Protein Structure and Post-Translational Modifications - Vocabulary Flashcards

A set of vocabulary flashcards covering key terms and concepts from the lecture notes on amino acids, protein structure (primary to quaternary), and common post-translational modifications.

Amino acid

The building blocks of proteins; consist of a central (alpha) carbon attached to an amino group, a carboxyl group, a hydrogen, and a variable side chain (R group).

R group (side chain)

The variable chemical group attached to the amino acid that determines identity and properties.

Peptide bond

Covalent bond linking two amino acids in a polypeptide; the backbone bond that is planar and has partial double-bond character.

Primary structure

The linear sequence of amino acids in a polypeptide; covalent connectivity.

Secondary structure

Local folded structures of the polypeptide backbone, including alpha helices and beta sheets, stabilized by backbone hydrogen bonds.

Alpha helix

Right-handed helical secondary structure stabilized by backbone N–H…O=C hydrogen bonds; about 3.6 residues per turn.

Beta sheet

Secondary structure formed by beta strands; can be parallel or antiparallel; stabilized by backbone hydrogen bonds between strands.

Parallel beta sheet

Beta strands run in the same N→C direction; hydrogen bonds are angled between strands.

Antiparallel beta sheet

Beta strands run in opposite directions; hydrogen bonds between strands are more linear.

Phi (φ) and Psi (ψ) angles

Dihedral angles describing rotation around bonds adjacent to the alpha carbon; define backbone conformation and secondary structure.

Ramachandran plot

A plot of allowed φ and ψ angle combinations for amino acids; shows favored and disallowed conformations.

Proline

Amino acid with a cyclic side chain that constrains φ angle; restricts certain conformations and often influences turns.

Tertiary structure

The overall three-dimensional folding of a single polypeptide, combining all secondary structure elements.

Quaternary structure

Arrangement and interaction of multiple polypeptide subunits (oligomers) into a functional protein complex.

Post-translational modification (PTM)

Chemical modifications of a protein after translation, such as phosphorylation, glycosylation, acetylation, and sulfation.

Phosphorylation

Addition of a phosphate group (often on Ser/Thr/Tyr) by kinases; introduces negative charge and modulates activity.

Kinases

Enzymes that catalyze the phosphorylation of target residues on proteins.

Sulfation (sulfotyrosine)

Addition of a sulfate group to tyrosine residues; introduces negative charge and affects interactions.

Glycosylation (N-linked)

Attachment of sugar moieties to asparagine residues (N-linked glycosylation); influences folding, stability, and signaling.

Glycosylated asparagine

Asparagine residue modified with a sugar moiety during N-linked glycosylation.

Acetylation (lysine)

Addition of an acetyl group to lysine, neutralizing its positive charge and affecting interactions such as DNA binding.

Hydroxyproline

Hydroxylated proline; increases polarity and hydrogen-bonding capability, common in certain proteins (e.g., collagen).

D/L nomenclature (Fischer projections)

Biochemical system for stereochemistry using D- and L- designations; often depicted with Fischer projections to convey orientation.

Glycine

The only standard amino acid that is achiral (has two hydrogens on its side chain) and lacks a stereocenter.

Chirality in amino acids

Most amino acids are chiral; glycine is the exception; L- and D- designations describe stereochemistry (not always matching R/S).

Amino acid sequence determines folding

The primary sequence (order of amino acids) guides how the polypeptide folds into its three-dimensional structure and function.

Amino acid backbone vs. side chains

Backbone consists of repeating N–Cα–C motifs; side chains (R groups) project outward and determine properties.

Protein folding diseases

Diseases linked to misfolded proteins, such as Alzheimer's, Huntington’s, Parkinson’s, and prion diseases like Creutzfeldt–Jakob.