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

http://www.labgrab.com/users/labgrab/blog/central-dogma-genetics-incomplete_id%3D904

Double stranded (DS) DNA

Single stranded (SS) RNA

Replication Transcription Translation

Nucleic Acids Amin Acids

Prokaryotes vs. Eukaryotes

• Smaller cells • Single-celled organisms• Ancient

http://www.phschool.com/science/biology_place/biocoach/cells/common.html

• Multi-cellular organisms• Has a nucleus

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?

Gene != Protein

The different mRNA molecules created by alternative splicing are called transcripts or isoforms.

Alternative splicing

GeneTranscript 1Transcript 2

Transcript 3

Protein 1Protein 2

Protein 3

Nucleic Acids Amino Acids

Alternative Splicing in EukaryotesProkaryotes 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 proteinsEach AA has traits that are reflected in the protein’s folding and function

https://www.mun.ca/biology/scarr/iGen3_06-02.htmlhttp://bio1151b.nicerweb.com/Locked/media/ch07/transmembrane.html

Neutral, Non polar Neutral, polar Basic

Acidic

Example: trans-membrane protein

Nucleic AcidsA G T C

Amino AcidsG A S T C V L I M P F Y W

D E N Q H K R

http://www.biogem.org/blog/rna-to-protein-translation-in-perl/

Regulation

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

• 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

Activatorbinding sites

Gene transcription start site

Brain cell 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!