DNA structure, replication and repair

Structure and properties of DNA
1. Genetic information is stored in DNA
  1. DNA is a macromolecule
    1. polymer
      1. Monomers are called nucleotides
        Consist of a Phosphate, sugar and base
  2. Information in DNA is digital
    1. Each position can be A, T, G or C
  3. Building Blocks of DNA
2. DNA stores information in all life forms
  1. Common mechanisms for storage, replication and expression of genetic information suggest a single origin for all life however, differences in detail are significant, especially between prokaryotes and eukaryotes
    1. Prokaryotic and eukaryotic cells
      1. Prokaryotes have no nucleus Prokaryotes carry less DNA Prolaryotes do not have membrane bound organelles Prokaryotes usually have 1 circular bacterial chromosome - eukaryotes usually have multiple linear DNA chromosomes Prokaryotes not complexed by histones Prokaryotic cell diameter is relatively small
3. DNA structure and organisation
  1. Must be stable and protected
    1. to store genetic information
    2. to prevent damage (mutation)
  2. Must be accessible
    1. information can be used to produce functional cells
4. Native DNA is a double helix of complementary antiparallel chains
  1. Linked by hydrogen bonds between the bases
  2. 3 H bonds in a G-C pair and 2 H bonds in an A-T pair
5. Supercoiling of DNA
  1. Separating the two strands of the DNA double helix causes supercoiling
    1. Regulated by Topoisomerases and Gyrases
6. DNA packing
  1. Nucleosomes
    1. Small regions of DNA are wrapped around protein cores
      1. Look like 'beads on a string'
    2. an octamer of two copies of each of the histones H2A, H2B, H3 and H4 (the nucleosomal histones)
      1. Histones are positively charged proteins.
      2. Histone H1 binds outside the nucleosome and has a structural role
  2. Role of DNA packing
    1. DNA is safely stored but easy to access for transcription and replication
DNA replication
1. DNA synthesis occurs in the 5’ to 3’ direction
  1. leading strand is replicated continuously
  2. lagging strand is replicated discontinuously
    1. Okazaki fragments
      1. RNA primer of each Okazaki fragment is replaced with DNA and the adjacent fragments are joined by DNA ligase
  3. DNA synthesis occurs in the opposite direction to movement of the replication fork
2. Nucleoside triphosphates are the substrates for DNA synthesis; pyrophosphate is released and the nucleoside monophosphate is joined onto the growing strand
3. Initiation of DNA replication requires many different proteins
  1. Initiator proteins
    1. Recruits the rest of the replication machinery
  2. Helicase
    1. Separates the two strands of the double helix (breaks hydrogen bonds)
  3. Topoisomerase (gyrase)
    1. Relieves supercoiling of DNA by breaking backbone (covalent bonds)
    2. Topoisomerase inhibitors
      1. Prevent DNA replication
        Blocks topoisomerase I so that supercoils accumulate ahead of the replication fork, preventing DNA replication
  4. Single stranded binding protein
    1. In a single stranded region of DNA where short regions of base paired 'hairpins' have been formed single stranded binding protein works to straighten the strand through cooperative protein binding
4. Initiated at origins
  1. Specific DNA sequence (Usually AT-rich)
  2. Origin sequences bound by DNA binding proteins (initiator proteins)
5. Proceeds bidirectionally
6. Elongation requires many different proteins
  1. Primase
    1. Primase is recruited to the origin when the strands have been separated by helicase
    2. Primers are laid down 5’ to 3’ on both strands (bidirectional replication)
  2. DNA polymerases
    1. DNA polymerase III
      1. Main replication polymerase
      2. Primer extension
      3. Coordination of leading and lagging strand synthesis
        The two molecules of DNA pol III (one on each strand) interact to ensure the two strands replicate together
    2. DNA polymerase I
      1. Replaces RNA primers with DNA
        Exonuclease activity 5’ to 3’ - One nucleotide at a time is removed from the 5’ end of the primer as one is added to the 3’ end of the preceding Okazaki fragment (DNA synthesis 5’ to 3’)
    3. Can back up and remove incorrectly paired bases
      1. use a 3’ to 5’ exonuclease activity to remove incorrect bases
        The 3’ end is then extended again as usual
    4. In eukaryotes
      1. DNA pol e on the leading strand and on the lagging strand DNA pol d
        High fidelity (proof-reading) enzymes
  3. DNA ligase
