BARANGIAN, RHEA BERANGEL

BIOCHEMISTRY
BS CHEMISTRY-PHYSICS II

MW: 1:30-5:00

Structure and Properties of Purines and

Pryimidines
Purines and pyrimidines are two of the building blocks of nucleic acids. Only two purines
and three pyrimidines occur widely in nucleic acids. Here are their structures in organic
chemists' line notation:
The Purines
Adenine

Guanine

The Pyrimidines
Cytosine

Thymine

Uracil

Crucial property: formation of hydrogen-bonded pairs composed of one purine and one
pyrimidine, such as guanine-cytosine (left, below) and adenine-thymine (right).

Guanine-Cytosine

Adenine-Thymine

Red dashes = the strong hydrogen bonds holding the dimers together

"Squiggly lines = position of attachment to the nucleic acid chains of DNA or RNA.

The dimers have exactly the same long dimension, enabling them to fit equally well
into the three dimensional structures derived from them.
o This steric "fit" is crucial to maintaining the helical structure of DNA

Tubular structures = ab initio MO calculated structures for the dimers.

Hydrogen bonding only possible in correct tautomers.

Remember: tautomers are isomers related by changing the positions of attachment

of a single hydrogen and a single double bond, in a three-atom system, such as the
keto- and enol tautomers of a ketone.

For example, the tautomers of adenine:

Tautomers A and C both have an aromatic 6-ring

Structures like C, which must be considered for adenine itself, are ruled out in the
nucleic acids by the attachment to the sugar.

Thus A is the favored tautomer for reasons of both stability and incorporation into
nucleic acids

The tautomers of guanine include the structure that hydrogen bonds well to a
pyrimidine (A), and an aromatic one (B)

Several that must be considered for guanine itself, but not for guanine incorporated
into a nucleic acid,

also can be drawn

Here are the tautomers of cytosine, thymine, and uracil:
Cytosine Tautomers

Thymine Tautomers

Uracil Tautomers

Again, these equilibria involving the "abnormal" tautomers have relevance only for the
individual pyrimidine in aqueous solution. The inter-base hydrogen bonds in the dimers
strongly stabilize the structure indicated in the base pairs.

DIFFERENCE BETWEEN PURINES AND PYRAMIDINES

Purines

Pyrimidines

Introduction (from
Wikipedia)

A purine is a heterocyclic
aromatic organic
compound, consisting of a
pyrimidine ring fused to an
imidazole ring.

Function

Production of RNA and

DNA, proteins and starches,
the regulation of enzymes
and cell signaling.
Adenine and guanine
A pyrimidine ring fused to a
imidazole ring. Contains two
carbon-nitrogen rings and
four nitrogen atoms.
214 C, 487 K, 417 F
Heterocyclic aromatic
organic compound
C5H4N4
120.11 g mol1

Pyrimidine is a heterocyclic
aromatic organic compound
similar to benzene and
pyridine, containing two
nitrogen atoms at positions 1
and 3 of the six-member
ring. It is isomeric with two
other forms of diazine.
Production of RNA
and DNA, proteins and
starches, the regulation of
enzymes and cell signaling.
Cytosine, thymine, uracil
Contains one carbonnitrogen ring and two
nitrogen atoms.

Nucleobases
Structure

Melting point
Type of Compound
Molecular formula
Molar mass

2022 C
Heterocyclic aromatic
organic compound
C4H4N2
80.088 g mol-1

MeSH
SMILES
CAS number
PubChem
Synthesis in Lab

Purine
c1c2c(nc[nH]2)ncn1
120-73-0
1044
Traube Purine Synthesis

Pyrimidine
C1=CN=CN=C1
289-95-2 Y
9260
Biginelli Reaction