DNA Structure

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Chapter 12

• DNA Structure Function

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Lets Set the Tone

• T.H. Morgans work - genes are found on
  chromosomes
• What are genes made out of? - the prevailing
  biological question from the 1920s to the 1950s
• DNA or protein

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Frederick Griffith - 1928

• Streptococcus pneumoniae - 2 strains, one
  harmless, one pathogenic
• heat-killed pathogenic strain
• mixed with harmless strain
• some of harmless strain were transformed
• what was the transforming factor?

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Oswald T. Avery - 1944

• Purified various chemicals from the heat-killed
  pathogenic bacteria, then tried to transform live
  nonpathogenic bacteria with each chemical
• Only DNA worked!
• Lots of nonbelievers.

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Hershey Chase - 1952

• Bacteriophages (just phages for short) - viruses
  that infect bacteria
• showed that DNA is the genetic material of phage
  T2
• T2 is made of DNA and protein
• radioactively labeled sulfur of some phages, and
  phosphorus of others
• Only the DNA enters the host cell

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The Hershey-Chase experiment
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The Hershey-Chase experiment phages
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Erwin Chargaff - 1947

• Found that DNA composition varies from one
  species to another - evidence of molecular
  diverisity!
• He also found that the amount of thymine always
  approximately equaled the amount of adenine, and
  the amount of guanine always approximately
  equaled the amount of cytosine - Chargaffs rules

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Watson Crick - 1953

• Discovery thanks to Maurice Wilkins and Rosalind
  Franklin, X-ray crystallographers
• Watson knew DNA was a double helix
• used wire models - eventually put bases in the
  middle (relatively hydrophobic)
• X-ray data suggested that DNA had uniform diameter

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Rosalind Franklin and her X-ray diffraction
photo of DNA
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Unnumbered Figure Purine and pyridimine
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Structure of Nucleic Acids

• DNA and RNA are polymers of nucleotides
• Nucleotide
• Phosphate group
• 5 carbon sugar deoxyribose or ribose
• Nitrogen bases adenine, thymine, cytosine,
  guanine and uracil

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More Nucleotides

• Purine 2 ring nitrogen compound, adenine and
  guanine
• Pyramidine 1 ring nitrogen compound, thymine and
  cytosine

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Base pairing in DNA
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Structure of DNA

• Double helix
• Adenine and thymine amounts equal
• Guanine and cytosine amounts equal
• A bonds with T (2 hydrogen bonds)
• G bonds with C (3 hydrogen bonds)
• Two strands of double helix run in opposite
  directions (strands are antiparallel)

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The double helix
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DNA Replication

• Semiconservative
• your cells have 6 billion base pairs to replicate
• very few errors - about one mistake per 1 billion
  nucleotides

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Possible Models for Replication
Semi Conservative
Conservative
Dispersive
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A model for DNA replication the basic concept
(Layer 4)
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Beginning Replication

• Origins of replication - special sites recognized
  by proteins that initiate DNA replication
• The proteins bond, separate the two strands -
  replication bubble
• replication then proceeds in both directions
• replication fork - at the end of each bubble

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Origins of replication in eukaryotes
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Elongation of New DNA

• DNA Polymerases - enzymes which add nucleotides
  to the growing strand of new DNA (50 per second
  in humans)
• source of energy?
• Elongation is a little more complicated because
  the strands of DNA are anti-parallel - they run
  in opposite directions

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Incorporation of a nucleotide into a DNA strand
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The two strands of DNA are antiparallel
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Consequences of Anti-Parallel-ism

• DNA polymerase can only add nucleotides at the 3
  end, not the 5 end thus a new strand of DNA can
  only elongate in the 5 to 3 direction
• leading strand - elongates continuously
• lagging strand - can only be made in little
  increments at a time - fragments are called
  Okazaki fragments
• DNA ligase joins Okazaki fragments

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Synthesis of leading and lagging strands during
DNA replication
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Priming DNA Synthesis

• DNA polymerases can NOT initiate DNA synthesis
  they can only ADD nucleotides to the end of an
  already-existing chain base-paired with the
  template strand
• primer - a short chain of RNA bonds to DNA
• Primase joins RNA nucleotides to make primers
  (about 10 nucleotides long)

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Priming DNA synthesis with RNA
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Other Important Proteins

• Helicase - an enzyme that untwists the double
  helix at the replication fork
• Single-stranded binding protein - line up along
  the unpaired DNA strands, holding them apart

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The main proteins of DNA replication and their
functions
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A summary of DNA replication
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DNA Proofreading

• Initial pairing errors occur at a rate of one in
  every 10,000 base pairs
• DNA polymerase proofreads its new strand against
  its template
• mismatch repair - cells use special enzymes to
  fix incorrectly paired nucleotides
• Over 130 enzymes involved!

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DNA Repair Mechanism

• Nuclease - cuts out a segment of DNA containing
  damage
• Gap is filled by DNA polymerase and ligase
• Nucleotide excision repair

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Telomeres

• Telomeres - special sequences of DNA found at the
  ends of chromosomes
• sequence of TTAGGG is repeated from 100 to 1,000
  times, so that there is no vital information
  contained there
• Telomerase - an enzyme that can lengthen the
  telomeres