Module 1
Introduction to Bioinformatics
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What is Life made of?
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Life begins with Cell
• A cell is a smallest structural unit of an
organism that is capable of independent
functioning
• All cells have some common features
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All Life depends on 3 critical
molecules
• DNAs
• RNAs
• Proteins
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DNA: The Code of Life
• Adenine (A), Guanine (G), Thymine (T), and Cytosine (C)
which pair A-T and C-G to form DNA and these molecules are
called as nucleic acids.
See Next Slide for More about DNA….
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DNA: The Basis of Life
• Deoxyribonucleic Acid (DNA)
– Double stranded with two strands A-T, C-G
• DNA is a polymer
– Sugar-Phosphate-Base
– Bases held together by Hydrogen bonding to the
opposite strand
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DNA, continued
• DNA has a double
helix structure which
composed of
– sugar molecule
– phosphate group
– and a base (A,C,G,T)
A - Adenine
C - Cytosine
G - Guanine
T - Thymine
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DNA: The basis of Life
DNA is Present in Chromosome
The figure shows how DNA is packed in chromosome….
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Central Dogma of Biology
The information for making proteins is stored in DNA. There is a process
(transcription and translation) by which DNA is converted to protein.
DNA
Transcription (the process of
formation of RNA from DNA)
RNA
Translation (the process of
formation of protein from RNA)
Protein
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RNA
• RNA is similar to DNA chemically. It is usually only a
single strand. DNA and RNA are similar in structure with
one difference. DNA consists of Adenine (A), Guanine
(G), Thymine (T), and Cytosine (C) and RNA consists of
Uracil (U), adenine (A), Guanine (G) & Cytosine (C).
Only difference is
T(hyamine) is
replaced by U(racil)
and it is single
strand & DNA is
double strand.
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Several types of RNA exists as mRNA, tRNA & rRNA
and each has its own significance.
Definition of a Gene
The important part of DNA,
which is responsible for “RNA
and protein” formation is
called “Gene” and Gene
consists of two parts
1. Exons:
2. Introns:
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Formation of RNA from a gene (gene is always present in DNA)
The process of breaking all introns to form mRNA is called “splicing”
& the most important region in mRNA which is reponsible for protein
formation is called “Open Reading Frame”.
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Protein:
Complex organic molecules made up
of amino acid subunits.
Protein is formed from 20 different
kinds of amino acids. Each has a 1
and 3 letter abbreviation.
Protein is also called as “polypeptide”
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Combination
of two or
more amino
acids can be
called as
proteins or
poly peptides.
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RNA  Protein: Translation
mRNA (messenger RNA) passes
through ribosome (A small organ
in a cell) and three nucleic acids
present in mRNA will produce
one amino acid and those three
nucleic acids are called codons.
In the figure you can see UUC,
GGA etc…. are coding for group
of amino acids.
Codon table is provided in the next slide which tells which codon codes for which
proteins.
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RNA  Protein: Translation
Protein is formed from RNA and three molecules in RNA, called as
codons, are responsible for producing one amino acid present in a
protein. As the codon number increases the formation of bigger
proteins takes place.
RNA codon ----- Amino Acid
UUA ----- Leucine
CGA ---- Arginine
UAG --- Stop Codon or
no amino acid
UGG --
Tryptophan.
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For more explanation (How protein is formed from mRNA)
tRNA enters into ribosome by carriing one
amino acid (in this case it is carrying
valine)
mRNA
As the amino acids number
increases the formation of
protein takes place.
(In the figure you can
observe a protein
consisting eight amino
acids)
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Proteins are represented by single letter alphabets...
(by using the table present in 14th slide)
Write down the name of corresponding amino acids
AGASPFMKLKKAGAKAHLKMSHFWYVHSIL
Example: A – alanine
G - Glycine
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DNA consists of four nucleotides Adenine, guanine, cytosine and thymine (and
they are represented by single letter alphabets.
Adenine ------Guanine ------Cytosine ------Thymine -------
A
G
C
T
Write down the names of nucleotides present in DNA
“AAAGAGACGTACGACGAGCGC”
Like: Adenine-Adenine-Adenine-Guanine-………..
