PHRD5025 Biochem - Lecture 1 Amino Acids & Protein Structure

  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. Image Upload 1
    glycine
  7. Image Upload 2
    alanine
  8. Image Upload 3
    valine
  9. Image Upload 4
    leucine
  10. Image Upload 5
    isoleucine
  11. Image Upload 6
    phenylalanine
  12. Image Upload 7
    proline
  13. Image Upload 8
    tryptophan
  14. Image Upload 9
    serine
  15. Image Upload 10
    threonine
  16. Image Upload 11
    methionine
  17. Image Upload 12
    cysteine
  18. Image Upload 13
    asparagine
  19. Image Upload 14
    glutamine
  20. Image Upload 15
    aspartic acid
  21. Image Upload 16
    lysine
  22. Image Upload 17
    tyrosine
  23. Image Upload 18
    glutamic acid
  24. Image Upload 19
    arginine
  25. Image Upload 20
    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 Image Upload 21 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. Image Upload 22
    bond angle for N-CImage Upload 23 bond
  61. Image Upload 24
    bond angle for CImage Upload 25-C bond
  62. direction of H-bonds in an Image Upload 26-helix
    parallel to helix long axis
  63. how many residues are H-bonds separated by in an Image Upload 27-helix
    4
  64. direction of side chains in an Image Upload 28-helix
    perpendicular to the helix long axis
  65. interactions that destabilize an Image Upload 29-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 Image Upload 30 and Image Upload 31 angles (high conformational flexibility)
  71. 2 least favored amino acids for a-helices
    Gly & Pro
  72. helix breaker, helix cap
    Pro
  73. parallel Image Upload 32-sheet
    • - aligned main chain atoms
    • - NON-linear H-bonds
    • - less stable
  74. how are parallel Image Upload 33-sheets connected?
    right handed connections

    -> shorter bend through smaller angles
  75. antiparallel Image Upload 34-sheet
    • - non-aligned main chain atoms
    • - LINEAR H-bonds 
    • - more stable
  76. how are antiparallel Image Upload 35-sheets connected?
    Image Upload 36-turns/hairpins
  77. # of residues in a Image Upload 37-turn
    4
  78. most favored amino acids in Image Upload 38-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 Image Upload 39-hairpin?
    Gly or Pro in a Image Upload 40-turn + stabilizing hydrophobic interactions between residues in adjacent Image Upload 41strands
Author
daynuhmay
ID
233495
Card Set
PHRD5025 Biochem - Lecture 1 Amino Acids & Protein Structure
Description
amino acids, protein structure
Updated