bio chem chapter 2

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theapk200
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234712
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bio chem chapter 2
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2013-09-14 00:51:01
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DNA replication repair
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  1. semiconservative replication
    • each of the parental strands are used as a template for syn of new strands
    • the daughter strands hav one new and one old strands
  2. origin of replication in prokary vs eukary
    • single ori in prokary
    • multiple in eukary
  3. final product of replication in pro vs eukary
    • in prokary - 2 seperate circular daughter DNAs
    • in eukary - sister chromatids that are connected at the centromere, to be seperated during mitosis
  4. replication forks
    • the origin of replication, opens two replication forks that move away from each other
    • thus replication is a bidirectional process
  5. polymerases and nucleases
    • polymerases: enzymes that syn nucleic acids by formin phophodiesterbonds
    • nucleases: break these bonds
    • exonucleases remove nucleotides from either 5` or 3` ends
    • endonucleases cut within the strand and release nucleic acid fragments
  6. features of DNA polymerase
    • syn DNA in 5` to 3` direction
    • req template is DNA that is copied from 3` to 5` direction
    • req deoxy nucleotide substrates
    • req primer is a RNA
    • has proof readin activity - 3`to 5` exonuclease activity
  7. features of RNA polymerase
    • syn rna in 5` to 3` direction
    • reads the DNA template in 3` to 5` direction
    • needs no primers
    • has no proof reading activity
  8. initiation of strand syn
    DNA polymerases cannot initiate strand syn where as RNA polymerses can do so
  9. steps of DNA replication
    • the base sequence at the origin is recognized
    • helicase: unwinds by breaking the hyd bonds - thus two replication forks are formed
    • single stranded binding proteins: bind to the single strands preventing them from reassociating and protecting them from degradation
    • primase: syn a short RNA primer in 5` to 3` direction startin at the ORI using parental strand as template
    • DNA polymerase III: starts makin DNA in 5` to 3` direction starting at 3` end of the primer
    • can make continously - leading strand
    • or discontinously - lagging strand (each discontinously made fragment called okazaki fragment - initiated with primer and made in 5` to3`)
    • RNA primers removed by RNAase H in eukaryotes and an uncharecterized DNA poly fills in the gap with DNA
    • in prokary DNA poly I removes both the primer and fills the gap
    • both eu and prokary DNA poly hav proof readin activity
    • DNA ligase: seals the nicks between okazaki fragments making them continous
    • DNA gyrase (topoisomerase II): provides a swivel in front of each replication fork
    • replication finished when the 2 replication forks meet on the other side of the circle opp the origin
  10. DNA gyrase and replication
    • provides a swivel in fornt of each of the replication forks
    • as helicase unwinds the DNA, the DNA ahead becomes overwound and positive supercoils appear
    • gyrase inserts negative supercoils in the strands
  11. drugs and DNA gyrase
    • quinolones block the action of topoisomerases
    • nalidixic acid kills bacteria by inhibiting DNA gyrase
    • inhibitors of eukaryotic topoisomerse II like etoposide and tenoposide are used as anticancer drugs
  12. eukaryotic DNA polymerases and their func
    • DNA α and δ work together to syn both leadin and lagging strands
    • DNA poly γ replicates mitochondrial DNA
    • DNA poly β and ε participate primarily in DNA repair
    • ε may substitute δ in some cases
  13. telomers and aging of cells
    • telomers - repetitive seq at the ends of linear DNA molecule
    • with each replication telomers are shortened as DNA poly cannot syn the 5` end of each strand
    • this causes aging of cells...ultimately telomeres become so short that chrmosomes cannot func and cells die
  14. telomerase
    • completes replication of the telomeric sequences at both ends of a eukaryotic chromosome
    • present in embryonic cells, fetal cells and certain adult stem cells; but not in adult somatic cells
    • inappropriately present in many cancer cells, contributing to their unlimited replication
    • it has a short RNA template complementary to the DNA telomers and telomerase reverse transcriptase activity
  15. syn of the DNA (both leading and lagging strands) in prokary is by
    DNA poly III
  16. removal of RNA primers
    • in prokary by dna poly I (5`to 3` exonuclease activity) 
    • in eukary by RNAase H (5` to 3` exonuclease activity)
  17. quinolones and fluroquinolones
    • prevent DNA gyrase and thus prevent DNA replication
    • most active against aerobic gram negative bacteria
    • eg levofloxacin, ciprofloxacin, moxifloxacin
    • currently used for rx of gonorrhea and upper and lower urinary tract infections in both sexes
  18. Antivirals and DNA replication
    • one chemotherapy for HIV is use of AZT (3`azido 2`,3`dideoxythymidine) or struc related comp
    • in cells, AZT converted to triphosphate derivative and used as a substrate for viral reverse transecriptase that makes DNA form its RNA genome
    • in AZT, an azide gr is at 3` postition instead of hydroxyl gr
    • this prevents further replication by effectively causing chain termination
    • this is possible as the reverse transcriptase though a DNA polymerse has no proofreading activity

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