Lecture 02

• What is the primary structure of a protein?

  Amino acid sequence stabilised by peptide bonds
• How is the primary structure of a protein encoded?

  By the nucleotide sequence of DNA
• What can result from the alteration of a single amino acid in a protein?

  It can cause disease
• What stabilises the primary structure of proteins?

  Peptide bonds
• What is the secondary structure of a protein?

  Folding of the polypeptide chain with hydrogen bonds
• What are the main types of secondary structure?

  α-helix, β-sheet, β-turns, loops

  
• How many residues are there per turn in an α-helix?

  3.6 residues per turn
• What type of bonding stabilises the α-helix structure?

  Hydrogen bonds between C=O and N-H groups
• What is the shape of an α-helix?

  Right-handed (clockwise)
• What charge does the dipole moment of an α-helix have at the N-terminus?

  Partial positive charge
• How do side chains extend in an α-helix?

  Radially from the α-helix core
• What is the shape of a β-sheet?

  Pleated shape
• What stabilises the β-sheet structure?

  Hydrogen bonds between C=O and N-H groups
• What distinguishes parallel β-sheets from anti-parallel β-sheets?

  Anti-parallel β-sheets are more stable

  
• What is the function of β-turns in protein structure?

  They reverse the direction of the polypeptide chain
• What stabilises β-turns?

  Hydrogen bonds between backbone atoms

  
• What is the characteristic of loops in protein structure?

  They are flexible and connect secondary structures
• How many residues are there per turn in a 310 helix?

  3 residues per turn
• What is the significance of the π-helix?

  It is a rare type of helix
• What is the definition of super secondary structure?

  Combinations of secondary structure elements
• What do motifs explain in protein structure?

  They explain structure but not function
• What is the tertiary structure of a protein?

  Overall three-dimensional structure of a protein
• What stabilises the tertiary structure of a protein?

  Bonds and interactions between side chains
• What is the quaternary structure of a protein?

  Arrangement of subunits in a protein
• How many polypeptide chains are in a tetramer of identical subunits?

  4 polypeptide chains
• What distinguishes a domain from a subunit in proteins?

  A single polypeptide can form several domains
• What is domain shuffling in protein evolution?

  Rearranging existing protein domains
• What is the role of exon shuffling in gene evolution?

  It rearranges exons to create new combinations
• What are the key points of protein structure?

  • Primary structure: amino acid sequence, stabilised by peptide bonds
  • Secondary structures: α-helix, β-sheet, β-turns, loops, stabilised by H-bonds
  • Super secondary structure: combination of secondary elements, performs functions
  • Tertiary structure: overall 3D structure, stabilised by side chain interactions
  • Quaternary structure: arrangement of subunits, stabilised by side chain interactions
• What are the characteristics of protein domains?

  • 80% of eukaryotic proteins are multidomain
  • Domains are stable and compact structures
  • A single polypeptide can form several domains but only one subunit
  • Domains are functional units of proteins
• What is the difference between domain movement and domain shuffling?

  • Domain movement: flexible connections allow movement between domains
  • Domain shuffling: rearranging existing domains to create new proteins