- absolute configuration at the alpha position
- L and D is different from R and S. L is not always S, and D is not always R.
- If the priority of NH2 > COOH > R, then L=S and D=R. For example, L-Alanine = S-Alanine.
- If the priority of NH2 > R > COOH, then L=R, and D=S. For example, L-Cysteine = R-Cysteine.
- L-amino acids are the more common in nature, and are the type found in proteins. D-amino acids are less common in nature, and are never found in proteins.
- amino acids as dipolar ions classification
- At low pH, amino acids exist in the cationic form.
- At high pH, amino acids exist in the anionic form.
- At pH = pI, amino acids exist in the zwitterion form, which is overall neutral.
- acidic or basic
- If the R group contains carboxylic acid, then it's an acidic amino acid. There are two acidic amino acids: aspartic acid and glutamic acid.
- If the R group contains an amine group, then it's a basic amino acid. There are three basic amino acids: lysine, arginine, and histidine.
- hydrophobic or hydrophilic
- Hydrophobic: If the R group doesn't contain any of the stuff below.
- Hydrophilic: If the R group contains acids, bases, amines or alcohols.
- synthesis of amino acids
- Strecker synthesis
- starting material: R-aldehyde
- reagents: cyanide (KCN), ammonium (NH4Cl)
- product: amino acid with the -R group originally on the aldehyde
- Gabriel synthesis
- starting material: R-halide
- reagents: 1. phthalimide, 2. NH2-NH2
- product: amino acid with the -R group originally on the halide
- Sulfur linkage for cysteine and cystine
- Cysteine = side chain with the thiol group
- cystine = 2 cysteines forming a disulfide bond
- peptide linkage
- Peptide bond = amide bond.
- The peptide bond is formed by the amine group attacking the carbonyl carbon.
- The peptide bond is very difficult to hydrolyze. It requires a strong base, or a biological enzyme.
- primary structure of proteins
- Primary structure = sequence.
- The primary structure of proteins is read from the N-terminus to the C-terminus.
- secondary structure of proteins
- Secondary structure = repetitive motifs formed by backbone interactions.
- Backbone interactions = hydrogen bonding between the NH and C=O
- The two most common secondary structures are α helices and β pleated sheets.
- The α helix is right-handed, with the R groups sticking outward.
- In β sheets, R groups stick out above and below the sheet.
- Tertiary structure
- 3D structure of proteins
- Caused electrostatic side chain - side chain interactions
- Quaternary structure
- Separate chains/subunits joining together
- Caused by covalent disulfide bonding of cysteine side chains
- Isoelectric point
- pH at which the molecule is neutral
- acidic amino acids and proteins with lots of acidic side chains have have a lower isoelectric point
- basic amino acids and proteins with lots of basic side chains have a higher isoelectric point