Nucleotide

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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 constituents of nucleotides are a nitrogenous base, a 5-carbon sugar and one or more phosphate group(s), the types of which vary between DNA and RNA. In DNA the base can be either one of the purines, adenine (A) or guanine (G), or one of the pyramidines, thymine (T) or cytosine (C). This is similar in RNA with the exception of one base; thymine is replaced with uracil. 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[1].

The presence of thymine in DNA rather than uracil is used to maintain the active repair system which corrects deamination of cytosine. The deamination of cytosine to form uracil (which occurs spontaneously in DNA) is potentially mutagenic as uracil is complementary to adenine. 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. Uracil is recognised as foreign to DNA by a repair system in order to prevent this mutation from occurring. The repair enzyme, uracil DNA glycosylase, hydrolyzes the glycosidic bond between uracil and deoxyribose but does not attack thymine-containing nucleotides. Once uracil is removed by the enzyme, cytosine is reinserted to repair the mutation. The methyl group on thymine enables theenzyme to distinguish between thymine and deaminated cytosine. If uracil was used in DNA rather than thymine, the uracil which was correctly placed would not be distinguishable from the potentially mutagenic uracil formed from deamination of cytosine. Thus, all uracil would be removed regardless of whether it was mutagenic or not and the fidelity of the genetic code would be decreased[2].

The base present in ATP is adenine and in GTP it is guanine. The sugar present in nucelotides is either deoxyribose in DNA or ribose in RNA; the sugar present in both ATP and GTP is the same as the sugar present in RNA, ribose. These are almost identical in structure except for one difference; in deoxyribose the 2' carbon has two hydrogen atoms attached, in RNA one of the hydrogen atoms on the 2' carbon is replaced with a hydroxyl (OH) group[3]. The final constituent which is present in the same form in both DNA and RNA is a phosphate group. In ATP and GTP 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, deoxyribose or ribose, on the 1' carbon and the phosphate group is attached to the 5' carbon of the relevant sugar. The multiple phosphate groups present in ATP and GTP are attached to one another. This altogether attachment is the final structure of a nucleotide. ATP and GTP are not always naturally found as triphosphates; they also exist as dipohosphates (ADP and GDP) and monophosphates (AMP and GMP) 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 phosphodiester bonds. Phosphodiester bonds form between a phosphate group 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[4]. These polynucleotide chains make up the DNA and RNA phosphate-sugar backbone.

References

  1. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman p109
  2. Berg Jeremy M., Tymoczko John L., Stryer Lubert., (2007) Biochemistry, Sixth Edition, New York, W.H. Freeman and Company. P809
  3. Hart D.L and Jones E.W (2009) Genetics: Analysis of Genes and Genomes, 7th Edition, Jones and Bartlett's Publishers, p.41
  4. Hartl D.L and Jones E.W (2009) Genetics: Analysis of Genes and Genomes, 7th Edition, Jones and Bartlett's Publishers, p.41
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