1. Associations of amphipathic molecules in aqueous solutions.

3. Ionic Mobilities in H 2 O at 25°C.

5. Mean lifetime of a hydronium ion is 10 -12 s This makes proton transfer reactions (acid base reactions) among the fastest in aqueous solutions.

6. Acid Base Chemistry HA + H 2 OH 3 O + + A - Conjugate acid Conjugate base K = [H 3 O + ][A - ] [HA][H 2 O] K = dissociation constant is a measure of the strength of an acid [H 2 O] = 55.5M K a = K[H 2 O] = [H + ][A - ] [HA] [H 3 O + ] = [H + ]

7. Water as an acid H2OH2OH + + OH - Conjugate acid Conjugate base K = [H + ][OH - ] [H 2 O] Pure water contains equimolar hydroxide ions and protons At 25ºC K w = 10 -14 M 2 [H + ] = [OH - ] = 10 -7 M [H 2 O] = 55.5M K w = K[H 2 O] =[H + ][OH - ]

8. Henderson Hasselbach and pH -log[H + ] pH = [H + ] =K a ([HA]/A - ]) pH =-log K a + log ([A - ]/[HA]) pH =pK a + log ([A - ]/[HA])

12. Titration curve of a 1L solution of 1M H 3 PO 4.

13. Thermodynamics First Law Energy is conserved ∆U = U final - U initial = q - w q = heat absorbed w = work done ∆U = 0 for any process that returns to its initial state Exothermic processes release heat Endothermic processes gain heat

14. H = U + PV Enthalpy is defined as: P = pressure (constant) ∆V = volume (insignificant) ∆H = ∆U + P∆V ∆H = ∆U = q - w ∆H = q w often is zero in biological systems q = heat transferred to/from the surroundings

15. Thermodynamics Second Law Entropy increases ∆S universe > 0

16. Two bulbs of equal volumes connected by a stopcock. N molecules of gas 2 N equally probable ways of distributing them

17. W L = N! L!(N-L)! W L = number of different ways of placing L of the N molecules in the left bulb For any N the most probable state is L = N/2 (half the gas in the left bulb) Probability = W L /2 N If N = 10 23 the probability that the # of molecules in the left and right bulbs differ by 1 molecule is 10 billion in 10 -434

18. Page 54 9 positions, 4 identical balls W = 987654321 = 126 (4321)(54321) Only 4 out of 126 possible arrangements have 4 balls touching each other W L = N! L!(N-L)! W L = number of different ways of placing L of the N molecules in the left bulb

19. S = k B ln W In a system where energy does not change a spontaneous process has ∆S > 0 W L = N! L!(N-L)! W is approximately 10 7x10 22 if the previous experiment uses a mole of real gas To make this more manageable entropy was “invented”

20. This does not mean that order cannot exist In a localized system. It means that order can only exist at the expense of surrounding systems. Biology gains order by disordering the nutrients that it consumes. ∆S system + ∆S surroundings = ∆S universe > 0

21. Free Energy G = H - TS ∆G = ∆H - T∆S ∆G ≤ 0 for a spontaneous process

22. Exergonic∆G < 0Spontaneous Endergonic∆G > 0Must input energy

23. Variation of Reaction Spontaneity (Sign of ∆G) with the signs of ∆H and ∆S.

24. How do we drive endergonic processes?

26. Greek lettering scheme used to identify the atoms in the glutamyl and lysyl R groups.

27. An  -amino acid

29. Glycine - The Simplest  -Amino Acid Fischer Projection    Preferred representation 

30. L-  -alanine or (-)-  -alanine (S)-  -alanine S = counterclockwise Alanine CC    

31.  -valine L-(-)-  -valine S-  -valine     Valine CC  

32.       -leucine L-  -leucine (-) -  -leucine S-  -leucine Leucine   CC

33. Isoleucine 2 chiral centers (2S,3S)-isoleucine       

34. Both centers are S CC CC

35. Methionine is non-polar but S-atom is reactive      -methionine L-methionine (-)-  -methionine S-methionine 

36. Methionine is non-polar but S-atom is reactive  -methionine L-methionine (-)-  -methionine S-methionine CC 

37. Proline is a cyclic imino acid  -proline L-proline (-)-  -proline S-proline     CC    2 + 2 + 2 + 2 +

39. Large non-polar aromatic  -phenylalanine L-phenylalanine (-)-  -phenylalanine S-phenylalanine         

40. Large and non-polar  -phenylalanine L-phenylalanine (-)-  -phenylalanine S-phenylalanine CC 

41. Large and non-polar             -tryptophan L-tryptophan (-)-  -tryptophan S-tryptophan 

42. Large and non-polar  -tryptophan L-tryptophan (-)-  -tryptophan S-tryptophan CC 

43. Uncharged Polar Amino Acids  -tyrosine L-tyrosine (-)-  -tyrosine S-tyrosine           +

44. Uncharged Polar Amino Acids  -tyrosine L-tyrosine (-)-  -tyrosine S-tyrosine CC 

46. Uncharged Polar Amino Acids   -serine L-serine (-)-  -serine S-serine  CC   +

47. Uncharged Polar Amino Acids - cysteine is often charged   -cysteine L-cysteine (-)-  -cysteine R-cysteine   CC   +

48. Uncharged Polar Amino Acids    -asparagine L-asparagine (-)-  -asparagine S-asparagine    CC   +

49. Uncharged Polar Amino Acids   -glutamine L-glutamine (-)-  -glutamine S-glutamine    CC   +

50. Threonine has 2 chiral centers (2S,3R)-threonine      

51. CC CC

53. Charged amino acids        -arginine L-arginine (-)-  -arginine S-arginine CC +  

54. Charged amino acids      -lysine L-lysine (-)-  -lysine S-lysine CC   +

55. Charged amino acids     -histidine L-histidine (-)-  -histidine S-histidine     CC   +

57. Charged amino acids    -glutamate L-glutamate (-)-  -glutamate S-glutamate    CC   +

58. Charged amino acids     -aspartate L-aspartate (-)-  -aspartate S-aspartate   CC   +

59. AlanineAlaA CysteineCysC GlycineGlyG HistidineHisH IsoleucineIleI LeucineLeuL MethionineMetM ProlineProP SerineSerS ThreonineThrT ValineValV ArginineArgR AsparagineAsnN AspartateAspD GlutamateGluE GlutamineGlnQ LysineLysK PhenylalaninePheF TryptophanTrpW TyrosineTyrY

60. Non-standard encoded amino acids Selenocysteine Sec, U Pyrrolysine Pyl, O   + +

61. Amino acids bear structural similarity to each other                   Asparate Asparagine Glutamate Glutamine + + + +

62. Amino acids bear structural similarity to each other Cysteine Selenocysteine Serine         Threonine + + + 

63. Amino acids bear structural similarity to each other Tyrosine Phenylalanine                  +

64. Amino acids bear structural similarity to each other Histidine Asparagine Glutamine Arginine Histidine Arginine

65. Amino acids bear structural similarity to each other Histidine Tryptophan

66. Amino acids bear structural similarity to each other Phenylalanine Tyrosine Phenylalanine Leucine

67. Glutamate, glycine –neurotransmitters D-serine –neurotransmitter S-adenosylmethionine –methyl transfer

68. Page 77 Non-peptide amino acids

69. Titration curve of glycine.

73. These values are the pKa’s of the free amino acids in aqueous solution. As we shall see later an aqueous solution may not represent reality

74. Hydrophobic pocket