Secondary Structure

Cards (26)

    • Alpha helix - peptide coil held together by H-bonds between carbonyl of residue and amine residue
    • R-groups point away from helical axis
    • Carbonyls point all in one direction while all amines point in one direction opposite of carbonyls
  • Amphipathic - one side polar the other non-polar
  • There must be chemical compatibility within residues stacked on each other
  • Alternating polarity can be seen every 2-3 amino acid residues’ R-groups in a-helicies
    • Beta sheets are extended compared to alpha helicies
    • Backbone of beta sheets zig-zag at tetrahedral alpha carbon
    • Beta sheets are also amphipathic
  • Anti-parallel beta sheet - One sheet will go from N-C terminal, the next will go from C-N terminal, and then N-C repeating pattern. 7 Armstrong. More strong compared to parallel due to co-linear H-bonds and dipole.
  • Parallel Sheet - pattern exhibits equal spacing between parallel residue groups (not backbones) 6.5 Armstrong. Less strong sheet.
  • This is an antiparallel beta sheet.
  • It is common to see two parallel beta sheets sandwiched together due to net dipole across sheets
  • Exterior unsatisfied H-bond beta sheet atoms achieve H2O interactions if on surface, if buried they will interact with other parts of protein (tertiary structure)
  • Hairpin connection - where connection between beta sheets re-enters on the same side where it left. Can be farther than adjacent beta sheets
  • Crossover connections - connection re-enters on the opposite side of beta sheet it left. Can occur farther than adjacent beta-sheets
  • Type I Beta turn - proline based at lower left (2) position.
    Type II Beta turn - glycine based at upper left (1) position.
    Both stabalized by intra-chain H-bonds
  • RNA ligase - glues & condenses pieces of RNA together
  • Peptide bonds are ~40% double bond character and are limited to ~1.33 Armstrong
  • Psi: The rotation of the carbonyl carbon to the alpha carbon: at 180 when fully extended, and 75% of conformational space is inaccessible
  • Phi: The rotation as described between the alpha carbon and the nitrogen: at 180 degrees when fully extended
  • Proline has a very limited range of phi angles (35-85 degrees) due to its cyclic imimo structure
  • -dH is favorable and creates bonds
  • H-bond acceptors are lone pairs, donors are H’s attached to e neg atoms
  • The pitch of an alpha helix is the distance per turn ~3.6 amino acid residues (~5.4 Armstrong)
  • A ribbon consists of 3-4 pitches (~12 residues): phi = -57 degrees; psi = -47 degrees
  • On a ribbon, all R-groups stick out to avoid interference with backbone
  • No prolines can be found in a-helix (except for terminus) as their amine does not have an H for H-bonding and therefore causes kink in structure
  • Beta sheet residues are ~3.5 armstrong apart, and have ~7 armstrong pitches
  • You can tell the difference between a-helix and beta-sheet by looking at primary structure
    • PNPNPNP… will be likely a beta sheet (polar vs. non-polar)
    • PPNNPPNNPP… will likely be an alpha helix