Chapter 3: Amino Acids, Peptides, and Proteins

Vocabulary flashcards covering amino acid structures, chemical properties, peptide synthesis, titration behavior, and protein characterization techniques.

Amino acid residue

The structure remaining in a peptide chain after two or more amino acids combine and the elements of water are removed during condensation.

$\alpha$-Amino acid

An amino acid containing both an amino group and a carboxylic acid group attached to the primary $\alpha$-carbon.

D,L-System

A configuration system that compares the stereochemistry of chiral molecules to that of glyceraldehyde.

Glycine

The only achiral amino acid; possesses a small hydrogen side chain that gives it conformational flexibility without contributing hydrophobic interactions.

Methionine

A nonpolar hydrophobic amino acid containing a thioether side chain that cannot form disulfide bonds.

Proline

An aliphatic amino acid with a cyclic secondary amino (imino) side group that restricts the conformational flexibility of polypeptide chains.

Lysine carbon designation

The system of designating amino acid side-chain carbons sequentially using Greek letters ($\alpha, \beta, \gamma, \delta, \epsilon$) or numbers ($1$ to $6$) starting from the carboxyl carbon.

Selenocysteine

The co-translationally incorporated 21st amino acid; encoded via context-dependent opal suppression and present as $99\%$ deprotonated at neutral pH.

Pyrrolysine

An amino acid encoded by the amber ($UAG$) stop codon, first identified in methanogenic archaea.

Ornithine and Citrulline

Non-protein amino acids that function as key intermediates in arginine biosynthesis and the urea cycle.

Zwitterion

A dipolar molecule containing both positively and negatively charged functional groups with an overall net electric charge of zero.

Amphoteric

The chemical property of a substance (such as an amino acid) enabling it to act as both an acid and a base.

Isoelectric point ($pI$)

The specific pH level at which a molecule carries no net electrical charge and is least soluble in water.

Peptide bond formation

A condensation reaction where the $\alpha$-amino group of one amino acid acts as a nucleophile to displace the hydroxyl group of another, releasing a water molecule.

Oligopeptide

A short peptide chain typically consisting of 4 to 10 amino acid residues.

Polypeptide

A long chain of amino acid residues joined by peptide bonds, containing more than 10 amino acids.

L-Aspartyl-L-phenylalanine methyl ester (aspartame)

A dipeptide derivative that functions as a synthetic commercial sweetener.

Multisubunit protein

A protein complex consisting of two or more noncovalently associated polypeptide chains.

Protomer

An identical repeating structural unit in an oligomeric protein, consisting of one or more polypeptide chains.

Conjugated protein

A protein that contains permanently attached non-amino acid chemical constituents in addition to polypeptide chains.

Prosthetic group

A non-amino acid moiety covalently or tightly bound to a conjugated protein required for its biological function.

Specific activity

The ratio of total enzyme activity units to the total mass of protein in milligrams, used as a measure of protein purity.

Sodium dodecyl sulfate (SDS)

An anionic detergent that unfolds proteins and coats them with negative charges to provide uniform mass-to-charge ratios during SDS-PAGE electrophoresis.

Isoelectric focusing

An electrophoretic technique that separates proteins based on their individual $ pI $ values along an immobilized pH gradient gel.

Edman degradation

A classical protein sequencing method involving stepwise N-terminal chemical modification, cleavage, and identification of individual amino acid residues.

Consensus sequence

A calculated order of most frequent amino acid or nucleotide residues found at each position in aligned, related sequences.

Signature sequence

A conserved motif of 10 to 50 amino acid residues linked to a specific structural fold or biological function in proteins.

Homologous proteins

Proteins that display detectable sequence similarity due to shared evolutionary origin.

Paralogs

Homologous proteins encoded by genes arising from gene duplication within the same species.

Orthologs

Homologous proteins found in different species that evolved from a common ancestral gene.

Lateral (or Horizontal) gene transfer

The transfer of genetic material between distinct organisms other than through direct vertical offspring transmission.