Nucleotide

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Nucleotide

Nucleotides are molecules that comprise the structural units of RNA

RNA

Ribonucleic acid is a type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nucleobase, a ribose sugar, and a phosphate....
and DNA

DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetics instructions used in the development and functioning of all known living organisms and some viruses....
. Additionally, nucleotides play central roles in metabolism

Metabolism

Metabolism is the set of chemical reactions that occur in living organisms in order to maintain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments....
. In that capacity, they serve as sources of chemical energy (adenosine triphosphate

Adenosine triphosphate

This article is about the chemical used by cells as an energy carrier. For other uses, see ATP .Adenosine-5'-triphosphate is a multifunctional nucleotide, and plays an important role in cell biology as a coenzyme that is the "molecule unit of currency" of intracellular energy transfer....
and guanosine triphosphate

Guanosine triphosphate

Guanosine-5'-triphosphate is a purine nucleotide. One role is as substrate for the synthesis of RNA during transcription . Its structure is similar to that of the guanine nucleoside, the only difference being that there are three phosphate groups attached to the 5' carbon....
), participate in cellular

Cell (biology)

The cell is the structural and functional unit of all known Life organisms. It is the smallest unit of an organism that is classified as living, and is often called the building bricks of life....
signaling (cyclic guanosine monophosphate

Cyclic guanosine monophosphate

Cyclic guanosine monophosphate is a cyclic nucleotide derived from guanosine triphosphate . cGMP acts as a second messenger much like cyclic AMP, most notably by activating intracellular protein kinases in response to the binding of cell membrane-impermeable peptide hormones to the external cell surface....
and cyclic adenosine monophosphate

Cyclic adenosine monophosphate

Cyclic adenosine monophosphate is a second messenger that is important in many biological processes. cAMP is derived from adenosine triphosphate and used for intracellular signal transduction in many different organisms....
), and are incorporated into important cofactors of enzymatic reactions (coenzyme A

Coenzyme A

Coenzyme A is a coenzyme, notable for its role in the Fatty acid metabolism#Synthesis and Fatty acid metabolism#.CE.B2-Oxidation of fatty acids, and the oxidation of pyruvic acid in the citric acid cycle....
, flavin adenine dinucleotide

FAD

In biochemistry, flavin adenine dinucleotide is a redox Cofactor involved in several important reactions in metabolism. FAD can exist in two different redox states and its biochemical role usually involves changing between these two states....
, flavin mononucleotide

Flavin mononucleotide

Flavin mononucleotide , or riboflavin-5'-phosphate, is a biomolecule produced from riboflavin by the enzyme riboflavin kinase and functions as prosthetic group of various oxidoreductases including NADH dehydrogenase....
, and nicotinamide adenine dinucleotide phosphate

Nicotinamide adenine dinucleotide phosphate

Nicotinamide adenine dinucleotide phosphate is used in anabolic reactions, such as lipid and nucleic acid synthesis, which require NADPH as a reducing agent....
).
cleotide is composed of a nucleobase

Nucleobase

Nucleobases are the parts of DNA and RNA that may be involved in pairing . The main ones are cytosine, guanine, adenine , thymine and uracil , abbreviated as C, G, A, T, and U, respectively....
(nitrogenous base) and a five-carbon sugar (either ribose

Ribose

Ribose, primarily occurring as D-ribose, is an organic compound that occurs widely in nature. It is an aldopentose, that is a monosaccharide containing five carbon atoms that, in its acyclic form, has an aldehyde functional group at one end....
or 2'-deoxyribose

Deoxyribose

Deoxyribose, also known as D-Deoxyribose and 2-deoxyribose, is an aldopentose — a monosaccharide containing five carbon atoms, and including an aldehyde functional group in its linear structure....
), and one to three phosphate

Phosphate

A phosphate, an inorganic chemical, is a Salt of phosphoric acid. Inorganic phosphates are mining to obtain phosphorus for use in agriculture and industry....
groups.

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Nucleotide structure

A nucleotide is composed of a nucleobase

Nucleobase

Ribose

Deoxyribose

Phosphate

A phosphate, an inorganic chemical, is a Salt of phosphoric acid. Inorganic phosphates are mining to obtain phosphorus for use in agriculture and industry....
groups. Together, the nucleobase and sugar comprise a nucleoside

Nucleoside

Nucleosides are glycosylamines consisting of a nucleobase bound to a ribose or deoxyribose sugar. Examples of these include cytidine, uridine, adenosine, guanosine, thymidine and inosine....
. The phosphate groups form bonds with either the 2, 3, or 5-carbon of the sugar, with the 5-carbon site most common. Cyclic nucleotides

Cyclic nucleotide

A cyclic nucleotide is any nucleotide in which the phosphate group is bonded to two of the sugar's hydroxyl groups, forming a cyclical or ring structure....
form when the phosphate group is bound to two of the sugar's hydroxyl groups

Hydroxyl

Hydroxyl in chemistry stands for a molecule consisting of an oxygen atom and a hydrogen atom connected by a covalent bond. The neutral form is a hydroxyl Radical and the hydroxyl anion is called a hydroxide....
. Ribonucleotides are nucleotides where the sugar is ribose

Ribose

Deoxyribose

Purine

Purine is a heterocyclic compound aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. Purines, including substituted purines and their tautomers, are the most widely distributed kind of nitrogen-containing heterocycle in nature....
or pyrimidine

Pyrimidine

Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring....
base.

