formamide could accumulate in sufficiently high amounts to serve as the building block and reaction medium for the synthesis of the first biogenic molecules.

References

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    From p. 329 Archived 2022-02-17 at the Wayback Machine : "Um eine rationelle Nomenklatur der so entstehenden zahlreichen Substanzen zu ermöglichen, betrachte ich dieselben als Abkömmlinge der noch unbekannten Wasserstoffverbindung CH3.C5N4H3 and nenne die letztere Methylpurin." (In order to make possible a rational nomenclature for the numerous existing substances, I regarded them as derivatives of a still unknown hydrogen compound, CH3.C5N4H3, and call the latter "methylpurine".)
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    From p. 2550 Archived 2020-10-18 at the Wayback Machine : "…hielt ich es für zweckmäßig, alle diese Produkte ebenso wie die Harnsäure als Derivate der sauerstofffreien Verbindung C5H4N4 zu betrachten, und wählte für diese den Namen Purin, welcher aus den Wörtern purum und uricum kombiniert war." (…I regarded it as expedient to consider all of these products, just like uric acid, as derivatives of the oxygen-free compound C5H4N4, and chose for them the name "purine", which was formed from the [Latin] words purum and uricum.)
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