BIOL or CHEM 3361 Biochemistry I Lecture Notes PDF

BIOL or CHEM 3361 Biochemistry I Proteins: Secondary, Tertiary, and Quaternary Structure Reading: Chapter 6 Secondary and Supersecondary Structures Secondary structures: Helices (particularly alpha) Beta sheets Beta turns Random coil Super-s...

BIOL or CHEM 3361 Biochemistry I Proteins: Secondary, Tertiary, and Quaternary Structure Reading: Chapter 6 Secondary and Supersecondary Structures Secondary structures: Helices (particularly alpha) Beta sheets Beta turns Random coil Super-secondary structures: Coiled coils Beta hairpin Beta-alpha-beta Helix-turn-helix, Greek keys, alpha-alpha hairpin, EF hand etc. The β-turn Allow protein chain to reverse direction Carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away (1st and 4th) Two types differ in orientation of middle peptide bond (Left: Type I (common); right: Type II) The β-Turn Proline and glycine are prevalent in β-turns Promote formation of antiparallel sheets Think of it as a three residue, zero pitch helix Proline phi is -60 Random Coil Helices and strands are connected by loop regions of various lengths and shapes often referred to as ‘random coil’ Not random or coiled, just no recurring bonding pattern These loops are at the surface of the protein C=O and N-H form H-bonds with water Rich in charged and polar residues Often not conserved Flexible and participate in binding events Amino Acid Preferences Amino acid residues exhibit only a preference for particular types of secondary structure; 50-80% accuracy Super-secondary Structures Beta-hairpin - Two adjacent anti-parallel strands joined by a 2-5 residue loop β-α-β Motif - Two adjacent parallel β-strands connected by an α-helix that is commonly positioned above the β-plane Coiled Coil - Two helices wound around each other in a supercoil or super-helix Left-handed twist of the structure reduces the no. of residues per turn to 3.5, sidechain positions repeat every 7 residues  α-Keratin A fibrous protein found in hair, fingernails, claws, horns and beaks Sequence consists of 311-314 residue alpha helical rod segments capped with non- helical N- and C-termini Primary structure of helical rods consists of 7-residue repeats: (a- b-c-d-e-f-g)n, where a and d are nonpolar. This structure promotes association of helices to form coiled coils Tertiary Structure - Protein Domains Secondary and supersecondary structures combine to make domains (