L20: Secondary and Tertiary structure

• What are the four hierarchical levels of protein structure?

  Primary, secondary, tertiary, and quaternary structure
• What defines the primary structure of a protein?

  The sequence of amino acids linked by covalent bonds
• How is secondary structure formed in proteins?

  It is created by hydrogen bonding in the backbone of the protein
• What is the tertiary structure of a protein?

  It refers to the overall 3D structure formed by interactions between secondary structure elements and side chains
• What is the quaternary structure of a protein?

  It describes how different polypeptide chains interact in multimeric proteins
• What does the 3D structure of a protein encode?

  It is encoded in the protein sequence
• What is AlphaFold used for?

  It allows us to predict protein structure based on the amino acid sequence
• What are the three main experimental methods for protein structure determination?

  X-ray crystallography, NMR spectroscopy, and electron microscopy
• Which experimental method is most commonly used today for protein structure determination?

  X-ray crystallography
• What are the three types of proteins mentioned?

  Membrane proteins, globular proteins, and fibrous proteins
• What characterizes globular proteins?

  They are water-soluble and have a roundish shape
• What are fibrous proteins typically described as?

  They are types of rope, such as collagen, silk, and keratin
• What is the purpose of secondary structure in proteins?

  It ensures the hydrophilic backbone can be buried in the hydrophobic core
• What is the bond character of the peptide bond?

  The peptide bond is partially double bonded
• What geometry does the peptide bond give to the protein structure?

  It gives planar geometry
• Which type of peptide bond is more common, cis or trans?

  Trans peptide bonds are more common
• Why are cis peptide bonds less common?

  Cis leads to steric clashes and is not permissible except for proline
• What makes proline unique in terms of peptide bond configuration?

  Proline has an unusual ring structure that makes the cis conformation more stable
• How does proline change from cis to trans configuration?

  The peptide bond is a single bond allowing free rotation, but enzymes are needed to catalyze the transition
• What are the torsion angles of the backbone called?

  Phi (φ) and Psi (ψ)
• What does the Ramachandran plot illustrate?

  It determines the angles of each amino acid in solved protein structures
• How are alpha-helices depicted in structural diagrams?

  As ribbons or cylinders
• What is the bonding pattern in an α-helix?

  Hydrogen bonds form between the C=O of residue i and the NH of residue i+4
• What is the rise per residue in an α-helix?

  1.5 Å per residue
• How many residues are typically in one turn of an α-helix?

  Approximately 3.6 residues
• What is the orientation of side chains in an α-helix?

  Side chains extend outward from the helix
• Why is proline considered a helix breaker?

  Proline lacks the N-H bond necessary to form hydrogen bonds
• What is an example of an α-helix in biological systems?

  It fits in the major groove of DNA
• How do β-strands interact with each other?

  They hydrogen bond with each other
• What is the typical arrangement of β-strands in a sheet?

  They can be arranged in parallel or anti-parallel configurations
• What is the geometry of a β-sheet?

  It is pleated due to the geometry of the peptide bond
• What is an example of a β-barrel structure?

  Porins are an example of a β-barrel structure
• What is a reverse turn or β-turn in protein structure?

  It allows the chain to sharply reverse direction, typically involving Pro and Gly
• Which amino acids are predominantly found in turns?

  Proline and glycine are predominantly found in turns
• What are the main elements of secondary structure?

  α-helix, β-strands, and β-turns
• What interactions hold the tertiary structure of proteins together?

  Noncovalent and covalent interactions, including disulfide bonds
• What role do salt bridges play in protein structure?

  They are interactions between opposite charges that help stabilize the structure
• What is a motif in protein structure?

  A combination of secondary structure elements, typically 10-30 amino acids
• What is the function of the zinc finger motif?

  It provides strong and specific binding to DNA
• How does the leucine zipper motif function in DNA binding?

  Hydrophobic interactions hold the helices together, allowing them to fit into the major groove of DNA