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In the graph of Fig. 1.10, nodes are atoms or groups of atoms, and edges represent
the chemical bonds between them. Table 1.4 gives the complete list of Nitrogen
Bases , which correspond to the letters of DNA and RNA alphabets.
In the deoxyribose molecule, Carbon at position 1 is connected to the nitroge-
nous base. Position 2 is where Oxygen is missing, respect to ribose, and position 5
is the position where Carbon shares an Oxygen with the phosphate group. Bases are
connected by means of a bond between Nitrogen and Carbon (a glycosidic bond)
which is established by liberating a water molecule.
When a nucleotide is linked to another nucleotide, then phosphate group becomes
the bridge between the 5 Carbon with the 3 Carbon of the other nucleotide. In this
link, OH molecule at position 3 of pentose (deoxyribose in DNA case, or ribose in
RNA case) is replaced by an Oxygen of the phosphate group.
Ta b l e 1 . 4 The nitrogen Bases of DNA. Uracil substitutes Thymine in RNA.
Adenine
A
C 5 H 5 N 5
Guanine
G
C 5 H 5 N 2 O 2
Thymine
T
C 5 H 6 N 2 O 2
Cytosine
C
C 4 H 5 N 3 O
Uracil
U
C 4 H 4 N 2 O 2
It is interesting that the nucleotide corresponding to the letter A of the DNA al-
phabet has a crucial role from the point of view of biological energy. In fact, the
Adenosine triphosphate is constituted by the adenine nucleotide, where deoxyri-
bose is replaced by ribose and the phosphate group is a triphosphate (see Fig. 1.12).
This molecule is the so-called unit of energetic currency in biomolecular trans-
formations. When energy is required, then a reaction, from ATP to the molecule
ADT (Adenosine diphosphate, with a diphosphate group) is simultaneously associ-
ated, which liberates both a phosphate group and an energy quantity (7 Kcal/mole
at 37 o Celsius). Figure 1.12 shows this transformation, which is essentially an
operation transforming a connected graph into another one with two connected
components.
RNA structure is similar to that of DNA, with the only difference that in RNA
the basic components are ribonucleotides (in a ribose the Carbon at 2' binds
H 2 O instead of H 2 ). Ribo-nucleotides concatenate each other, by providing RNA
strands.
DNA nucleotide concatenate in double strands, according to the schema of Fig.
1.13, where a nucleotide of a strand is paired with a nucleotide of the other strand
if the two corresponding bases are a complementary pair. The two complementary
pairs are
(a pairing of a DNA strand with a RNA strand is also
possible, according to the complementarity
{
A
,
T
}
and
{
C
,
G
}
). The three principles of
this molecule arrangement are: bilinearity, complementarity, and antiparallelism .
{
A
,
U
}
,
{
C
,
G
}
 
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