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We all know that three Nucleotides codes for single amino acid then for
example like "UUU" codon produces "Phenylalanine Amino Acid“.
By using the above table find the protein sequence of the following RNA
starting from first "A" only.
AAGAGARGACGUGCGACGACGUCGAGUCAAAAACGUCGA
Clue: AAG ---- See the corresponding amino acid in the above table
it is “Lys” or “K”…. Like wise select three codons and
get amino acids
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Bioinformatics:
Bioinformatics is generally defined as the analysis, prediction, and
modeling of biological data with the help of computers
What is biological data and how to put
protein into computer?
Biological data is nothing but protein and
nucleic acid sequences represented by
alphabets.
Example: Protein Sequence
(consists twenty amino acids)
AAGHWTILKWGRSH
DNA sequence (Consists four nuclic acids)
AAGAGTCGCGAGAGGACG
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What is Computational Biology?
This branch of biology involves the use of
techniques including applied mathematics,
informatics, statistics, computer science,
artificial
intelligence,
chemistry,
and
biochemistry to solve biological problems
usually at the molecular level.
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Bioinformatics is multidisciplinary
Mathematics/
computer
science
Genomics
Molecular
biology
Bioinformatics
Biophysics
Biomedicine
Ethical, legal,
and social
implications
Molecular
evolution
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From chromosomes
to sequence data
Large scale DNA
sequencing
CGCCAGCTGGACGGGCACACCATGAGGCTGCTGACCCTCCTGGGCCTTCTG
TGTGGCTCGGTGGCCACCCCCTTAGGCCCGAAGTGGCCTGAACCTGTGTTC
GGGCGCCTGGCATCCCCCGGCTTTCCAGGGGAGTATGCCAATGACCAGGAG
CGGCGCTGGACCCTGACTGCACCCCCCGGCTACCGCCTGCGCCTCTACTTC
ACCCACTTCGACCTGGAGCTCTCCCACCTCTGCGAGTACGACTTCGTCAAG
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Some Terminology……..
Genome: In biology the genome of an organism is its whole hereditary information
and is encoded in the DNA (or, for some viruses, RNA). Genomes can be
represented as base pairs (AT or CG) of nucleic acids.
Human Genome consists of 3 Billion Base Pairs.
etc…….
Genomics is the study of an organism's entire genome. The field includes intensive
efforts to determine the entire DNA sequence of organisms.
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Genome sequencing and analysis
(genomics)
Genomics generates a vast amount of DNA
sequence data. Sophisticated algorithms are
used to predict gene regions. Only ~3% of the
vertebrate genome codes for proteins.
Genbank hold sequences from over 800
organisms. There are currently 113 complete
genomes.
The completion of a "working draft" of the
human genome was announced in June 2001.
•Estimates of 38 - 120,000 genes (40, 000)
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Genome Size as in base pairs….
ORGANISM
CHROMOSOMES
GENOME SIZE
GENES
Homo sapiens
(Humans)
23
3,200,000,000
~ 30,000
Mus musculus
(Mouse)
20
2,600,000,000
~30,000
Drosophila
melanogaster
(Fruit Fly)
4
180,000,000
~18,000
Saccharomyces
cerevisiae (Yeast)
16
14,000,000
~6,000
Zea mays (Corn)
10
2,400,000,000
???
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1. Draw the figure present in sixth slide?
2. Draw the table giving proteins (14th slide)
3. Search what is tRNA in google.com
4. Literature Collection:
Type www.google.com in the web site.
Type NCBI home page in the google
Go to home page of NCBI
Click on pubmed in the search space and type any key word you are
interested in to look for, for eg., lung cancer, human genome project,
polymerase, immunoglobins etc.
Window will display your result
Click on each of the result to read abstract or full text of your interest.
5. Go to www.answers.com and type transcription and see the
explanation.
6. Go to google.com and type “ppt introduction to bioinformatics” and
collect more than five powerpoint presentation.
(if you add ppt to any keywork you will get PowerPoint presentations)
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Reference:
1. http://en.wikipedia.org/wiki/Bioinformatics
2. PowerPoint Slides from internet
http://www.bioalgorithms.info/presentations.old/Ch03_Molecula
r_Biology_Primer.ppt
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