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

Hydrogen bonds also form between other polar bonds Figure 2.4

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.

An electrostatic interaction formed between charged residues in a protein.

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.

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

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

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????

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

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

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

Water has a slight tendency to ionize  

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 10-16 M at 25oC 1.8 x 10-16 M (55.5 M) = 1.0 x 10-14 M2 = [H+][OH-] Kw = 1.0 x 10-14 M2 Since water is electrically neutral, [H+] = [OH-] Kw = 1.0 x 10-14 M2 = [H+]2 or [H+] = 1.0 x 10-7 M

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

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

The relationship between pH and pKa Henderson-Hasselbalch equation    

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.

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

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).

Calculations involving the Henderson-Hasselbalch equation 1. Pick a conjugate acid-base pair in Figure 2.11. 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?

Maintenance of Blood pH in Humans pKa = 6.1

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.

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.

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

Blood Concentrations Ratio of HCO3- : H2CO3 = 20 : 1  This results in pH = 7.4 (pKa = 6.1 at metabolic temperatures) HCO3- = 24 - 27 mM H2CO3 = 1.20 - 1.35 mM Clinicians often monitor blood pH, HCO3- and CO2 concentrations.

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