Basics of Bioinformatics
Patricia Francis-Lyon
Assistant Professor of Health Informatics
University of San Francisco
Bioinformatics
• Original definition (1979 by Paulien Hogeweg):
“application of information technology and computer
science to the field of molecular biology”
• Using information technology, designing novel algorithms
and methods of analyses (computational biology)
• Establishing innovative software and databases of
information, allowing open access to the records held
within them
(bioinformatics)
Bioinformatics is interdisciplinary
Mathematics
Statistics
Computer Science
Biomedicine
Molecular
Biology
Structural
Biology
Ethical,
legal and
social implications
Bioinformatics
Biophysics
Evolution
Patrice Koehl
Genomics: genes give rise to proteins
• The ~25,000 genes of the human genome
encode > 100,000 polypeptides
• Not all of the DNA in a genome encodes
protein
microbes: 90% coding gene
human: 3% coding gene
• About ½ of the non-coding DNA in humans is
conserved (functionally important)
Central Dogma of Molecular Biology
Genotype
Replication
DNA
Transcription
RNA
Translation
Protein
Phenotype
Patrice Koehl
DNA structure
RNA structure
Protein structure
mRNA synthesis
The mRNA is formed by adding nucleotide that are complementary
to the template strand
DNA coding strand
DNA
5’
3’
3’
3’
G U C A U U C G G
5’
DNA template strand
5’
RNA
Patrice Koehl
Translation: mRNA -> protein
TRANSLATION
• The process of reading the mRNA sequence and creating the protein
is called translation
• Protein are made of amino acids (20 different, 9 “essentials”)
• 3 bases or nucleotides make one codon
• Each codon specifies one amino acid : genetic code
Patrice Koehl
3-letter Codon -> amino acid
Translation : initiation
Patrice Koehl
Translation : initiation
tRNA
Patrice Koehl
Translation : elongation
tRNA
Patrice Koehl
Translation : elongation
Patrice Koehl
Translation : elongation
Patrice Koehl
Translation : elongation
Patrice Koehl
Translation : termination
Patrice Koehl
Translation : termination
Protein
Patrice Koehl
Summary
1) Bioinformatics as a field arose as massive amounts of data on
proteins and genes became publicly available
2) Central Dogma of Molecular Biology:
DNA -> RNA -> protein
3) DNA is in the nucleus of each cell, RNA can go where needed
4) Transcription: DNA -> RNA (alphabet: ACTG -> ACUG)
5) Translation: mRNA -> protein (RNA codon -> amino acid)