Chapter 9 The Mutability and Repair of DNA

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Chapter 9 The Mutability and Repair of DNA
? Replication errors and their Repair ? DNA
damage ? Repair of DNA damage
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Life and Biodiversity Depend on a Happy Balance
between Mutation and Its Repair
What do we learn from this chapter? ?
Causes of mutation ? The systems
responsible for reversing or correcting and
minimizing the damage
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Life and Biodiversity Depend on a Happy Balance
between Mutation and Its Repair

Inaccuracy in DNA replication
arise from tautomerization Sources
Chemical damage to the genetic material Of
spontaneous damage , natural and
unnatural Mutation chemicals and
radiation Transposons

insertions generated by DNA elements
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Consequences

• Permanent changes to DNA (mutation)
• generally become manifest only in the
  progeny
• Some chemical alterations to the DNA prevent its
  use for replication and transcription
• have immediate effects on cell function
  and survival

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The twofold challenge

• Scan the genome to detect errors
• Mend the lesions
• we should consider how the alteration to
  the genetic material is detected and how it is
  properly repaired

A few important questions we must take with us
while
learning this chapter are on page 236. Remember
them.
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Replication errors and their repair

• Some conceptions
• transitions pyrimidine-to-pyrimidine,
  purine-to-purine substitutions
• transversions pyrimidine-to-purine,
  purine-to-pyrimidine substitutions
• point mutations mutations that alter a
  single nucleotide
• hotspots some sites on the chromosome
  where mutations arise at high frequency
• DNA microsatellites sequences contain
  repeats of simple di-, tri- or tetranucleotide
  sequences

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Replication errors and their repair

• Although the replication machinery has a
  remarkably high degree of accuracy , some
  misincorporated nucleotides escape detection .
  And if these misincoporated nucleotides isnt
  subsequently detected and replaced , the sequence
  change will become permanent in the genome.

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Mismatch repair removes errors that escape
proofreading

• The mismatch repair system increases the accuracy
  of DNA synthesis by an additional two to three
  orders of magnitude.
• In E.coli ,mismatches are detected by MutS ,which
  scans the DNA and recognize the mismatch . MutS
  induces a pronounced kink in the DNA and MutS
  itself. This complex recruits MutL , which
  activates MutH, an enzyme that causes nick near
  the site of the mismatch. Then the helicase
  unwinds the DNA, producing a single-standard gap.

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How does the repair system know which nucleotide
to replace ?
E.Coli tags the parental strand by transient
hemimethylation. The enzyme Dam methylase
methylates A residues on both strands of the
sequence 5-GATC-3. After replication for a few
minutes before it catch up, the daughter DNA will
be hemimethylated.
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DNA damage

• DNA damage is also a factor of mutation.
• Mutagens radiation , some chemical agents and
  so on. (The Ames Test)
• DNA is damaged by alkylation, oxidation,radiation.
  
• Mutations are also caused by base analogs and
  intercalating agents.

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Repair of DNA damage

• General statement
• repair mechanism concerns three mode
• 1. simply reverses the damage by a repair
  enzyme
• 2. excision repair systems
• 3. recombinational repair

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1.Direct Reversal of DNA Damage

• To illustrate this type of repair, simply
  consider the two examples below.
• 1. photoreactivation with the energy captured
  from the light, DNA photolyase break the covalent
  bonds linking adjacent pyrimidines.
• 2. Removal of methyl group methyltransferase
  removes the methyl group from the guanine residue
  by transferring it to one of its own cystenine
  residues.

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Base-Flipping Mechanism of base excision repair
enzymes

• Critical enzyme glycosylase
• mechanism hydrolyzing the glycosidic bond
• HOWEVER! There comes a riddle!
• How could the enzyme to act on the base buried in
  the helix?!

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Nature gives the answer!

• With the remarkable flexibility of DNA, the
  damaged base projects away from the double helix,
  which could delicately and properly sit in the
  specificity pocket of glycosylase. Thus, the
  beautiful repair arises!

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Nucleotide Excision Repair Enzyme

• Differences from the former
• 1. do not recognize any particular lesion but
  function based on the detection of distorted
  shapes of double helix.
• 2. Not remove single nucleotide but a short
  single-stranded segment including the lesion.

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Recombination repair

• Another problem while excision enzyme uses the
  undamaged DNA as template for repair, how could
  the double-strand breaks be repaired?.
• Nature has its solution double-strand break
  repair pathway

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Answer !

• Although the two strand have been damaged, the
  cell could retrieve sequence information from the
  sister chromosome.

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Life always involves challenge

• What if there is no sister chromosome available
  in the nascent period of cell cycle?
• Nonhomologous end joining (NHEJ)
• directly link the two ends of broken DNA by
  misalignment between single strands protruding
  from the broken ends.

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Translesion DNA synthesis

• In light of the incomplete efficiency of repair
  system, how to action faced with the residual
  unrepaired damage?
• Cell faces two choice
• cease the replication
• translesion synthesis

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Smart cell choose the better latter

• How to achieve this seems impossible goal?
• A specialized class of DNA polymerase
  enable this goal to be accessible through the
  independence of base pairing.
• Evidently , this method involves high error
  rate
• Thus , this is the last resort.