Amino Acids Study Notes PDF

Structural Features Basic structure Each amino acid (AA) is composed of one alpha, or central, carbon bonded to: o One alpha amine group o One alpha carboxyl group o One hydrogen atom o One R group, which varies between AAs and gives them their unique properties Stereochemis...

Structural Features Basic structure Each amino acid (AA) is composed of one alpha, or central, carbon bonded to: o One alpha amine group o One alpha carboxyl group o One hydrogen atom o One R group, which varies between AAs and gives them their unique properties Stereochemistry o Isomers: molecules with identical formulas but different structures o Stereochemistry: property of molecules with the same formula and sequence of atoms but different 3-dimensional orientations in space o Chirality: property of molecules that are non-superimposable on their mirror images  AAs have D and L isomers.  Almost all proteinogenic AAs are found in the L configuration.  The chiral center of every AA is the alpha carbon, except for glycine (because its R group is a hydrogen atom). R groups or side chains R groups determine the differences in structure, function, and biological interactions of AAs. R groups can be classified in 2 ways: 1. Hydrophobic or hydrophilic:  Non-polar or hydrophobic R groups: side chains do not interact with water; the protein folds so that these AAs are toward the core of the molecule. Grouped according to structure:  Aromatic R groups (a cyclic compound called a benzene ring)  Aliphatic R groups (branched or straight open-chain compound)  Polar or hydrophilic R groups: Side chains interact with water; found on the surface of the molecule. Grouped according to ionic charge:  Uncharged R groups (neutral at physiological pH)  Positively charged R groups (basic amine groups)  Negatively charged R groups (acidic carboxyl groups) 2. Hydrophobic, hydrophilic, and ionic:  Hydrophobic: non-polar AAs containing aromatic or aliphatic R groups  Hydrophilic: polar AAs with neutral charge containing hydroxyl, sulfhydryl, or carboxamide R groups  Ionic: AAs that acquire a positive (amines) or negative (carboxylates) charge by ionizing at physiological pH Classifications R-group categories Chemical Properties of Amino Acids o Ionization: formation of ions and the acquiring of a negative or positive charge by the gain or loss of electrons. For AAs, this depends on the level of pH. o pKa: pH at which half of the ionizable molecules have a proton and half do not o AAs are amphoteric molecules: possess basic and acidic properties  Carboxyl and amino groups have the same strength of acidity and basicity o At neutral pH, the carboxyl group of an AA is missing a proton, while the amino group has a proton (zwitterion form or dipolar ion). o Zwitterion: a molecule with one positively charged functional group (amine) and one negatively charged group (carboxyl), and a net charge of zero   Have high melting temperatures and good water solubility  pI: pH at which the AA is in its zwitterion form  If the pH value < pI, the nitrogen atom of the amine group gains a proton and AA → cation  If the pH value > pI, the carboxyl group loses a proton and AA → anion  The presence of other carboxylic acids, amine, and hydroxyl groups in the side chains also contributes to the degree of ionization in varying pH values.