Protein Structure and Function Flashcards

Vocabulary practice flashcards covering the key terms, structural levels, chemical bonds, and biological functions of proteins from the lecture notes.

Primary Structure

The linear sequence of amino acids in a polypeptide chain joined by covalent peptide bonds.

Secondary Structure

The local folding or coiling of regions within a polypeptide backbone into repeating conformation motifs, primarily the $\alpha$-helix and $\beta$-sheet, stabilized by hydrogen bonds between backbone atoms.

Tertiary Structure

The overall three-dimensional folded structure of a single polypeptide chain, stabilized by interactions among amino acid side chains (R groups).

Quaternary Structure

The three-dimensional assembly formed by the interaction and combination of more than one folded polypeptide subunit (e.g., the $\alpha_2\beta_2$ tetramer of hemoglobin).

Peptide Bond

A rigid, planar covalent bond with partial double bond character formed between the carboxyl carbon of one amino acid and the amino nitrogen of another, usually in a trans configuration.

Condensation Reaction

A dehydration synthesis reaction in which the carboxyl group of one amino acid reacts with the amino group of another to form a peptide bond with the simultaneous release of a water molecule ($H_2O$).

N-terminus

The end of a polypeptide chain that terminates with an amino acid having a free amino group ($-NH_3^+$).

C-terminus

The end of a polypeptide chain that terminates with an amino acid having a free carboxyl group ($-COO^-$).

Alpha-helix ($\alpha$-helix)

A regular right-handed helical secondary structure with $3.6$ amino acid residues per turn and a pitch of $0.54\,nm$, stabilized by hydrogen bonds between the carbonyl oxygen of one peptide bond and the N-H hydrogen of the 4th peptide bond downstream.

Beta-pleated sheet ($\beta$-sheet)

A secondary structure element composed of extended linear peptide strands linked side-by-side by hydrogen bonds between backbone amino and carboxyl groups, with side chains alternating above and below the sheet plane.

Beta-hairpin bend ($\beta$-hairpin bend)

A tight structural turn widespread in globular proteins that connects adjacent antiparallel $\beta$-strands.

Collagen Triple Helix

A fibrous structural protein assembly composed of three left-handed helices coiled together with $3$ residues per turn, stabilized by interchain hydrogen bonds and characterized by repeating Gly-X-Y sequence motifs (where X is mainly proline and Y is mainly hydroxyproline).

Supersecondary Structure

Common recurring combinations or spatial arrangements of $\alpha$-helices and $\beta$-sheets that form recognizable structural folds in proteins, such as $\alpha/\beta$-barrels, $\beta$-barrels, or Rossmann folds.

Structural Domain

A compact, independently folded region of a single polypeptide chain that functions as a distinct structural, catalytic, or regulatory unit.

Pyruvate Kinase

An enzyme consisting of a single polypeptide chain organized into three distinct domains: Domain 1 ($\alpha/\beta$-barrel catalytic domain), Domain 2 ($\beta$-barrel active site cap), and Domain 3 ($\alpha/\beta$-sheet regulatory domain).

Electrostatic Interactions (Salt Bridges)

Non-covalent ionic bonds with a typical stabilization energy of $250\,kJ\,mol^{-1}$ that form at physiological pH between oppositely charged amino acid side chains (e.g., Asp/Glu carboxyl groups and Lys/Arg amino groups).

Van der Waals Forces

Weak, non-covalent attractive or repulsive forces (typical energy $2\,kJ\,mol^{-1}$) generated by temporary electron charge fluctuations that induce complementary dipoles in neighboring non-bonded atoms.

Hydrophobic Effect

The principal thermodynamic driving force for the folding of soluble cytosolic proteins, characterized by the sequestration of nonpolar hydrophobic side chains into the internal protein core to minimize entropic penalty from water ordering.

Disulfide Bridge

A covalent bond formed by the oxidation of sulfhydryl groups between two cysteine (Cys) residues, providing robust structural stability within or between polypeptide chains (e.g., in insulin).

Protein Denaturation

The disruption and loss of a protein's functional native three-dimensional tertiary/quaternary structure caused by external stressors such as heat, extreme pH, or detergents.

Amyloid Proteins

Misfolded proteins that associate into highly stable, insoluble fibrillar aggregates and plaques, contributing to neurodegenerative disorders like Alzheimer's disease.

Prion Protein Isoforms ($\text{PrP}^{\text{C}}$ vs $\text{PrP}^{\text{Sc}}$)

$\text{PrP}^{\text{C}}$ is the normal, soluble, predominantly $\alpha$-helical cellular form of prion protein, whereas $\text{PrP}^{\text{Sc}}$ is the pathogenic, protease-resistant, $\beta$-sheet-rich misfolded form that induces neurotoxic aggregation.

Creutzfeldt-Jakob Disease (CJD)

A fatal neurodegenerative disease caused by the infectious polymerization and accumulation of pathogenic prion protein ($\text{PrP}^{\text{Sc}}$), resulting in neurological symptoms like ataxia and psychological changes like depression and insomnia.

Carnosine

A naturally occurring dipeptide found in muscle and brain tissue consisting of $\beta$-alanine and histidine synthesized by carnosine synthase using ATP.

Glutathione

A naturally occurring tripeptide (Glu-Cys-Gly) that acts as a vital intracellular antioxidant.

Dystrophin

A large structural muscle protein comprising $3684$ amino acids with a molecular weight of $427\,kDa$.