Protein Structure 7

Question 1

Levels of protein structure

Answer 1

• proteins are defines as polypeptide chains containing over 50 residues
• primary structure determines all higher order structures
• Protein sequence are always written from amino (N) to carboxy (C) terminus

Question 2

Peptide bonds and flexibility

Answer 2

• each aa along the polypeptide backbone contributes 3 bonds: N-C, C-C, C-N (peptide bond)
• peptide bond is planar due to electron resonance (40% double bond character)

Question 3

Dihedral angles

Answer 3

• some dihedral angles are preferred
• rotation about he dihedral angles is contradicted by steric hindrance
• some dihedral angles are favoured

Question 4

Alpha helix

Answer 4

-stabilized by H bonds

Question 5

Beta sheet

Answer 5

• extended zig-zag conformation with H bonds between chains and R groups projecting from both faces
• amino acids have properties to form either helix or sheet
• can be parallel or antiparallel
• Hbonds in straight line are strongest
• antiparallel is more stable

Question 6

Conformational diseases

Answer 6

• Alzheimer’s (Human amyloid native conformation becomes destabilized to form B amyloid fibril)
• Prions (Mad cow)

Question 7

Supersecondary structure: motifs and domains

Answer 7

• Motifs: small regions with a defined sequence or structure, often serving a common function in different proteins
• Domain: sub-regions of single polypeptide chains that can fold and function independently (sometimes correlated with exons)

Question 8

Forces that stabilize protein tertiary structure

Answer 8

• helical structure
• sheet structure
• metal ion coordination
• hydrophobic interactions
• disulfide bonds
• electrostatic attraction
• side chain hydrogen bonding

Question 9

Protein stability and denaturation

Answer 9

• Native
  
  • the native sate of a protein is specified by its primary structure
  • stabilized by non-polar side chains, optimized Hbonding, maximized side chain packing, and intracranial S-S bonds
  • most polar and charged residues are on the surface of globular proteins, exposed to aqueous environment
• Denatured
  
  • denatured state is stabilized by increased conformational entropy of the unfolded chain
  • can be denatured by heat, chemicals, extreme pH, mutations
  • protein denaturation is often irreversible because of side reaction such as proteolysis and precipitation

Question 10

Protein folding

Answer 10

• anfinsen experiment: native structure of RNase only recovered if urea removed before/during removal of reducing agent… but not after
• Levi that paradox: all possible conformations of a 100-residue protein would take the age of the universe to sample
  
  • but proteins fold in seconds
• initial formation of 2 degree structure elements which restrict further possibilities
• some folding intermediates may promote mis folding and aggregation
• some proteins are intrinsically disordered: only fold upon interaction with binding partners

Question 11

Chaperoning-assisted protein folding

Answer 11

• while the primary structure of a protein dictates its 3D structure, many larger proteins require some assistance to explore their conformational space
• chaperone allows protein to fold properly
• uses ATP
• makes folding more efficient