Amino Acids – Structure, Properties & Metabolism

Vocabulary cards covering essential terms, structures, chemical properties, modifications, and metabolic classifications of amino acids as presented in the lecture.

Amino Acid

Organic molecule with an α-carbon attached to an amino group, a carboxyl group, a hydrogen, and a distinctive side chain (R-group).

Essential Amino Acids

Nine amino acids (e.g., lysine, leucine, tryptophan) that cannot be synthesized by humans and must be obtained from the diet.

Non-Essential Amino Acids

Amino acids that humans can synthesize de novo (e.g., alanine, glutamine, serine).

α-Carbon

The central carbon of an amino acid to which the amino, carboxyl, hydrogen, and R-group are bonded.

α-Amino Acid

Standard amino acid in which both the amino and carboxyl groups are bonded to the same (α) carbon.

R-Group (Side Chain)

Variable group of an amino acid that determines its chemical properties and classification.

Chiral (Asymmetric) Center

A carbon atom bonded to four different substituents, giving rise to stereoisomers (D and L forms).

L-Amino Acid

The stereoisomeric form of amino acids predominantly found in biological proteins.

D-Amino Acid

Mirror-image stereoisomer rarely found in proteins but present in some bacterial cell walls and antibiotics.

Non-Polar (Aliphatic) Amino Acids

Hydrophobic residues such as alanine, valine, leucine, isoleucine, methionine, glycine, and proline.

Aromatic Amino Acids

Residues with aromatic rings: phenylalanine, tyrosine, and tryptophan.

Hydroxyl Amino Acids

Serine, threonine, and tyrosine, each containing an –OH group capable of hydrogen bonding or phosphorylation.

Sulfhydryl Amino Acid

Cysteine, which carries a reactive –SH group that can form disulfide bonds.

Carboxamide Amino Acids

Asparagine and glutamine; contain amide side chains derived from aspartate and glutamate.

Ionizable R-Group

Side chain capable of gaining or losing a proton within physiological pH (e.g., Asp, Glu, Lys, Arg, His, Cys, Tyr).

pKa

The pH at which half of a given ionizable group is protonated and half is deprotonated.

Isoelectric Point (pI)

The pH at which an amino acid carries no net electric charge.

Peptide Bond

Amide linkage formed between the α-carboxyl of one amino acid and the α-amino of another, releasing water.

Proteinogenic Amino Acids

The 20 standard amino acids incorporated into proteins during translation.

Rare (21st & 22nd) Amino Acids

Selenocysteine (Sec) and pyrrolysine (Pyl), inserted by unique recoding mechanisms.

Selenocysteine

Sec; cysteine analog with selenium replacing sulfur, present in some redox enzymes.

Pyrrolysine

Pyl; lysine derivative with a pyrroline ring, found in certain methanogenic archaeal enzymes.

Carnitine

Non-protein amino acid that transports fatty acids into mitochondria for β-oxidation.

Disulfide Bond

Covalent –S–S– link formed by oxidation of two cysteine residues, stabilizing protein structure.

Hydroxyproline

Post-translationally hydroxylated proline critical for collagen stability.

γ-Carboxyglutamate

Vitamin K–dependent modification adding a second carboxyl to glutamate, enhancing Ca²⁺ binding in clotting proteins.

Phosphoserine

Serine residue bearing a phosphate group; common regulatory modification.

Phosphothreonine

Phosphorylated threonine involved in signal transduction pathways.

Phosphotyrosine

Tyrosine residue phosphorylated by tyrosine kinases; key in cell signaling.

Glucogenic Amino Acid

Amino acid whose catabolism yields intermediates that can be converted to glucose (e.g., alanine → pyruvate).

Ketogenic Amino Acid

Amino acid degraded solely to acetyl-CoA or acetoacetate, yielding ketone bodies (e.g., leucine, lysine).

Glucogenic/Ketogenic Amino Acid

Amino acid giving rise to both glucose and ketone precursors (e.g., isoleucine, phenylalanine, tryptophan).

Aspartate & Glutamate

Acidic amino acids with carboxylate side chains; pKa ≈ 4.1, negatively charged at physiological pH.

Lysine & Arginine

Basic amino acids with high pKa (~10.5 & 12.5); positively charged at physiological pH.

Histidine

Amino acid with imidazole ring (pKa ≈ 6.0) that can switch charge near physiological pH, useful in enzyme catalysis.

Cysteine pKa

Approximately 8.2; its –SH can deprotonate to form a thiolate anion, important in catalysis and redox.

Tyrosine pKa

Approximately 10.5; phenolic –OH can ionize at high pH.

Titration Curve

Plot of amino-acid charge versus added base, showing pKa inflection points and pI plateau.

Aliphatic R-Group

Non-aromatic hydrocarbon side chain providing hydrophobic character (e.g., leucine).

Ionization State

The charging pattern of amino acid functional groups at a given pH.

Protein Charge Modulation

Changes in pH alter ionizable residues, affecting protein activity (e.g., pepsin active at low pH, trypsin at high pH).

Peptide N-Terminus

End of a peptide chain with a free amino group; written on the left in sequences.

Peptide C-Terminus

End with a free carboxyl group; written on the right of peptide sequences.

Post-Translational Modification (PTM)

Covalent change to a protein after translation (e.g., phosphorylation, hydroxylation, glycosylation).

Carbohydrate-Asparagine Adduct

N-linked glycosylation where a carbohydrate attaches to the amide nitrogen of asparagine.

Protein Functions

Key cellular roles including catalysis, signaling, structural support, and energy/gradient generation.

Ionizable Amine R-Groups

Side chains containing amino functionality that can accept protons (Lys, Arg, His).

Ionizable Carboxyl R-Groups

Side chains containing carboxyl groups that lose protons (Asp, Glu).

Equivalents of OH⁻

Amount of base added per mole of amino acid during titration, used to calculate pKa values.

Peptide Bond Hydrolysis

Reaction that breaks peptide bonds, consuming water; reverse of peptide bond formation.