Adopted from Nilsen and cox – Lehninger principles of biochemistry (sixth edition)

1. Chapter 2 : Water “I believe that as the methods of structural chemistry are further applied to physiological problems, it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature.” –Linus Pauling, The Nature of the Chemical Bond, 1939 Adopted from Nilsen and cox – Lehninger principles of biochemistry (sixth edition)

2. Learning Objectives • What kind of interactions occur between different type of molecules in water. • Why water is a good medium for life • Why nonpolar moieties aggregate in water • How dissolved molecules alter properties of water • How weak acids and bases behave in water: to be able to solve weak acid problems with the Henderson-Hasslebalch equation. • How buffers work and why we need them • How water participates in biochemical reactions

4. Structure

5. ice Hydrogen bonding in ice. In ice, each water molecule forms four hydrogen bonds, the maximum possible for a water molecule, creating a regular crystal lattice. By contrast, in liquid water at room temperature and atmospheric pressure, each water molecule hydrogen-bonds with an average of 3.4 other water molecules. This crystal lattice structure makes ice less dense than liquid water, and thus ice floats on liquid water.

6. Common H-bonds in Biological system The hydrogen acceptor is usually oxygen or nitrogen; The hydrogen donor is another electronegative atom.

7. Some Biologically Important H-bonds

8. H-bond Strength and Alignment

9. Importance of Hydrogen Bonds • Source of unique properties of water • Structure and function of proteins • Structure and function of DNA • Structure and function of polysaccharides • Binding of substrates to enzymes • Binding of hormones to receptors • Matching of mRNA and tRNA

10. Water as a Solvent • Water is a good solvent for charged and polar substances • amino acids and peptides • small alcohols • carbohydrates • Water is a poor solvent for nonpolar substances • nonpolar gases • aromatic moieties • aliphatic chains

12. Solvation and Hydration Spheres

14. Flickering Clusters and Clathrate Cages

15. The Hydrophobic Effect • Refers to the association or folding of nonpolar molecules in the aqueous solution • Is one of the main factors behind: • protein folding • protein-protein association • formation of lipid micelles • binding of steroid hormones to their receptors • Does not arise because of some attractive direct force between two nonpolar molecules

17. Substrates Must Displace Water to Bind Enzymes 

18. Approximate Bond Strength, kJ/mole 12-30 20 <40 0.4 – 4.0 Distance,nm 0.3 0.25 - 0.2

19. Water Bound to Hemoglobin Hb purified from water Hb with Water Removed

20. Water Bound in a Protein Channel (Cytochrome f) Facilitates Proton Hopping – see later in Photosynthesis

22. Osmotic Pressure

23. Cell Response to Osmotic Pressures

24. Proton Hop and Hydronium

25. Plants Use Osmotic Pressure

26. Plants Use Osmotic Pressure Protection Against Wind

27. Ionization of Water Keq = [H+][OH-] / [H2O] = 1.8 x 10-16 M Concentration of water - one liter = 1,000g Mole Wt Water = 18.015 [H2O] = 55.5 M Kw = [H+][OH-] = Keq x [H2O] = 1 x 10-14 M2 for pure water [H+] = [OH-] so, [H+] = 10-7 M pH is negative log [H+] , for pure water = 7.0

30. Weak Acids HA ↔ H+ + A- K e = [H+][A-] / [HA] = Ka Henderson-Hasselbalch Equation Rearranges Ka pH = pKa + log ( [A-] / [HA] ) when pKa = pH … [A-] = [HA]

32. A

33. The titration curve of acetic acid.

34. Weak acids have different pKas

35. Ionization of histidine. The amino acid histidine, a component of proteins, is a weak acid. The pKa of the protonated nitrogen of the side chain is 6.0.

36. Enzymes have pH optima Related to their Function

38. Water as a Reactant

39. Problem 18 in Chapter 2 1 liter of 0.1 M glycine. a. What pH is glycine a good buffer due to its amino group: NH3+ Glycine = CH2-COO- pKa’s = 2.34 and 9.6 So it would be good +/- 1.0 from each pKa which would be from 1.3 to 3.3 and 8.6 to 10.6 for the amino group.

40. Problem 18 in Chapter 2 NH3+ Glycine = CH2-COO- pKa’s = 2.34 and 9.6 • I liter of 0.1 M glycine. • b. in a 0.1 M solution, pH 9.0 what fraction has the amino group as –NH3+ ? • Example of a Clicker Question: R-NH3+ is • HA • A- • H2O • H+ • OH-

41. Problem 18 in Chapter 2 NH3+ Glycine = CH2-COO- pKa’s = 2.34 and 9.6 I liter of 0.1 M glycine. b. in a 0.1 M solution, pH 9.0 what fraction has the amino group as –NH3+? pH = pKa + log A/HA 9.0 = 9.6 + log A/HA log A/HA = -0.6  A/HA = 0.25  0.25HA = A HA + A = 0.1M so HA + 0.25HA = 0.1 M :: 1.25HA = 0.1M so HA = 0.08 M…and that is 80% of 0.1M so  not asked: A = 0.02 M or 20%

42. Problem 18 in Chapter 2 NH3+ Glycine = CH2-COO- pKa’s = 2.34 and 9.6 I liter of 0.1 M glycine. c. How much 5M KOH is needed to change pH from 9 to 10 for 1 Liter of 0.1M glycine? pH = pKa + log A/HA 10 = 9.6 + log A/HA so: log A/HA = 0.4 thus A/HA = 2.5  2.5HA = A HA + A = 0.1 M  HA + 2.5 HA = 0.1 M  3.5HA= 0.1M so HA at pH 10 = 0.029 moles/L from pH 9 HA is converted to A by adding OH-, that is HA is lowered from 0.08M to 0.029M or a change of 0.051 moles 0.051 moles/5 moles/L = 0.01 L  10 ml of 5M KOH

43. Problem 18 in Chapter 2 NH3+ Glycine = CH2-COO- pKa’s = 2.34 and 9.6 I liter of 0.1 M glycine. d. When 99% of glycine is in its –NH3+ form, what is the pH of solution due to it’s amino group? (functionally reworded from the text) pH = pKa + log A/HA so this is easy HA dominates, so it will be on the acid side of the pKa. A is only 1% or 0.01 so the log of A/HA ≈ -2 thus pH = 9.6 – 2 = or 7.6

44. Things to Know • General Chemical Properties of Water. • pH definition and what it means + how to calculate it. • Strong vs Weak Acids. • Henderson-Hasselbalch Equation and how to do calculations with it. • Weak bonds and their relative bond strength.

45. For more updates regulary.