Proteins : The primary worker molecule in the body

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. 20 different types R2 R1 R acid amino NH2 NH2 NH2 Ca Ca Ca COOH COOH COOH H H H R1 R2 NH2 Ca CO NH Ca COOH H H Polypeptide Protein Amino acid Amino Acid Chemistry

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. Keq, Kw and pH As H2O 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: H2O <-------> H+ + OH-Eqn. 1 • The equilibrium constant can be calculated as for any reaction: • Keq = [H+][OH-]/[H2O] Eqn. 2 • Since the concentration of H2O 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, Kw: • Kw = [H+][OH-] Eqn. 3

6. Keq, Kw and pH (cont.) This term is referred to as the ion product. In pure water, to which no acids or bases have been added: Kw = 1 x 10-14 M2Eqn. 4 • As Kw 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 Ka. Ka = [H+][A-]/[HA] Eqn. 8 The equilibrium is also sometimes expressed as the dissociation constant Kd = 1/Ka.

8. pKa As in the case of the equilibrium of H+ and OH- in water, the equilibrium constant Ka can be expressed as a pKa: pKa = -logKaEqn. 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: • -logKa = -log[H+][A-]/[HA] Eqn. 10 Since as indicated above -logKa = pKa and taking into account the laws of logarithms: pKa = -log[H+] -log[A-]/[HA] Eqn. 11 pKa = pH -log[A-]/[HA] Eqn. 12

9. The Henderson-Hasselbalch Equation By rearranging the above equation we arrive at the Henderson-Hasselbalch equation: pH = pKa + 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 = pKa + log[1] Eqn. 14 • The log of 1 = 0. Thus, at the mid-point of a titration of a weak acid: • pKa = pH Eqn. 15 • The term pKa is that pH at which an equivalent distribution of acid and conjugate base (or base and conjugate acid) exists in solution.

10. 1.0 .8 Added base .6 .4 pKa .2 .0 2 3 4 5 6 7 8 pH Buffering It should be noted that around the pKa 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 pKa near the pH optimum for the experiment.

11. Thinking beyond the lecture • 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

12. R acid amino NH2 Ca COOH H NH2 COO- NH3+ COOH pKa ~ 9.4 pKa ~ 2.2 R +NH3 Ca COO- H At physiological pH, amino acids are zwitterions Amino Acid Chemistry The free amino and carboxylic acid groups have pKa’s

13. Amino Acid Chemistry

14. Glycine Gly - G 2.4 9.8 Alanine Ala - A 2.4 9.9 Valine Val - V 2.2 9.7 Leucine Leu - L 2.3 9.7 Isoleucine Ile - I 2.3 9.8 • Amino Acids with Aliphatic R-Groups pKa’s

15. Non-Aromatic Amino Acids with Hydroxyl R-Groups Serine Ser - S 2.2 9.2 ~13 Threonine Thr - T 2.1 9.1 ~13 Amino Acids with Sulfur-Containing R-Groups Cysteine Cys - C 1.9 10.8 8.3 Methionine Met-M 2.1 9.3 • Amino Acids with Polar R-Groups

16. Aspartic Acid Asp - D 2.0 9.9 3.9 Asparagine Asn - N 2.1 8.8 Glutamic Acid Glu - E 2.1 9.5 4.1 Glutamine Gln - Q 2.2 9.1 • Acidic Amino Acids and Amide Conjugates

17. Arginine Arg - R 1.8 9.0 12.5 Lysine Lys - K 2.2 9.2 10.8 Histidine His - H 1.8 9.2 6.0 • Basic Amino Acids

18. Phenylalanine Proline Pro - P Phe - F 2.0 10.6 2.2 9.2 Tyrosine Tyr - Y 2.2 9.1 10.1 Tryptophan Trp-W 2.4 9.4 • Aromatic Amino Acids and Proline