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Protein Structure

Protein Structure. C483 Spring 2013. 1. Which statement is false about a globular protein that performs its biological function as a single independent polypeptide chain?

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Protein Structure

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  1. Protein Structure C483 Spring 2013

  2. 1. Which statement is false about a globular protein that performs its biological function as a single independent polypeptide chain? A) Its tertiary structure is likely stabilized by the interactions of amino acid side chains in non-neighboring regions of the polypeptide chain. B) It could contain α-helices that are stabilized by hydrogen bonding. C) It likely has extensive quaternary structure to maintain its globular shape. D) Non-covalent forces are the primary source of stability for the secondary and tertiary structure. 2. The conformation of the backbone of a polypeptide is described completely by the angle(s) of rotation about which bond(s)? A) The peptide bond only. B) N-Cα only. C) N-Cα, Cα-C and C-N bonds. D) N-Cα and Cα-C bonds only. 3. Which structure indicates the proper hydrogen-bonding pattern between amino acids in an α-helix? (Dashed lines represent the hydrogen bonds.)

  3. 4. What would you expect about the formation of an α-helix for a segment of a protein chain that contains lysine approximately every fourth residue with all other residues being mostly hydrophobic? • A) Helix formation would be favored at low pH. • B) Helix formation would be favored at high pH. • C) Helix formation would be favored at neutral pH. • D) Helix formation would never occur regardless of pH. • 5. Supersecondarystructures that contain recognizable combinations of α-helices, β-strands and loops (e.g. the Greek Key) are called ________. • A) domains • B) folds • C) homologous regions • D) motifs • 6. The principle forces holding subunits of an oligomeric protein to each other are ________. • A) peptide bonds • B) hydrophobic interactions • C) covalent bonds • D) disulfide bonds

  4. Protein Structure • Configuration and conformation • Native structure • Fibrous • Globular • Atomic level and cartoon level

  5. Structural Determination • Crystallography • NMR

  6. Structural Hierarchy

  7. C483 goals • Secondary structure dictated by • Peptide bond structure • Atomic level intermolecular interactions • Tertiary and quaternary structure • Importance to protein folding and activity • Familiar with vocabulary so that you can read a paper to learn the details

  8. Peptide Bond • Resonance • 6 planar atoms form a unit • Highly polar • Trans vscis conformation

  9. Conformational Flexibility • If each peptide bond is relatively locked, backbone conformation can be defined by phi and psi • NOT cis/trans • Both stuctures to the right are trans

  10. Ramachandran Plots

  11. Alpha Helix • Right handed • Polarity • Phi = -57o and psi = -47o • n and n + 4 • Ala vs. Tyr • Gly and Pro

  12. The average a-helix is 12 residues long. What is its length in nm? • How many amino acids/turn of an alpha helix?

  13. Amphipathic Helices Structural Implications Placement in Protein Coiled-Coil

  14. Beta-Sheets

  15. Real Beta Sheets • Technically, often tertiary structure • Generally bent/twisted • Alternating sidechains can lead to amphipathic sheets

  16. Loops and Turns • Nonrepeating • Change of direction • Turns have about 4 residues • Internal H-bonds • Gly, Pro

  17. Tertiary Structure • Longer range interactions of secondary features • Driven by hydrophobic effect • Disulfide bridges • Diversity

  18. Tertiary Structure • Too many shapes to memorize • But not an infinite number of possibilities • Take away the ability to read a paper • Discussions of motifs and why important • Discussion of domains and why important

  19. Motifs (Super Secondary Structure) • Recognizable combinations of helices, loops, and sheets • Match • Helix-loop-helix • Helix bundle • Hairpin • b-sandwich

  20. Studying Motifs • Some Motifs are highly studied • Know the Lingo • Leucine zipper • Zinc finger • Often have recurring applications

  21. Domains • Discrete, independently folded unit (may maintain shape when cleaved on loop) • May have separate activities: “ATP binding domain” or “catalytic domain” • Similar activity = similar structure across many proteins • Binding pockets at interfaces How many domains?

  22. Common Domains

  23. Quaternary Structure a2 • Multiple subunits: Oligomers • Homodimer, heterotrimer • Advantages • Economy • Stability • regulation a3 a2b2

  24. From your discussion paper…

  25. Answers • C • D • B • B • D • B

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