ch18 part1

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ch18 part1
2013-11-01 20:47:33

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  1. What
    did Erwin Chargaff learn when he compared the base composition of DNA from
    various sources?
    • Chargaff’sObservations, 1944-1952:
    • 1. DNA isolated fromdifferent cells of a given species has the same % of each of the four bases.
    • 2. For all DNA samples,# of A = # of T and # of G = # of C.
    • 3. A+G = C + T (or Ratio of A+G to C+T is always 1)
  2. Understand
    the structure of DNA. Include nucleotide, sugar-phosphate backbone, phosphodiester
    bond, the purines and the pyrimidines, complementary base pairing, number
    of hydrogen bonds between complementary bases, length of one nucleotide
    pair, length of one helical turn, number of base pairs/turn, major and
    minor groove, antiparallel nature, 5'-3' polarity, and handedness.
    • –10 nucleotide pairs or 3.4nm per
    • helical turn (0.34nm/base pair x 10)
    • –2nm in diameter
    • –Major and minor grooves
    • Right-handed helix

    • •Sugar-phosphate
    • backbone (phosphodiester bond)
    • • 5’-3’ polarity
    • • Antiparallel
    • • Complementary
    • base-pairing
    • A-T (2 H bonds)
    • G-C (3 H bonds)
  3. Contrast positive and negative supercoiling.
    Which form allows more access of the DNA to proteins?
    • Negative supercoil: extra twist in the
    • opposite direction as the double helix
    • Positive supercoil: extra twist in the
    • same direction as the double helix

    • Negative supercoiling is associated with
    • unwinding and allows increased access to proteins.
  4. Can supercoiling occur in circular DNA? In
    linear DNA?
    • Although supercoiling is easiest to study
    • in circular DNA, it occurs in linear DNA as well.
  5. Which
    type of DNA (circular or linear, + or - supercoiling) is found in viruses,
    bacteria, mitochondria, and chloroplasts?
    Circular DNA found innature (including those of viruses, bacteria, mitochondria, and chloroplasts)are negatively supercoiled.
  6. What
    functions do topoisomerases I and II serve? How do these two enzymes
  7. What is meant by DNA denaturation, renaturation,
    melting, reannealing, and reassociation?
    • •DNA denaturation
    • –aka DNA melting
    • –Occurs with increase in
    • temperature or pH in the laboratory
    • –Tm increases with proportion of G+C
    • bases, length of DNA, and ionic strength of solution.
    • •DNA renaturation or reannealing occurs when ss DNA reassociate
  8. What happens to absorbance of DNA at 260nm when
    it undergoes denaturation?
  9. In the
    laboratory, what are typically done to induce DNA denaturation? What is Tm
    and how is it related to G-C content, length of DNA and salt concentration
    of solutions?
    • Increase temp or PH
    • temp at which DNA splits
    •   positively corrilated
  10. How do
    concentration and length of DNA affect the rate of DNA reassociation?
    Concentrated and lengthy DNA increases the rate of DNA reassociation
  11. What
    is deduced from experiments comparing the renaturation of DNA from
    bacteria and calf?
    • 40% of calf DNA renatures more rapidly than
    • bacterial DNA does. Those DNA consists of repeated sequences.
  12. What is meant by genome?
    • Genome
    • - one complete copy of all the genetic information of an organism or virus.
  13. In
    comparing the genome from various organisms, what can be learned about the
    relationships of genome size, gene number, and chromosome number
    respectively to the complexity of organism?
    • There is some
    • correlation between genome size and complexity of organism.

    • There is also some
    • correlation between gene number and complexity of organism.

    • There is no
    • correlation between chromosome number and complexity of organism.
  14. How is
    bacterial chromosomal DNA organized in the cell?
    • •Most commonly, single
    • circular DNA
    • •Negatively supercoiled
    • •Bound to small
    • amounts of histone-like basic proteins
    • and RNA
    • •Folded into extensive
    • loops and anchored to the nucleoid region
  15. What
    is a bacterial plasmid? What DNA sequences does it carry?
    • •Small
    • circular ds DNA separate from the bacterial
    • chromosome
    • •One
    • or more per cell
    • •Contains
    • own origin of replication so it can replicate autonomously
    • •Carry
    • specialized genes (e.g. drug resistance, genes for metabolic enzymes, etc.)
  16. How is
    eukaryotic genomic/chromosomal DNA organized in the cell?
    • •DNA + histone and nonhistone proteins
    • • Nucleosome: linker DNA (about
    • 50 nucleotide pairs) + DNA (146 nucleotide pairs) wrapped almost twice around a
    • complex of 8 histones (octamer, 2 of each of H2A,H2B, H3, and H4)
    • • Histone H1 packs the nucleosomes into a 30nm
    • chromatin fiber.
    • • Chromatin fibers
    • fold into loops and attach to a non-histone
    • protein scaffold.

    • •Chromatin
    • condenses into chromosomes during mitosis.

    • Each chromosome has two chromatids since DNA has been
    • duplicated.
  17. What are
    Molecules that DNA uses to wrap around.
  18. What is a nucleosome consisted of?
    DNA + Histone
  19. How do
    heterochromatin and euchromatin differ?
    Looped chromatin may be more tightly packaged into heterochromatin (if transcriptionally inactive)Or loosely packaged into euchromatin (if transcriptionally active).
  20. Know all
    of the different levels of eukaryotic DNA packaging.
    • 1.Nucleosome
    • 2. 30 nm chromasome fiber
    • 3. Looped Domains
    • 4. Heterochromatin
    • 5. Highly condense, duplicated chromosomes of dividing cell.
  21. How
    many fold of compaction is the mitotic chromosome compared to a stretched
    out DNA molecule?
    15,000 fold
  22. How is
    mitochondrial or chloroplast DNA organized in the organelle? Does it
    encode for all of the proteins needed by the organelle?
    • –Usually circular
    • –Lack histones
    • –Genome codes for some of the
    • polypeptides needed by the organelles