Protein Structure and Function - Vocabulary Flashcards

Key vocabulary terms and concise definitions covering protein structure, folding, function, regulation, and common experimental methods.

Conformation

The three-dimensional shape of a protein; correct folding is essential for function; function derives from structure.

Primary structure

Linear sequence of amino acids in a protein; contains intrinsic information on how folding occurs.

Secondary structure

Local folding patterns stabilized mainly by hydrogen bonds; includes alpha helices, beta sheets, beta turns, and random coils.

Alpha helix

Right-handed helical structure with about 3.6 amino acids per turn; carbonyl oxygens hydrogen-bond to amide nitrogens; R groups project outward and the helix has a dipole.

Beta sheet

Pleated sheet formed by hydrogen bonds between backbone of adjacent strands; can be parallel or antiparallel; 5–8 residues per strand.

Beta turn

A tight turn (often four amino acids) that reverses the direction of the polypeptide chain; glycine and proline are common here.

Amphipathic

Molecule or region with both hydrophilic (polar) and hydrophobic (nonpolar) parts, often seen in helices.

Random coil

Irregular, flexible region connecting regular secondary structures; lacks a well-defined structure.

Peptide bond

Planar bond between carboxyl carbon of one amino acid and amino nitrogen of the next; has partial double-bond character.

Polypeptide

A polymer of many amino acids linked by peptide bonds; can fold to form a protein.

Amino acid

Monomer building block of proteins; contains an amino group, a carboxyl group, and a side chain (R).

Hydrophobic interactions

Driving force for protein folding; burying nonpolar side chains away from water into the protein core.

Hydrogen bonds

Noncovalent bonds between hydrogen donors and acceptors; stabilize secondary and tertiary structures.

Ionic interactions

Electrostatic attractions (salt bridges) between oppositely charged side chains; contribute to stability.

Van der Waals interactions

Weak noncovalent forces between close nonpolar atoms; contribute to tight packing.

Disulfide bonds

Covalent bonds between cysteine residues; stabilize folded protein structure.

Domain

A distinct structural/functional module within a protein; can fold independently.

Motif

A short, recurring structural feature within proteins; part of a domain and often linked to function.

Leucine zipper (coiled coil motif)

Amphipathic alpha-helical region with a heptad repeat (often Leu) that drives dimerization.

EF-hand motif

Ca2+-binding helix-loop-helix motif found in many calcium-binding proteins.

Helix-loop-helix motif

A common DNA-binding or dimerization motif consisting of two helices separated by a loop.

Zinc-finger motif

A motif with coordinating Zn2+ ions (often Cys/His) that binds DNA or RNA.

Alpha helical wheel

A visual representation of side-chain properties around an alpha helix, highlighting amphipathicity.

Parallel/antiparallel beta sheets

Two arrangements of beta strands relative to each other; affects hydrogen-bond geometry.

Protein folding

Process by which a polypeptide folds into its native three-dimensional structure under thermodynamic control.

Native state

The most thermodynamically stable, functional conformation of a protein.

Denaturation

Loss of protein structure due to heat, pH change, or chemicals; can be reversible or irreversible.

Renaturation

Refolding of a denatured protein back toward its native state (not always possible).

Proline isomerases

Enzymes that catalyze cis-trans isomerization of peptide bonds at X-Pro, influencing folding.

Molecular chaperone

Proteins that assist the folding of other proteins without being part of the final structure.

Hsp70

A molecular chaperone that binds unfolded proteins and uses ATP to drive folding.

Hsp90

A molecular chaperone that stabilizes and folds many client proteins.

Chaperonin

Large protein complexes that provide an isolated folding chamber for substrates.

GroEL/GroES

Bacterial chaperonin system forming a folding chamber with an encapsulated substrate.

TRiC (CCT)

Eukaryotic chaperonin complex aiding folding of many cytosolic proteins.

