1

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

3

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

5 Predicting the effect of temperature on reaction rates (Arrhenius equation). k=A*e (-Ea/R*T) Δ Go = - RTln(Keq) Δ G = Δ Go + RTln(Q) Predicting the amount of energy released in a chemical reaction Chemistry Biology

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

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

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

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

10 Reproduction Cannot reproduce itself Can reproduce itself

11 Darwin’s finches Focusing on differences to learn about nature

12 Common denominator? Focusing on similarities to learn about nature

13 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

14

15

16

17

18

19

20

21

22

23

24

25

26 Alive?

27

28 Cell theory end

29 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.

30 membonly OutsideInside

31 Mem+nuc Organelles without membranes

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

33 A cell 10 microns

34 Sizes Skin cell ~ 10 micrometers (microns, um) in diameter –Millimeter (mm) = 1/1000 of a meter: e.g., head of a pin –Micron = meters (1 millionth of a meter, 1/1000 of a millimeter): e.g., cells –Nanometer (nm) = 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)

35 bactcell0 A bacterial cell A bacterium

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

37 Prokaryotes: (mostly bacteria) Pneumococcus (pathogen) Rhizobium (nitrogen fixation) Escherichia coli (lab) Eukaryotes: Amoeba (pond) Paramecium (pond) Plasmodium (malaria) Yeast (beer, 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

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

39 ~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? ~5000 types of molecules

40 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

41 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

42 ~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 in one hour” ~5000 types of molecules Net synthesis of an E. coli cell

43 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

44 gu

45 1cell Exponential growth

46 1cellbigger

47 2cells

48 2cellsbigg er

49 4cells

50 1 generation

51 2 generation

52 So, starting with one cell, after 1 generation, get 2 cells, after 2 gens., 4 cells, after 3 gens, 8 cells, etc. 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

53 Growth: linear

54 Growth: semilog A semi-log plot N=N o 10 kt N/No = 10 kt log(N/No) = kt Note: just k used here not k’, k defined in context logN N

55 Growth phases Real life

56 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: 2 = e kt D. Taking the natural logarithm of both sides: ln2=kt D, or k=ln2/t D, so the constant comes out exactly as before as well.

57 water E. Coli molecule #1 H2OH2O HOH O H H 105 o Our first “functional group”: hydroxyl, -OH

58 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

59 waterHbonds

60 waterHbonds Hydrogen bond

61 Ethanol and Water

62 R= any group of atoms amide3 R-CONH 2 is an “amide”, -CONH 2 is an amide group (another functional group - the whole –CONH2 together) O is more electronegative than C

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

64 The functional groups used in this course must be memorized. See the Functional Groups handout. This is one of very few memorizations required.