Nucleic Acids

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  1. What are the three forms of DNA? What are their characteristics?
    • B - Common - Narrow(ish) diameter, major/minor grooves
    • A - Fatter DNA, equal(ish) grooves
    • Z - Thin, Shallow grooves, left handed
  2. How many torsion angles shape DNA? Why is it not more flexible?
    6, because of constrains from the double helix (steric inteference)
  3. Is DNA a perfect double helix? Why?
    No, local variations can induce small in the shape of the helix
  4. What are some examples of base pair geometries? What are their properties?
    • Twist - 26-43 degrees (36 degrees ave.)
    • Propellor twist - (-23)-(-7) degrees
    • Roll - 14-17 degrees
  5. How does stacking affect DNA bending?
    Smaller stacking makes DNA less stiff, therefore making it more bendable.
  6. How can DNA be bent?
    • - Sequence structure (AT rich)
    • - Protein binding
  7. What are some examples of DNA bending proteins?
    • Catabolite gene activator protein (CAP) - 90 degree
    • Lac repressor - 45 degree
  8. How are Holliday junctions formed?
    • Homologous recombination
    • Nickec strands cross over
  9. What are some properties of RNA?
    • 2' OH
    • Single stranded
    • Uracil
    • Labile
    • RNA-11 (like A-DNA)
  10. What is a stem loop?
    A single strand of RNA that has base paired with itself
  11. What is a Ribozyme?
    A catalytic RNA
  12. What are four key types of RNA?
    • mRNA
    • rRNA
    • tRNA
    • Other (often catalytic)
  13. Give an example of a stem loop RNA
  14. What are the levels of RNA structure? What are their properties?
    • Primary - Sequence
    • Secondary - Base paring
    • Tertiary - Long range interactions
  15. What are the three edges of a base?
    • Watson Crick
    • Hoogsten
    • Sugar
  16. Are all RNAs coding?
    No some have other functions (rRNA, tRNA etc)
  17. Where is the riboswitch found?
    The 5' UTR
  18. How does the Riboswitch work?
    TPP binds, preventing ribosome binding and therefore translation (like a snorlax on the promoter)
  19. Give one key example of a Ribozyme. What does it do?
    Hammerhead Ribozyme - Cleaves itself before cytidine-17, yields cyclic phosphodiester
  20. What are group II introns?
    Self splicing introns, possibly spliceosome precursor
  21. What sites in the Ribosome are made of RNA (mostly)
    Decoding and peptidyltransferase
  22. What catalytic mechanisms take place in the ribosome?
    Mainly Proximity and Orientation, as well as preferential transition state binding
Card Set:
Nucleic Acids
2014-12-16 05:01:46

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