Nucleic acid

Nucleic acid

A nucleic acid is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within Cell ....
s are polymeric macromolecules made from nucleotide monomers. In DNA

DNA

Adenine

Adenine is a nucleobase with a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate and the cofactor s nicotinamide adenine dinucleotide and flavin adenine dinucleotide , and Protein biosynthesis, as a chemical component of DNA and RNA....
and guanine

Guanine

Guanine is one of the five main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, thymine, and uracil. In DNA, guanine is paired with cytosine....
, while the pyrimidines are thymine

Thymine

Thymine is one of the four bases in the nucleic acid of DNA that make up the letters GCAT. The others are adenine, guanine, and cytosine. Thymine always pairs with adenine....
and cytosine

Cytosine

Cytosine is one of the five main bases found in DNA and RNA. It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached ....
. RNA

RNA

Ribonucleic acid is a type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nucleobase, a ribose sugar, and a phosphate....
uses uracil

Uracil

Uracil is a common and naturally occurring pyrimidine derivative. Originally discovered in 1900, it was isolated by hydrolysis of yeast nuclein that was found in bovine thymus and spleen, herring, sperm, and wheat germ....
in place of thymine.

Synthesis

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

In vitro

In vitro refers to the technique of performing a given procedure in a controlled environment outside of a living organism. Some may argue that in vitro refers to a process that is created in a "test tube"; however, Robert Kail and John Cavanaugh on page 58 in the 4th edition of Human Development: A Life-Span View cite that in fact th...
and in vivo

In vivo

In vivo means that which takes place inside an organism. In science, in vivo refers to experimentation done in or on the living tissue of a whole, living organism as opposed to a partial or dead one or a in vitro....
. In vivo, nucleotides can be synthesised de novo

De novo synthesis

De novo is a Latin phrase, meaning "from the new," anew, or from the beginning. De novo synthesis refers to the synthesis of complex molecules from simple molecules such as sugars or amino acids, as opposed to their being recycled after partial degradation....
or recycled through salvage pathways. Nucleotides undergo breakdown such that useful parts can be reused in synthesis reactions to create new nucleotides. In vitro, protecting group

Protecting group

A protecting group or protective group is introduced into a molecule by chemical modification of a functional group in order to obtain chemoselectivity in a subsequent chemical reaction....
s may be used during laboratory production of nucleotides. A purified nucleoside

Nucleoside

Phosphoramidite

Nucleoside phosphoramidites are used to oligonucleotide synthesis short nucleic acid chains.The chemical process allows several modifications, such as linker arms or using Nucleic acid analogues, such as LNA or morpholino or 2' group modified or abasic, non-canon bases or bases with a fluorescent group, linker arm to attach a fluorescent...
, which can then be used to obtain analogues not found in nature and/or to synthesize an oligonucleotide

Oligonucleotide synthesis

Oligonucleotide synthesis is the non-biological, chemical synthesis of defined short sequences of nucleic acids. It is extremely useful in laboratory practice covering a wide range of molecular biology applications and in pharmaceutical research....
.

Pyrimidine ribonucleotides

Pyrimidine nucleotide synthesis starts with the formation of carbamoyl phosphate from glutamine and CO₂. The cyclisation reaction between carbamoyl phosphate reacts with aspartate yielding orotate in subsequent steps. Orotate reacts with 5-phosphoribosyl a-diphosphate

Phosphoribosyl pyrophosphate

Phosphoribosyl pyrophosphate is a Sugar phosphates.It is formed from ribose 5-phosphate by the enzyme ribose-phosphate diphosphokinase.It plays a role in transferring phosphate groups in several reactions:...
(PRPP) yielding orotidine monophosphate (OMP) which is decarboxylated to form uridine monophosphate (UMP). It is from UMP that other pyrimidine nucleotides are derived. UMP is phosphorylated to uridine triphosphate (UTP) via two sequential reactions with ATP. Cytidine monophosphate (CMP) is derived from conversion of UTP to cytidine triphosphate (CTP) with subsequent loss of two phosphates.

