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BTW: Turn on the recorder

BTW: Turn on the recorder. Note to myself for Lec. 1: Web site is required reading (at least twice a week) Problem book Problem book Web lectures Email questions, Q&A database, office hours Evening vs. morning lectures Recitation sign-up

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BTW: Turn on the recorder

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  1. BTW: Turn on the recorder

  2. Note to myself for Lec. 1: Web site is required reading (at least twice a week) Problem book 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

  3. What is expected of you as a student If you can: then you will:

  4. Physics

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

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

  7. ΔG = ΔGo + RTln(Q) ΔGo = - RTln(Keq) Biology Predicting the amount of energy released in a chemical reaction [products] Q = [reactants]

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

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

  10. 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.

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

  12. dust 2. Chemical interaction with the environment CO2 O2 NO3- H2O Real Artificial

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

  14. 3. Reproduction Can reproduce itself Cannot reproduce itself

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

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

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

  18. ? ? ?

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

  20. membonly ‘ ‘ Outside Inside

  21. Mem+nuc

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

  23. A cell 10 microns

  24. Skin cell ~ 10 micrometers (microns, um) in diameter Millimeter (mm) = 1/1000 of a meter: e.g., head of a pin Micron = 10-6meters (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) Sizes

  25. bactcell0 A bacterial cell A bacterium

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

  27. 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

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

  29. ~20,000,000 molecules in 2 cells ~10,000,000 molecules in 1 E. coli cell ~5000 types of molecules types of molecules ~5000 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 . . .

  30. A minimal medium for E. coli C6H12O6 glucose, a sugar KH2PO4 MgSO4  NH4Cl ammonium chloride H2Owater +trace elements (e.g., Zn, Fe, Cu, Se, … ) potassium phosphate magnesium sulfate

  31. MM with glucose A minimal medium for E. coli C6H12O6 glucose, a sugar KH2PO4 MgSO4  NH4Cl ammonium choride H2Owater +trace elements (e.g., Zn, Fe, Cu, Se, … ) potassiumphosphate magnesium sulfate

  32. Net synthesis of an E. coli cell ~20,000,000 molecules in 2 cells ~10,000,000 molecules in 1 cell ~5000 types of molecules types of molecules ~5000 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”

  33. 1. Whatis 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. Preview Large molecules Organic chemicals Small molecules

  34. 1cell Exponential growth

  35. 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: 21=2, 22 = 4, 23 = 8, … and so in general, N = 1 x 2g And if we start with 100 cells, then have 200, 400, 800, etc, so N = 100 x 2g : Or in general: N = No x 2gAnd to express growth in terms of real time: g = t/tDwheretD= the doubling time, or generationtime. So the number of cells as a function of time is : N =No2t/tD Or:if we let k= 1/tD,thenN =No2kt But 2 is not a common base, so we can also write: N = No10k’t, but here k’ = log(2)/tD rather than 1/tD(“log” = log base 10) Or we can use the natural log, e: N = Noek”t where k” = ln(2)/tD And if we take the log of both sides, we get (base 10 case): log(N/No) = k’t (k’ = log(2)/tD = 0.3/tD) and ln(N/No) = k”t (k” = ln(2)/tD = 0.69/tD) See exponential growth handout

  36. Growth: linear N = No10kt

  37. Growth: semilog A semi-log plot N logN 8 7 6 5 4 3 2 1 0 log(N/No) = kt N=No10ktN/No = 10ktlog(N/No) = kt Note: just used k here not k’, k defined in context in general

  38. Got this far

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

  40. 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 No = kt - 0, or ln(N/No) = kt, or N = Noekt, 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 No has exactly doubled; in that case: N/No = 2 and t = tD, so: N = Noekt 2 = ektD To solve for k, take the natural logarithm of both sides: ln2=ktD, or k=ln2/tD, so the constant comes out exactly as before as well. See exponential growth handout

  41. Our first “functional group”: hydroxyl, -OH H O H Covalent bond (strength = ~100 kcal/mole) E. coli molecule #1 water H2O HOH 105o

  42. Waterdeltas Negative pole Positive pole 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)

  43. waterHbonds

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

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

  46. amide3 O is more electronegative than C R= any group of atoms R-CONH2 is an “amide”, -CONH2 is an amide group (another functional group - the whole –CONH2 together)

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

  48. 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. O || -C -- OH “carboxyl” Me You

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