2012 October 15

==Matters arising==
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==Review of sources for genetics projects==
==Origin of life and evolution of species==
#What does genome-scale sequence information tell us?
#Classical model: Vertical transmission
#Contemporary model: Vertical plus lateral (horizontal) transmission
==Genome organization: Prokaryotes vs. Eukaryotes==
==Organization of genomes in prokaryotes==
#Transcription units, operons, translational initiation
#Lateral gene transfer mechanisms
#Mobile genetic elements
#Introns and RNA splicing
#Plasmids
#Bacteriophage: DNA and RNA genomes
#The bacterial core genome, pan-genome and genome evolution
==Organization of genomes in eukaryotes==
#Transcription units, translational initiation
#Processing of polyproteins vs. operons
#Introns and RNA splicing
#Mobile genetic elements
#DNA rearrangements
#Plasmids
#Viruses
#Gene organization in mitochondria and chloroplasts=
==Class notes==
Molecular Orgins of Cellular Life
The earth is ~4.2 billion years old. By using geological and archaeological data, the origin of life is suspected to have risen ~3-3.5 billion years ago.
The three large domains of life that are believed to have come from a common ancestor are: Eukaryotes, Bacteria & Archea. Bacteria & Archea are both classified as prokaryotes. Proof that we all share a common ancestor lies in the fact that we all use DNA and common cell machinery (DNA pol, RNA pol, Robosomes, tRNA, etc.). The most solid evidence is in a conserved sequence in the large ribosomal subunit. Every ribosome has the same nucleotide sequence that codes for the peptidy-transfer site (site where peptide bonds are created between amino acids).
The Tree of Life
*It is believed that the oldest common ancestor probably looked something like a prokaryote.
*Bacteria were the first of the three classes to branch out from the common ancestor.
*Archea & Eukaryotes are more closely related than either of them to bacteria.
*Although the tree of life is based on vertical transmission, horizontal transfer of genes is evedent  from bacteria to plants (i.e. cyanobacteria-chloroplast), and bacteria to vertebrates (i.e. alpha-proteobacteria-mitochondrion). 
Endosymbiosis: Mitochondria & Chloroplasts
*Some bacteria were able to infect eukaryotic cells. alpha-proteobacteria really like to invade eukaryotic cells & are not thought to be our mitochondria.
*Mitochondria provide ATP synthesis via oxidative phosphorylation for the host cell and in turn get a cozy, safe environment where they probably have a higher chance of survival than they would outside of the cell.
*Some mitochondrial genes snuck into the cell nucleus. These genes are now coded for by the nucleus and then delivered to the mitochondria.
*Cyanobacteria provided the chloroplast to the plant cell. This happened later than mitochondrial integration.
*Mitochondria & Chloroplasts share some similar DNA sequences.
*The mitochondrial genome varies in size between species. Animals have the most compact mitochondrial DNA.
DNA Transmission: Vertical vs. Horizontal
*Vertical Transmission: Transmission of DNA from parent to offspring.
*Horizontal Transmission: Also known as lateral transmission. The transmission of DNA between species within a single generation. ie. bacteria to human.
*Most modern organisms are genetic mosaics. For example: Some nuclear DNA came from mitochondria, which came from bacteria.
*Because DNA has been spread around via horizontal transmission, the tree of life may be better represented as a 'web of life', showing how evolution occurred not only by genetic variation leading to divergence of species, but also by transmission of DNA between species.
Differences between Eukaryotic nuclear genes and Prokaryotic nuclear genes and genomes:
Bacterial genes and genomes:
*circular chromosomes in most bacteria
*single DNA + plasmids
*less DNA (about 0,5 to 10Mbp)
*genes are  closely spaced (the intergenic distance is from 10 to 200nt)
*single DNA replication origin
*no intrones - intrones are very rare, but they do exist , e.g. Phage T4 has 3 self-splicing genes with introns.
Eukaryotic genes and genomes:
*linear DNA molecules
*multiple chromosomes
*complex folding structure
*more DNA > 100Mbp)
*more distantly spaced genes (100 bs- millions) 
*multiple origins
*intrones: eukaryotes have multiple intrones, alternative patterns of RNA splicing and splicing machinery - spliceosomes. Yeast is among organisms with the least number of introns. 
==Assignments for Wed 17 October==
#Continue work on the Genetics project. Class presentations will begin Monday 22 October
#Finish reading Lesk chapter 4
#Add wiki content as you wish