Purine ribonucleotides

The atoms which are used to build the purine nucleotides come from a variety of sources:

	The biosynthetic origins of purine ring atoms N1 arises from the amine group of Asp Aspartic acid Aspartic acid is an a-amino acid with the chemical formula HO2CCHCH2CO2H. The carboxylate anion of aspartic acid is known as aspartate.... C2 and C8 originate from formate Formate Formate or methanoate is the ion CHOO− or HCOO− . It is the simplest carboxylate anion.A formate is a salt or ester of formic acid.... N3 and N9 are contributed by the amide group of Gln Glutamine Glutamine is one of the 20 amino acids encoded by the standard genetic code. Its side chain is an amide formed by replacing the side-chain hydroxyl of glutamic acid with an amine functional group.... C4, C5 and N7 are derived from Gly Glycine Glycine is the organic compound with the chemical formula NH2CH2COOH. It is the smallest of the 20 amino acids commonly found in proteins, coded by codons GGU, GGC, GGA and GGG.... C6 comes from HCO₃^- (CO₂)

The de novo synthesis

De novo synthesis

De novo is a Latin phrase, meaning "from the new," anew, or from the beginning. De novo synthesis refers to the synthesis of complex molecules from simple molecules such as sugars or amino acids, as opposed to their being recycled after partial degradation....
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

Imp

An imp is a mythology being similar to a fairy or demon, frequently described in folklore and superstition. The word may perhaps derive from the term ympe, used to denote a young grafting tree....
, the nucleotide

Nucleotide

Nucleotides are molecules that comprise the structural units of RNA and DNA. Additionally, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy , participate in cell signaling , and are incorporated into important cofactors of enzymatic reactions ....
of the base hypoxanthine

Hypoxanthine

Hypoxanthine is a naturally occurring purine derivative. It is occasionally found as a constituent of nucleic acids where it is present in the anticodon of tRNA in the form of its nucleoside inosine....
. AMP

Amp

Amp or AMP may refer to:...
and GMP

GMP

There are several expansions of the abbreviation GMP:*Airport code for Gimpo International Airport in Seoul, South Korea*Gay Men's Press*Global Marshall Plan...
are subsequently synthesized from this intermediate via separate, two step each, 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
Phosphoribosylglycinamide formyltransferase

Phosphoribosylglycinamide formyltransferase is an enzyme involved in the synthesis of purines.External links...
(reactions 2, 3, and 5)
PAICS
Phosphoribosylaminoimidazole carboxylase

Phosphoribosylaminoimidazole carboxylase is an enzyme involved in nucleotide synthesis.It catalyzes the conversion of 5'-phosphoribosyl-5-aminoimidazole into 5-phosphoribosyl-4-carboxy-5-aminoimidazole ....
(reactions 6, and 7)
ATIC
Inosine monophosphate synthase

5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase, also known as ATIC and Inosine monophosphate synthase, is a human gene....
(reactions 9, and 10)

Reaction 1. The pathway starts with the formation of PRPP. PRPS1 is the enzyme

Enzyme

Enzymes are biomolecules that catalysis chemical reactions. Almost all enzymes are proteins. In enzymatic reactions, the molecules at the beginning of the process are called Substrate , and the enzyme converts them into different molecules, the products....
that activates R5P, which is primarily formed by the pentose phosphate pathway

Pentose phosphate pathway

The pentose phosphate pathway is a process that serves to generate NADPH and the synthesis of pentose sugars. There are two distinct phases in the pathway....
, to PRPP by reacting it with ATP

Adenosine triphosphate

ATP

ATP may refer to:...
to C1

C1, C01, C.I or C-1 may refer to:* C1, an international standard paper size defined in ISO 216 * Bills C-1 and S-1, a pro forma bill normally introduced at the start of a parliamentary session in the Canadian House of Commons....
of R5P and that the product has the a configuration about C1

C1, C01, C.I or C-1 may refer to:* C1, an international standard paper size defined in ISO 216 * Bills C-1 and S-1, a pro forma bill normally introduced at the start of a parliamentary session in the Canadian House of Commons....
. This reaction is also shared with the pathways for the synthesis of the pyrimidine nucleotides, Trp

Tryptophan

Tryptophan is one of the 20 List of standard amino acids, as well as an essential amino acid in the human diet. It is encoded in the standard genetic code as the codon UGG....
, and His

Histidine

Histidine is one of the 20 standard amino acids present in proteins. In the nutritional sense, in humans, histidine is considered an essential amino acid, but only in children....
. As a result of being on (a) such (a) major metabolic crossroad and the use of energy, this reaction is highly regulated.

Reaction 2. In the first reaction unique to purine nucleotide biosynthesis, PPAT catalyzes the displacement of PRPP's pyrophosphate

Pyrophosphate

In chemistry, the anion, the salts, and the esters of pyrophosphoric acid are called pyrophosphates. Pyrophosphates were originally prepared by heating phosphates: the prefix pyro- derived from Greek, means "fire" in this context....
group (PP_i) by Gln's amide nitrogen. The reaction occurs with the inversion of configuration about ribose C1, thereby forming ß-5-phosphorybosylamine (5-PRA) and establishing the anomeric form of the future nucleotide. This reaction which is driven to completion by the subsequent hydrolysis of the released PP

PP, pp, Pp, or Pp may refer to:...
_i, is the pathway's flux generating step and is therefore regulated too.

External links

(IUPAC)
(IUPAC)

Nucleotide

Nucleotide structure

Synthesis

Pyrimidine ribonucleotides

Purine ribonucleotides

See also

External links