BIOL 3030 – Protein Structure and Function - LEC 2 - Stevens

Vocabulary flashcards covering major concepts of amino-acid chemistry, hierarchical protein structure, folding mechanisms, binding and catalysis, enzyme kinetics, and regulatory strategies discussed in Lectures 2 and 3.

Amino Acid

The monomeric building block of proteins, composed of an α-carbon, amino group, carboxyl group, hydrogen, and variable R (side-chain) group.

R Group (Side Chain)

The variable part of an amino acid that determines its chemical properties and classification.

L-Isomer

The naturally occurring optical isomer of amino acids incorporated into proteins.

Optical Isomer (Enantiomer)

One of a pair of non-superimposable mirror-image molecules produced by an asymmetric carbon.

Hydrophobic Amino Acid

An amino acid with a non-polar side chain that avoids water and is usually buried inside proteins.

Hydrophilic Amino Acid

An amino acid with polar or charged side chains that interact favorably with water.

Charged Amino Acid

An amino acid whose side chain is positively or negatively charged at physiological pH.

Peptide Bond

The covalent amide linkage joining two amino acids between the carboxyl carbon of one and the amino nitrogen of the next.

N-Terminus

The end of a polypeptide with a free amino group; written first in primary sequences.

C-Terminus

The end of a polypeptide with a free carboxyl group; written last in primary sequences.

Primary Structure

The linear sequence of amino acids in a polypeptide chain.

Secondary Structure

Local repetitive folding of the backbone into α-helices, β-sheets, or β-turns stabilized by hydrogen bonds.

α-Helix

A right-handed secondary-structure spiral with 3.6 residues per turn and side chains projecting outward.

β-Sheet

Secondary structure formed by hydrogen bonding between backbone strands arranged in parallel or antiparallel orientation.

β-Turn

A short secondary-structure motif that reverses the direction of a polypeptide chain, often containing glycine or proline.

Tertiary Structure

The overall three-dimensional conformation of a single polypeptide stabilized by side-chain interactions and disulfide bonds.

Motif

A recurring short amino-acid sequence and corresponding structural pattern found in many different proteins.

Domain

A large, independently folding and often functionally distinct region within a protein.

Quaternary Structure

The arrangement and interaction of multiple polypeptide chains (subunits) in a protein complex.

Supramolecular Complex (Molecular Machine)

A large assembly of many proteins (and often RNA) that carries out a coordinated biological function, such as the ribosome or proteasome.

Protein Family

A group of homologous proteins sharing similar primary sequence and three-dimensional structure, indicating common ancestry.

Molecular Chaperone

A protein that binds nascent or unfolded polypeptides to prevent misfolding and promote correct folding, using ATP.

Chaperonin

A cylindrical chaperone complex that encloses unfolded proteins in an ATP-dependent folding chamber.

Hsp70

An ATP-dependent molecular chaperone that binds short hydrophobic regions of nascent chains to aid folding.

GroEL/GroES

The bacterial chaperonin complex that forms a double-ring folding chamber capped by GroES.

Ligand

Any molecule that specifically binds to a protein.

Specificity

The preference of a protein to bind one ligand over others.

Affinity

The strength of binding between a protein and its ligand, often expressed by the dissociation constant (Kd).

Antibody

An immunoglobulin protein that specifically binds antigens through variable regions and CDR loops.

Antigen

A molecule recognized and bound by an antibody.

Enzyme

A protein (or RNA) catalyst that accelerates chemical reactions by lowering activation energy without altering ΔG.

Active Site

The region of an enzyme where substrate binding and catalysis occur, often comprising binding and catalytic subsites.

Vmax

The maximum reaction velocity achieved by an enzyme at saturating substrate concentration.

Km (Michaelis Constant)

The substrate concentration at half-maximal velocity; inversely related to enzyme-substrate affinity.

Michaelis–Menten Kinetics

The quantitative relationship describing how reaction rate varies with substrate concentration for many enzymes.

Scaffold Protein

A protein that holds multiple enzymes of a metabolic pathway in close proximity, enhancing flux.

Allostery

Regulation of protein activity through ligand-induced conformational changes at a site distinct from the active site.

Cooperativity

A form of allostery where ligand binding to one subunit alters affinity in other subunits, as in O₂ binding to hemoglobin.

Proteasome

An ATP-dependent macromolecular machine that degrades polyubiquitinated proteins into short peptides.

Ubiquitin

A 76-residue polypeptide covalently attached to lysine residues of target proteins to signal degradation or other fates.

Polyubiquitination

Attachment of a chain of ubiquitin molecules to a protein, with linkage type dictating function (e.g., Lys48 for degradation).

Phosphorylation

Reversible covalent addition of a phosphate group (often to Ser, Thr, or Tyr) that modulates protein activity.

Proteolytic Cleavage

Irreversible cutting of a polypeptide backbone that activates or inactivates a protein (e.g., zymogen activation).

GTP-Binding Protein (G-Protein)

A molecular switch that cycles between active GTP-bound and inactive GDP-bound states to regulate signaling.

Calmodulin

A calcium-binding switch protein whose Ca²⁺-induced conformational change modulates target proteins.