Nucleotides are organic compounds that consist of three joined structures: a nitrogenous base, a sugar, and a phosphate group. An organic compound is any member of a large class of Chemical compounds whose Molecules contain Carbon. Sugar is a class of edible Crystalline substances mainly Sucrose, Lactose, and Fructose. A phosphate, an Inorganic chemical, is a salt of Phosphoric acid. The most common nucleotides can be divided into two groups (purines and pyrimidines) based on the structure of the nitrogenous base. Purine ( 1) is a heterocyclic Aromatic Organic compound, consisting of a Pyrimidine ring fused to an Imidazole ring Pyrimidine is a Heterocyclic Aromatic Organic compound similar to Benzene and Pyridine, containing two Nitrogen Atoms The joined sugar is either ribose or deoxyribose. Ribose (ɹˈaɪbəʊs ɹˈaɪbəɹʊs primarily seen as D-ribose, is an Aldopentose — a Monosaccharide containing five Carbon Deoxyribose, also known as D-Deoxyribose and 2-deoxyribose, is an Aldopentose &mdash a Monosaccharide containing five Carbon
Nucleotides are the structural units of RNA and DNA. Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known They also serve as important cofactors in cellular signaling and metabolism. The cell is the structural and functional unit of all known living Organisms It is the smallest unit of an organism that is classified as living and is often called Metabolism is the set of Chemical reactions that occur in living Organisms in order to maintain Life. These cofactors include CoA, flavin adenine dinucleotide, flavin mononucleotide, adenosine triphosphate and nicotinamide adenine dinucleotide phosphate. Coenzyme A ( CoA, CoASH, or HSCoA) is a Coenzyme, notable for its role in the synthesis and oxidation of Fatty acids In Biochemistry, flavin adenine dinucleotide ( FAD) is a Redox cofactor involved in several important reactions in Metabolism. Flavin mononucleotide (FMN or riboflavin-5′-phosphate, is produced from Riboflavin (vitamin B2 by the enzyme Riboflavin kinase and Adenosine-5'-triphosphate ( ATP) is a multifunctional Nucleotide that is most important as a " molecular currency" of intracellular Energy Nicotinamide adenine dinucleotide phosphate ( NADP+, in older notation triphosphopyridine nucleotide TPN) is used in anabolic reactions such as Lipid
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Nucleotide synthesis and structure
A nucleotide is composed of a ring of nitrogen, carbon and oxygen atoms, a five carbon sugar (together referred to as a nucleoside) and one phosphate group. Basic aromatic rings are aromatic rings in which the Lone pair of Electrons of a ring- Nitrogen Atom is not part of the Aromatic A pentose is a Monosaccharide with five Carbon Atoms They either have an Aldehyde Functional group in position 1 ( aldopentoses See also Adenosine triphosphate (ATP A phosphate, an Inorganic chemical, is a salt of Phosphoric acid. Nucleotides can be synthesized through a variety of methods both in vitro and in vivo. In vitro ( Latin: within the glass refers to the technique of performing a given experiment in a controlled environment outside of a living Organism In vivo ( Latin: within the living means that which takes place inside an organism. This can involve salvage synthesis (the re-use of parts of nucleotides in resynthesizing new nucleotides through breakdown and synthesis reactions in order to exchange useful parts), or the use of protecting groups in a laboratory. A protecting group or protective group is introduced into a molecule by chemical modification of a Functional group in order to obtain Chemoselectivity In the latter case, a purified nucleoside or nucleobase is protected to create a phosphoramidite, and can be used to obtain analogues not present in nature and/or to create an oligonucleotide. See also Adenosine triphosphate (ATP Structure The "skeleton" of adenine Nucleoside phosphoramidites are used to synthesise short Nucleic acid chains Oligonucleotide synthesis is the non-biological chemical synthesis of defined short sequences of Nucleic acids It is extremely useful in laboratory procedures covering a wide
The first step of nucleotide synthesis is the formation of a nucleoside (the nitrogenous base joined to a sugar). The sugar involved in the synthesis and structure of a nucleotide may be either ribose or deoxyribose; in the latter case, the prefix 'deoxy' may be added before the name of the nucleoside in all cases except Uracil. Ribose (ɹˈaɪbəʊs ɹˈaɪbəɹʊs primarily seen as D-ribose, is an Aldopentose — a Monosaccharide containing five Carbon Deoxyribose, also known as D-Deoxyribose and 2-deoxyribose, is an Aldopentose &mdash a Monosaccharide containing five Carbon Uracil is a common and naturally occurring Pyrimidine derivative A functional group of phosphate is then esterified to the sugar, creating a nucleotide. In Organic chemistry, functional groups are specific groups of Atoms within Molecules that are responsible for the characteristic Chemical reactions Esterification is the general name for a Chemical reaction in which two reactants (typically an alcohol and an acid form an Ester as the reaction product The phosphate group may consist of one, two, or three phosphates, forming monophosphates, diphosphates, or triphosphates, respectively.
