PHRD5025 Biochem - Lecture 2 Protein Function

  1. molecule bound reversibly by a protein
  2. structural adaptation that occurs between ligand and protein to make the binding site more complementary to the ligand
    induced fit
  3. # of polypeptide chains Hb contains (& types)

    2 Image Upload 1-chains, 2 Image Upload 2-chains
  4. what binds to O2 in Hb?
    each polypeptide chain contains 1 heme group that binds
  5. If a ligand specifically binds to one of the 2 states, equilibrium between those states will be shifted in favor of the state with bound ligand with the increase of ligand concentration
    Wyman Linkage relationship
  6. cyclic organic ring structure bound to Fe to generate heme
  7. what state of Fe binds to oxygen?
  8. what prevents the conversion of ferrous iron Fe2+) to ferric (Fe3+)?
    the 4 nitrogen atoms bound to Fe in heme
  9. 2 conformations of Hb
    • 1) T state - low O2 affinity
    • 2) R state - high O2 affinity
  10. conformational change in Hb R state
    Image Upload 3 subunit pairs slide past each other and rotate, narrowing the pocket between the Image Upload 4subunits
  11. 2 axial ligands to Fe in heme
    • 1) sidechain N of a His residue
    • 2) O2 binding site
  12. equation for the fraction of total binding sites occupied in Hb
    Image Upload 5
  13. protein in which the binding of a ligand to one site affects the binding properties of another site in the same protein
    allosteric protein
  14. Hill coefficient nH>1
    positive cooperativity
  15. positive cooperativity
    ligand binding at one site promotes the ligand binding at another site
  16. Hill coefficient nH=1
    no cooperativity
  17. negative cooperativity
    binding of one ligand impedes the binding of others
  18. any molecule capable of eliciting an immune response
  19. percentage of blood protein made up of antibodies
  20. 5 classes of antibodies
    • 1) IgG
    • 2) IgA
    • 3) IgD
    • 4) IgE
    • 5) IgM
  21. major class of antibody
  22. antibody found in saliva, tears, and milk
  23. 3 fragments of IgG when cleaved by papain
    • 1) Fc (constant Ab stem)
    • 2) 2 Fab's (antigen-binding fragments
  24. a particular molecular structure within an Ag that binds to an individual antibody or TCR
    antigenic determinant/epitope
  25. what is binding specificity of an antibody determined by?
    amino acid sequences in the variable domains
  26. what activates the macrophage to engulf a foreign body?
    IgG binding to an antigen -> receptors on the macrophage surface recognize and bind the Fc region of IgG
  27. proteins that interact with partially folded or improperly folded polypeptides, facilitating correct folding pathways
  28. what to chaperones bind to on improperly folded proteins?
    regions rich in hydrophobic residues
  29. do chaperones actively promote folding of a protein?
    no, they just prevent aggregation
  30. what is the difference between chaperones and chaperonins?
    chaperonins provide a cavity for the folding of an isolated substrate (ex: GroEL/GroES)
  31. GroEL
    double donut shaped protein, with 7 polypeptide chains per donut (14 total)
  32. two-stroke system
    during 1 cycle, 2 substrate molecules are folded
  33. when does the conformational change occur in the GroEL/ES system?
    GroES binding to one of the GroEL rings
  34. where is the chemical energy for muscle contraction derived from?
    ATP hydrolysis
  35. percentage of protein mass of muscle actin and myosin make up
  36. motor domain that makes muscle contraction possible
    myosin head group (globular domain)
  37. myosin subunits
    • - 2 heavy chains
    • - 4 light chains
  38. myosin heavy chain structure
    @ C-term: extended Image Upload 6 helices, wrapped around each other in a left-handed coiled coil

    @N-term: each chain has a large globular domain containing an ATP hydrolysis site
  39. location of myosin light chains
    associated with the globular domains of heavy chains
  40. myosin aggregates in muscle cells
    thick filaments
  41. bipolar structure of a thick filament
    several hundred myosin molecules associate their fibrous tails, with globular domains projecting from either end
  42. thin filament makeup
    F-actin (+ other proteins)
  43. F-actin
    filamentous actin

    associated globular actin (G-actin) proteins
  44. binds ATP and hydrolyzes it to ADP, which helps in the assembly of filaments
    G-actin (globular actin)
  45. binds tightly and specifically to 1 myosin head group
    each actin monomer in the thin filament
  46. slide along actin thin filaments during contraction
    myosin thick filaments
  47. what causes dissociation of myosin head from actin?
    ATP binding to myosin head
  48. conformational change in the myosin head that moves actin and myosin filaments relative to one another
    power stroke
  49. triggers power stroke
    Pi release from the myosin head
  50. structure serving as an anchor to which thin filaments are attached
    Z disk
  51. arises from the thick filament
    A band
  52. arises from the thin filaments
    I band
  53. during contraction, Z disks in neighboring __bands draw closer together
    I bands
  54. # heme groups in myoglobin
  55. myoglobin cooperativity
    nH=1, since there is only 1 ligand binding site
Card Set
PHRD5025 Biochem - Lecture 2 Protein Function
protein function