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This chapter explains in short some of the common biological terms
absolutely essential to get a clear understanding of what exactly is
Bioinformatics all about. I have avoided getting into the intricacies
of Genetics because the basic aim of this report is to know the latest
developments in the field of Bioinformatics, try to visualize where it
is heading, understand what it has got to offer to the community, and
exploit the opportunities available in this field.

2.1 Nucleotide

A nucleotide is a macromolecule made up of three sub-units: a pentose
sugar, a nitrogen base and a phosphate. Nucleic acids are polymers of
nucleotides. Pentose sugar is either ribose or deoxyribose (this
decides whether the genetic material formed is RNA or DNA). Nitrogen
bases are of two types: Purines (Adenine (A), Guanine (G)) and
Pyramidines (Cytosine (C), Thymine (T) and Uracil (U))

2.2 Amino acid

It is the fundamental building block of proteins. There are 20
naturally occurring amino acids in animals and around 100 more found
only in plants. A sequence of three nucleotides forms one amino acid.
The logic behind this is as follows: There are four types of
nucleotides depending on the nitrogenous base: (A,G,C,T) in DNA and
(A,G,C,U) in RNA. 20 different amino acids are to be coded using
permutations of 4 types of nucleotides. So obviously, 3 nucleotides
are required to signify one amino acid (43 > 20), because less than 3
will be insufficient and more than 3 will cause redundancy. The
sequence of three nucleotide specifying an amoni acid is called a
triplet code or codon (coding unit). All 64 codons specify something
or the other. Most of them specify amino acids, but a few are
instructions for starting and stopping the synthesis.

2.3 Properties of Genetic Code

1. Three nucleotides in a DNA molecule code for one amino acid in the
corresponding protein. Such a triplet is called a codon.
2. The code is read from a fixed starting point.
3. Codes for starting and stopping are present, but not for a pause in
the middle, or
comma.
4. The nucleotides are read three at a time in a non-overlapping manner.
5. Most of the 64 possible nucleotide triplets stand for one amino
acid or the other.
6. A few triplets stand for starting and stopping the synthesis.
7. There are two or more different codons for the same amino acid.
Because of this,
the genetic code is said to be degenerate.
8. The code has polarity because it can be read only in one direction.
9. The code is universal. Practically all the organisms use the same code.

2.4 DNA (Deoxy-ribonucleic Acid)

The long, thread-like DNA molecule consists of two strands that are
joined to one another all along their length. Each strand is a polymer
made up of repeated sub-units (nucleotides). Hence each strand is also
called a polynucleotide. DNA is the basic genetic material in all the
living material existing on this earth. The two essential mechanisms
possessed by DNA are (1) Transmission of hereditary characters and (2)
Ability of self-duplication. In the DNA molecule, tow long
polynucleotide chains are spirally twisted around each other. This is
also called helical coiling and the DNA is often referred to as a
double helix. A polynucleotide chain has polarity and the two strands
of a DNA molecule run in opposite directions, hence they are said to
be anti parallel. The two chains are joined together by hydrogen bonds
existing between the nitrogenous bases on the inside. Adenine (A)
forms a bond only with Thymine (T) and Guanine (G) can form a bond
only with Cytosine (C). Because of the base pairing restriction, the
two strands are always complementary to each other.
The sequence of bases along the polynucleotide is not restricted in
any way. An infinite variety of combinations is possible. It is the
precise sequence of bases that determines the genetic information.
There is no theoretical limit to the length of a DNA molecule.

2.5 Chromosomes
Chromosomes are the paired, self-replicating genetic structures of
cells that contain the cellular DNA; the nucleotide sequence of the
DNA encodes the linear array of genes.

2.6 Gene
A gene is the fundamental physical and functional unit of heredity. A
gene is an ordered sequence of nucleotides located in a particular
position on a particular chromosome that encodes a specific functional
product (i.e. a protein or RNA molecule).

2.7 Protein
Protein is a molecule composed of one or more chains of amino acids
in a specific order. The order is determined by the base sequence of
nucleotides in the gene coding for the protein. Proteins are required
for the structure, function and regulation of cells, tissues and
organs, each protein having a specific role (e.g., hormones, enzymes
and antibodies).
DNA carries the hereditary material and the only thing that they do
is to synthesize proteins, and thereafter, all the hereditary
characteristics get reflected in the activities of the body cells
because of proteins.

2.8 Sequencing
Sequencing means the determination of the order of nucleotides (base
sequences) in a DNA or RNA molecule, or the order of amino acids in a
protein.

2.9 Genome
Genome of an organism means all the genetic material in its
chromosomes. Its size is generally given as its total number of base
pairs. Genomes of different organisms can be compared to identify
similarities and disparities in the strategies for the 'Logic of
Life'.

2.10 Clone
Clone is an exact copy made of biological material such as a DNA
segment, a whole cell or a complete organism. The process of creating
a clone is called as cloning.

2.11 Model Organism

Saccharomytes cerevisiae commonly known as the baker's yeast have
emerged as the model organism. It has demonstrated the fundamental
conservation of the basic informational pathways found in almost all
the organisms. From the detailed study of the genomes of these
organisms (which is possible today), we can gain an insight into their
functioning. All this data will lead to the fundamental insights into
human biology.
Vast amount of genetic data available on this species provides
important clues helpful for the ongoing research on human genetics.
Saccharomytes cerevisiae has become the workhorse of many
biotechnology labs. It can exist either in a haploid or a diploid
state and divides by the vegetative process of budding. Yeast cultures
can be easily propagated in labs. It has become the model organism
partly because of the ease with which genetic manipulations can be
carried out. Random mutations can be induced into the genome by the
treatment of live cells with chemicals such as ethyl-methanesulphone
or by exposure to ultra-violet rays. Targeted gene inactivations can
also be carried out; this property is very important during
experiments for the unambiguous assignments of gene functions.
Saccharomytes cerevisiae has a compact genome of 12 lakh base pairs
of DNA present on 16 chromosomes. This presented a reasonable goal for
complete sequencing and analysis of it's genome. The Saccharomytes
genome database (SGD) was established at the Stanford University in
1995.
Knowing the complete sequence of a genome is only the first step in
understanding how the huge amount of information contained in genes is
translated into functional proteins.