Nucleotide

Nucleotides are the fundamental building blocks of DNA and RNA.  They are similar to the structure of nucleosides but differ in the fact that they have one or more phosphate group(s) added.

A compound consisting of a nitrogenous base, a phosphate group and a sugar. Nucleotides are bonded together by phosphate-sugar linkages to form DNA or RNA.

Structure

The contituents of nucleotides are a nitrogenous base, a 5-carbon sugar and one or more <a href="Phosphate">phosphate</a> group(s), the types of which vary between DNA and RNA. In DNA the base can be either one of the purines, <a href="Adenine">adenine</a> (A) or <a href="Guanine">guanine</a> (G), or one of the pyramidines, <a href="Thymine">thymine</a> (T) or <a href="Cytosine">cytosine</a> (C). This is similar in RNA with the exception of one base; thymine is replaced with <a href="Uracil">uracil</a>.The base of each nucleotide is joined to C1' of the sugar by a beta-glycosidic linkage from either N-9 of a purine or N-1 of a pyrimidine. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman p109

The presence of thymine in <a href="DNA">DNA</a> rather than uracil is used to maintain the active repair system which corrects deamination of <a href="Cytosine">cytosine</a>. The <a href="Deamination">deamination</a> of <a href="Cytosine">cytosine</a> to form <a href="Uracil">uracil</a> (which occurs spontaneously in <a href="DNA">DNA</a>) is potentially mutagenic as <a href="Uracil">uracil</a> is complementary to <a href="Adenine">adenine</a>. This means that during replication one of the daughter strands would contain a U-A base pair instead of the original C-G base pair. <a href="Uracil">Uracil</a> is recognised as foreign to <a href="DNA">DNA</a> by a repair system in order to prevent this mutation from occurring. The repair enzyme, <a href="Uracil DNA glycosylase">uracil DNA glycosylase</a>, hydrolyzes the <a href="Glycosidic bond">glycosidic bond</a> between <a href="Uracil">uracil</a> and <a href="Deoxyribose">deoxyribose</a> but does not attack thymine-containing nucleotides. Once <a href="Uracil">uracil</a> is removed by the <a href="Enzyme">enzyme</a>, <a href="Cytosine">cytosine</a> is reinserted to repair the mutation. The methyl group on <a href="Thymine">thymine</a> enables the enzyme to distinguish between <a href="Thymine">thymine</a> and <a href="Deaminated cytosine">deaminated cytosine</a>. If <a href="Uracil">uracil</a> was used in <a href="DNA">DNA</a> rather than <a href="Thymine">thymine</a>, the <a href="Uracil">uracil</a> which was correctly placed would not be distinguishable from the potentially mutagenic <a href="Uracil">uracil</a> formed from deamination of <a href="Cytosine">cytosine</a>. Thus, all <a href="Uracil">uracil</a> would be removed regardless of whether it was mutagenic or not and the fidelity of the genetic code would be decreased Berg Jeremy M., Tymoczko John L., Stryer Lubert., (2007) Biochemistry, Sixth Edition, New York, W.H. Freeman and Company. P809.

The base present in <a href="ATP">ATP</a> is <a href="Adenine">adenine</a> and in <a href="GTP">GTP</a> it is <a href="Guanine">guanine</a>. The sugar present in nucelotides is either <a href="Deoxyribose">deoxyribose</a> in <a href="DNA">DNA</a> or <a href="Ribose">ribose</a> in <a href="RNA">RNA</a>; the sugar present in both <a href="ATP">ATP</a> and <a href="GTP">GTP</a> is the same as the sugar present in <a href="RNA">RNA</a>, <a href="Ribose">ribose</a>. These are almost identical in structure except for one difference; in <a href="Deoxyribose">deoxyribose</a> the 2' carbon has two <a href="Hydrogen">hydrogen</a> <a href="Atom">atoms</a> attached, in <a href="RNA">RNA</a> one of the <a href="Hydrogen">hydrogen</a> <a href="Atom">atoms</a> on the 2' carbon is replaced with a hydroxyl (OH) group Hart D.L and Jones E.W (2009) Genetics: Analysis of Genes and Genomes, 7th Edition, Jones and Bartlett's Publishers, p.41. The final constituent which is present in the same form in both <a href="DNA">DNA</a> and <a href="RNA">RNA</a> is a <a href="Phosphate">phosphate</a> group. In <a href="ATP">ATP</a> and <a href="GTP">GTP</a> there is not just one phosphate group present but three phosphate groups, hence the name triphosphate. In all nucleotides, the base is attached to the relevant sugar, <a href="Deoxyribose">deoxyribose</a> or <a href="Ribose">ribose</a>, on the 1' carbon and the phosphate group is attached to the 5' carbon of the relevant sugar. The multiple phosphate groups present in <a href="ATP">ATP</a> and <a href="GTP">GTP</a> are attached to one another. This altogether attachment is the final structure of a nucleotide. <a href="ATP">ATP</a> and <a href="GTP">GTP</a> are not always naturally found as triphosphates; they also exist as dipohosphates (<a href="ADP">ADP</a> and <a href="GDP">GDP</a>) and monophosphates (<a href="AMP">AMP</a> and <a href="GMP">GMP</a>) where either two (a pyrophosphate) or only one phosphate groups are attached respectively.

Polynucleotide chains can be formed which are simply repeating units of nucleotides which are joined by bonds called <a href="Phosphodiester bond">phosphodiester bonds</a>. <a href="Phosphodiester bond">Phosphodiester bonds</a> form between a phosphate groups and two 5-carbon sugars each from a different nucleotide. The phosphate group, which is already attached to one sugar at the 5' carbon forms a bond with an OH group on the 3' carbon of another sugar Hartl D.L and Jones E.W (2009) Genetics: Analysis of Genes and Genomes, 7th Edition, Jones and Bartlett's Publishers, p.41. These polynucleotide chains make up the <a href="DNA">DNA</a> and <a href="RNA">RNA</a> phosphate-sugar backbone.