Amyloid

Misfolded protein aggregates that can form fibrils and plaques linked to neurodegenerative diseases.

Ligand

Molecule that binds specifically to a protein, often modulating function.

Substrate

Reactant molecule that binds to an enzyme in a catalytic process.

Affinity

Strength of binding between a protein and its ligand; related to the dissociation constant.

Kd

Dissociation constant; lower values indicate tighter binding between protein and ligand.

Km

Michaelis constant; substrate concentration at 1/2 Vmax; reflects enzyme affinity for substrate.

Vmax

Maximum velocity of an enzyme-catalyzed reaction at saturating substrate.

Kcat (turnover number)

Number of substrate molecules processed per enzyme molecule per second.

Michaelis–Menten equation

v = Vmax [S] / (Km + [S]); describes how rate depends on substrate concentration.

Allosteric regulation

Regulation of protein activity via binding at a site other than the active site, often cooperative.

Allosteric switch

Noncovalent conformational change that toggles a protein between active and inactive states.

Calmodulin

A Ca2+-binding protein that activates target enzymes when bound to Ca2+.

Ca2+

Calcium ion; acts as a second messenger in many allosteric and signaling processes.

Ras/Ran GTPases

Small GTP-binding proteins that regulate signaling; activity controlled by GEFs and GAPs.

GEF

Guanine nucleotide exchange factor; promotes GDP→GTP exchange to activate GTPases.

GAP

GTPase-activating protein; accelerates GTP hydrolysis to GDP, inactivating GTPases.

Phosphorylation

Covalent addition of a phosphate group to serine, threonine, or tyrosine, regulating activity.

Ubiquitination

Covalent attachment of ubiquitin to lysine; marks proteins for degradation or signaling roles.

Proteasome

Proteolytic complex that degrades ubiquitinated proteins in the cytosol.

Ubiquitin

Small 76-aa protein that tags other proteins for ubiquitination; can form chains.

Proteolytic cleavage

Proteases cleave proteins to activate or inactivate function; often crucial in maturation.

cAMP

Cyclic adenosine monophosphate; a second messenger activating PKA and other targets.

Regulatory vs catalytic subunits

Subunits that regulate or execute activity; in PKA, regulatory subunits inhibit catalytic ones until cAMP binding occurs.

PKA (Protein Kinase A)

A cyclic-AMP–dependent kinase; regulates many targets via phosphorylation.

Allosteric cooperativity

Binding of a ligand to one subunit increases affinity at other subunits; e.g., hemoglobin and PKA regulatory subunits.

Hemoglobin

Oxygen transport protein with cooperative, allosteric O2 binding across subunits.

Heme

Iron-containing prosthetic group in hemoproteins; binds gases like O2.

X-ray crystallography

Technique to determine precise 3D structure by diffraction of X-rays by a crystal.

Cryo-electron microscopy

High-resolution imaging technique that freezes samples in vitreous ice to determine structures.

NMR (Nuclear Magnetic Resonance)

Technique to determine molecular structure from magnetic properties of nuclei; best for smaller proteins.

Mass spectrometry

Analytical method to determine mass/sequence of proteins and peptides (MALDI-TOF, ESI, MS/MS).

MALDI-TOF

Matrix-assisted laser desorption/ionization mass spectrometry; rapid mass measurement of biomolecules.

ESI

Electrospray ionization mass spectrometry; suitable for analyzing large biomolecules.

LC-MS/MS

Liquid chromatography with tandem mass spectrometry; separates and sequences complex mixtures.

2D gel electrophoresis

Technique separating proteins by isoelectric point (IEF) and size, enabling high resolution.

Edman degradation

Sequential method to identify the N-terminal amino acid of a protein.

Pulse-chase

Experiment labeling newly synthesized proteins and tracking their fate over time.

Domain modularity

Proteins often consist of multiple domains that can be mixed and matched across proteins.

Proteomics

Study of the protein content of a cell or tissue, often involving large-scale identification and quantification.