L21: Quaternary structure and folding

• What is the primary structure of a protein?

  Covalent structure and sequence of amino acids
• How is secondary structure in proteins created?

  By hydrogen bonding in the backbone
• What does tertiary structure refer to in proteins?

  The overall 3D structure formed by interactions between secondary structure elements and sidechains
• What is quaternary structure in proteins?

  How different polypeptide chains interact in multimeric proteins
• What is an example of a protein with quaternary structure?

  Hemoglobin tetramer
• Why is the quaternary structure of hemoglobin essential for its function?

  It allows for the interaction of two different chains, α and β
• What is the function of GAPDH in its tetrameric form?

  It is catalytically active
• What is the sequence pattern of collagen?

  Gly-X-Y where X and Y are often Pro or hydroxy-Pro
• Why is hydroxy-Pro important in collagen?

  Its modification requires vitamin C
• What is RNase and its function?

  A small digestive protein that hydrolyzes RNA to nucleotides
• What was added to RNase solution in Anfinsen's experiment to disrupt hydrogen bonding?

  8M Urea
• What effect does urea have on protein structure?

  It disrupts hydrogen bonding and weakens hydrophobic interactions
• What happens to RNase when urea and β-mercaptoethanol are removed through dialysis?

  The protein refolds
• What does Anfinsen's experiment suggest about protein folding?

  Protein folding is spontaneous and requires energy
• What is the conclusion of Anfinsen's experiment regarding protein structure?

  Proteins adapt their native structure spontaneously based on their sequence
• What is Levinthal's paradox in relation to protein folding?

  It suggests that proteins cannot fold through random exploration due to the vast number of conformations
• What is the process of nucleation in protein folding?

  Hydrophobic regions condense, leading to short stretches of secondary structure
• What happens to unfolded proteins in the cell?

  They become sticky due to exposed hydrophobic surfaces
• What is the role of chaperones in protein folding?

  They look after other proteins when not fully folded
• Who demonstrated the binding of proteins to chaperones?

  Prof John Ellis
• What is the function of Protein Disulphide Isomerase (PDI)?

  It catalyzes oxidation and isomerization of disulfide bonds
• What is the role of proline cis-trans isomerase?

  It catalyzes the slow conversion between cis and trans forms of proline
• How does Anfinsen's conclusion about protein folding relate to the need for cellular machinery?

  Proteins cannot fold spontaneously without guidance, despite Anfinsen's conclusion
• What is a consequence of protein misfolding?

  It can cause disease
• What disease can result from eating meat from BSE affected animals?

  vCJD (variant Creutzfeldt-Jakob disease)
• What type of protein aggregates are found in the brain associated with diseases?

  Abnormal β sheets and aggregates
• What happens to hemoglobin in sickle cell anemia?

  It aggregates to form long chains that distort the shape of the cell
• What are the key messages regarding protein structure and folding?

  • Quaternary structure is important for many functions of proteins
  • Anfinsen’s experiment is key to understanding protein folding
  • Protein folding is an ordered process depending on hydrophobic collapse
  • The cell is a suboptimal environment for protein folding, hence machinery exists to prevent misfolding