Secondary structure

• Define the secondary structure of a protein

  Initial folding of the primary sequence
• What are the two types of secondary structures

  Alpha helixes and Beta [pleated] sheets.
• What are the bonds involved in the secondary structure

  Hydrogen.
• Which groups are bonded in an alpha helix.

  N-H and C=O.
• Where do hydrogen atoms form in an alpha helix.

  Between every 4th Amino acid.
• Which way do amino acid residues point in an alpha helix.

  Out of the helix.
• Define a Beta sheet structure

  Hydrogen bonds between non-continuous regions [Beta strands].
• What are the two types of Beta sheets

  Parallel and Anti-parallel.
• Where do hydrogen bonds form in Beta sheets

  Between the C=O and N-H groups.
• What is a parallel Beta sheet.

  All strands are running in the same direction.
• What is an anti-parallel Beta sheet

  Strands run in opposite directions
• What are the features of a parallel sheet

  Hydrogen bonds are evenly spaced
• What are the features of an anti-parallel sheet

  Hydrogen bonds are narrowly spaced and separated by large gaps
• Describe the pleated structure

  Chiral carbons lie successively above and below the plane
• What are loop regions

  Structures that link secondary structures
• What are the types of loop regions

  • Long
  • Short
  • Proline
  • Glycine
• Describe a short loop region

  Highly flexible random coils
• Describe a short loop region


  Hairpin loops [Beta turns]
• What do short loop regions link

  Anti-parallel Beta strands
• Describe a proline loop region

  Locked ring structure with kinks
• Describe a glycine loop region

  Small residue allows for the formation of turns
• What is a Beta-alpha-Beta motif

  Parallel beta strands linked by alpha helixes.
• Give examples of post-translational modifications

  • Production of rare amino acids
  • Formation of lipoproteins
  • Glycosylation to form glycoproteins