DNA Structure part 2

  1. __ is the average conformation (of a double helix) seen in physiological conditions

    • Depending on the sequence of DNA, the B-form may change to some extent affecting the major and minor grooves.
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  2. __ sometimes occur in DNA protein interactions & is more similar to RNA if it makes a double strand structure
    • A-form
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  3. __ is a left handed helix with a zigzag structure
    • Z DNA
    • This happens if the sequence is made of purine and pyrimidine alternates in a solution with high concentration of charged ions (Na+).
  4. __ has the largest diameter & __ has the smallest diameter.
    • A DNA (A-form); Z DNA
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  5. __ has the largest distance per complete turn & rise per base pair and __ has the smallest distance per complete turn & rise per base pair.
    • Z DNA; A DNA (A-form)
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  6. number of base pairs per complete turn: B DNA __, A DNA __, Z DNA __
    10, 11, 12
  7. In __ DNA, in purine & pyrimidine alternates, the __ is in anti & __ is in syn.
    • Z; pyrimidine; purine
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  8. In __, DNA the position is always in anti conformation.
    • B-DNA
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  9. syn conformation → __
    left hand helix
  10. anti-syn alternates → __
    zigzag appearance
  11. denaturation
    • separating the 2 strands of DNA from each other
    • can happen by breaking hydrogen bonds by high temperature or high pH
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  12. The two strands can be attached with each other again (renaturation) if __. This reattachment is by restoration of __ and is known as __
    • The temperature or pH are brought down;
    • hydrogen bonds;
    • hybridization or annealing

    (For this hybridization the sequences of both strands should be complementary.)
  13. Absorption of UV light is by the __
  14. In the double strand DNA, due to the stack of bases that makes them unavailable to UV, the UV absorption is __ compared to 2 separate single strands of DNA (denatured DNA)
    • 40% less
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  15. Increasing temperature will cause a rapid __ in absorption.
    • increase
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  16. What factors increase the melting temp of DNA?
    • higher G:C = more hydrogen bonds = higher melting pointAlso in base pair stacks, G:C has more interaction with adjacent base pairs.
    • ionic strengths: higher salt concentration = higher melting temp. High levels of positively charged ions surround the negatively charged phosphates in DNA backbone, therefore its is easier for both strands to not repel each other
  17. What factors decrease the melting temp of DNA?
    shorter DNA fragments = lower melting temp
  18. Chromosomes of eukaryotes are __
    long linear DNA molecules plus their associated proteins
  19. Chromosomes of most of __ are circular.
    • - prokaryotes, genetic materials of some viruses, DNA of mitochondria, and plasmids
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  20. A circular DNA can be generated by __
    • covalently joining both ends of a DNA molecule (covalently closed circular DNA (cccDNA)
    • Circular DNA is in topological constrict (cannot very freely rotate)
  21. If the linking number (LK) = twist number (Tw) – Wr (writhe number), __
    linking number is less than no writhe “relaxed.” Supercoil is negative.
  22. If the linking number (LK) = twist number (Tw) + Wr (writhe number), __
    linking number is greater than no writhe “relaxed.” Supercoil is positive
  23. DNA can be long or short which changes the LK value, thus to normalize the LK, the __ is calculated.
    • super helical density  (σ)
    • σ = ΔLK / LK°
  24. DNA in __ can be unwind (separation of two strands) easier than __ DNA.
    negative supercoil; relaxed

    Organisms keep the DNA in negative
  25. The thermophile bacteria living in hot springs have __.
    positive supercoil

    (preventing denaturation of DNA in the very high temperature of theenvironment )
  26. The supercoil can be resolved by making a temporary break in__ bond(s) of one or both DNA strand(s). This is done usually by __ enzymes.
    • phosphodiester;
    • topoisomerase

    • After the release of the supercoil (decreasing LK) the phosphodiester bond is restored.
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  27. __ introduce a break in one strand’s phosphodiester bond (a nick) and pass the second strand through the generated gap. The two ends of thebroken strand are then re-aligned.
    • Type I topoisomerases
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  28. __ break both strands of the double helix, creating a “gate” through which a second segment of the double helix is passed. Requires the use of ATP
    • Type II topoisomerases
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  29. Bacteria also have the enzyme __ which is a type of topoisomerase. Instead of relaxing the DNA, it induces negative supercoil which is favorable for DNA replication and transcription.
  30. 2 circular DNA can __ with each other especially during the replication of circular DNA
    • catenate
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  31. __ can decatenate (separate) 2 circular DNA
    Topoisomerase II

    • (If there is already a nick in 1 DNA, topoisomerase I also can decatenate them.)
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  32. Linear chromosomes of eukaryotes can get entangled especially during DNA replication. __ untangles 2 newly made DNA from each other.
    Topoisomerase II

    • (can also remove knots. If DNA has a nick, then topo I can also undo the knot)
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  33. During the activity of topoisomerases, one end of each cut polynucleotide becomes covalently attached to a __ at the active site of the enzyme (held tightly in place) while the __ is being manipulated. This assures __. Then open __ on the other side of the cut attacks the __ restoring the bond and realigning the 2 pieces of DNA together
    • tyrosine amino acid;
    • free end;
    • to rejoin the strand and prevents a permanent cut in the DNA;
    • hydroxyl;
    • phosphotyrosine
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  34. steps of topo enzyme activity
    • 1. cleavage of DNA
    • 2. strand passage
    • 3. DNA rejoining

    • Topo binds to the melted DNA cleavage by topo and phosphotyrosine formation (covalent bond of enzyme & DNA) and holding the other side of broken DNA strand. Change of enzyme conformation and moving the intact strand through the broken one.
    • Change of conformation again and rejoining the 2 sides of broken DNA (no change in DNA sequence but change in supercoiling). The same mechanism for topo II except the enzyme is a dimer or tetramer and makes cuts on both strands
  35. DNA topoisomers
    circular DNA of the same size by different linking number
  36. Relaxed circular DNA moves __ in gel electrophoresis than linear DNA. Supercoiled DNA moves __.
    • slower;
    • faster (as it is more compact)

    • The more supercoiled, the faster it moves
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  37. EtBr
    • intercalates between bases and unwinds them
    • decreases the twist of DNA (from 36 degrees to 10 degrees per base pair)
    • decreases the negative supercoil (Wr is increased), makes it close to 0 & if more EtBr is added, the DNA becomes positively supercoiled.
    • affects movement of cccDNA in the gel
  38. Negative supercoiled + EtBr →
    more relaxed → slower movment
  39. Less negative supercoiled + EtBr →
    going beyond the relaxed to become positive supercoiled → fast movment
Card Set
DNA Structure part 2
Week 1