Amino Acids Lecture Notes PDF

Department of Biochemist Faculty of Pharmacy, Suez Ca University Amino Acids  Protein Function Proteins are the most abundant molecules in living systems Some functions of proteins: 1. Enzymes: biological catalysts, increase reaction rates 2. Polype...

Department of Biochemist Faculty of Pharmacy, Suez Ca University Amino Acids  Protein Function Proteins are the most abundant molecules in living systems Some functions of proteins: 1. Enzymes: biological catalysts, increase reaction rates 2. Polypeptide hormones: direct and regulate metabolism 3. Contractile proteins: in muscles, allow movement 4. Structural proteins: in bone, collagen forms framework for calcium deposition  Protein Function 5. Transport and storage: hemoglobin and myoglobin transport oxygen in the blood, plasma albumin transports fatty acids 6. Immunoglobulins: fight infection Proteins are made from amino acids  Structure of Amino Acids Amino acids consist of a primary amino group, a carboxyl group, a hydrogen atom and a distinctive side chain (R group)bonded to a carbon atom The carbon is called the α-carbon, because it is adjacent to the carboxyl group  Properties of Amino Acids At physiological pH (~ pH 7.4): – The carboxyl group is dissociated forming the negatively charged carboxylate ion COO- – The amino group is protonated NH3+ Under normal cellular conditions (pH 7.4), amino acids are zwitter ions (dipolar ions): – Carboxyl group = COO- – Amino group = NH3+  Properties of Amino Acids In proteins, carboxyl group of one amino acid is bound to the amino group of the adjacent amino acid in the peptide linkage Carboxyl and amino groups of amino acids are usually not involved in chemical reactions except hydrogen bond formation  Properties of Amino Acids Chemical properties and role of an amino acid is dependent on the side chain, R-group Amino acids are classified according to the properties of the side chain: 1. Amino acids with non-polar side chains 2. Amino acids with uncharged polar side chains 3. Amino acids with acidic side chains 4. Amino acids with basic side chains 1. Amino Acids with Non-Polar Side Chains (9) Side chain does not bind protons Side chain does not release protons Side chain does not participate in hydrogen or ionic bonds 1. Amino Acids with Non-Polar Side Chains (9) Aliphatic side groups 1. Amino Acids with Non-Polar Side Chains (9) Aromatic side groups Cyclic  1. Amino Acids with Non-Polar Side Chains Side chains of non-polar amino acids cluster together in the interior of the protein due to hydrophobicity of the side group Membrane proteins: non-polar groups are on outside surface of protein, interact with non-polar lipid membrane  1. Amino Acids with Non-Polar Side Chains Proline Side chain and α-amino nitrogen form a rigid 5- membered ring Proline has a secondary amino group Proline plays a large role in structure of collagen 2. Amino Acids with Uncharged Polar Side Chains (6) Zero net charge at neutral pH hydroxyl group participates in hydrogen bond formation hydroxyl of serine, threonine serves as site of attachment for phosphate groups in proteins hydroxyl of serine, threonine serves as site of attachment for oligosaccharides in glycoproteins 2. Amino Acids with Uncharged Polar Side Chains (6) Zero net charge at neutral pH carbonyl and amide groups participate in hydrogen bonds sulfhydryl (-SH) group loses proton at alkaline pH amide group of asparagine serves as site of attachment of oligosaccharides in glycoproteins 2. Amino Acids with Uncharged Polar Side Chains (6) Disulfide bond: – Sulfhydryl (-SH) group of cysteine plays role in active site of enzymes – -SH groups of two cysteines can become oxidized to the dimer cystine – Cystine contains disulfide bond (- S – S -)  3. Amino Acids with Acidic Side Chains (2) proton donors: side chains are fully ionized and negatively charged at physiological pH 4. Amino Acids with Basic Side Chains (3) proton acceptors: side chains are fully protonated and positively charged at physiological pH 4. Amino Acids with Basic Side Chains (3) weak base amino acid is mostly uncharged at physiological pH side chain can either be positively charged or neutral depending on the ionic environment Amino Acid Abbreviations Amino Acid Abbreviations Amino Acid Abbreviations Amino Acid Abbreviations  Optical Properties of Amino Acids α-carbon of amino acids is chiral or optically active Glycine is the exception amino acids have D-forms and L-forms (stereoisomers, optical isomers, enantiomers) Amino acids in mammals are in L-form  Acid Base Properties of Amino Acids Amino acids contain weakly acidic α-carboxyl groups and weakly basic α-amino groups Acidic and basic amino acids contain ionizable groups in the side chain Amino acids can act as buffers Buffers are weak acids or bases (with ionizable groups) which resist small changes in pH  Acid Base Properties of Amino Acids: Henderson-Hasselbalch