1. BTW: Turn on the recorder 1

3. 3 Note to myself for Lec. 1: Web site is required reading (at least twice a week) Problem book Web lectures Email questions, Q&A database, office hours Evening vs. morning lectures Recitation sign-up Note exam dates and times (drop an exam); note final date Transparency Exam topics, nature

4. What is expected of you as a student 1) Repeat what you have heard exactly as it was presented, know all the terms and the definitions we or the texts have provided Probably fail 2) Repeat what you have heard in your own words, showing you have some understanding of the concepts and not just the words Probably pass with up to a B- 3) Apply what you have learned to a new situation you have never seen before thus proving that you have understood the concept and not just learned how to describe it. B to A 4) Synthesize a new application yourself or extend what you have learned to a new situation of your own design A If you can: then you will:

5. 5 Physics

6. 6 Hydrogen atom Schrodinger equation: Probability of finding an electron at a given position Chemical Physics

7. 7 http://www.wou.edu/las/physci/ch336/lecture/lect10.htm Chemistry

8. 8 ΔG o = - RTln(K eq ) ΔG = ΔG o + RTln(Q) Predicting the amount of energy released in a chemical reaction Biology [products] [reactants] Q =

9. 9 Chemistry and Math for this course basic atomic structure and bonding ions salts moles molecular weight stoichiometry chemical equilibria, equilibrium constants pH etc.? and: exponents logarithms algebra no calculus

10. 10 Characteristics of living things 1) Structure = complex 2) Metabolism = chemical interaction with the environment 3) Reproduction = duplication of the complex, metabolizing structure

11. 11 Artificial rubber plant vs. a real one: 1. complexity Artificial: polypropylene polyester 5 dye molecules_____ 7 different distinguishable molecules Real: 20,000 different distinguishable molecules And each one is doing a job.

12. 12 Characteristics of living things 1) Structure = complex 2) Metabolism = chemical interaction with the environment 3) Reproduction = duplication of the complex, metabolizing structure

13. 13 CO 2 H2OH2O O2O2 Artificial Real 2. Chemical interaction with the environment NO 3 - dust

14. 14 Characteristics of living things 1) Structure = complex 2) Metabolism = chemical interaction with the environment 3) Reproduction = duplication of the complex, metabolizing structure

15. 15 3. Reproduction Cannot reproduce itself Can reproduce itself

16. 16 Darwin’s finches 1. Focusing on differences to learn about nature Consider 2 approaches to studying biology:

17. 17 Common denominator? 2. Focusing on similarities to learn about nature Reductionism

18. 18 Chemistry analogy: basic building block is the molecule Corn syrup sweet Take smaller bits a molecule + Not glucose not sweet (lost it) 2 different molecules

19. 19 ? ? ?

20. 20 Cell Theory All living things are made up of cells (or their by-products), and all cells come from other cells by growth and development.

21. 21 membonly OutsideInside ‘ ‘

22. 22 Mem+nuc

23. 23 Mem+nuc+org Organelles “mitochondria” “lysosomes” “ribosomes” etc. Organelles with membranes Organelles without membranes

24. 24 A cell 10 microns

25. 25 Sizes Skin cell ~ 10 micrometers (microns, um) in diameter –Millimeter (mm) = 1/1000 of a meter: e.g., head of a pin –Micron = 10 -6 meters (1 millionth of a meter, 1/1000 of a millimeter): e.g., cells –Nanometer (nm) = 10 -9 meters (1 billionth of a meter, 1/1000 of a micron): e.g., diameter of molecules –Angstrom (A) = 1/10 of a nanometer: e.g, distance between 2 atoms in a molecule Smallest cells ~ 1 micron in diameter (so volume = ~1/1000 of skin cell)

26. 26 bactcell0 A bacterial cell A bacterium

27. 27 bactcell1 No. of cells in the whole organism = ~ 1 (unicellular) Prokaryote, prokaryotic No nucleus (DNA is in the cytoplasm) No membrane-bound organelles

28. 28 Prokaryotes: (mostly bacteria) Pneumococcus (pathogen) Rhizobium (nitrogen fixation) Escherichia coli (lab) Eukaryotes: Amoeba (pond) Paramecium (pond) Plasmodium (malaria) Yeast (beer, wine, bread, lab) Prokaryotes: Very few examples Eukaryotes: Human being Worm (C. elegans) Fruit fly (Drosophila) Zebra fish Mustard plant (Arabidopsis) Mouse (these are all popular research organisms) Unicellular Multicellular

29. 29 binfission  ---------------------------------------------------- One hour --------------------------------------------  1 2 One net bacterial cell in 1 hour (in minimal medium) Escherichia coli E. coli

30. 30 ~10,000,000 molecules in 1 E. coli cell ~5000 types of molecules ~20,000,000 molecules in 2 cells Net increase = 10,000,000 organic molecules, synthesized in one hour What are these molecules and whence do they come? The newly synthesized stuff must come from the stuff that’s in the medium... ~5000 types of molecules

