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