Proteins

  1. torsion angle coordinates for beta strands & alpha helices in a Ramachandran plot
    • (-phi,+psi) for beta strands
    • (-phi,-psi) for alpha helices

    Beta strands are in the +y region, alpha helices are in the -y region. They both only occur on the -x axis side. See slide #13
  2. Why are certain torsion angle combinations not allowed from the Ramachandran plot?
    The protein structures would be unstable due to large possibility of steric clashes between atoms.
  3. How many intrahelical H bonds are present with 18 residues?
    14

    (# of H bonds) = (# of residues) - 4

    See slide #4
  4. How many residues are there per helical turn?
    3.6

    • Ex. 1: 18 residues x (1 turn/3.6 residues) = 5 turns
    • Ex. 2: 7 turns x (3.6 residues/1 turn) = 25 residues when rounded to the nearest whole #
  5. amino acids whose side chains can participate in favorable electrostatic interactions
    DEKR (all charged molecules)

    (also participate in H bonding)
  6. functional significance of a disulfide bond
    strengthens the shape of a protein or peptide

    1 disulfide bond = 2 Cysteines
  7. Which secondary protein structure never occurs alone (self-stabilizes) & why?
    Beta strands. There would be steric constraints between the H bonds within 1 strand. Interstrand H bonding occurs between 2 strands to help them stabilize.

    See slide #10
  8. Which secondary protein structures are self-stabilizing?
    Alpha helixes & beta turns. In alpha helixes, intrahelical H bonding occurs between the carbonyl O & amide N

    See slide #3 & 11A
  9. How many residues are in one helical layer?
    18 (See slide #6)
  10. An alpha helix has 35 intrahelical H bonds. How many layers will it occupy? (3 sig figs)
    • 35 H bonds + 4 = 39 residues.
    • 39 residues x (1 layer/18 residues) = 2.17 layers
  11. An alpha helix has 8 turns. How many helical layers will it occupy? (3 sig figs)
    • 8 turns x (3.6 residues/1 turn) = 28.8 residues
    • 28.8 residues x (1 layer/18 residues) = 1.60 layers
  12. A coiled coil has 42 residues. How many total a & d positions will there be?
    42/7 = 6 perfect heptad repeats. Each heptad has 2 a & d residues making a total of 12 a & d positions.

    See slide #9
  13. A coiled coil has 8 a & d positions. How many total residues would there be? Assume it has perfect heptad repeats.
    A heptad has 2 a & d positions so there would be 4 heptad repeats. Each heptad has 7 residues so 4 x 7 = 28 residues
  14. Phi is defined by __ & controls __ distance.
    N-C(alpha); carbonyl C
  15. Psi is defined by __ & controls __ distance
    C(alpha)-C; amide N
  16. Omega is defined by __ & controls __ distance
    C-N (no rotation due to partial double bond); alpha C
Author
sophathida
ID
350791
Card Set
Proteins
Description
Proteins
Updated