DNA and the Gene

  1. Hershey and Chase experiment conclusion
    DNA entered the bacterial cells, not protein so DNA functions as genetic material
  2. Primary structure of DNA
    • 5' end starts with a phosphate; 3' is the other side
    • Sugar-phosphate is the backbone of DNA strand
    • Phosphodiester bond links deoxyribonucleotides
    • Bases (A,T,C,G) project from the backbone
  3. Complementary base pairing
    • Sugar-phosphate backbone of dna
    • Complementary base pairs held together by hydrogen bonding
    • Antiparallel strands (their 5' -> 3' polarities run in opposite directions)
  4. DNA replication
    Specific base-pairing is functionally significant, but the actual mechanism is still a mystery
  5. Three predictions from the Mendelson-Stahl Experiment
    • Semiconservative replication
    • Conservative replication
    • Dispersive replication
  6. Semiconservative replication
    • In this model, the two strands of DNA unwind from each other, and each acts as a template for synthesis of a new, complementary strand. This results in two DNA molecules with one original strand and one new strand.
    • The results in DNA that are hybrids
  7. Results after 2 generations from semiconservative replication
    • 1/2 low-density DNA
    • 1/2 intermediate-density DNA (hybrid)
  8. Conservative replication
    • this model, DNA replication results in one molecule that consists of both original DNA strands (identical to the original DNA molecule) and another molecule that consists of two new strands (with exactly the same sequences as the original molecule).
    • This looks like 2 pairs of homozygous
  9. Results of conservative replication after 2 generations
    • 1/4 high-density DNA
    • 3/4 low-density DNA
  10. Dispersive replication
    • In the dispersive model, DNA replication results in two DNA molecules that are mixtures, or “hybrids,” of parental and daughter DNA. In this model, each individual strand is a patchwork of original and new DNA.
    • Results in molecules that are all hybrid (the spotted one)
  11. Results after 2 generation in dispersive replication
    All intermediate-density DNA (hybrid)
  12. Image Upload 1
    • Semiconservative
    • Conservative
    • Dispersive
  13. DNA replication
    • Begins at specific sites= origins of replication
    • -Bacterial chromosomes have one origin of replication
    • -Eukaryotes have multiple origins along chromosome (speeds up replication)
    • Replication proceeds in both directions from origin
  14. Replication fork
    • DNA is unwound to form this in order to replicate
    • Helicase- untwists the double helix and separates the strands
    • Single-strand DNA- binding proteins (SSBPs)- bind to separated DNA strands to prevent reparing
  15. Topoisomerase
    Relieves strain ahead of replication fork caused by unwinding by breaking, swiveling and rejoining DNA strands
  16. Where does DNA synthesis occur?
    Enzymes which synthesize DNA cannot start a new chain. They can only add to an existing strand (need -OH group)
  17. Primase
    • Lays down an RNA primer which is complementary to the template strand
    • Provides the initial chain so replication can proceed
  18. DNA polymerases
    • Enzymes which catalyze the synthesis ob DNA by adding nucleotides to an existing chain
    • -Can only add dNTPs in 5' to 3' direction
  19. DNA polymerase III
    Adds a nucleotide to the RNA primer and then keeps adding complementary nucleotides to the growing strand
  20. Why does orientation matter?
    • DNA strands are antiparallel because DNA polymerases can only add nucleotides to the free 3' end (they need the free OH to attach the next base)
    • So, a new strand can only be synthesized in the 5' -> 3' direction
  21. Two strands of DNA that must be synthesized differently due to their different orientations
    • Leading strand
    • Lagging strand
  22. Leading strand
    • Synthesized towards the replication fork
    • Occurs continuously
    • Requires one primer
  23. Lagging strand
    • Synthesized away from the replication fork
    • Discontinuous
    • -New fragment cannot be started until fork moves forward and exposes template
    • Creates okazaki fragments
  24. What does the lagging strand require for each fragment?
    A primer such as DNA pol I and DNA ligase
  25. DNA pol I
    Replaces the RNA primer with DNA nucleotides
  26. DNA ligase
    Joins all of the fragments into a continuous strand
  27. Replisome
    • Many enzymes involved in replication form this large macromolecular machine
    • Image Upload 2
  28. Which of the enzymes synthesizes short segments of RNA?

    C) Primase
  29. If this is replicated what would it be 3'-AAGTCAGT-5'?
  30. Problems with copying the ends of linear chromosomes?
    • DNA unwinding completed
    • Leading strand completed
    • Lagging strand nears completion
    • Lagging strand is too short because there is no primer for DNA polymerase- unreplicated and is eventually lost shortening chromosomes
  31. What is the solution for copying linear chromosomes?
  32. Telomeres
    • Consist of a short nucleotide sequence (TTAGGG in humans) repeated between 100-1,000 times
    • "Buffers" at the ends of eukaryotic chromosomes
    • Do NOT encode any genes
    • Once they reach a critical limit the cell enters senescence
  33. Telomerase
    • Active during embryonic development but shut off in most somatic cells at later stage.
    • Male germ cells, activated lymphocytes and some stem cells still have enzyme
    • Active in ~90% of tumors
  34. What is telomerase composed of?
    • Composed of protein and RNA
    • Telomerase reverse transcriptase (TERT)
    • Telomerase RNA (TERC)
  35. The DNA of Telomeres has been highly conserved throughout the evolution of eukaryotes. What does this most probably reflect?

    C) The critical functions of telomeres must be maintained
  36. Proofreading and Repair
    • Overall error rate only 1 mistake per 1 billion nucleotides
    • Initial errors between incoming bases and the template strand are much more common
  37. Why are initial errors between incoming bases and the template strand much more common?
    • Occurs 1 every 100,000 bases
    • DNA polymerases proofread each base as soon as it is added
    • If incorrectly paired, it is removed and synthesis resumes
  38. Mismatch Repair (MMR)
    • Other enzymes remove and replace incorrectly paired nucleotides
    • Defects in these enzymes are linked to cancer
    • -Hereditary non-polyposis colon cancer (HNPCC)
  39. What happens if the error arises after replication (sun, smoke, carcinogens, etc.)?
    • DNA is constantly monitored and repaired
    • Nucleotide excision repair (NER)
  40. Nucleotide excision repair (NER)
    Damaged segment is cut out by a nuclease and the gap is filled in by DNA polymerase and ligase using the undamaged strand as a template
  41. Seroderma pigmentosum
    • Damage from UV light causes thymine dimers which interfere with replication
    • This disorder is caused by inherited defect in NER)
    • -Hypersensitivity to light
    • -Increased risk of skin cancer (1000x-2000x)
  42. Benzopryene in cigarette smoke binds to DNA replication. Which repair mechanism would most likely be used to repair the damage caused by this chemical?

    D) Nucleotide excision repair
Card Set
DNA and the Gene