Protein Structure

• Proteins in any of their functional, folded conformations are called native proteins.
• Stability is the tendency to maintain a native conformation
• The unfolded stated of a protein is characterized by a high degree of conformational entropy.
• The rigid peptide bonds limit the range of conformations possible for a polypeptide chain.
• In an a-helix structure amino acid residues protrude outward from the helical backbone.
• Each helical turn in an a-helix includes 3.6 amino acid residues
• Dihedral angles in the backbone, determines a-helix conformation.
• Extended left-handed a-helices are less stable.
• One fourth of all amino acid residues in proteins are found in a-helices.
• Glutamate residues repel each other, thus preventing formation of a-helix
• The bulk and shape of ser, asn, thr, and cys residues can destabilize an a-helix if they are close together.
• Proline and Glycine will not be seen in an a-helices
• Fibrous proteins are polypeptide chains arranged in long strands or sheets.
• Globular proteins are polypeptide chains folded into a spherical or globular shape.
• All fibrous proteins are insoluble in water.
• Silk fibroin is an example of B conformation
• B-conformation characteristics soft, flexible filaments.
• Keratin is a right-handed a-helix
• Keratin is rich in hydrophobic residues.
• In keratin, cross-links stabilizing quarternary structure are disulfide bonds.
• How can fibrous proteins strength be enhanced? By covalent cross-links
• Collagen is left-handed and has 3 amino acid residues per urn.
• Gelatin is derived from collagen
• Collagen contains a lot of proline and glycine residues.
• Proline permits the sharp twisting in collagen.
• As you get older, connective tissue becomes more rigid and brittle dued to accumulated covalent cross-links.
• Silk fibroin is rich in alanine and glycine residues.
• Silk does not stretch, because the B conformation is already highly extended.
• A loss of 3-D structure that causes loss of function is called denaturation.
• Circular dichroism measures the amount of helical structure in a protein.
• Urea disrupts hydrogen bonds.
• Organic solvents, urea, and detergents disrupt hydrophobic aggregation of nonpolar amino acid side chains, which produces the stable core of globular proteins.
• Extremes of pH alter the net charge on a protein, causing electrostatic repulsion and the disruption of some hydrogen bonding.
• Protein precipitation is a consequence of protein aggregate formation as exposed hydrophobic surfaces associate.
• Unfolded states have a high degree of conformational entropy and high free energy.
• Chaperones facilitate correct folding
• Peptide C-N bonds have partial double bond character, meaning they cannot rotate freely.
• B turns connect the ends of two adjacent segments of antiparallel B sheets.
• Glycine and Proline are often found in B-Turns.
• The light-absorbing entity is also referred to as chromophore.