Equation + - HA  H +A weak proton conjugate acid base The dissociation constant, Ka of the acid is: + - [H ] [A ] Ka = [HA] the larger the Ka, the stronger the acid, since all the acid would have dissociated into protons and conjugate base  Acid Base Properties of Amino Acids: Henderson-Hasselbalch Equation [H+ ] [A- ] Ka = [HA] By solving for H+: + K a [HA] [H ] = [A - ]  Acid Base Properties of Amino Acids: Henderson-Hasselbalch Equation By taking the logarithm of each side: +  K a [HA]  log[ H ] = log    [A- ]    Rearranging: log[H+ ] = logK a + log[HA] − log[A− ]  Acid Base Properties of Amino Acids: Henderson-Hasselbalch Equation By multiplying each side by -1: + − − log[H ] = −logK a − log[HA] + log[A ] Rearranging: − + [A ] − log[H ] = −logK a + log [HA]  Acid Base Properties of Amino Acids: Henderson-Hasselbalch Equation Since pH = -log [H+] and pKa = -log Ka, we obtain the Hendersen-Hasselbalch equation − [A ] pH = pK a + log [HA]  Acid Base Properties of Amino Acids Buffers Resist small changes in pH on addition of acid or base Formed by mixing a weak acid (HA) with its conjugate base (A-): – If acid is added, A- neutralizes it forming HA – If base is added, HA neutralizes it, forming A- Maximum buffering capacity occurs at pH equal to Ka ± 1 unit Acid Base Properties of Amino Acids Buffers Acetic acid (HA) + acetate (A-) has pKa 4.8 Buffer region only between pH 3.8 – 5.8 pH < pKa: HA is predominant pH > pKa: A- is predominant  Acid Base Properties of Amino Acids Titration of Amino Acids Amino acids have a pK value for every dissociable group Alanine: α- carboxyl group and α-amino group Acid pH: both groups are protonated Neutral pH: carboxyl group dissociates, loses proton Basic pH: amino group dissociates, loses proton  Acid Base Properties of Amino Acids Titration of Alanine Alanine has two titratable groups (α-carboxyl and α-amino) Dissociation constant for carboxyl group is called K1 [A − ] [II] pH = pK + log a pH =pK1 +log [HA] [I]  Acid Base Properties of Amino Acids Titration of Alanine Dissociation constant for amino group is called K2 [A − ] p H = pK 2 + log [III] pH = pK + log a [HA] [II]  Acid Base Properties of Amino Acids Titration of Alanine: pK’s Alanine has two pK’s pK is equal to the pH where half of the protons is removed from the group pK1 = 2.3: at pH 2.3, half of the carboxyl groups in solution are dissociated pK for the most acidic group is the smallest, pK increases with increasing basisity Titration Curve of Alanine 1. Buffer pairs: -COOH/COO- is a buffer pair in the acid pH range, -NH3+/-NH2 pair buffers in the basic pH range 2. pH = pK: if pH = pK1, then equal amounts of forms I and II are present 3. Isoelectric point (pI): pI is pH at which form II is predominant, with equal amounts of forms I and III pI is average of pK1 and pK2 alanine exists in dipolar form II at neutral pH. Net charge is zero  Acid Base Properties of Amino Acids Most amino acids have a net charge of zero at physiological pH – Negatively charged α - carboxyl (–COO-) – Positively charged α – amino (-NH3+) Isoelectric point (pI): pH at which the molecule has a net charge of zero Amino acids are called zwitter ions (carry both a positive and negative charge) Amino acids are amphoteric: can act as acids or bases Glu, Asp, His, Arg and Lys have additional charged side groups, thus are not zwitter ions  Other Applications of the Henderson-Hasselbalch Equation − [A ] pH = pK a + log [HA] Can be used to estimate change in pH in response to changes in concentration of a weak acid or its conjugate base e.g. bicarbonate buffer system  The Bicarbonate Buffer System CO2 + H 2O  H2CO3  H + + HCO 3− − [HCO3 ] pH = pK + log [H2CO3 ] Pulmonary embolism causes an increase in carbon dioxide in the blood → increase in H2CO3 → decrease in pH (Respiratory acidosis) An increase in bicarbonate conc. causes an increase in pH  Effect of pH on Drug Absorption Drugs pass through membranes readily in their uncharged form Drugs are either weak acids or weak bases: – Weak acid: HA ↔ H+ + A- – Weak base: BH+ ↔ B + H+ Aspirin is a weak acid, permeates membrane in the HA, undissociated, form Morphine is a weak base, permeates membrane in its B, dissociated form  Effect of pH on Drug Absorption Effective concentration of a drug at the absorption site depends on the concentration of the dissociated and undissociated forms Concentration of dissociated and undissociated forms depends on: – pH at absorption site – pKa of the ionizable group (i.e. how strong the acid or base)  Effect of pH on Drug Absorption Aspirin, the weak acid is protonated in the acidic environment of the stomach, is absorbed in the stomach  Effect of pH on Drug Absorption The Hendersen-Hasselbalch equation is used to estimate how much of a drug is present on either side of a membrane that separates between environments with different pH Stomach Blood pH 1.5 pH 7.4 A- HA HA HA HA H+ + A- HA HA A - HA A- A- A- HA A-