General Index
Bases, Nucleosides and Nucleotides
The complete enzymatic hydrolysis of a nucleic acid gives a mixture of Nucleotides. The complete hydrolysis of a
nucleotide gives an equimolar mixture of:
- One Heterocyclic Nitrogen Base, that can be of two types: Purine or Pyrimidine
- One Pentose, that can be either D-Ribose or 2-D-Deoxyribose
- Ortophosphate
The union of the base with the pentose gives a type of glycosides called Nucleosides. The esterification by
phosphate of the alcoholic groups of the pentose gives Nucleotides.
Nitrogen Bases
The nitrogen bases of the nucleic acids are heterocyclic compounds of one of two families, Pyrimidines and
Purines.
Pyrimidines are formed by the Pyrimidine Ring:
It is a planar ring of six atoms, four carbons and two nitrogens. The numbering of the pyrimidine ring is: N1:
The different pyrimidine bases are obtained by substitution of the heterocycle with
oxo groups (=O), amino groups (-NH2) or methyl groups (-CH3).
The other family of nitrogen bases is based on the Purine Ring:
It is a plnar system of nine atoms, five carbons and four nitrogens. The purine
ring can be viewed as an pyrimidine ring fused to a imidazol cycle. The numbering of the ring is
as follows: N1:
Let's see now the structure of the main nitrogen bases:
Pyrimidines |
2-oxo 4-amino pyrimidine
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2,4 dioxo pyrimidine
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2,4-dioxo 5-methyl pyrimidine
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Purines |
6-amino purine
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2-amino 6-oxo purine
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6-oxo purine
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2,6-dioxo purine
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Of all these bases, in the nucleic acids appear cytosine, thymine, guanine and adenine
in DNA; cytosine, uracil, adenine and guanine in RNA. xanthine and hypoxanthine are metabolic forms of the
purines, and sometimes appear as constituents of RNA.
The end product of purine degradation in Primates is Uric Acid:
Uric acid is 2,6,8 trioxo purine. Pyrimidines are completely degraded to water, carbon dioxide
and urea.
Nitrogen bases can appear in Tautomeric forms caused by Keto/enol Isomerism.
Normally the oxo group appears as a keto group -C=O, but rarely can appear as enol group -OH.
For example, Thymine present two tautomeric forms. The keto form is:
This is by far the most abundant form. The enol form is:
The presence of rare tautomeric forms in nucleic acid may be a cause of Spontaneous
Mutations through incorrect Watson-Crick base pairings.
Nucleosides
The union of a nitrogen base with a pentose gives the compounds called Nucleosides.
Note the suffix -oside (from glycoside), The pentose can be either D-Ribose (D-Ribofuranose),
in the case of Ribonucleosides or 2-D-Deoxyribose (2-D-Deoxyribofuranose) in the case of
Deoxyribonucleosides.
All nucleosides are of the b anomeric type. We can
see as an example the structure of Adenosine, a ribonucleoside of the base Adenine (that is,
b-ribofuranosyl adenine:
The atoms of the pentose are numbered as 1', 2', 3', 4' and 5', to avoid confusion
with the atoms of the base. These atoms are 1':
The glycosidic bond allows rotation of the base, thus giving different conformations.
The model of adenosine is in the anti- conformation, in which the furanose and the purine
ring are at opposite sides of the glycosidic bond.
Sometimes, mainly in DNA-Z, tha base and the furanosic ring are on the same side of
the glycosidic bond. This is the syn- conformation:
The table below presents the structures of the different Ribonucleosides. Pay
attention to nomenclature. Ths suffix osine is applied to the radical name of the base in the case
of purine nucleosides, and so is the suffix idine in the case of pyrimidine nucleosides. As exceptions,
thymine ribonucleoside is called Ribothymidine and hypoxanthine ribonucleoside is called Inosine.
Pyrimidine Nucleosides |
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Purine Nucleosides |
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Deoxynucleosides are named placing the preffix Deoxy- before the name of
the nucleoside. Is an exception thymine deoxynucleoside, called Thymidine. Their structures are:
Pyrimidine Deoxynucleosides |
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Purine Deoxynucleosides |
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Nucleotides
When a phosphate group esterifies to any of the alcoholic groups of a nucleoside,
the resulting structure is called Nucleotide. In ribonucleosides, phosphate can be esterified to
three positions; 2', 3' and 5'. Let's see the adenosine monophosphates:
Adenosine 5'-monophosphate (AMP)
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Adenosine 3'-monophosphate (3'-AMP)
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Adenosine 2'-monophosphate (2'-AMP)
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Adenosine 3',5'cyclic monophosphate (cAMP)
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Ih this case, phosphate esterifies simultaneously hydroxyl groups in 3' and 5'. These
are Cyclic Nucleotides.
Very often nucleosides appear esterified to a polyphosphate. In the case of
adenosine:
Adenosine 5'-monophosphate (AMP)
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Adenosine 5'-diphosphate (ADP)
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Adenosine 5'-triphosphate (ATP)
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In the case of deoxyribonucleosides, nucleorides can only be formed by esterification
to 3' and 5', 2' not being available because lacks a -OH group. These are the deoxynucleotides of the
four bases that enter in the composition of DNA:
Deoxyadenosine-5'-monophosphate (dAMP)
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Deoxyguanosine-5'-monophosphate (dGMP)
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Deoxycytidine-5'-monophosphate (dCMP)
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Thymidine-5'-monophosphate (TMP)
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