Strings and Genomes - Infobiotics: Information in Biotic Systems - page 27

between two monomers is obtained by connecting the head of a monomer with the
tail of another monomer in a resulting component which is the bridge of the com-
posed structure. When the link is performed we get a polymer, or more precisely a
dimer, having a head and a tail: the head is the head of the monomer which fused its
tail in the bridge, while the tail is the tail of the monomer which fused its head in the
bridge (see Fig. 2.1 and Fig. 2.2). In this construction we have a result the linear ar-
rangement of the two flags of the linked monomers, and we can continue the process
by linking, in the same way, the obtained polymer with another monomer or with
another polymer. This means that the flag is the variable component of monomers,
or what makes its specific role in the construction of polymers.
The reader is invited to verify that this structure is present in the nucleotide given
in Fig. 1.10, where the body is the sugar, the head and also the bridge is the phos-
phate group, the tail is the oxhydryl group OH in 3', while flags are the nitrogenous
bases.
For peptides we have that the body is a Carbon-Hydrogen group, the head is the
amine group NH 2 , the tail is the carboxyl group COOH , the bridge is the group
CONH , and flags are the 20 peptide residues.

Fig. 2.1 The structure of a biological monomer

2.2 DNA Strings and DNA Helix

DNA molecules realize a special structure of strings. For this reason, DNA ma-
nipulation can be formally described in terms of string operations. However, DNA
strings are more precisely double strings and their physical nature implies their spe-
cific geometric form of a helix. In the following section we discuss these aspects.