Chapter 22, Macromolecules and aggregates

1. Chapter 22, Macromolecules and aggregates Entropy and order Simplicity of small systems and complexity of real systems Ideality and reality Dealing with large systems

2. Proteins

3. DNA

4. Amyloids and Cellucoses

5. Liposome

6. Artificially Synthetic macromolecules

7. Common synthetic polymers

8. Contents Structure and dynamics 22.1 different levels of structure 22.2 Random coils 22.3 The structure of proteins 22.4 The structure of nucleic acids 22.5 The stability of biological polymers Determination of shape and size 22.6 Mean molar mass 22.7 Mass spectroscopy 22.8 Laser light scattering 22.9 Ultracentrifugation 22.10 Electrophoresis 22.11 Size exclusion chromatography 22.12 Viscosity Self-assembly 22.13 Colloids 22.14 Micelles and biological membranes 22.15 Surface films

9. Assignment for chapter 22 • 22.1(b) • 22.5(a)

10. Structure and dynamics Configuration Structural features elated to a given arrangement of chemical bonds It can be changed only by breaking Chemical bonds and forming new ones. Conformation Spatial arrangement of the different parts of a chain. It can be changed into another by Rotating one part of a chain around a bond.

11. Different levels of structure Primary structure (sequence) Secondary structure (helix, sheet etc.) Tertiary structure (overall 3D structure) Quaternary structure (formed by different 3D structures)

12. Random coils All bond angles are arbitrary. Free rotation.

13. Random coils (a more realistic model) Bond angle is fixed. Free rotation. Freely jointed chain model

14. l Measure of size Contour length:

15. Measure of size 1D chain, N units, each with length l, The probability that the ends are nl apart:

16. Proof Number of chains pointing to the right: NR Number of chains pointing to the left: NL Effective length: (NR-NL)l=nl N=NR+NL The number of ways forming a chain with end-to-end distance nl: The probability that the ends are nl apart: With Stirling’s approximation:

17. l nl 3D case P(RR+dR)=fdR

18. Measure of size Root mean square separation: (classroom exercise)

19. Measure of size Radius of gyration: Rij: separation of atoms i and j

21. Exercise • Calculate the mean separation of the ends of a freely jointed chain of N bonds pf length l.

22. Conformational entropy The most probable conformation is the one with n=0:

23. Constrained chains For tetrahedral bonds, For polyethylene with M=56 kg/mol, N=4000, l=154 pm (C-C bond),

24. The structure of proteins Classroom question: How many standard amino acids are most commonly found in living things? Corey-Pauling rules

25. α helix

26. Conformational energy Bond stretching: Bond bending: Bond torsion: Coulomb forces between partial charges: Dispersion and repulsive forces: Hydrogen bonding:

27. Potential Energies

28. vibration b • Kb :bond force constants • b : bond length

29. bending • Kθ :angle force constant • Θ: bond angle Θ

30. torsion • KX :dihedral angle force constant • X: dihedral angle

31. Improper torsion • Kimp : improper dihedral angle • Φ: improper torsion angle (e.g., angle between ab and acd) b c a d

32. Intermolecular forces (van der Walls forces) • εij : Lennards-Jones well depth • σij : Distance at the Lennards-Jones minimum between atoms i and j. • qi : Partial atomic charge • ε0 : Dielectric constant • r ij : The distance between atoms i and j

33. Lower energy means more stable

34. Typical distribution of torsion angles(Ramachandran plot)

35. Glycyl residue

36. Alanyl residue

37. βsheet Parallel and anti-parallel sheets

38. Higher-order structure Four-helix bundle

39. Higher-order structure β-barrel

40. The structure of nucleic acids

48. Secondary structure of DNA

49. Higher-order structure of DNA

50. The stability of biological polymers Denaturation and renaturation