Protein Structure and Function Flashcards

Vocabulary practice flashcards covering key terms and concepts in protein structure, folding, function, and regulation.

Polypeptide Backbone

The repeating core of atoms ($-N-C-C-$) in a protein chain formed by amino acids joined by peptide bonds.

N-terminus

The end of a polypeptide chain that carries a free amino group.

C-terminus

The end of a polypeptide chain that carries a free carboxyl group.

Amino Acid Side Chain

The variable R group attached to an amino acid's $\alpha$-carbon that gives the amino acid its unique identity, charge, reactivity, and polarity.

Hydrophobic Force

The force that drives nonpolar amino acid side chains together into the interior core of a folded protein to avoid contact with the aqueous environment.

Conformation

The final three-dimensional folded structure adopted by a polypeptide chain that minimizes free energy.

Denaturation

The unfolding of a protein molecule resulting in loss of its three-dimensional structure due to the disruption of noncovalent bonds.

Renaturation

The spontaneous refolding of a denatured protein back into its original native conformation when normal conditions are restored.

Chaperone Proteins

Specialized proteins that assist newly synthesized or partially folded polypeptides to fold into their most energetically favorable conformation, often using isolation chambers to prevent aggregation.

Primary Structure

The linear sequence of amino acids linked together in a polypeptide chain.

Secondary Structure

Regular local folding patterns formed within a polypeptide chain, specifically $\alpha$-helices and $\beta$-sheets.

Tertiary Structure

The full three-dimensional conformation formed by an entire single polypeptide chain.

Quaternary Structure

The complete protein structure formed by the assembly and interaction of multiple polypeptide chains (subunits).

$\alpha$-Helix

A common protein secondary structure forming a right-handed spiral stabilized by hydrogen bonds between every $4\text{th}$ amino acid, completing a turn every $3.6$ amino acids.

Coiled-Coil

A stable structural motif formed when two or three $\alpha$-helices wrap around each other to bury their nonpolar hydrophobic side chains away from the aqueous environment.

$\beta$-Sheet

A rigid secondary structure formed by hydrogen bonds between neighboring polypeptide segments running in either parallel or antiparallel directions.

Amyloid Structure

An insoluble protein aggregate formed when $\beta$-sheets stack together with amino acid side chains interdigitated like zipper teeth.

Prion

An infectious, misfolded protein containing amyloid structures that binds to normal forms of the protein and converts them into the abnormal misfolded conformation.

Protein Domain

Any segment of a polypeptide chain (typically $40$ to $350$ amino acids long) that can fold independently into a compact, stable structure.

Protein Families

Groups of proteins that share similar amino acid sequences and structural domains, each having a distinct enzymatic or physiological function.

Subunit

An individual polypeptide chain that binds noncovalently with other polypeptide chains to construct a multi-chain protein complex.

Collagen

A fibrous protein composed of three peptide chains wound in a triple helix with glycine at every third position, forming strong overlapping fibrils in the extracellular matrix.

Elastin

A fibrous extracellular protein formed by loose, unstructured polypeptide chains covalently cross-linked into an elastic meshwork that allows tissues to stretch without tearing.

Disulfide Bridges

Covalent linkages formed between two cysteine side chain $-\text{SH}$ groups that reinforce protein structures exported outside the cytosol.

Ligand

Any substance or molecule that is bound selectively and noncovalently by a protein.

Binding Site

A cavity or surface region on a protein that associates noncovalently with a specific ligand.

Substrate

A ligand molecule that specifically binds to an enzyme and undergoes a chemical transformation.

Active Site

The specialized binding site on an enzyme where the substrate molecule attaches and undergoes catalysis.

Transition State

The distorted physical conformation of an enzyme-substrate complex during catalysis that lowers the reaction's activation energy.

Metabolic Pathway

A linked sequence of enzymatic reactions where the product of one enzyme becomes the reactant substrate for the next.

Cofactor

A small inorganic molecule or metal ion (such as iron or zinc) required by an enzyme to assist catalysis.

Coenzyme

A small organic nonprotein molecule (often derived from vitamins, like biotin or retinal) that assists enzymes during chemical reactions.

Feedback Inhibition

A regulatory mechanism where an enzyme functioning early in a metabolic pathway is inhibited by a product synthesized later in the pathway.

Allosteric Protein

A protein that exists in multiple alternative conformations, whose activity is regulated when ligand binding at one site changes its shape to affect binding at another site.

Protein Kinase

An enzyme that transfers a phosphate group from ATP onto an amino acid side chain (such as serine) of a target protein.

Protein Phosphatase

An enzyme that removes a phosphate group from a phosphorylated protein, reversing its conformational change.

GTP-Binding Protein

A regulatory protein that acts as a molecular switch, being active when bound to GTP and becoming inactive when GTP is hydrolyzed to GDP.

Motor Protein

A protein that drives unidirectional physical movement along cell structures by coupling ATP hydrolysis to irreversible conformational changes.

Scaffold Protein

A large protein containing multiple binding sites that brings interacting proteins together to accelerate cellular processes in a specific area.

Biomolecular Condensates

Fluid, membrane-less intracellular compartments held together by weak interactions between protein and RNA scaffolds to concentrate client molecules.

Affinity Chromatography

A protein purification technique that isolates target proteins from a cell extract based on their specific binding to a ligand coupled to a matrix column.

Mass Spectrometry

An analytical method used to identify proteins by measuring the mass-to-charge ratio ($m/z$) of tryptic peptide fragments.

Ribbon Model

A structural model of a protein that highlights secondary structures like $\alpha$-helices and $\beta$-sheets along the polypeptide backbone.