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Nucleobase

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Definition

noun

plural: nucleobases


(biochemistry) The base in the nucleic acid, e.g. purines and pyrimidines


Details

Overview

A nucleic acid is a biopolymer composed of monomeric units of nucleotides. Each nucleotide that makes up a nucleic acid is comprised of phosphoric acid, sugar (5-carbon), and nucleobase. The chains of nucleotides in a nucleic acid are linked by 3', 5' phosphodiester linkages. This means that the 5'-phosphoric group of one nucleotide is esterified with the 3'-hydroxyl of the adjoining nucleotide.


A nucleobase is a nitrogen-containing compound. They may also form nucleosides when they are attached to a five-carbon sugar ribose or deoxyribose. Nucleosides are components of nucleotides. Nucleotide is the monomeric unit of nucleic acid, e.g. DNA and RNA. In two-stranded nucleic acids like DNA, the nucleobases are paired. The two nucleobases that are complementary are connected by a hydrogen bond.


Classification

The nucleobases can be grouped into two major forms: purines and pyrimidines. While both purines and pyrimidines are heterocyclic aromatic compounds, they can be differed from each other based on the chemical structure. The purines occur as two carbon rings whereas the pyrimidines occur as one carbon ring. The purine has a pyrimidine ring fused to an imidazole ring. The pyrimidine has only a pyrimidine ring. Thus, the purine has four nitrogen atoms whereas the pyrimidine has two.

Purines are adenine and guanine whereas the nitrogenous bases of pyrimidines are cytosine, thymine, and uracil. These five nitrogenous bases are regarded as primary or canonical since they are the fundamental units of the genetic code. The nitrogenous components are one of the major distinctions used to distinguish DNA from RNA molecules. In DNA, thymine complementary pairs with adenine whereas in RNA, uracil matches with adenine. The thymine differs from uracil in having a methyl group, which the uracil lacks.


Canonical nucleobases

The nucleobases adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) are referred to as primary or canonical. They are the fundamental nucleobases of the genetic code. DNA specifically has A, C, G, and T whereas RNA has A, C, G, and U. Thus, one of the ways to distinguish DNA from RNA is the presence of thymine. Instead of uracil, DNA has thymine that complementary pairs with adenine. The nucleobase cytosine pairs with guanine in both DNA and RNA. The pairings of nucleobases C-G and A-T (or A-U in RNA) are referred to as base complements.


One of the possible explanations why DNA has thymine instead of uracil is associated with the conversion of cytosine into uracil by spontaneous deamination. Cytosine can turn into uracil when it loses its amine group. This deamination of cytosine is a common occurrence. Nevertheless, the error is corrected through an inherent DNA repair systems. If not repaired though, it could lead to a point mutation. If uracil is present in the DNA, the repair systems may not be able to distinguish the original uracil from the cytosine-turned-uracil and therefore may fail to discern which uracil to correct. The presence of methyl group in thymine (which is absent in uracil) helps avert this from happening, thereby, preserving the integrity and stability of the genetic code.


Non-primary nucleobases

The nucleic acids may contain other nucleobases. Examples of non-primary pyrimidine nucleobases are 5-methylcytosine (m5C), 5,6-dihydrouracil, and 5-hydroxymethylcytosine. As for the non-primary purine nucleobases, hypoxanthine, xanthine, and 7-Methylguanine are examples.


non-primary pyrimidines nucleoside features
5-Methylcytosine 5-Methylcytidine (m5C) A modified cytosine, i.e. a methylated cytosine
5,6-Dihydrouracil Dihydrouridine (D) A modified uracil


An intermediate in uracil catabolism

5-Hydroxymethylcytosine Derived from cytosine


non-primary purines nucleoside features
Hypoxanthine Inosine (I) A modified adenine
Xanthine Xanthosine (X) A modified guanine
7-Methylguanine 7-Methylguanosine (m7G) A modified guanine


m5C is the most common non-primary nucleobase in DNAs whereas Ψ, D, I, and m7G occur in RNA (particularly, tRNA). Hypoxanthine may form from spontaneous deamination of adenine. Similarly, xanthine is a purine nucleobase that forms by deamination, but in this case, of guanine. Other sources of xanthine are hypoxanthine (via the enzymatic activity of xanthine oxireductase) and xanthosine (via purine nucleoside phosphorylase). The presence of mutagens may promote the formation of hypoxanthine and xanthine. Hypoxanthine, in particular, may faulty base pairs with cytosine because of its likeness to adenine (which pairs up naturally with thymine). When this happens, one of the ways by which DNA is repaired is by base excision repair mechanism as initiated by the enzyme N-methylpurine glycosylase.


Artificial nucleobases

Certain nucleobases are artificially produced. Examples of nucleobase analogues are isoguanine and isocytosine. Isoguanine is an isomer of guanine that can be produced by oxidative damage to DNA. One of its applications is for use as a nucleobase in hachimoji nucleic acids. Isocytosine is an isomer of cytosine that can be synthesized from guanidine and malic acid. One of its uses is for use as a nucleobase in hachimoji RNA.


Common biological reactions

Biosynthesis

Ribonucleotides (i.e. nucleobases attached to ribose 5-phosphate) are precursors to nucleobases. Purines such as adenine and guanine are derived from the nucleotide inosine monophosphate (IMP). IMP, in turn, is formed from a ribose phosphate.


One of the biosynthetic pathways to produce pyrimidines is de novo synthesis pathway. In the de novo synthesis, the six-member ring is synthesized first and ends in the formation of uridine monophosphate (UMP). The six major steps are as follows:[1]

  1. Carbamoyl phosphate synthesis
  2. Carbamoyl aspartate synthesis
  3. Ring closure to yield dihydroorotate
  4. Addition of ribose phosphate moiety
  5. Decarboxylation to yield UMP

Down in the biosynthetic pathway, uridine triphosphate (UTP), cytidine triphosphate (CTP), and thymidine triphosphate (TTP) are produced as catalyzed by certain enzymes.


Degradation and Salvage

Pyrimidines are degraded into CO2, water, and urea. The metabolic fates of pyrimidines are as follows:

  • Cytosine » uracil » N-carbamoyl- β-alanine » β-alanine, CO2, and ammonia
  • Thymine » β-aminoisobutyrate » » Citric acid cycle

As for the purines guanine and adenine, they are degraded generally as follows:

  • Guanine (via guanase) » xanthine (via xanthine oxidase) » uric acid
  • Adenosine »» inosine (via purine nucleoside phosphorylase) » hypoxanthine (via xanthine oxidase) » xanthine (via xanthine oxidase) » uric acid

Purines from catabolism may be salvaged and re-used as follows:

  • Adenine is salvaged by the enzyme adenine phosphoribosyltransferase (APRT)
  • Guanine and hypoxanthine are salvaged by the enzyme hypoxanthine-guanine phosphoribosyltransferase (HGPRT)


Biological importance

The nucleobases are one of the fundamental components of nucleic acids, such as DNA. Nucleic acids such as DNA and RNA molecules contain the genetic information that are important for all cellular functions and heredity.


Supplementary

Etymology

  • origin: word (translation, "meaning")

Synonym(s)

  • nitrogenous base
  • nitrogen base


Further reading

See also

Mention(s)


Reference

  1. "Pyrimidine Synthesis". (2017, May 3). Biochemistry Den. Retrieved from Biochemistry Den website: [Link]



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