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Tutorial 1. Biology background for the course. Genome sizes and number of genes. Orthologs vs. Paralogs. Orthologs – Genes in different genomes with a common origin Paralogs – Genes in the same genome with a common origin.

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Tutorial 1

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Tutorial 1

Tutorial 1

Biology background

for the course


Genome sizes and number of genes

Genome sizes and number of genes


Orthologs vs paralogs

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

The Central Dogma

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

Transcription

Translation

Replication

Single stranded

(SS) RNA

Double stranded

(DS) DNA

Amin Acids

Nucleic Acids


Prokaryotes vs eukaryotes

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

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


Tutorial 1

Alternative splicing

~100,000 proteins and only ~20,000 genes.

How can that be?

Gene != Protein

Protein 1

Transcript 1

Protein 2

Gene

Transcript 2

Nucleic Acids

Amino Acids

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

Transcript 3

Protein 3


Alternative splicing in eukaryotes

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

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

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


Tutorial 1

Amino Acids

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

Nucleic Acids

A G T C

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


Regulation

Regulation

  • 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?

  • Chimps and humans share 98.5% of the DNA sequence – why are they so different?


Regulation1

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.


Tutorial 1

Brain cell

Muscle cell

Gene transcription start site

Repressor binding sites

Activator

binding sites


Real life is a lot more complex

Real life is a lot more complex…

E. Davidson, Current Opinion in Genetics & Development, 2009


Notes for cs students

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

Enjoy the course!


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