Biochem 3

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Biochem 3
2011-12-02 18:48:27
Biochem Nucleic Acids

Biochem 3- Nucleic Acids
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  1. What charge does a phosphate group have a neutral pH?
    Negatively charged
  2. Where is the phosphate group attached to a nucleotide?
    Attached to C5' position on the ribose (pentose) ring
  3. How many phosphate groups do nuleic acids contain?
    Nucleic acids contain one phosphate group per nucleotids
  4. What is Pentose?
    A five-carbon sugar
  5. What is deoxyribose?
    A pentose molecule with no O atom on carbon 2'
  6. Why are carbon atoms in pentose numbered with primes?
    Has carbon atoms numbered with primes to distinguish them from the atoms in nitrogen bases
  7. What are nucleobases?
    Derivatives of pyrimidine or purine
  8. Are nucleo bases planar?
    yes, they are planar or almost planar structures
  9. What kind of light do nucleobases absorb?
    Absorb UV light around 250-270nm
  10. What is the general structure of a nucleobase?
    Nitrogen-containing heteroaromatic molecules
  11. In all nucleotides, where is the phosphate group located?
    At the 5' position
  12. What is the backbone of DNA/RNA made of?
    Alternating phosphate and sugar groups
  13. As a rule, how are DNA/RNA polymers written?
    From 5' to 3'
  14. How are nucleosides in DNA/RNA polymers linked?
    By a phospho-diester linkage
  15. Which end of the DNA/RNA poymers are phosphorylated?
  16. What are DNA/RNA polymers less than 50 nucleotides refered to as?
  17. What are DNA/RNA polymers sensitive to?
    Alkaline hydrolysis
  18. Which is more sensitive to Alkaline hydrolysis, DNA or RNA?
    RNA, due to 2' OH
  19. What do phosphodiester bonds do in DNA?
    Link successive nucleotide units
  20. Why are nucleic acids highly polar?
    The backbone of alternating pentose and phosphate groups
  21. Why are the ends named 5' and 3'?
    The 5' and of the macromolecule lacks a nucleotide at the 5' position and the 3' end lacks a nucleotide at the 3' position
  22. What happens in RNA hydrolysis under Alkaline conditions?
    • The 2' hydroxul acts as a nucleophile in an intamolecular displacement.
    • The 2',3'- cyclic monophosphate derivative is further hydrolyzed to a mizture of 2'- and 3'-monophosphates
  23. Why is DNA stable under Alkaline conditions?
    It lacks 2' hydroxyls
  24. What do nucleic acid polymers do?
    Mediate the storage and transfer of genetic material
  25. What are the 3 'game-changer' experiments?
    • Griffit- 'Transforming Principle'- 1928
    • Avery-McLaeod-McCarty- 'DNA fractions'-1943
    • Hershey and Chase- Bacteriophage- 1952
  26. Who discovered the 'transforming principle'?
  27. What was the conclusion of the 'Transforming Principle' experiment?
    A transforming material (unlikely proteins) crossed from the heat ikilled virulent S strain to the non-virulent R live strain
  28. What was the conclusion of Aver-McLaeod-McCarty expriment?
    The transforming factor is DNA
  29. What is the conclusion of the Hershey and Chase experiment?
    The injected material from the Bacteriophage was 32P labeled. Consequently, DNA is responsible for the storage and transferred of genetic material
  30. Who discovered the double helix?
    James Watson and Francis Crick
  31. What was the key to the discoverey of the double helix?
    Recognition of base pairing
  32. What is Chargaff's rule?
    • The percentge of G+Cs and A+Ts were equal
    • A+G=T+C
  33. How are base pairs joined?
    Hydrogen bonds
  34. Is the double helix right-handed or left-handed?
  35. What points towards the outside of the double helix?
    phosphate groups
  36. What is the width of the double helix?
    2.0nm (20A)
  37. How far apart are the bases along the helix axis?
    0.34 nm (3.4A)
  38. How long is the pitch of the helix?
    3.6nm (36A)
  39. How many nucleotides per turn of the helix?
  40. What is 'Central Dogma'?
    refers to the flow of information from genes to proteins
  41. What is the first step in the 'Central Dogma'?
    DNA replication
  42. What were the postulated methods of DNA replication?
    • Semi-conservative
    • Conservative
    • Dispersive
  43. What was the conclusion of the Meselson-Stahl experiment (1957)?
    Experimental evidence confirmed that DNA replication is Semi-conservative
  44. Is DNA bidirectional?
  45. What does DNA polymerase do?
    Catalyze the stepwise addition of deoxyribonucleotides (5'-3')
  46. What are the characteristics of DNA Polymerase I?
    • It has 5'-3' polymerase activity
    • It has 3'-5' exonuclease activity (proof reading)
    • It has 5'-3' exonuclease activity (removes added primers)
    • Requires a DNA template
    • It is moderately processive (dissociates after adding 20 dNTPs)
    • All three activites on a single polypeptide
  47. What are the characteristics of DNA polymerase II?
    • It has 5'-3' polymerase activity
    • It has 3'-5' exonuclease activity (proof reading)
    • Does NOT 5'-3' exonuclease activity
    • Requires DNA template
    • It is highly processice (synthesizes 1000 dNTPs/second)
    • It is made up of 10 subunits
  48. Which enzyme is responsible for the unwinding of the DNA double helix?
    DNA helicase
  49. What is used to keep the DNA strands separate?
    Single Strand Binding proteins
  50. What releases the stress of the DNA unwinding through transient DNA cut and ligation?
  51. Which enzyme does not require a free 3'OH group to add compimerntary base pairs?
  52. What are Okazaki fragments?
    Short DNA fragments compimentary to the lagging strang sequence
  53. How is the RNA primer removed?
    Removed by 5'-3' exonuclease activity of DNA Polymerase I
  54. What enzyme joins the DNA fragments on the lagging strand?
    DNA Ligase
  55. How can DNA be denatured?
    Changes to pH or temperature?