7_27 Lecture 2 Proteins 2.txt

  1. author "Joshua Ellis"
  2. tags "HUCM"
  3. description ""
  4. fileName "7/27 Lecture 2 Proteins 2"
  5. freezingBlueDBID -1.0
  6. What is the difference between conservative and non-conservative mutations? Give an example.
  7. Conservative doesn't change structure too much
    whereas non-conservative does and is often deleterious.
  8. ie: conservative would be to change Leu to Ile... as both structure simply have a strand of CH2 chains.
  9. non-conservative would be to change glu to val... which is sickle cell anemia in hemoglobin
  10. What is a major character of the Peptide bond between proteins? What are its characteristics? (5) What is the common configuration? and the exception?
  11. The partial double bond.
  12. Shorter
  13. No rotation
  14. Flat
  15. 6 atoms lie in the same plane.
  16. Flexible but conformationally restricted
  17. Trans is the common configuration. Prolyl residue is the exception. (must complete the ring)
  18. In the alpha helix how many residues are in each turn? What is the pitch and its actual number? What is rise and its actual number?
  19. There are 3.6 residues per turn (3.6 amino acid per turn)
  20. The pitch is the distance between each turn and is 5.4
  21. The rise/ residue is the distance for each amino acid and is 1.5
  22. How long is a 10 amino acid chain?
  23. Rise is 1.5... so 10 * 1.5 = 15 angstroms
  24. Alpha helix right/left hand rule
  25. point thumb and curl fingers.
  26. What is amphipathic
    and how are alpha helices amphipathic?
  27. It is when one half is polar and the other half is non polar. The side chains of the helix stick outside the axis
    and carry the properties with it
  28. What is the pitch and and residue amount in each turn of a Beta strand?
  29. n=2 residues per "turn"
  30. p= 6.8 angstrom
  31. What is the difference between parallel and anti-parallel Beta sheets. How do they stack
  32. They stack with chains projecting above and below... allowing sheets to form.
  33. What is a Beta turn and a Beta loop
  34. A Beta reverse turn occurs when a 1st residue hydrogen bonds to a 4th. (Type I and Type II)
  35. Beta loop is more elaborate. Located on surface of proteins but do not have regular structure.
  36. What are the Simple Tertiary Structures
  37. Alpha domain proteins (contain mostly alpha helices)
  38. Beta domain proteins (contain mostly beta helices)
  39. Alpha/Beta domain proteins (contain both)
  40. Supersecondary Structures
  41. Otherwise known as motifs... in between secondary and tertiary.
  42. ie:
  43. helix-loop-helix
    zinc finger
  44. Ways to determin protein structure
  45. X-ray Crystallography
  46. NMR--advantage cuz you can look at things in solution
  47. Helix-Loop-Helix
  48. Feature of some transcription factors proteins that bind to DNA and direct transcription
  49. Zinc-Finger DNA Binding Motif
  50. 2 his and 2 cys residues connected to Zn++ ion. Has a DNA binding region.
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7_27 Lecture 2 Proteins 2.txt
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