BIOL 443/543 LEC SLIDES 10 (Proteins and Enzymes - Structure and Function)

Vocabulary practice flashcards covering amino acid properties, levels of protein structure, bonding mechanisms, folding, and protein domains based on lecture notes.

Amino Acid

The monomer unit of proteins consisting of a central $\alpha$-carbon, amino group, carboxyl group, hydrogen atom, and variable side chain ($R$ group); 20 standard types are used in protein synthesis.

L-amino acid

The specific stereo-isomer (optical isomer) form of amino acids exclusively found and utilized in natural proteins.

Peptide Bond

An amide linkage that joins amino acids together, possessing partial double-bond character that restricts C-N rotation and forms a rigid planar unit of four atoms.

Primary Structure ($1^0$)

The specific linear sequence of amino acids linked together by peptide bonds in a polypeptide chain, written from the N-terminus to the C-terminus.

Secondary Structure ($2^0$)

Local structural conformations formed by hydrogen bonding between H and O atoms along the peptide backbone, such as $\alpha$-helices and $\beta$-sheets.

$\alpha$-helix

A right-handed spiral secondary structure stabilized by backbone hydrogen bonds, featuring side chains pointing outward, approximately $3.6$ amino acids per turn, and a pitch of $0.54\,\text{nm}$.

$\beta$-strand

An extended polypeptide chain with side chains projecting perpendicularly (up and down) that interacts with neighboring strands via hydrogen bonds to form $\beta$-sheets or $\beta$-barrels.

Loops and Turns

Short stretches of amino acids connecting $\alpha$-helices and $\beta$-strands that enable bending and folding of the polypeptide chain, often containing proline or charged side chains.

Intrinsically Disordered Proteins (IDP)

Abundant cellular proteins that lack a rigid or ordered secondary structure in isolation, but may adopt defined structures upon environmental changes or substrate binding.

Tertiary Structure ($3^0$)

The overall three-dimensional folding and spatial arrangement of a single polypeptide chain, driven by hydrophobic interactions, non-covalent forces, and covalent disulfide bridges.

Protein Motif

A common pattern or combination of secondary structures (super-secondary structure) appearing across unrelated proteins, such as the zinc finger or hairpin loop.

Protein Domain

A compact, stable, and independently folding region of a polypeptide chain that serves as a modular building block and often executes a distinct function.

Matrix Metalloproteinases (MMPs)

A family of 23 human modular enzymes (17 soluble/secreted and 6 membrane-associated) that vary in structural domain architecture, substrate specificity, and tissue expression.

Denaturation

The process of unfolding a protein's three-dimensional structure, disrupting its biological function, caused by heat, extreme pH, heavy metals, detergents, or urea.

Disulfide Bridge

A covalent linkage formed via oxidation between the thiol (-SH) groups of two cysteine residues within the same polypeptide or between different polypeptides.

Quaternary Structure ($4^0$)

The higher-order level of protein structure formed by the interaction and association of two or more individual polypeptide subunits into a functional multimeric protein.

Homopolymer vs. Heteropolymer

A homopolymer is a multimeric protein composed of identical polypeptide subunits, whereas a heteropolymer is composed of two or more different types of subunits.