Amino Acids in Principles of Biochemistry - Study Guide | BC 351, Study notes of Biochemistry

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Lecture 2 Amino acids The building blocks of proteins Amino acids are α-amino substituted carboxylic acidsamino substituted carboxylic acids 20 naturally occurring amino acids in proteins Incorporated while the protein is being made Encoded in genome A residue is an amino acid in the context of a protein General structure of an amino acid α-amino substituted carboxylic acidscarbon (C-amino substituted carboxylic acidsα), central carbon 4 different groups bound to it α-amino substituted carboxylic acidsamino group NH 3 +^ @ pH 7 (biological setting) α-amino substituted carboxylic acidscarboxyl group COO-amino substituted carboxylic acids^ @ pH 7 Proton R group Similar to figure 3 – 3a The R – group (aka side chain) is the group that differentiates the 20 amino acids Carbons labeled (β, γ, δ, ε) Amino acid stereochemistry A chiral center is an atom with 4 different groups bound to it 2 different ways to arrange groups around a chiral center Stereoisomers are chemical compounds that have the same chemical make-amino substituted carboxylic acidsup and connectivity but different spatial arrangements

Glycine is the only amino acid that does not exhibit stereochemistry Only L amino acids are used in proteins The twenty amino acids Nomenclature: Glycine, Gly, G Table 3 – 1 Grouped based on nature of side chain Nonpolar, aliphatic R groups Aliphatic – hydrocarbon chain; opposite of aromatic Glycine, alanine, proline, valine, leucine, isoleucine, methionine Glycine does not have stereochemistry Glycine is conformationally flexible Proline is least conformationally flexible amino acid For the most part, nonpolar environments – protein interior Aromatic R groups Phenylalanine, tyrosine, tryptophan Phenylalanine – very hydrophobic Tyrosine and tryptophan have hydrophilic sections Polar, uncharged R groups Typically found on protein exteriors Serine, threonine, cysteine, asparagine, glutamine Cysteine is only amino acid that can form covalent bonds with other amino acids Figure 3 – 7 Disulfide bond/bridge Positively charged R groups Lysine, arginine, histidine

Can form ionic bonds (with negative charges) Negatively charged R groups Aspartate, glutamate Can form ionic bonds (with positive charges) Acid/base chemistry of amino acids Acid and base definitions Acids are proton donors Bases are proton acceptors General acid and base reactions HA ↔ H+^ + A-amino substituted carboxylic acids

Ka = ¿ ¿

A-amino substituted carboxylic acids^ is conjugate base to HA “Ionization reaction” – starts with something not an ion, ion is created Ka (dissociation constant) The equilibrium constant for an ionization reaction

[ P ]

[ R ]

Represents the affinity of a conjugate base for a proton Affinity – strength of interaction -amino substituted carboxylic acidslog Ka = pKa Small Ka / large pKa – base Large Ka / small pKa – acid Protonation and deprotonation of amino acid groups Carboxyl group R-amino substituted carboxylic acidsCOOH ↔ R-amino substituted carboxylic acidsCOO-amino substituted carboxylic acids^ + H+

α-amino substituted carboxylic acidscarboxyl group Glutamate (E) Aspartate (D) pKa 1.5 – 4. Amino group R-amino substituted carboxylic acidsNH 3 +^ ↔ R-amino substituted carboxylic acidsNH 2 + H+ α-amino substituted carboxylic acidsamino group Histidine (H) Arginine (R) Lysine (K) pKa 8 – 12. Titration of amino acids Le Chatelier’s principle (aka mass action) states that when a stress is applied to a system at equilibrium the equilibrium will adjust to minimize the effects of the stress. H 2 O ↔ H+^ + OH-amino substituted carboxylic acids^ pKa = 16. [H] down (pH up) [HA] down [A-amino substituted carboxylic acids] up Midpoint pH = pKa [HA] = [A-amino substituted carboxylic acids] α-amino substituted carboxylic acidscarboxylic group designated pK 1 α-amino substituted carboxylic acidsamino group designated pK 2 Side chain designated pKR