DNA TECH: GENOMICS

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DNA TECH GENOMICS

• Review for Lecture P162

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most important concept

•      
• DNA -gtmore DNA --gt RNA -gt protein
• This "central dogma" of today's molecular biology
  has applications
• in medicine and biotechnology.

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HUMAN GENOME PROJECT

• a "rough draft" (published 2001 in Science and
  Nature) of the base sequences of all 30,000 human
  genes
• maps of where these genes are located on
  chromosomes

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but

• they don't yet know what all of these genes do--
• for many of the genes they don't know which ones
  are for which proteins
• or what effect they have on phenotypic traits
• or where some disease alleles are.

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http//www.ornl.gov/TechResources/Human_Genome/pro
ject/info.html

• The human genome contains 3164.7 million base
  pairs
• The average gene consists of 3000 bases, but
  sizes vary greatly, with the largest known human
  gene being dystrophin at 2.4 million bases.
• The total number of genes is estimated at 30,000
  to 35,000much lower than previous estimate
• Almost all (99.9) nucleotide bases are exactly
  the same in all people.
• The functions are unknown for over 50 of
  discovered genes.

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http//www.ornl.gov/TechResources/Human_Genome/pro
ject/info.html

• The Wheat from the Chaff
• Less than 2 of the genome codes for proteins.
• Repeated sequences that do not code for proteins
  ("junk DNA") make up at least 50 of the human
  genome.
• Repetitive sequences are thought to have no
  direct functions, but they shed light on
  chromosome structure and dynamics. Over time,
  these repeats reshape the genome by rearranging
  it, creating entirely new genes, and modifying
  and reshuffling existing genes.
• During the past 50 million years, a dramatic
  decrease seems to have occurred in the rate of
  accumulation of repeats in the human genome.

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http//www.ornl.gov/TechResources/Human_Genome/pro
ject/info.html

• How Humans Compare with Other Species
• Unlike the human's seemingly random distribution
  of gene-rich areas, many other organisms' genomes
  are more uniform, with genes evenly spaced
  throughout.
• Humans have on average three times as many kinds
  of proteins as the fly or worm because of mRNA
  transcript "alternative splicing" and chemical
  modifications to the proteins. This process can
  yield different protein products from the same
  gene.

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http//www.ornl.gov/TechResources/Human_Genome/pro
ject/info.html

• How Humans Compare with Other Species
• Humans share most of the same protein families
  with worms, flies, and plants, but the number of
  gene family members has expanded in humans,
  especially in proteins involved in development
  and immunity.
• The human genome has a much greater portion (50)
  of repeat sequences than the mustard weed (11),
  the worm (7), and the fly (3).

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http//www.ornl.gov/TechResources/Human_Genome/pro
ject/info.html

• How Humans Compare with Other Species
• Although humans appear to have stopped
  accumulating repeated DNA over 50 million years
  ago, there seems to be no such decline in
  rodents. This may account for some of the
  fundamental differences between hominids and
  rodents, although gene estimates are similar in
  these species. Scientists have proposed many
  theories to explain evolutionary contrasts
  between humans and other organisms, including
  those of life span, litter sizes, inbreeding, and
  genetic drift (which well study after fall
  break).

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http//www.ornl.gov/TechResources/Human_Genome/pro
ject/info.html

• The ratio of germline (sperm or egg cell)
  mutations is 21 in males vs females. Researchers
  point to several reasons for the higher mutation
  rate in the male germline, including the greater
  number of cell divisions required for sperm
  formation than for eggs.

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http//www.ornl.gov/TechResources/Human_Genome/pro
ject/info.html

• The draft sequence already is having an impact on
  finding genes associated with disease. A number
  of genes have been pinpointed and associated with
  breast cancer, muscle disease, deafness, and
  blindness. Additionally, finding the DNA
  sequences underlying such common diseases as
  cardiovascular disease, diabetes, arthritis, and
  cancers is being aided by the human variation
  maps (SNPs) generated in the HGP in cooperation
  with the private sector. These genes and SNPs
  provide focused targets for the development of
  effective new therapies.

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http//www.ornl.gov/TechResources/Human_Genome/pro
ject/info.html

• http//doegenomestolife.org/

The Next Step Functional Genomics
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TEXTBOOK POINTS

• 1. How they did the sequencing
• 2.More Important What have we learned and what
  else will we learn?

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Newer methods (chapter 16)

• Dyes on different nucleotides instead of
  radioactivity
• (still electrophoresis, but no longer 4 bands)
• machine scanner tabulates color sequences
  (instead of error-prone human looking at film)

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sequencing machines
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Fig16.3
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• These last steps are done by computers.

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Latest genome dogs

• Less detail than human genome (shotgun pattern
  overlaps sampled less)
• newer techniques meant faster results
• other genomes coming real soon now

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DNA used for genetic engineering is
always recombinant DNA, involving genes from
natural sources

• partly because real genes are too long to be
  synthesized practically
• and partly because the proteins which would be
  translated do not fold into functional and
  predictable tertiary shapes. Scientists don't
  know enough about proteins yet. We still need
  cells.

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MORE IMPORTANT

• WHAT THEY LEARNED AND WHAT THEY WILL LEARN FROM
  THE GENOME PROJECT

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Lateral Transfer

• Genomes getting genes from unrelated critters
  and viruses
• important because
• germs and parasites become more toxic
• and more resistant to antibiotics and pesticides
• makes tracing ancestry trickier

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Junk DNA?

• Hypervariable
• because of transposons
• and because it does not affect phenotype (like
  silent mutations)
• used for DNA fingerprints because its
  hypervariable
• Probably not junk but spare parts and homologous
  species exclusion tickets

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Where ALL the genes are

• Not finished yet.
• Big research now Functional Genomics
• which genes are being expressed (transcribed)
• when and where
• proteonomics how the translated products
  function
• Best Tool chip!

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future

• http//doegenomestolife.org/

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Biotech TOOLS

• restriction endonuclease enzymes
• nucleic acid fragments (RFLPs, etc.)
• electrophoresis
• probes
• PCR
• sequencing
• ligase enzyme
• synthetic nucleotides
• BACs and plasmids
• cDNA
• libraries
• chips
• more later

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Biotech TOOLS

•   For each, know
• what it does
• why anybody would use it
• how or why it works especially if it involves
  something relevant to the natural structure and
  function of DNA.

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most important concept

•      DNA -gtmore DNA --gt RNA -gt protein
• the natural processes of replication can be used
  in the laboratory to synthesize bits of DNA for
  analyzing more DNA--
• disorders,
• forensics,
• archaeology and paleontology,
• pure research on how cells work....