Tutorial 1 Biology background for the course. Genome sizes and number of genes OrganismGenome...
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Transcript of Tutorial 1 Biology background for the course. Genome sizes and number of genes OrganismGenome...
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!