Protein Structure and Solvation - Key Terms (Video Notes)

Vocabulary flashcards covering the levels of protein structure, oligomerization, and solvation concepts discussed in the video notes.

Primary structure

The linear sequence of amino acids in a polypeptide, linked by peptide bonds; the starting blueprint for higher-order protein structure.

Secondary structure

Local regular structures stabilized by backbone hydrogen bonds, including alpha helices, beta sheets, and beta turns/loops.

Alpha helix

A right-handed coiled backbone structure stabilized by intra-chain hydrogen bonds between the N–H and C=O groups four residues apart.

Beta sheet

A sheet-like arrangement of beta strands connected by hydrogen bonds; can be parallel or antiparallel; side chains project above and below the plane.

Beta turn

A short loop that reverses direction between beta strands, typically four amino acids long.

Loop / unstructured region

Regions lacking a defined secondary structure; flexible segments often called loops.

Parallel beta sheet

Beta strands run in the same N→C direction with hydrogen bonds between strands.

Antiparallel beta sheet

Beta strands run in opposite directions with nearly linear inter-strand hydrogen bonds.

Quaternary structure

The arrangement of two or more polypeptide subunits in a protein complex.

Oligomer

A protein complex composed of multiple polypeptide chains; can be homo- or heterooligomeric.

Dimer

A protein complex composed of two subunits; can be homo- or heterodimer.

Trimer

A protein complex composed of three subunits.

Tetramer

A protein complex composed of four subunits.

Homotetramer

A tetramer made up of four identical subunits.

Heterotetramer

A tetramer made up of different subunits.

Isoelectric point (pI)

The pH at which a molecule carries no net electric charge; solubility often lowest at the pI.

Solvation

Interaction of a solute (protein) with a solvent (water), including hydrogen bonding and ionic/dipole interactions.

Hydrophobic effect

Tendency of nonpolar regions to avoid water, driving aggregation and folding; largely entropy-driven.

Hydrophobic collapse

Early protein folding step where nonpolar residues cluster to minimize water exposure.

Ion-dipole interaction

Electrostatic interaction between an ion and a polar molecule’s dipole; intermediate strength.

Dipole-dipole interaction

Electrostatic attraction between two polar molecules; hydrogen bonds are a strong special case.

Hydrogen bond

A strong dipole-dipole interaction between a hydrogen donor and an acceptor, critical in protein–water interactions.

Ionic interaction

Electrostatic attraction between oppositely charged groups; among strongest non-covalent interactions.

Amphiphilic

Molecules with both hydrophilic and hydrophobic parts (e.g., detergents) that interact with water and nonpolar regions.

Detergent

An amphiphilic molecule that solubilizes hydrophobic regions by forming micelles in water.

Chromatography

Separation technique based on differential interactions with a stationary phase or solvent, often used to separate proteins by charge or polarity.

Gel electrophoresis

Separation technique that uses an electric field to move charged molecules; influenced by size and charge.

Salt effect (salting out/in)

Salt concentration can shield charges and alter solubility; high salt can precipitate proteins (salting out) by reducing solvation.

pKa

The acid dissociation constant; the pH at which a group is half-protonated/deprotonated, influencing charge state.

Protonation / deprotonation

Gain or loss of a proton from a functional group, changing its charge state and interactions.

Peptide bond

Covalent bond linking the carboxyl group of one amino acid to the amino group of the next, forming the protein backbone.

Domain

An independently folding unit within a protein that often corresponds to a specific function.

Motif

A short, conserved sequence/structure within a protein that is associated with a particular function.