Life Science: Organisms

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Life Science Organisms
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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

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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_euk
aryotic_genomes http//www.ornl.gov/sci/techresour
ces/Human_Genome/home.shtml
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Biological Systems

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

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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

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A Cell

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

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• 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.

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Central Dogma http//www.accessexcellence.org/RC/
VL/GG/protein_synthesis.html
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DNA
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DNA
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RNA
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Central Dogma http//www.accessexcellence.org/RC/
VL/GG/protein_synthesis.html
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Translation RNA to Protein
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Proteins
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Gene to Protein
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Sites of Regulation
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Sites of Regulation
DNA Chromosome packing Methylation Transcription factor binding sites Protein Post-translational modification Structural modifications, cleavage Protein-protein interactions Co-factors
RNA Capping, Poly adenylation Editing, splicing Transport from nucleus Promotors, Ribosome binding Metabolites Co-factor and substrate concentration Transport

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• How do we measure it?
• presence, concentration, activation state, etc.
  of specific biological molecules.
• How do we measure the variations?

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DNA

• Sequencing
• Genomic library
• Genome sequencing
• PCR
• SNPs
• Linkage analysis

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Life Science
http//www.genomenewsnetwork.org/articles/06_00/se
quence_primer.shtml
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Life Science
http//www.genomenewsnetwork.org/articles/06_00/se
quence_primer.shtml
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http//mekentosj.com/4peaks/science.html
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Genomic Library
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Genome sequencing and Display

• http//www.genomenewsnetwork.org/articles/06_00/se
  quence_primer.shtml
• BAC-to-BAC method
• whole genome shotgun sequencing
• UCSC Genome Browser
• http//genome.ucsc.edu/

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Life Science
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Microarray
Probe hybridization to DNA on chips Probes bind
to unique features on chips Flourescent labels
highlight bound probes
http//www.affymetrix.com
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RNAi RNA silencing
http//fig.cox.miami.edu/cmallery/150/gene/how_si
RNA_works.htm
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Life Science
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Proteomics Mass Spectrometry
http//www.proteomesoftware.com/Proteome_software_
ed_mass_spec.html
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Proteomics Mass Spectrometryhttp//www.academy
savant.com/cmsp.htm
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Yeast 2 hybrid used to measure protein-protein
interactions.
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Life Science

• Flow of information

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Life Science

• Flow of information

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NCBI Derivative Sequence Data (Maureen J. Donlin,
St. Louis University)
C
C
Curators
GA
GA
ATT
C
GA
GA
ATT
C
RefSeq
TATAGCCG
ACGTGC
TATAGCCG AGCTCCGATA CCGATGACAA
ATTGACTA
CGTGA
TTGACA
Labs
TTGACA
TTGACA
ACGTGC
Genome Assembly
TATAGCCG
ACGTGC
TATAGCCG
ATTGACTA
CGTGA
CGTGA
ATTGACTA
TATAGCCG
CGTGA
ATTGACTA
TTGACA
ATTGACTA
TATAGCCG
ATTGACTA
TATAGCCG
TATAGCCG
TATAGCCG
TATAGCCG
ATT
C
GenBank
GA
UniGene
AT
GA
C
C
Algorithms
ATT
C
C
GA
GA
ATT
GA
GA
ATT
C
C
GA
ATT
GA
GA
ATT