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2013-10-29 19:49:43

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  1. What are proteins composed of?
    amino acids
  2. COOH and NH3 are both what
    weakly acidic
  3. Why are there usually 2 forms of a molecule
    Bc the C is the chiral center
  4. What are the two forms?
    • D-right side
    • L-left side
    • Found in ALL proteins
  5. What is the L (leurotary)-form based on?
    The configuration of NH3
  6. How are amino acids classified?
    • basis of 'D' groups 
    • based on polarity
  7. How many classes of AAs are there and what are they?
    • 5 classes:
    • Non-polar, Aromatic, Polar, Positive charged (basic), and Negative charged (acidic)
  8. Non-polar AAs
    • akly side chains (hydrocarbons)
    • hydrophobic bonding in proteins
  9. Aromatic AAs
    • aromatic ring structure 
    • hydrophobic bonding
  10. Polar AAs
    • dipole but no formal charge (+/-) [h bonding]
    • hydrophilic 
    • freq found on the surface of "soluble" proteins
  11. Positive AAs
    • Full (+) charge on R group
    • variation on Nitrogen-containing FG
  12. Negative AAs
    Full (-) on R groups
  13. How many AAs are there
    20 AAs
  14. What do non-standard do?
    have biochemical roles
  15. What are the biochemical roles and how were they created?
    • modification of standard AAs
    • they are metabolic roles
  16. What is Isoelectric point?
    pH at which a molecule has a net charge of 0
  17. What is the net charge?
    Sum of (+ charges) - (- charges)
  18. What is the pI?
    sum of all the pk values/2
  19. pH < pI
    net charge will be +
  20. pH > pI
    net charge will be -
  21. What are peptides?
    Short polymers of AAs
  22. What does partial double bind pressure do? 
    limits rotation about bond 
  23. What is the peptide/protein rotation also limited by?
    by steric hindrance (R' groups) 
  24. What is the Ramachandran plot?
  25. What are the proteins/peptide ends?
    • Amino terminal (N terminal)
    • Carboxyl (C terminal)
  26. Long peptides assume what configurations?
    native, active 3D configurations 
  27. What does entropy play a role in?
    "driving" folding as protein folds
  28. What occurs after the protein folds 
    • more H2O is released from solvation "shell" 
    • greater freedom=^ randomness=^ entropy 
  29. Which are weak bonds?
    H-bonding, H-phobic, ionic bonding
  30. What about weak bonds
    maximized in folded, native structures 
  31. What about soluble (aqueous) proteins?
    H-phobic AAs more prevalent in interior of protein 
  32. H-bonding, ionic bonding 
    FG in protein interior have to have a bonding partner 
  33. What do small proteins often have?
    disulfide bonds (covalent) stabilized folded structures 
  34. Hierarchal levels of proteins of all proteins 
    • 1, 2, 3 are in all proteins 
    • 4 is only in some 
  35. 1 level
    • in covalent structures 
    • location of disulfides 
  36. 2 level
    • local 3D structures
    • only part of the protein 
  37. How is level 2 defined?
    by the set of structures 
  38. i AA double helix
    polypeptide winds itself around an imaginary axis 
  39. How are things stabilized 
    H bonding among peptide bonds
  40. What can destabilize the helix
    • incompatible 'R' groups 
    • 4AA apart 
  41. Larger groups=
    steric hindrance 
  42. Which AAs dont perform well in double helix 
    Gly and Pro
  43. What are B-strands/sheets 
    linear stretches of AAs that fold back upon one another to forms sheets 
  44. How can steric hindrance be reduced 
    • r groups will be perpendicular
    • alternate position in up/down 
  45. B turns 
    • tight turn 
    • short seq of AA 
    • common is about 4 AAs
  46. Where are B turns usually seen 
    freq seen on the surface of proteins 
  47. What do B turns usually contain
    small flexible AAs
  48. What are super-secondary structure
    • common structural patterns that include multiple representations of 2o
  49. What are the rules for super-secondary structure of 2o
    2 seq are usually close together in 1o
  50. 2o do NOT form what?
    doesn't form knots 
  51. 3structure