Tutorial 1
Biology background
for the course
Genome sizes and number of genes
Organism
Genome Size
No. of genes
E. coli
4.6 Mb
~4,300 genes
Baker’s Yeast
12 Mb
~5,700 genes
C. elegance
100 Mb
~20,000 genes
Rice
430 Mb
~40,000 genes
Mouse
2.8 Gb
~21,000 genes
Human
3.3 Gb
~21,000 genes
Orthologs vs. Paralogs
Orthologs – Genes in different genomes with a common origin
Paralogs – Genes in the same genome with a common origin
http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2010/Rydberg/Orthologs.html
The Central Dogma
Replication
Transcription
Double stranded
(DS) DNA
Nucleic Acids
Translation
Single stranded
(SS) RNA
Amin Acids
http://www.labgrab.com/users/labgrab/blog/central-dogma-genetics-incomplete_id%3D904
Prokaryotes vs. Eukaryotes
• Smaller cells
• Single-celled organisms
• Ancient
• Multi-cellular organisms
• Has a nucleus
http://www.phschool.com/science/biology_place/biocoach/cells/common.html
RNA splicing in Eukaryotes
Only exons form the final mRNA that the protein
will be translated from.
Exons << Introns
http://en.wikipedia.org/wiki/File:Pre-mRNA_to_mRNA.svg
~100,000 proteins and only ~20,000 genes.
How can that be?
Alternative splicing
Gene
Transcript 1
Transcript 2
Protein 1
Protein 2
Transcript 3
Protein 3
Nucleic Acids
Gene != Protein
Amino Acids
The different mRNA molecules created by alternative
splicing are called transcripts or isoforms.
Alternative Splicing in Eukaryotes
Prokaryotes usually have smaller and more compact
genomes. Eukaryotes “can afford” to have alternative splicing.
http://commons.wikimedia.org/wiki/File:DNA_alternative_splicing.gif
What are proteins?
Biological molecules with a variety of functions:
• Chemical and metabolic reactions Enzymes in the
gut, replication of DNA
• Signal transductions Receptors on cells
• Structural proteins For example collagen and keratin in
hair, nails and feathers
• Binding ligands Antibodies that bind foreign antigens
Amino acids form proteins
Each AA has traits that are reflected in the
protein’s folding and function
Neutral, Non polar
Neutral, polar
Basic
Example:
trans-membrane protein
Acidic
https://www.mun.ca/biology/scarr/iGen3_06-02.html
http://bio1151b.nicerweb.com/Locked/media/ch07/transmembrane.html
Nucleic Acids
AGTC
Amino Acids
GASTCVLIMPFYW
DENQHKR
http://www.biogem.org/blog/rna-to-protein-translation-in-perl/
1. If all the cells in our body have the same DNA
code – why is a brain cell, a muscle cell and a
skin cell different from one another?
2. Chimps and humans share 98.5% of the DNA
sequence – why are they so different?
Regulation
Regulation
• Only ~1% of the DNA sequence encodes for
proteins. Some of the rest is used for regulation
of gene expression.
The DNA sequence to which a
protein binds is called a binding site.
Regulation can both activate or
repress expression.
Repressor
binding
sites
Brain cell
Activator
binding
sites
Gene transcription start site
Muscle cell
Real life is a lot more complex…
E. Davidson, Current Opinion in Genetics & Development, 2009
Notes for CS students
• The challenge in this course is not in
algorithms or mathematical proofs, but in
understanding the biological questions and
applying appropriate computational
methodologies to solve them.
• Most of the topics we will talk about is under
constant research.
Enjoy the course!