1. In trans peptide bond the amide proton is opposite from the carbony oxygen. In a cis peptide bond they are on the same side. The close contacts between the a carbons and other side-chain atoms cause the cis bond to be higher in energy.
2. The peptide bond before a proline is unfavourable as either cis or trans due to crowding. The energy of the trans bond is increased such that it is now only slightly more favourable than the cis configuration.
3. a-Helix
   • Usually right-handed
   • 3.6 residues/turn
   • 5.4 A rise/turn
   • i, i+4 residues form H-bonds
   • H-bonds || to helical axis
4. 3-10 helix
   i, i+3 residues form H-bonds
   • Hbonds not || not || to helical axis
   • Thinner than a-Helix
5. b-Strand
   • Highly extended (F,Y=180)
   • 2 residues/'turn'
   • 6.6 A rise/turn
   • no intra-hydrogen bonds
6. b-Sheets
   • Two types, || and anti-||
   • inter-chain hydrogen bonds
   • zig-zag pattern
   • Side chains alternate up-and-down

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