1. Proteins : The primary worker molecule in the body Transport- hemoglobin in blood Storage- ferritin in liver Immune response- antibodies Receptors- sense stimuli, e.g. in neurons Channels- control cell contents Structure- collagen in skin Enzymes- catalyze biochemical reactions Cell functions- multi-protein machines

2. Proteins are amino acid polymers 20 different amino acids: many combinations Proteins are made in the RIBOSOME

3. Amino Acid Chemistry NH 2 CC R1R1 CO H NHCC R2R2 COOH H NH 2 CC R COOH H amino acid 20 different types Amino acid PolypeptideProtein NH 2 CC R1R1 COOH H NH 2 CC R2R2 COOH H

4. Water, pH and pKa’s The following sections are taken from a website created by Dr. Michael W. King at Indiana University School of Medicine http://www.indstate.edu/thcme/mwking/home.html

5. K eq, K w and pH As H 2 O is the medium of biological systems one must consider the role of this molecule in the dissociation of ions from biological molecules. Water is essentially a neutral molecule but will ionize to a small degree. This can be described by a simple equilibrium equation: H 2 O H + + OH - Eqn. 1 The equilibrium constant can be calculated as for any reaction: K eq = [H + ][OH - ]/[H 2 O] Eqn. 2 Since the concentration of H 2 O is very high (55.5M) relative to that of the [H + ] and [OH - ], consideration of it is generally removed from the equation by multiplying both sides by 55.5 yielding a new term, K w : K w = [H + ][OH - ] Eqn. 3

6. K eq, K w and pH (cont.) This term is referred to as the ion product. In pure water, to which no acids or bases have been added: K w = 1 x 10 -14 M 2 Eqn. 4 As K w is constant, if one considers the case of pure water to which no acids or bases have been added: [H + ] = [OH - ] = 1 x 10 -7 M Eqn. 5 This term can be reduced to reflect the hydrogen ion concentration of any solution. This is termed the pH, where: pH = -log[H + ] Eqn. 6

7. pKa Acids and bases can be classified as proton donors (A-H  A - + H + ) and proton acceptors (B + H +  BH + ). In biology, various weak acids and bases are encountered, e.g. the acidic and basic amino acids, nucleotides, phospholipids etc. Weak acids and bases in solution do not fully dissociate and, therefore, there is an equilibrium between the acid (HA) and its conjugate base (A - ). HA A - + H + Eqn. 7 This equilibrium can be calculated and is expressed in terms of the association constant K a. K a = [H + ][A - ]/[HA] Eqn. 8 The equilibrium is also sometimes expressed as the dissociation constant K d = 1/K a.

8. pKa As in the case of the equilibrium of H + and OH - in water, the equilibrium constant K a can be expressed as a pK a : pK a = -logK a Eqn. 9 Therefore, in obtaining the -log of both sides of the equation describing the association of a weak acid, we arrive at the following equation: -logK a = -log[H + ][A - ]/[HA] Eqn. 10 Since as indicated above -logK a = pK a and taking into account the laws of logarithms: pK a = -log[H + ] -log[A - ]/[HA] Eqn. 11 pK a = pH -log[A - ]/[HA] Eqn. 12

9. By rearranging the above equation we arrive at the Henderson-Hasselbalch equation: pH = pK a + log[A - ]/[HA] Eqn. 13 The pH of a solution of any acid can be calculated knowing the concentration of the acid, [HA], and its conjugate base [A - ]. At the point of the dissociation where the concentration of the conjugate base [A - ] = to that of the acid [HA]: pH = pK a + log[1] Eqn. 14 The log of 1 = 0. Thus, at the mid-point of a titration of a weak acid: pK a = pH Eqn. 15 The term pK a is that pH at which an equivalent distribution of acid and conjugate base (or base and conjugate acid) exists in solution. The Henderson-Hasselbalch Equation

10. Buffering It should be noted that around the pK a the pH of a solution does not change appreciably even when large amounts of acid or base are added. This phenomenon is known as buffering. In most biochemical studies it is important to perform experiments, that will consume H + or OH - equivalents, in a solution of a buffering agent that has a pK a near the pH optimum for the experiment. Added base 2345678 1.0.8.6.4.2.0 pKa pH

11.  Clinical significance of blood buffering  Role of kidneys in acid-base balance See Dr. King’s website: http://www.indstate.edu/thcme/mwking/ionic- equilibrium.html Thinking beyond the lecture

12. Amino Acid Chemistry NH 2 CC R COOH H amino acid The free amino and carboxylic acid groups have pKa’s COOH COO - pKa ~ 2.2 NH 2 NH 3 + pKa ~ 9.4 At physiological pH, amino acids are zwitterions + NH 3 CC R COO - H

13. Amino Acid Chemistry

14. GlycineGly - G 2.49.8 AlanineAla - A 2.49.9 ValineVal - V 2.29.7 LeucineLeu - L 2.39.7 IsoleucineIle - I 2.39.8 Amino Acids with Aliphatic R-Groups pKa’s

15. Amino Acids with Polar R-Groups Non-Aromatic Amino Acids with Hydroxyl R-Groups SerineSer - S 2.29.2 ~13 ThreonineThr - T 2.19.1 ~13 Amino Acids with Sulfur-Containing R-Groups CysteineCys - C 1.910.8 8.3 MethionineMet-M 2.19.3

16. Acidic Amino Acids and Amide Conjugates Aspartic AcidAsp - D 2.09.9 3.9 AsparagineAsn - N 2.18.8 Glutamic AcidGlu - E 2.19.5 4.1 GlutamineGln - Q 2.29.1

17. Basic Amino Acids ArginineArg - R 1.89.0 12.5 LysineLys - K 2.29.2 10.8 HistidineHis - H 1.89.2 6.0

18. Aromatic Amino Acids and Proline PhenylalaninePhe - F 2.29.2 TyrosineTyr - Y 2.29.1 10.1 TryptophanTrp-W 2.49.4 ProlinePro - P 2.010.6