Summary: Mboc Samenvatting

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  • 1 DNA replication, sequencing and PCR

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  • Why is DNA replication considered semi-conservative?

    Because every new double stranded molecule consist of one old and one new strand
    • the old strand is the template 
  • What is the chemical reaction behind DNA synthesis?

    The formation of phosphodiester bonds while hydrolysing the matching dNTP molecule of the template strand
  • What are the frequency of mistakes?

    1. Without proof-reading: 1 in 10^5
    2. with proof-reading: 1 in 10^7
    3. with strand-directed mismatch repair: 1 in 10^10
  • What is strand-directed mismatch repair?

    When there is a error in the new strand, mismatch proofreading proteins will bind to DNA and detects error in strand. The error will be removed and the DNA strand will be repaired.
  • What causes permanent changes in the template strand?

    Chemical changes in DNA bases can cause mutation in the DNA
    • depurination: loss of purine bases (A and G), will cause deletion in mutated strand
    • deamination: C -> U
  • What are the main differences between DNA sequencing and PCR?

    DNA sequencing determine the order of the bases, while PCR amply the DNA
  • What is shotgun sequencing?

    The method involves randomly breaking up the genome into small DNA fragments that are sequenced individually. A computer program looks for overlaps in the DNA sequences, using them to reassemble the fragments in their correct order to reconstitute the genome.
    • works well for small genomes that lack repetitive DNA
  • What are the difference between different sequencing platform?

    Read length and error rate
  • What are the advantages and restrictions of PCR?

    Advantages: sensitive and fast
    Restrictions: fragment length <20kb and homologous DNA sequences
  • What are the techniques for detecting DNA polymorphism?

    PCR-based: VNTR
    PCR and sequencing-based/melting curve: SNP

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