Deoxyribonucleotide

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Definition

noun

plural: deoxyribonucleotides

de·ox·y·ri·bo·nu·cle·o·tide, [diˌɒk sɪˌraɪbəʊˈnjuːklɪəˌtaɪd]

A form of nucleotide in which the sugar component is a deoxyribose (as opposed to ribonuleotide that has a ribose as its sugar)


Details

Overview

A nucleotide is regarded as the basic building block of nucleic acids (e.g. DNA and RNA). A nucleic acid is one of the major groups of biomolecules [the others are carbohydrates (especially, polysaccharides), proteins, and amino acids]. Nucleic acids are involved in the preservation, replication, and expression of hereditary information. The fundamental structure of a nucleotide is a nitrogenous base, a pentose sugar, and phosphate group(s). Based on the pentose sugar component, the nucleotide may either be a ribose or a deoxyribose. Nucleotides with a ribose sugar make up the RNA whereas those with a deoxyribose make up the DNA molecule.


Structure/Characteristics

A deoxyribonucleotide is a nucleotide that has a deoxyribose as its sugar component. As for the nitrogenous base (or nucleobase) component, the common forms are adenine (A), guanine (G), cytosine (C), and thymine (T). Depending on the number of phosphates that make up the compound, the deoxyribonucleotide may be designated as monophosphate (having only one phosphate group), diphosphate (having two phosphate groups), or triphosphate (having three phosphate groups). Thus, the common deoxyribonucleotides include the following:


Without the phosphate group(s), the compound is referred to as a nucleoside (i.e. a nucleobase + pentose sugar). Adenine and guanine nucleotides are purines whereas cytosine and thymine nucleotides are pyrimidines.


Common biological reactions

Biosynthesis

The deoxyribonucleotides may be derived from dietary sources or they can be biosynthesized via the de novo pathway. In particular, purines (i.e. nucleotides with adenine and guanine nucleobases) are derived from the nucleotide inosine monophosphate (IMP). IMP, in turn, is produced from a pre-existing ribose phosphate that forms mainly from the amino acids glycine, glutamine, and aspartic acid. Ribose 5-phosphate reacts with ATP to produce 5-Phosphoribosyl-1-pyrophosphate (PRPP) (which is also involved in pyrimidine biosynthesis). PRRP though becomes committed particularly to purine biosynthesis when PRRP is converted into 5-phosphoribosyl amine by having the pyrophosphate of PRRP replaced by the amide group of glutamine. IMP is then converted into either adenosine monophosphate (AMP) or guanosine monophosphate (GMP). AMP can then be reduced to dAMP catalyzed by ribonucleotide reductase. GMP, in turn, when reduced is converted into dGMP.


As for pyrimidines such as thymine and cytosine nucleotides, the biosynthesis involves a series of steps that begins in the formation of carbamoyl phosphate catalyzed by the enzyme carbamoyl phosphate synthetase. The carbamoyl phosphate is then converted into carbamoyl aspartate through the catalytic activity of aspartate transcarbamylase. Carbamoyl aspartate is next converted into dihydroorotate, which is then oxidized to produce orotate. Orotate then reacts with PRPP to form orotidine-5-monophosphate (OMP). OMP is decarboxylated by the enzyme OMP decarboxylase to yield uridine monophosphate (UMP). Eventually, uridine diphosphate (UDP) and uridine triphosphate (UTP) are produced down the biosynthetic pathway by kinases and dephosphorylation of ATPs. Amination of UTP leads to the formation of cytidine triphosphate (CTP) by the action of the enzyme CTP synthetase. Breaking down of CTP (by losing two phosphates through the action of RNAse) leads to the formation of CMP. In order to synthesize thymidine, uridine is reduced first to deoxyuridine (by the enzyme ribonucleotide reductase). After which, it is methylated by the enzyme thymidylate synthase to form thymidine.


DNA synthesis

DNA synthesis is the process of linking together of nucleotides (as deoxyribonucleotide triphosphates) to form DNA. In vivo, most synthesis is by DNA replication, but incorporation of precursors also occurs in repair. The polymerization of nucleotides to produce DNA involves the binding of the phosphate group from one nucleotide to the 3' carbon of the adjacent nucleotide. The chemical bond between the two nucleotides is a phosphodiester bond. The direction of DNA synthesis proceeds from 5' to 3'.


Biological importance

Deoxyribonucleotides are essential in being the basic building blocks of DNA. In DNA, adenine pairs with guanine whereas cytosine pairs with thymine.


Supplementary

Etymology

  • ribo (denotes ribose) + nucleo- ("nucleus") + -ide (chemical suffix)


Further reading

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