Molecular and Cellular Biology (1)

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  1. What is the central dogma of DNA?
    DNA is an informational molecule

    genes are composed of DNA

    genes code for proteins

    transcription -- RNA using DNA template

    RNA processed to mRNA

    mRNA translated into protein by ribosome
  2. Describe the characteristics of B-DNA.
    Double-stranded uniform polymer

    Right handed double helix

    Two DNA strands of double helix antiparallel

    Directionality 5’ --> 3’

    Monomers are nucleotides (A, T, G, C)

    Core of stacked base-pairs with edges exposed

    10 base pairs per turn

    Highly negatively charged phosphodiester backbone

    H-bonds, hydrophobic and VDW contribute to stability

    Major Groove - Width (13.6 Å) & Depth (5.8 Å)

    Minor Groove - Narrow (9.6 Å) & Depth (6.7 Å)

    Persistence length of DNA ~150 base pairs

    Bending preference of A-T stretches (4-6 nucleotides)
  3. List the 2 types of protein DNA interactions.
    1. Non specific DNA interactions

    2. Specific DNA interactions
  4. Describe Non specific DNA interactions.
    Protein interacts with phosphate or sugar of DNA without selecting a specific site on the strand.
  5. Describe specific DNA interactions.
    Proteins interact with specific nucleotides in the DNA strand.
  6. Describe direct readout (base readout) interactions.
    proteins discriminate between different bases in a DNA sequence via direct interactions with the DNA bases.
  7. Describe indirect readout (shape readout) interactions.
    sequence dependent deformability or structural differences between DNA molecules that contribute to their discrimination by proteins.
  8. Describe Higher Order Multi-protein Recognition Codes.
    mechanisms by which genomic targeting is encoded in multi-protein complexes.
  9. Compare A-DNA to B-DNA.
    wider and shorter

    wider and deeper major groove

    more narrow and shallower minor groove

    RNA-DNA & RNA-RNA duplexes
  10. What functional groups are found in major and minor grooves?
    H bond donor

    H bond accepter 


  11. Where does the name nucleic acid come from?
    It is due to the acid character of the phosphate group, which is deprotonated at the neutral pH, producing H+.
  12. What makes make DNA more stable than RNA?
    The 2' hydrogen makes DNA more stable than RNA.
  13. True or false: the 2' OH in RNA results in slow hydrolysis of phosphodiester bond.
  14. Can DNA function as a catalytic molecule?
    No, but RNA can due to the 2' OH.
  15. What are the 3 methods utilized in denaturation of DNA?
    Increasing temperature, breaks H bonds

    Agents that destabilized H bonds (formamide or urea)

    extreme pH changes, this causes repulsions between bases.
  16. How do high cation concentrations stabilize duplex DNA?
    They shields negative charges of the DNA backbone.
  17. DNA is ___ in water.

    DNA is ___ in alcohol.

  18. DNA molecules longer than ___ kb tend to break if not handled gently.
Card Set
Molecular and Cellular Biology (1)
DNA: Structure, Topology, and Chemistry
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