Information Technology Reference
In-Depth Information
do, although I recommend the third edition of
Biochemistry
by Mathews et
al. (1999) for its clarity and elegant presentation.
1.1 The Entities of Biological Gene Expression
In the cell, the expression of the genetic information is a very complex proc-
ess involving hundreds of molecules. For our purposes, though, it is enough
to know the basics about the structure and function of the main players:
DNA, RNA, and proteins.
DNA is the carrier of the genetic information and the proteins read and
express that information. RNA is a working copy of DNA and, although its
existence makes sense in the environment of the cell, its equivalent is of
little use in a computer system like GEP. Nonetheless, it is important to know
the structure and properties of this molecule in order to understand the fun-
damental difference between GEP and the other genetic algorithms.
1.1.1 DNA
DNA molecules are long, linear strings of four nucleotides (represented by A,
T, C, and G). Each DNA molecule is, in fact, a double helix in which one of
the strings is the complementary of the other and, thus, adds nothing to the
information contained in a single string. In the structure of the double helix,
A pairs with T, and C with G (Figure 1.1). The double-stranded, complemen-
tary nature of DNA is fundamental for the replication of the genetic informa-
tion in the cell, but is of little importance in a computer system like GEP or
GAs. Indeed, the chromosomes of both GEP and GAs are single-stranded
and their replication is done by simple program instructions.
The information stored in DNA consists of the sequence of the four
nucleotides, which is called the primary structure of DNA. The secondary
structure of DNA consists of the different kinds of double helixes it can form
and, most important to us, DNA lacks a tertiary structure, which consists of
a unique three-dimensional arrangement of the molecule. Indeed, DNA mol-
ecules fold, forming random coils. And because complex functionality such
as catalytic activity is closely related to tertiary structure, DNA molecules
are useless for doing much of the work that needs to be done in a cell.
However, the simple DNA molecule is excellent to store information. In
the structure of the double helix, the complementary nucleotides face each
