Quiz 2: Definitions

1. Quiz 2: Definitions • Monosaccharide • Disaccharide • Oligosaccharide • Polysaccharide • Aldose • Ketose • Lipid • Fatty Acid • Amphiphillic • Amphipathic • Saturated • Unsaturated

2. Quiz 2: Identification (Carbs)

3. Quiz 2: Identification (Lipids)

4. Protein Structure III

5. Relevent Interactions • Hydrophobic Forces • Electrostatic forces • Ion Pairs • Dipole–Dipole Interactions • Hydrogen Bonding • Covalent Bonds

6. Hydrophobic Forces(Entropic) Minimizes order of solvent H2O which occurs when hydrophobic molecules are in aqueous environment Primary Determinant of Tertiary and Quaternary Structures

7. Hydrophobic Interactions Not “bonds”; exclusion of water Buried in interior Important in tertiary structure

8. Electrostatic Forces • Ion Pairs • Attractive or Repulsive • Coulomb’s Law (strength proportional to 1/r2 • Competition between buried ionic interactions and hydrated ionic species on the surface

9. Ion Pairs Strength dependent on magnitude of charges, dielectric constant, and distance Modest strength Contribute little to native protein structure

10. Ion Pairs or Salt Bridges(Myoglobin) Figure 6-36

11. Ion-Polar Bonds Similar to electrostatic bonds Alternative to interactions with water Contribute little to native protein structure

12. Dipole-Dipole Interactions • Van der Waals Attractions • Strength proportional to 1/r6 • Dipole–Dipole Interactions • Dipole-Induced Dipole Interactions • Induced Dipole-Induced Dipole Interactions (London Dispersion Forces) Significant Contribution to Protein Native Structure

13. Dipole-Dipole Interactions

14. Typical Hydrogen Bonds between side chains(unshared electron pair: N and O)

15. Hydrogen Bonds Strength greatest in a polar environment Contribute greatly to secondary structure

16. Other Hydrogen Bonds(e.g. –SH)Similar electronegativity as –CH3More polarizable than –CH

17. Covalent Bonds Disulfide Bonds

18. Covalent (Disulfide) Bonds Do not need to be adjacent in primary structure Strong Intra- or Interchain

19. Sum of Forces Conformational Stability e.g. linking of fingers

20. Flexibility(conformational changes possible) Interaction (binding) of small molecules (effectors) Modification of protein amino acids – e.g. phosphorylation of serine

21. Cys2–His2 Zinc Finger Motif Stabilization of Small Domain Figure 6-37

22. Molecular Dynamics of Myoglobin Proteins Are Dynamic Structures Figure 6-38

23. Tertiary Structure Folding and ordering of a polypeptide chain due to interactions involving the amino acid side chains

24. Characteristics of Tertiary Structure • May contain both helices and  sheets • Structural characteristics • Nonpolar residues: interior • Charged residues: surface (hydrated) • Polar residues: surface (hydrated) or interior (hydrogen-bonded) • Compact: little or no internal space for water molecules • Domain Structure

25. Side Chain Distribution in Horse Heart Cytochrome c Figure 6-27

26. Tertiary Structures Contain Combinations of Secondary Structure Motifs

27. Super Secondary Structural Motifs Greek Key  hairpin  Figure 6-28

28. All a-Helix Proteins

29. All b-Sheet Proteins

30. a/b Proteins

31. Large Proteins Form Domains

32. Two Domain Protein(glyceraldehyde-3-P dehydrogenase) Figure 6-31

33. Quaternary Structure Specific association of polypeptide chains Subunits

34. Characteristics of Quaternary Structure • Identical or nonidentical subunits • Subunits usually associate noncovalently • Subunits are symmetrically arranged • Efficient means of producing highly complex proteins • Basis for regulatory behavior of many enzymes

35. Quaternary Structure of Hemoglobin (22) Figure 6-33

36. Three Broad Categories of Proteins • Fibrous Proteins • Globular Proteins • Membrane Proteins

37. Characteristics of Fibrous Proteins • Rod-like • Insoluble • due to hydrophobic AAs both inside and outside • Structural

38. -Keratin: Evolved for Strength (Hair, Wool, Nails) Right handed a-helix Left handed coiled coil

39. Coiled Coil non-polar residues Figure 6-15a

40. -Keratins - Crosslinked by Disulfide Bonds

41. Collagen — A Triple Helical Cable • Component of connective tissue • Distinctive amino acid compostion • ~33% glycine • 15-30% 4-hydroxyproline • Some 3-hydroxyproline & 5-hydroxylysine • Right-handed triple helix • Organized into fibrils • Fibrils are covalently cross-linked • Collagen defects are responsible for a variety of human diseases

42. Collagen: in connective tissue, cartilage, gelatin • left-handed-helix • 3 AA per turn • 3 -chains are supertwisted • mainly Gly, Ala, Pro • (Gly-X-Y motif) • 6% hydroxy-proline confers thermostability

43. Proline Hydroxylase Requires ascorbic acid (vitamin C) Scurvy

44. Globular Proteins

45. Properties of Globular Proteins • Majority of proteins • Dynamic Functions, i.e. enzymes • Mixture of secondary structures • Soluble • hydrophobic core, polar surface

47. Membrane Proteins: receptors, transporters, enzymes, ion channels Hydrophobic Water (aqueous) Non-Polar Water (aqueous)

48. Determination of Tertiary Structure X-Ray Crystallography Nuclear Magnetic Resonance (NMR)

49. Protein Crystals

50. X-Ray Diffraction Pattern Figure 6-21