1. Water is a Polar Molecule
Hydrogen Bond
Figure 2.1
Space-filling structure of a water molecule. (b) Angle between the covalent bonds of a water molecule. Two of the sp3 hybrid orbitals of the oxygen atom participate in covalent bonds with s orbitals of hydrogen atoms. The other two orbitals are occupied by lone pairs of electrons.
H2Te: -2.2oC (28oF) H2Se: -41.2oC (-42.2oF) H2S: -60oC (-76oF) H2O: +100oC (212oF)
Figure 2.1

2. Hydrogen bonds also form between other polar bonds
Figure 2.4

3. Ionic and polar substances dissolve in water
Example: Dissolution of sodium chloride in water
Figure 2.3
Figure 2.6
Dissolution of sodium chloride (NaCl) in water. (a) The ions of crystalline sodium chloride are held together by electrostatic forces. (a) Water weakens the interactions between the positive and negative ions, and the crystal dissolves. Each dissolved Na+ and Cl– is surrounded by a solvation sphere. Only one layer of solvent molecules is shown. Interactions between ions and water molecules are indicated by dashed lines.
Water encapsulates dissolved
Ions.

4. An electrostatic interaction formed between charged residues in a protein.

5. Molecules can form hydrogen bonds with each other or water
Dynamic equilibrium
Relatively weak electrostatic interactions
Protein secondary structures
Glucose contains five hydroxyl groups and a ring oxygen, each of which can form hydrogen bonds with water.

6. Hydrogen bonding between bases in DNA Figure 2.8
Hydrogen bonding between the complementary bases guanine and cytosine in DNA.

7. Van der Waals forces are weak noncovalent interactions between any two atoms
Figure 2.12
Effect of internuclear separation on van der Waals forces. Van der Waals forces are strongly repulsive at short internuclear distances and very weak at long internuclear distances. When two atoms are separated by the sum of their van der Waals radii, the van der Waals attraction is maximal.
Figure 2.6

8. The HYDROPHOBIC EFFECT
Why do water and canola oil (or any hydrophobic material)
spontaneously separate when first mixed?
Figure 2.9-Entropy increases when nonpolar molecules aggregate.
WHY????

9. The HYDROPHOBIC EFFECT
The hydrophobic effect drives the formation of micelles from amphipathic molecules
Sodium dodecyl sulfate (SDS), a synthetic detergent.
Amphipathic molecules, such
As detergents, have a polar and
A nonpolar end.
Water

10. The HYDROPHOBIC EFFECT
- The formation of plasma membranes
Phosphate group
Figures 1.4
and 1.9

11. The HYDROPHOBIC EFFECT
Figure 2.10 Protein folding into the 3D structure
Hydrophobic groups aggregate while “squeezing” H2O
out of interior of protein.

12. Water has a slight tendency to ionize

13. How do we determine the amount of ions present in water?
What is the concentration of H2O?
1 liter of water = 1000g and 1 mol of water = 18 g
Therefore,
[H2O] = 55.5 mol/L or 55.5 M
Keq = 1.8 x M at 25oC
1.8 x M (55.5 M) = 1.0 x M2 = [H+][OH-]
Kw = 1.0 x M2
Since water is electrically neutral, [H+] = [OH-]
Kw = 1.0 x M2 = [H+]2 or [H+] = 1.0 x 10-7 M

15. Strong acids completely dissociate in water.
Example: Hydrochloric acid (HCl)

16. Weak acids dissociate in water with a characteristic acid dissociation constant (Ka).
Example: Acetic acid, present in vinegar

17. The relationship between pH and pKa
Henderson-Hasselbalch equation

18. Titration of acetic acid with aqueous base (OH-) Figure 2.12
The buffering region
is +/- 1 pH unit from
the pKa
Figure 2.16
Titration of acetic acid (CH3COOH) with aqueous base (OH–). There is an inflection point (a point of minimum slope) at the midpoint of the titration, when 0.5 equivalent of base has been added to the solution of acetic acid. This is the point at which [CH3COOH] = [CH3C00–] and pH = pKa. The pKa of acetic acid is thus 4.8. At the endpoint, all the molecules of acetic acid have been titrated to the conjugate base, acetate.

19. Figure 2.11 Variety of conjugate acid-base pair important
in biochemistry
H2CO3 – in blood chemistry the pKa = 6.1

20. Titration of a polyprotic acid (phosphoric acid) w/ aqueous base.
Figure 2.18
Titration curve for phosphoric acid H3PO4. Three inflection points (at 0.5, 1.5, and 2.5 equivalents of strong base added) correspond to the three pKa values for phosphoric acid (2.2, 7.2, and 12.7).

21. Calculations involving the Henderson-Hasselbalch equation
1. Pick a conjugate acid-base pair in Figure Calculate the pKa using the Ka.
2. What is the weak acid in the reaction and what is the conjugate base of that acid?
3. What is the pH of a solution containing equal amounts of the acid and base?
4. What is the pH of a solution containing 10 times more acid than base?
5. What is the ratio of base to acid at pH = 7?
6. Draw a titration curve for the addition of base (OH-) added to a solution of acid.
7. In what pH range is the conjugate acid-base pair an effective buffer?
8. What is the pH of a solution containing 10 times more weak acid than conjugate base?

22. Maintenance of Blood pH in Humans
pKa = 6.1

23. Regulation of blood pH in mammals
Figure 2.20
Regulation of the pH of blood in mammals. The pH of blood is controlled by the ratio of [HCO3–] to pCO2 in the air spaces of the lungs. When the pH of blood decreases due to excess HM, pCO2 increases in the lungs, restoring the equilibrium. When the concentration of HCO3– rises because the pH of blood increases, CO2 (gaseous) dissolves in the blood, again restoring the equilibrium.

24. Role of the lungs and kidneys in regulation of physiological pH
Respiratory Lungs
Metabolic Kidneys
Problems occur when pH drops (acidosis) or if pH increases (alkalosis).
Acidosis (decrease pH of blood):
Lungs: control supply of H2CO3 in the blood by the amount
of CO2 exhaled.
When blood level HCO3- decreases the pH drops, the
breathing rate must increase which increases CO2 expelled.
Respiratory acidosis-if too much CO2 is retained
in the blood.
Kidneys: Control [HCO3-] by excrete more acidic urine.
if [HCO3-] is too low Metabolic acidosis
Causes: hypoventilation, emphysema, congestive heart failure, kidney
failure, too much acidic drugs (aspirin) are taken.

25. Causes: hyperventilation, kidney disease, high fevers
Alkalosis (increase pH of blood):
Lungs: control supply of H2CO3 in the blood by the amount
of CO2 exhaled.
When blood level HCO3- increase, the breathing rate
must decrease which increases CO2(aqueous).
Respiratory alkalosis- to little CO2 (H2CO3) in blood)
Kidneys: Control [HCO3-] by excrete less acidic urine.
if [HCO3-] is too high Metabolic alkalosis
Causes: hyperventilation, kidney disease, high fevers

26. Blood Concentrations
Ratio of HCO3- : H2CO3 = 20 : 1  This results in pH = 7.4
(pKa = 6.1 at metabolic temperatures)
HCO3- = mM
H2CO3 = mM
Clinicians often monitor blood pH, HCO3- and CO2 concentrations.

27. Assignment Read Chapter 2 Read Chapter 3 Topics not covered:
Making Buffers in the Lab – Page 30