31. 31 C 6 H 12 O 6 glucose, a sugar KH 2 PO 4 MgSO 4 NH 4 Cl ammonium chloride H 2 O water +trace elements (e.g., Zn, Fe, Cu, Se, … ) potassium phosphate magnesium sulfate A minimal medium for E. coli

32. 32 C 6 H 12 O 6 glucose, a sugar KH 2 PO 4 MgSO 4 NH 4 Cl ammonium choride H 2 O water +trace elements (e.g., Zn, Fe, Cu, Se, … ) potassium phosphate magnesium sulfate A minimal medium for E. coli MM with glucose

33. 33 ~10,000,000 molecules in 1 cell ~5000 types of molecules ~20,000,000 molecules in 2 cells Net increase = 10,000,000 organic molecules, synthesized in one hour What are they and from whence do they come? “You can make an E. coli cell from glucose (OK, and salts) in one hour” ~5000 types of molecules Net synthesis of an E. coli cell

34. 34 Preview 1. What is an E. coli cell? –Polysaccharides, –Lipids, –Nucleic Acids, –Proteins, –Small molecules 2. How do we get those chemicals (in minimal medium)? -- From glucose, -- via biosynthetic chemical reactions (= metabolism). 3. Where does the energy for this process come from? -- From glucose, via energy metabolism. 4. Where does E. coli get the information for doing all this? -- it's hard-wired in its DNA. Organic chemicals Large molecules Small molecules

35. 35

36. 36 1cell Exponential growth

37. 37 So, starting with one cell, after 1 generation, get 2 cells, after 2 gens., 4 cells, after 3 gens, 8 cells, etc. Looks like 2 is a key number: 2 1 =2, 2 2 = 4, 2 3 = 8, … and so in general, N = 1 x 2 g And if we start with 100 cells, then have 200, 400, 800, etc, so N = 100 x 2 g : Or in general: N = N o x 2 g And to express growth in terms of real time: g = t/t D where t D = the doubling time, or generation time. So the number of cells as a function of time is : N = N o 2 t/t D Or: if we let k= 1/t D, then N = N o 2 kt But 2 is not a common base, so we can also write: N = N o 10 k’t, but here k’ = log(2)/t D rather than 1/t D (“log” = log base 10) Or we can use the natural log, e: N = N o e k”t where k” = ln(2)/t D And if we take the log of both sides, we get (base 10 case): log(N/N o ) = k’t (k’ = log(2)/t D = 0.3/t D ) and ln(N/N o ) = k”t (k” = ln(2)/t D = 0.69/t D ) See exponential growth handout

38. 38 Growth: linear N = No10 kt

39. 39 Growth: semilog A semi-log plot N=N o 10 kt N/No = 10 kt log(N/No) = kt Note: just used k here not k’, k defined in context in general logN 8 7 6 5 4 3 2 1 0 N log(N/No) = kt

40. Got this far

41. 41 Growth phases Real life (linear on a semi-log plot)

42. 42 Use calculus if you know it, it’s more natural: dN/dt = kN Separating variables: dN/N = kdt Integrating between time zero when N = No and time t, when N = N,  dN/N =  kdt, we get: lnN - ln N o = kt - 0, or ln(N/N o ) = kt, or N = N o e kt, which is exactly what we derived above. But is this k the same k as before? We can now calculate this constant k by considering the case of the time interval over which N o has exactly doubled; in that case: N/N o = 2 and t = t D, so: N = N o e kt  2 = e kt D To solve for k, take the natural logarithm of both sides: ln2=kt D, or k=ln2/t D, so the constant comes out exactly as before as well. See exponential growth handout

43. 43 water E. coli molecule #1 H2OH2O HOH O H H 105 o Our first “functional group”: hydroxyl, -OH Covalent bond (strength = ~100 kcal/mole)

44. 44 Waterdeltas δ+ = partial charge, not quantified Not “ + ”, a full unit charge, as in the formation of ions by NaCl in solution: NaCl  Na+ + Cl - Water is a POLAR molecule (partial charge separation) Negative pole Positive pole

45. 45 waterHbonds

46. 46 waterHbonds Hydrogen bond “H-bond” (strength = ~ 3 kcal/mole )

47. 47 Ethanol and Water 3 2 3 2 hydroxyl group again

48. 48 R= any group of atoms amide3 R-CONH 2 is an “amide”, -CONH 2 is an amide group (another functional group - the whole –CONH 2 together) O is more electronegative than C

49. 49 an amide ethanol, an alcohol Hydrogen bonds between 2 organic molecules Water often out-competes this interaction (but not always)

50. 50 The chemical structures of the functional groups used in this course must be memorized. See the Functional Groups handout. This is one of very few memorizations required. “carboxyl” Me You O || -C -- OH