Structural Biochemistry/Nucleic Acid/Nitrogenous Bases/Pyrimidines

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What is a Pyrimidine?[edit]

A pyrimidine is a nucleotide (nucleoside + phosphate group) whose basic structure is cyclohexane with Nitrogen atoms positioned at 1 and 3. This molecule is also aromatic, and planar. Pyrimidine is isomeric with two other forms of diazine. Cytosine(C), Uracil(U), and Thymine(T) are all examples of pyrimidines; each with different chemical groups. Pyrimidine attaches itself to a phosphate sugar group such as ribonucleotides(which have a hydroxy group positioned axially at carbon-2) or deoxyribonucleotide(which have a hydrogen atom at C-2) at the 1st Nitrogen.

Pyrimidine.  Two of the bases found in DNA, cytosine (C) and thymine (T), and a base found only in RNA, uracil (U), are derivatives of pyrimidine.


Correct mistake: 2. It needs carbonyl phosphate synthetase, which is located in the cytoplasm.

Pyrimidine Biosynthesis[edit]

1. Unlike in purine, the ring is synthesized first then conjugated after.

2. It needs carbamoyl phosphate synthetase, which is located in the cytoplasm.

3. It also needs an enzyme in order for the reaction to work, but the enzyme should be controlled in 2 steps:

  • controlled level at where the reaction occurs & transcriptions must be reduced
  • the pyrimidine nucleotides which produces the feedback inhibition level also must be controlled

4. The ring then closes.

5. The C-C bond is formed when the ring oxidizes.

Thymine base
Cytosine base
Uracil base

Chemical Properties[edit]

Pyrimidine has similar properties to that of pyridines. One similarity is that as the number of nitrogen atoms in the ring increase, the ring pi electrons become less energetic and, as a result, electrophilic aromatic substitution gets more difficult while nucleophilic aromatic substitution gets easier. One example is the displacement of the amino group in 2-aminopyrimidine by chlorine and its reverse reaction. Reduction in resonance stabilization of pyrimidines leads to the addition and ring cleavage reactions, and not substitutions. An example of this is in the Dimroth arrangement. Pyrimidines are less basic than pyridines and the N-alkylation and N-oxidation are more difficult in pyrimidines as well.