1. Lecture 1

2. Self-organization of biological systems Self-organization of biological systems: self-assembly into compartments active transport molecular specificity

3. Cell types: 1. Cells are fundamental units of life 2. Cells use chemical or solar energy to function, grow, and reproduce 3. Cells are macromolecular factories 4. Cells move, divide (mitosis), and sense environmental conditions

4. Courtesy of Dr. Julian Heath.

5. ©1982. Used by permission of Jones and Bartlett Publishers, Sudbury MA.

6. ©1993. Used by permission of Springer-Verlag. Prokaryotic cells

7. ©1993. Used by permission of Springer-Verlag.

8. Eukaryotic cells

9. (b) ©1980. Used by permission of Elsevier Science. Mitochondria are organelles that metabolize conversion of chemical energy from food into ATP.

10. Chromatin and cell nucleus

11. Chromatin under the microscope Electron micrograph of D.Melanogaster chromatin: arrays of regularly spaced nucleosomes, each ~80 A across. Section of a chromosome: central scaffold + lateral loops High-resolution image of a human chromosome

12. Structure of the nucleosome core particle (NCP) T.J.Richmond: K.Luger et al. Nature 1997 (2.8 Ǻ); T.J.Richmond & C.A.Davey Nature 2003 (1.9 Ǻ) Left-handed superhelix: 1.84 turns, 147 bp, R = 41.9 A, P = 25.9 A. PDB code: 1kx5

13. Molecular composition of bacterial cells by weight Molecular composition of bacterial cells by weight: Small molecules 74% water 70% amino acids, sugars, fatty acids, ions 4% Macromolecules 26% proteins 15% RNA 6% DNA 1% lipids 2% polysaccharides 2% Molecular “parts list”

15. ©1991 Larry Gonick.

16. ©1982, American Association for the Advancement of Science. Used by permission.

19. 20 types of amino acids in proteins

20. Protein Data Base accession code 1VII ({C.J. McKnight, D.S. Doering, P.T. Matsudaira, P.S. Kim, J. Mol. Biol. 260 126 (1996)).

21. Protein 3D structure Protein Data Bank (PDB) http://www.rcsb.org

22. Elastic rod model DNA looping induced by a Lac repressor tetramer

23. Protein Data Base accession code 1EHZ (H. Shi and P.B. Moore, RNA 6 1091 (2000)).

24. ©1993. Used by permission of Springer-Verlag.

25. Fatty acids Cellulose (polysaccharide)

26. Lecture 2

27. A single peptide (protein building block) A polypeptide chain

28. A tyrosine (TYR) amino acid (one of 20 naturally occurring amino acids)

29. Peptide torsion angles and secondary structure omega = 180 deg, phi & psi are variable minimize E({phi,psi}) – protein folding problem

30. Secondary structure elements: alpha & 3-10 helices

31. Secondary structure elements: beta sheets

32. Turns of the polypeptide chain

33. The Ramachandran plot

34. Side chain conformations

35. Protein 3D structure (second look) Protein Data Bank (PDB) http://www.rcsb.org Protein functions: enzymes, gene regulation

36. Protein folding: I

37. Protein folding: II

39. Microtubules (25 nm): cytoskeleton Actin filaments (F-actin; 7 nm): actin cortex

41. Cell membranes are crowded: channels, receptors, pumps, actin cortex attachment points

43. DNA & RNA

44. The genetic code

47. ©1993. Used by permission of Springer-Verlag.