Synthesis
Nucleotides can be synthesized through a variety of methods both in vitro and in vivo. In vitro ( Latin: within the glass refers to the technique of performing a given experiment in a controlled environment outside of a living Organism In vivo ( Latin: within the living means that which takes place inside an organism. This can involve salvage synthesis (the re-use of parts of nucleotides in resynthesizing new nucleotides through breakdown and synthesis reactions in order to exchange useful parts), or the use of protecting groups in a laboratory. A protecting group or protective group is introduced into a molecule by chemical modification of a Functional group in order to obtain Chemoselectivity In the latter case, a purified nucleoside or nucleobase is protected to create a phosphoramidite, and can be used to obtain analogues not present in nature and/or to create an oligonucleotide. See also Adenosine triphosphate (ATP Structure The "skeleton" of adenine Nucleoside phosphoramidites are used to synthesise short Nucleic acid chains Oligonucleotide synthesis is the non-biological chemical synthesis of defined short sequences of Nucleic acids It is extremely useful in laboratory procedures covering a wide
Types of bases
Nucleotides can be synthesized with both purine and pyrimidine as bases. Biosynthesis is a phenomenon wherein Chemical compounds are produced from simpler Reagents Biosynthesis unlike Chemosynthesis, takes place within living Purine ( 1) is a heterocyclic Aromatic Organic compound, consisting of a Pyrimidine ring fused to an Imidazole ring Pyrimidine is a Heterocyclic Aromatic Organic compound similar to Benzene and Pyridine, containing two Nitrogen Atoms In DNA, the purine bases are adenine and guanine, while the pyrimidines are thymine and cytosine. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Adenine is a Purine with a variety of roles in Biochemistry including Cellular respiration, in the form of both the energy-rich Adenosine Guanine is one of the five main Nucleobases found in the Nucleic acids DNA and RNA, the others being Adenine, Cytosine, Thymine is one of the four bases in the Nucleic acid of DNA that make up the letters ATGC Cytosine is one of the five main bases found in DNA and RNA. It is a Pyrimidine derivative with a Heterocyclic Aromatic ring RNA uses uracil rather than thymine (thymine is produced by adding a methyl to uracil). Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units Uracil is a common and naturally occurring Pyrimidine derivative The nucleotide passes through numerous biochemical steps while being processed, adding and removing atoms through the use of numerous enzymes. History See also Atomic theory, Atomism The concept that matter is composed of discrete units and cannot be divided into arbitrarily tiny Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins
Pyrimidine ribonucleotides
The synthesis of a single pyrimidine is complex; the diagram to the left demonstrates the synthesis of a single pyrimidine.
Purine ribonucleotides
The atoms which are used to build the purine nucleotides come from a variety of sources:
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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. De novo is a Latin phrase, meaning "from the new" anew or from the beginning Hypoxanthine is a naturally occurring Purine derivative It is occasionally found as a constituent of Nucleic acids where it is present in the Anticodon AMP and GMP 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:
Reaction 1. Phosphoribosylglycinamide formyltransferase is an enzyme involved in the synthesis of Purines Phosphoribosylaminoimidazole carboxylase (or AIR carboxylase) is an enzyme involved in Nucleotide synthesis 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase, also known as ATIC and Inosine monophosphate synthase, is a human Gene The pathway starts with the formation of PRPP. Phosphoribosyl pyrophosphate (PRPP is a pentosephosphate. It is formed from Ribose 5-phosphate by the enzyme Ribose-phosphate diphosphokinase. PRPS1 is the enzyme that activates R5P, which is primarily formed by the pentose phosphate pathway, to PRPP by reacting it with ATP. Ribose-phosphate diphosphokinase (or phosphoribosyl pyrophosphate synthetase) is an enzyme which converts Ribose 5-phosphate into Phosphoribosyl pyrophosphate Ribose 5-phosphate is both a product and an intermediate of the Pentose phosphate pathway. The pentose phosphate pathway (also called Phosphogluconate Pathway or HexoseMonophosphate Shunt shunt is a process that serves to generate NADPH and the synthesis of pentose Adenosine-5'-triphosphate ( ATP) is a multifunctional Nucleotide that is most important as a " molecular currency" of intracellular Energy 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 the pyrimidine nucleotides, Trp, and His. Tryptophan (abbreviated as Trp or W) is one of the 20 standard amino acids, as well as an Essential amino acid in the Human diet Histidine (abbreviated as His or H) is one of the 20 standard Amino acids present in Proteins In the Nutritional sense in 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 group (PPi) by Gln's amide nitrogen. Amidophosphoribosyltransferase (or phosphoribosyl pyrophosphate amidotransferase) is an enzyme which converts Phosphoribosylpyrophosphate (PRPP into 5-phosphoribosylamine 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. Phosphoribosylamine (5PRA is an intermediate in Purine metabolism. This reaction which is driven to completion by the subsequent hydrolysis of the released PPi, is the pathway's flux generating step and is therefore regulated too.
See also
External links
- Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents (IUPAC)
- Provisional Recommendations 2004 (IUPAC)
- Chemistry explanation of nucleotide structure
Dictionary
nucleotide
-noun
- (biochemistry) the monomer comprising DNA or RNA biopolymer molecules. Each nucleotide consists of a nitrogenous heterocyclic base (or nucleobase), which can be either a double-ringed purine or a single-ringed pyrimidine; a five-carbon pentose sugar (deoxyribose in DNA or ribose in RNA); and a phosphate group.
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