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Biological and Biochemical Foundations of Living Systems

Amino Acids


Absolute configuration at the α position

An alpha-carbon is so named because it is the first carbon attached to a functional group. In the case of amino acids, the α-carbon is also the central carbon, making up the backbone in a polypeptide chain with a bond to an amino group (NH2) on one side and a carboxyl group (COOH) on the other.

As a tetrahedral atom, an amino acid's α-carbon holds bonds to four substituents (the NH2, the COOH, the H, and the R group), thereby making it a chiral center in all but one amino acid, glycine, whose R group is a second hydrogen atom.

The spatial organization of substituents around the chiral α-carbon determines the absolute configuration of the amino acid. The absolute configuration distinguishes between the amino acid's two enantiomers (stereoisomers that are non-superimposable mirror images). There are a few naming conventions for chirality, each of which is determined independently (i.e, R is not necessarily D, etc):

  • R/S notation is determined by the clockwise arrangement of priority groups when approaching the α-carbon from the lowest priority group (the hydrogen)
  • D/L notation is determined by analogy to the D and L forms of glyceraldehyde . This is the most commonly used notation for amino acids.
  • d/l or +/- notation is determined by optical activity (the rotation of a plane of polarized light)

All of the amino acids naturally found in proteins are of the L-configuration.

Amino acids as dipolar ions

In aqueous environments (e.g. physiological conditions), the amino and carboxyl groups of an amino acid will be ionized. In an acidic environment (low pH), the amino acid will take a cationic form with an extra hydrogen on it amino group (NH3+) and the carboxyl group holding its hydrogen (COOH). In a basic environment (high pH), the amino acid will take an anionic form with its amino group in its neutral state (NH2) and the carboxyl group releasing its hydrogen (COO-). At a neutral pH, the amino acid will exist as a neutral zwitterion or dipolar ion, holding a positive charge on its amino group (NH3+) and a negative charge on its carboxyl group (COO-).

EnvironmentpHAmino groupCarboxyl groupForm of amino acid (excludes R group)


Amino acids can be classified in several ways.

Acidic or basic

An amino acid will be acidic or basic if it has electrically charged side chains.

As such, aspartic acid (aspartate as an anion) and glutamic acid (glutamate as an anion) are acidic amino acids because of the carboxyl group in their side chains, and arginine, histidine, and lysine are basic amino acids because of the amine in their side chains.
Acidic amino acidsAspartic acid
Glutamic acid
Basic amino acidsArginine
Hydrophobic or hydrophilic

Amino acids have a range of hydrophobicity (a measure of how soluble the amino acid is in water) based on their side chains. Side chains that are non-polar or mainly hydrocarbons are generally more hydrophobic. Side chains that are polar or with a group that participates in hydrogen bonding, such as a hydroxyl, a carboxyl, or an amine are generally more hydrophilic.

Hydrophobic amino acids are generally found within the interior of a protein or exposed in a non-polar local environment such as a lipid membrane. Hydrophilic amino acids are readily found on the exterior of a protein, exposed to an aqueous environment.


Sulfur linkage for cysteine and cystine

A covalent disulfide bond can form between the sulfur containing R-groups (CH2SH) on two cysteine molecules, producing the amino acid cystine. Disulfide bonds between cysteine residues can affect protein folding and stability.

Peptide linkage: polypeptides and proteins

Amino acids form polypeptide chains via peptide bonds, which are formed when the amine of one amino acid forms a covalent amide bond with the carbonyl carbon on a second amino acid, releasing a molecule of H20 in the process. Peptide bond formation is thus an example of a dehydration synthesis reaction because of the generation of water as a result of the linkage.


Breaking a peptide bond requires the addition of a hydrogen to one amino acid's amine group and a hydroxyl to the other amino acid's carbonyl carbon (the breaking of water), thus classifying it as a hydrolysis.

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