2 February, 2007

Life Science: Organisms

2 February, 2007

Genomics

“The genetic blueprints of all people generally have the same information, with approximately 99% of one human genome sequence being identical to all others. That makes the 1% of places in the genetic code that account for human variation very interesting…”

Momentum Winter 2006-2007, DNA Rubic “Some geneticists have calculated the differences in human and

chimpanzee DNA as just over 1%, some at 1.6%, and others at 1.8%.”

Momentum Winter 2006-2007, What we learn from Chimpanzees

2 February, 2007

Genomics

Organism Genome size Number of genes

Human 3.2 Gb 25,000

Rat 2.7 Gb 25,000

Mouse 2.5 Gb 24,000

Dog 2.4 Gb 19,300

Puffer fish 390 Mb 25,000

Fruit fly 165 Mb 13,600

Arabidopsis (plant) 120 Mb 25,500

C elegans 97 Mb 19,000

Slime mold 34 Mb 12,500

Yeast 12 Mb 6,300

http://en.wikipedia.org/wiki/List_of_sequenced_eukaryotic_genomeshttp://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

2 February, 2007

Biological Systems

http://www.innerbody.com/htm/body.html

2 February, 2007

Cell types

The human embryonic stem cells cultured have been observed to randomly differentiate in culture into a variety of different cell types, including (A) gut, (B) neural cells, (C) bone marrow cells, (D) cartilage, (E) muscle and (F) kidney cells.

www.news.wisc.edu/packages/

stemcells/3327.html

2 February, 2007

A Cell

http://micro.magnet.fsu.edu/cells/animalcell.html

2 February, 2007

They are all the same cells – They all have the same genetic material,The only difference is what is turned on and

what is silent.

2 February, 2007

Central Dogma http://www.accessexcellence.org/RC/VL/GG/protein_synthesis.html

2 February, 2007

DNA

2 February, 2007

DNA

2 February, 2007

RNA

2 February, 2007

Central Dogma http://www.accessexcellence.org/RC/VL/GG/protein_synthesis.html

2 February, 2007

Translation RNA to Protein

2 February, 2007

Proteins

2 February, 2007

Gene to Protein

2 February, 2007

Sites of Regulation

2 February, 2007

Sites of Regulation

DNAChromosome packing

Methylation

Transcription factor binding sites

ProteinPost-translational modification

Structural modifications, cleavage

Protein-protein interactions

Co-factors

RNACapping, Poly adenylation

Editing, splicing

Transport from nucleus

Promotors, Ribosome binding

MetabolitesCo-factor and substrate concentration

Transport

2 February, 2007

How do we measure it?

presence, concentration, activation state, etc. of specific biological molecules.

How do we measure the variations?

2 February, 2007

DNA

Sequencing Genomic library Genome sequencing PCR SNPs Linkage analysis

2 February, 2007

Life Science

http://www.genomenewsnetwork.org/articles/06_00/sequence_primer.shtml

2 February, 2007

Life Science

http://www.genomenewsnetwork.org/articles/06_00/sequence_primer.shtml

2 February, 2007 http://mekentosj.com/4peaks/science.html

2 February, 2007

Genomic Library

2 February, 2007

2 February, 2007

Genome sequencing and Display

http://www.genomenewsnetwork.org/articles/06_00/sequence_primer.shtml

BAC-to-BAC method

whole genome shotgun sequencing

UCSC Genome Browser http://genome.ucsc.edu/

2 February, 2007

2 February, 2007

Life Science

2 February, 2007

Microarray

Probe hybridization

to DNA on chips

Probes bind to unique features on chips

Flourescent labels highlight bound probeshttp://www.affymetrix.com

2 February, 2007

RNAi : RNA silencing

http://fig.cox.miami.edu/~cmallery/150/gene/how_siRNA_works.htm

2 February, 2007

Life Science

2 February, 2007

Proteomics: Mass Spectrometry

http://www.proteomesoftware.com/Proteome_software_ed_mass_spec.html

2 February, 2007

Proteomics: Mass Spectrometry

http://www.academysavant.com/cmsp.htm

2 February, 2007

Yeast 2 hybrid

used to measure

protein-protein

interactions.

2 February, 2007

Life Science

Flow of information

2 February, 2007

Life Science

Flow of information

2 February, 2007

NCBI Derivative Sequence Data (Maureen J. Donlin, St. Louis University)

ATTGACTA

TTGACA

CGTGAAT

TGACTA

TATAGCCG

ACGTG

C

ACGTGC

ACGTGC

TTGACA

TTGACA

TTGACA

CGTGA

CGTGA

CGTGA

ATTGACTA

ATTGACTA ATTGACTA

ATTGACTA

TATAGCCG

TATAGCCG

TATAGCCG

TATAGCCG

GenBank

TATAGCCG TATAGCCGTATAGCCGTATAGCCG

ATGA

CATT

GAGA

ATT

ATTCC GAGA

ATTCC

GA

GA

ATTC GAGA

ATTC

GAGA

ATTCC GAGA

ATTCC

UniGene

RefSeq

GenomeAssembly

Labs

Curators

Algorithms

TATAGCCGAGCTCCGATACCGATGACAA