Tutorial 1 Biology background for the course

Genome sizes and number of genes OrganismGenome SizeNo. of genes E. coli4.6 Mb~4,300 genes Baker’s Yeast12 Mb~5,700 genes C. elegance100 Mb~20,000 genes Rice430 Mb~40,000 genes Mouse2.8 Gb~21,000 genes Human3.3 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

The Central Dogma Double stranded (DS) DNA Single stranded (SS) RNA Replication Transcription Translation Nucleic Acids Amin Acids

Prokaryotes vs. Eukaryotes Smaller cells Single-celled organisms Ancient 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

~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 Gene Transcript 1 Transcript 2 Transcript 3 Protein 1 Protein 2 Protein 3 Nucleic AcidsAmino Acids

Alternative Splicing in Eukaryotes Prokaryotes usually have smaller and more compact genomes. Eukaryotes “can afford” to have alternative splicing.

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 polarNeutral, polarBasic Acidic Example: trans-membrane protein

Nucleic Acids A G T C Amino Acids G A S T C V L I M P F Y W D E N Q H K R

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 Activator binding 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!