    1. Seals the nick between two Okazaki fragments
7. Nucleases - Enzymes that cut nucleic acids (DNA or RNA)
  1. Exonuclease – cuts off one nucleotide at a time from the end of a DNA molecule
  2. Endonuclease – cuts internally in a DNA molecule (may be sequence specific)
8. Replication errors and mismatch repair
  1. Mismatch repair
    1. operates soon after replication and distinguishes the newly replicated strand (carrying the incorrect base) from the parental, correct strand
      1. Mismatch repair assumes that the parental strand is correct
        Newly synthesised DNA is methylated but not immediately so Mismatch repair acts on the non-methylated strand, soon after DNA replication
    2. Hereditary non-polyposis colon cancer (HNPCC) is due to inherited defects in mismatch repair genes
  2. Replication strand slippage
    1. misalignment of the template and newly synthesised strand and results in unequal daughter strands
Replication of chromosome ends
1. The last RNA primer on the lagging strand cannot be replaced
2. Chromosomes have repeated sequences at each end, called telomeres
  1. G-rich (on strand with its 3’ end at the chromosome end)
  2. Short repeats (6-10 bp)
3. Telomerase
  1. Reverse transcriptase
    1. enzyme that uses an RNA template to make a complementary DNA strand
  2. an enzyme that extends chromosome ends by adding telomere repeat sequences.
  3. Extends DNA so that strand remains same size (fills in gap left by lost rna polymerase)
Mutation and DNA repair
1. Mutations
  1. in germ cells will be passed on to offspring
  2. in somatic cells may cause cancer
    1. Mutations that disrupt regulation of cell division may lead to cancer
  3. Base mismatches
    1. Base excision repair
      1. the first step is removal of the base
      2. Incorrect/modified bases are recognised; different errors are recognised by different glycosylases
        A uracil specific glycosylase removes uracil in the first step.
        This is why DNA contains Thymine. It makes the repair system able to distinguish a problem much more easily
    2. Deamination changes base pairing properties. This occurs spontaneously but the rate can be increased by some chemicals
      1. Can lead to point mutations
2. Causes of mutation
  1. Replication errors
    1. Mispairing or small insertions and deletions
  2. Spontaneous chemical change to DNA
  3. Chemical mutagens
  4. Radiation
    1. UV light causes pyrimidine dimers to form – usually thymine
      1. A single unrepaired thymine dimer can be lethal because progress of high fidelity DNA polymerases is blocked
      2. Photoreactivation: direct repair
        Not present in humans
        An enzyme (photoreactivating enzyme) uses energy from visible light to break the bonds between the two pyrimidine residues
        Direct repair involves reversing the chemical reaction causing the DNA damage
        Photolyase (or photoreactivating enzyme) splits the dimer to regenerate normal DNA
      3. Nucleotide excision repair
        Detects and repairs bulky lesions in DNA, eg thymine dimers and modified bases
        1. Recognition of damage 2. Single strand binding protein binds 3. Endonuclease cuts out damaged region 4. New DNA synthesised
      4. Translesion synthesis
        Bases are randomly incorporated opposite the lesion (commonly A)
        error-prone mechanism that introduces mutations
        New strand is complete but likely to carry a mutation
        May leave pyrimadine dimer unrepaired leading to cell death
        Bypasses the blockage of DNA replication
    2. Double-stranded DNA breaks
      1. Repaired by Homologous recombination or Nonhomologous end-joining
        Homologous recombination results in exchange of genetic information between homologous chromosomes
        Recombination provides a means to generate new combinations of genes
        generates genetic diversity
        Blocks of genes are exchanged between homologous chromosomes
        Can be used as a repair system
        When there is a Double stranded break on one chromosome The other is used as a template for repair, resulting in exchange of genetic material
        Nonhomologous end-joining Protein recognise broken chromosomes and join the ends together (no base pairing involved)
        Error prone
        Wrong ends could be joined, causing translocations
        Insertions or deletions may occur during joining

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DNA structure, replication and repair

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