PHRD5025 Biochem - Lecture 1 Amino Acids & Protein Structure

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PHRD5025 Biochem - Lecture 1 Amino Acids & Protein Structure
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2013-09-08 15:21:58
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amino acids protein structure
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amino acids, protein structure
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  1. What is almost all drug action targeted at?
    proteins
  2. Virtually all amino acids in proteins are which chiral conformation/enantiomer?
    L-stereomers
  3. Why is it important to synthesize a drug that contains predominantly 1 chiral conformation?
    • -increase its efficiency
    • -decrease toxic effects
  4. # of naturally occurring amino acids
    20
  5. 5 groups of side chains
    • 1) nonpolar, aliphatic (hydrophobic)
    • 2) aromatic (hydrophobic)
    • 3) polar, uncharged (hydrophilic)
    • 4) positively charged (basic, hydrophilic)
    • 5) negatively charged (acidic, hydrophilic)
  6. glycine
  7. alanine
  8. valine
  9. leucine
  10. isoleucine
  11. phenylalanine
  12. proline
  13. tryptophan
  14. serine
  15. threonine
  16. methionine
  17. cysteine
  18. asparagine
  19. glutamine
  20. aspartic acid
  21. lysine
  22. tyrosine
  23. glutamic acid
  24. arginine
  25. histidine
  26. G
    • glycine, Gly
    • nonpolar, hydrophobic
  27. A
    • alanine, Ala
    • nonpolar hydrophobic
  28. P
    • proline, Pro
    • nonpolar, hydrophobic
  29. V
    • valine, Val
    • nonpolar, hydrophobic
  30. L
    • leucine, Leu
    • nonpolar, hydrophobic
  31. I
    • isoleucine, Ile
    • nonpolar, hydrophobic
  32. M
    • methionine, Met
    • nonpolar, hydrophobic
  33. F
    • phenylalanine, Phe
    • aromatic, hydrophobic
  34. Y
    • tyrosine, Tyr
    • aromatic, hydrophobic
  35. W
    • tryptophan, Trp
    • aromatic, hydrophobic
  36. S
    • serine, Ser
    • polar, hydrophilic
  37. T
    • threonine, Thr
    • polar, hydrophilic
  38. C
    • cysteine, Cys
    • polar, hydrophilic
  39. N
    • asparagine, Asn
    • polar, hydrophilic
  40. Q
    • glutamine, Gln
    • polar, hydrophilic
  41. K
    • lysine, Lys
    • positively charged, hydrophilic
  42. H
    • histidine, His
    • positively charged, hydrophilic
  43. R
    • arginine, Arg
    • positively charged, hydrophilic
  44. D
    • aspartic acid, Asp
    • negatively charged, hydrophilic
  45. E
    • glutamic acid, Glu
    • negatively charged, hydrophilic
  46. amino acid that forms disulfide bonds
    cysteine
  47. cystine
    • 2 cysteines bonded together
    • nonpolar (unlike cysteine)
  48. protein that consists of 2 polypeptide chains stabilized by 3 disulfide bonds between cysteines
    insulin
  49. hormone produced by the pineal gland that regulates sleep-wake cycles and is a tryptophan derivative
    melatonin
  50. 2 tryptophan derivatives
    serotonin, melatonin
  51. 4 tyrosine derivatives
    DOPA -> dopamine -> norepinephrine -> epinephrine

    *catecholamine neurotransmitters
  52. tyrosine derivative used to treat dystonia (movement disorder)
    DOPA
  53. tyrosine derivative used to treat cardiac arrest
    epinephrine
  54. arginine derivative used to store high energy phosphate
    creatine
  55. arginine derivative that is toxic to the body & excreted in the kidneys
    creatinine
  56. how are peptide bonds formed between amino acids?
    condensation/dehydration
  57. structure around an amino acid  carbon
    tetrahedral
  58. configuration of virtually all peptide bonds in proteins
    trans configuration
  59. geometric configuration of C-N in the primary structure
    planar
  60. bond angle for N-C bond
  61. bond angle for C-C bond
  62. direction of H-bonds in an -helix
    parallel to helix long axis
  63. how many residues are H-bonds separated by in an -helix
    4
  64. direction of side chains in an -helix
    perpendicular to the helix long axis
  65. interactions that destabilize an -helix (2)
    • 1) steric hindrance (large R groups)
    • 2) electrostatic repulsion (++ or -- close to one another)
  66. interaction between oppositely charged side chains
    salt bridges
  67. helices prefer ___ charged amino acids at the N-terminus
    Negatively charged
  68. helices prefer ___ charged amino acids at the C-terminus
    positively charged
  69. residue with highest helix propensity
    alanine (smallest side chain, next to Gly)
  70. why is Gly not favored in a helix?
    it can occupy too many  and  angles (high conformational flexibility)
  71. 2 least favored amino acids for a-helices
    Gly & Pro
  72. helix breaker, helix cap
    Pro
  73. parallel -sheet
    • - aligned main chain atoms
    • - NON-linear H-bonds
    • - less stable
  74. how are parallel -sheets connected?
    right handed connections

    -> shorter bend through smaller angles
  75. antiparallel -sheet
    • - non-aligned main chain atoms
    • - LINEAR H-bonds 
    • - more stable
  76. how are antiparallel -sheets connected?
    -turns/hairpins
  77. # of residues in a -turn
    4
  78. most favored amino acids in -turns
    Gly & Pro
  79. 2 major groups of proteins
    • 1) fibrous
    • 2) globular
  80. fibrous protein
    • - long strands/sheets
    • - provide support, shape, external protection
    • - highly insoluble (high # of hydrophobic residues)
  81. globular protein
    • - spherical or globular shape
    • - several types of secondary & tertiary structures
  82. collagen secondary structure
    • - 3 left-handed helices forming a right-handed supertwist
    • - 3 amino acids per turn
  83. amino acid sequence in collagen
    repeating tripeptide unit: Gly-X-Y
  84. type of protein that has a well-packed, compact interior similar to that of crystal
    globular
  85. supersecondary structure characterized by involving 2 or more secondary structural elements and the connections between them
    motif
  86. all connections in a motif are ____ handed
    right-handed
  87. what constitutes a stable -hairpin?
    Gly or Pro in a -turn + stabilizing hydrophobic interactions between residues in adjacent strands

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