CHEMICAL BONDS, INTERMOLECULAR FORCES, PROPERTIES OF WATER, BUFFER SOLUTIONS

1. BASIC CELL BIOLOGY I CHEMISTRY of LIFE CHEMICAL BONDS, INTERMOLECULAR FORCES, PROPERTIES OF WATER, BUFFER SOLUTIONS

2. Lecture 3 CHEMICAL BONDS, INTERMOLECULAR FORCES, PROPERTIES OF WATER, BUFFER SOLUTIONS • Covalent bond • Van der Waals forces • Hydrophobic interactions • Hydrogen bond • Biologically important properties of water • pH, acids and bases • Buffer solutions

3. Lecture 3 Chemical bond In forming chemical bonds, atoms donate, acquire, or share electrons.

4. Lecture 3 Chemical bond : ionic bond The electron from the outer shell of sodium atom is transferred to the outer shell of the chlorine atom. The number of the electrons which can be donated or accepted determine the valence of the atom. Sodium and chlorine are monovalent atoms.

5. Lecture 3 Chemical bond : ionic bond Not only the atoms, also functional groups can be ionised through donation or acceptance of the proton.

6. Lecture 3 Chemical bond : ionic bond Ionic bond participates in the formation of the secondary structure of the proteins

7. Lecture 3 Chemical bond : covalent bond Sharing of the pair of electrons through formation of the common electron shells One common pair of the electrons Formation of the bond Structural formula Energy: ~80 kcal/mole

8. Lecture 3 Chemical bond : covalent bond Sharing of the pair of electrons through formation of the common electron shells Two common pairs of the electrons Formation of the bond Structural formula Energy: ~150 kcal/mole

9. Lecture 3 Chemical bond : covalent bond Sharing of the pair of electrons through formation of the common electron shells Three common pairs of the electrons Formation of the bond Structural formula Energy: ~200 kcal/mole

10. Lecture 3 Chemical bond : covalent bond Formation of the covalent bond between different atoms: carbon and hydrogen Formation of the bond Structural formula Spatial structural formula

11. Lecture 3 Chemical bond : covalent bond Formation of the covalent bond between different atoms: carbon and oxygen Formation of the bond Carbon atom forms four, oxygen atom forms two common pairs of electrons. Structural formula

12. Lecture 3 Chemical bond : covalent bond Formation of the covalent bond between different atoms: carbon and oxygen Formation of the bond Structural formula Nitrogen atom forms three, hydrogen atom forms one common pairs of electrons. Spatial structural formula

13. Lecture 3 Chemical bond : covalent bond Covalent bonds make the backbone of the organic molecules and ensure their stability

14. Lecture 3 Chemical bonds The valence of the atom at ionic bonding is determined by the number of donated or accepted electrons. The valance of the atom at covalent bonding is dertemined by the number of formed common electron pairs.

15. Lecture 3 Intermolecular forces Van der Waals forces The movement of the electrons in the molecule or atom creates instant non-uniformity of the charge distribution, the molecule or the atom gets polarised, instant dipole is formed.

16. Lecture 3 Intermolecular forces Van der Waals forces Instantly negative part of a molecule interacts with instantly positive part of another molecule or induces dipole in another electro-neutral molecule. Two dipoles are mutually stabilising. In macromolecules (polymers) the force of these electrostatic forces can reach considerable values. Van der Waals forces have essential role in the formation of the structure of biopolymers.

