Secondary Structure

• • 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