17. Lecture 3 Intermolecular forces Van der Waals forces Energy: 1 - 2 kcal/mole

18. Lecture 3 Intermolecular forces Hydrogen bond Polar molecules: unequal spatial distribution of the electrons Non-polar molecule: symmetrical spatial distribution of the electrons

19. Lecture 3 Intermolecular forces Hydrogen bond H2O Energy: 3 - 5 kcal/mole

20. Lecture 3 Intermolecular forces Hydrogen bond electrostatic interaction between partially electronegative atoms (O, N, P) of the polar molecules or functional groups within molecules and partially electropositive hydrogen atoms. H R O H N R H s+ s- R O H O R s+ s-

21. Lecture 3 Intermolecular forces Hydrogen bond within the structure of the biological macromolecules Complementary interactions of the base pairs in the nucleic acid structure

22. Lecture 3 Intermolecular forces Hydrogen bond within the structure of the biological macromolecules a-spiral of the proteins

23. Lecture 3 Intermolecular forces Hydrogen bond

24. Lecture 3 Biologically important properties of the water Surface tension

25. Lecture 3 Biologically important properties of the water Cohesion

26. Lecture 3 Biologically important properties of the water High heat capacity

27. Lecture 3 Biologically important properties of the water High heat capacity

28. Lecture 3 Biologically important properties of the water Cooling through evaporation

29. Lecture 3 Biologically important properties of the water Reduced density at freezing

30. Lecture 3 Biologically important properties of the water Reduced density at freezing

31. Lecture 3 Biologically important properties of the water Capability to dissolve polar compounds

32. Lecture 3 Biologically important properties of the water Capability to dissolve polar compounds Polar compounds are hydrophilic The concentration of the solutions is measured in moles per litre

33. Lecture 3 Biologically important properties of the water Repulsion of from the surfaces covered with non-polar compounds Non-polar compounds are hydrophobic

34. Lecture 3 Intermolecular forces Hydrophobic interactions Many molecules are water-insoluble (hydrocarbons, fats) or contain hydrophobic parts (several amino acids). Such molecules tend to aggregate in the water environment and to diminish the surface which is exposed to the water (oil drops in the water). Minimal surface are which is exposed towards the water support the energetically favourable conformation of the hydrophobic (water-insoluble) molecules.

35. Lecture 3 Intermolecular forces Hydrophobic interactions Micelle of the fatty acids Energy: 3 - 4 kcal/mole

36. Lecture 3 The dissociation of the water, pH H2O H+ + OH- The concentration of hyrogen (hydronium) and hydroxide ions is 10-7 M Only one out of 554 million water molecules is dissociated in pure water

37. Lecture 3 The dissociation of the water, pH H2O H+ + OH- The product of the hydrogen and hydroxide ion concentrations in solutions is constant In pure water [H+] · [OH-] = 10 -14 M2 pH = - log [H+] For pure water pH= -log10-7 = -(-7) = 7

38. Lecture 3 The dissociation of the water, pH pH values of different solutions

39. Lecture 3 The dissociation of the water, pH Acids and bases Acid Conjugated base Strong acids dissociate completely, week acids dissociate partially

40. Lecture 3 The dissociation of the water, pH Acids and bases Week acids dissociate only partially pK = the constant of dissociation, the smaller is pK, the stronger is the acid. pK numerically identical to pH at which half of the acid molecules are dissociated. For two and three-valent acids each step of dissociation has its own pK.

41. Lecture 3 The dissociation of the water, pH Acids and bases

42. Lecture 3 The dissociation of the water, pH Buffer solutions Solutions of a week acid and conjugated base which are capable to resist rush changes of pH upon addition of small amounts of strong acids or bases.

43. Lecture 3 The dissociation of the water, pH Buffer solutions Henderson – Haselbach equation:

44. Lecture 3 The dissociation of the water, pH Buffer solutions When small amount of a strong acid is added to the buffer solution:

45. Lecture 3 The dissociation of the water, pH If HCl to 0.01 M final concentrationis aded in water final pH will be 2. If HCl is aded to 0.01 M final concentrationin 0.05 M phosphate buffer solution at pH 7.2 final pH will be : pH = 7.2 + log 0.67 = 7.2 + (-0.174) = ~ 7.0

46. Lecture 3 The dissociation of the water, pH Buffer solutions When small amount of a strong base is added to the buffer solution:

47. Lecture 3 The dissociation of the water, pH Buffer solutions Buffer capacity of the solution is maximal within the interval of one pH unit around pK point.