Cell Biology: The Endomembrane System, Protein Trafficking, and Cytoskeleton

Comprehensive vocabulary flashcards reviewing the endomembrane system, cotranslational translocation, vesicular trafficking, lysosomes, the cytoskeleton, molecular motors, and nuclear transport based on the Fall 2026 Review Seminar 2 lecture notes.

Endomembrane System

A coordinated network of internal membranes and organelles in eukaryotic cells that collaborates to modify, package, and transport lipids and proteins while maintaining protein orientation via post-translational modifications such as glycosylation.

Rough Endoplasmic Reticulum (RER)

The ribosome-studded region of the endoplasmic reticulum responsible for protein synthesis, protein folding and quality control via molecular chaperones, initial glycosylation, and phospholipid synthesis.

Smooth Endoplasmic Reticulum (SER)

The ribosome-lacking compartment of the endoplasmic reticulum primarily involved in lipid synthesis, steroid hormone production, detoxification, and the sequestration and storage of $Ca^{2+}$.

ER Signal Sequence

A peptide sequence located at the amino-terminus (N-terminus) of a nascent polypeptide containing several consecutive hydrophobic amino acids that targets the translation complex to the rough ER membrane.

Signal Recognition Particle (SRP)

A ribonucleoprotein complex that recognizes and binds the exposed ER signal sequence on a nascent polypeptide, transiently halting translation until it docks with the SRP receptor on the rough ER membrane.

Translocon

A proteinaceous transmembrane channel in the rough ER membrane through which the nascent polypeptide chain is threaded into the ER lumen during cotranslational translocation.

BiP

An ER-resident molecular chaperone that assists in protein folding and quality control within the ER lumen to prevent improper polypeptide folding or aggregation.

Signal-Anchor Sequence

An internal hydrophobic sequence within an integral membrane protein that halts transfer through the translocon and integrates into the ER lipid bilayer, forming a permanent transmembrane domain.

TOM Complex

The Translocase of the Outer Mitochondrial Membrane; an outer-membrane translocon complex that recognizes and imports mitochondrial proteins synthesized on free cytoplasmic ribosomes.

Anterograde Transport

Forward directional vesicular movement within the endomembrane system, traveling from the endoplasmic reticulum to the Golgi complex (cis to medial to trans) and on toward the plasma membrane or lysosomes.

Retrograde Transport

Backward directional vesicular movement within the endomembrane system, carrying components from the Golgi back to the ER or from later to earlier Golgi cisternae.

cis-Golgi Network (CGN)

The proximal entry cisternae of the Golgi apparatus that functions as a sorting station determining whether proteins proceed along the secretory pathway or are retrieved back to the ER.

trans-Golgi Network (TGN)

The distal exit cisternae of the Golgi apparatus that sorts fully processed cargo into specialized transport vesicles destined for the plasma membrane, secretory granules, or lysosomes.

Constitutive Secretion

An unregulated, continuous secretory pathway present in all eukaryotic cells that operates without requiring an external signal, steadily delivering membrane lipids, membrane proteins, and extracellular matrix components like collagen.

Regulated Secretion

A specialized secretory pathway in endocrine, exocrine, and neuronal cells where cargo is concentrated in dense-core secretory granules and released via exocytosis only in response to a specific trigger, such as a hormone, neurotransmitter, or elevated cytosolic $Ca^{2+}$.

COPII Coat

A vesicle coat protein complex that drives vesicle budding from the rough ER and mediates anterograde transport toward the cis-Golgi network.

COPI Coat

A vesicle coat protein complex that directs retrograde transport from the Golgi apparatus back to the endoplasmic reticulum or from distal to proximal Golgi cisternae.

Clathrin

A polymeric coat protein that forms curved polyhedral lattices on vesicles budding from the trans-Golgi network, endosomal compartments, and the plasma membrane during receptor-mediated endocytosis.

SNARE Proteins

Membrane-anchored fusion proteins consisting of vesicle-associated v-SNAREs and target-associated t-SNAREs that zipper together into a bundle to drive membrane apposition and fusion.

Lysosome

A membrane-bound digestive organelle ranging from $25\,\text{nm}$ to $1\,\mu\text{m}$ in size, maintaining an internal pH of $4.6$ via an $H^+\text{-ATPase}$ proton pump and containing glycosylated membrane proteins to resist autodigestion.

Acid Hydrolases

A class of hydrolytic enzymes found within lysosomes that catalyze the degradation of proteins, nucleic acids, lipids, and carbohydrates optimally at an acidic pH.

Endocytic Pathway

An outside-in trafficking route where plasma membrane proteins and extracellular substances are internalized into endocytic vesicles, traffic through early and late endosomes, and are ultimately degraded in lysosomes.

Autophagy

The cellular self-degradation pathway for organelle turnover, in which an ER-derived isolation membrane (phagophore) engulfs cytoplasmic cargo into an autophagosome, which then fuses with a lysosome to form an autolysosome.

Phagocytosis

A specialized form of endocytosis in which phagocytic cells extend pseudopods to engulf large particles or microbes into phagosomes, which subsequently fuse with lysosomes to form phagolysosomes for destruction.

Plant Vacuole

A large fluid-filled, membrane-bound organelle that can occupy up to $90\%$ of a plant cell's volume, responsible for maintaining turgor pressure, storing solutes and malate, and carrying out hydrolytic degradation at pH $5.0$.

Microtubules

Rigid, hollow cylinders approximately $25\,\text{nm}$ in diameter composed of 13 parallel protofilaments made of $\alpha\text{-tubulin}$ and $\beta\text{-tubulin}$ heterodimers, featuring distinct plus (+) and minus (-) ends.

Microtubule-Organizing Center (MTOC)

The primary eukaryotic nucleation site for microtubule assembly that anchors the minus (-) ends of microtubules, exemplified by centrosomes, spindle poles, and basal bodies.

Microfilaments (Actin Filaments)

The thinnest cytoskeletal components, measuring approximately $7\,\text{nm}$ in diameter, formed by the head-to-tail polymerization of globular actin (G-actin) into double-stranded helical filamentous actin (F-actin).

Treadmilling

A steady-state dynamic process in polarized actin microfilaments where ATP hydrolysis causes subunit dissociation at the slower-growing minus (-) end at the same rate as new ATP-bound subunits assemble at the plus (+) end.

Intermediate Filaments

Tough, rope-like structural fibers approximately $10\,\text{nm}$ in diameter composed of eight laterally bundled anti-parallel tetramers; they lack structural polarity, provide mechanical integrity, and do not associate with motor proteins.

Kinesin

An ATP-dependent motor protein family that moves outward toward the plus (+) end of microtubules to mediate anterograde transport of secretory vesicles, organelles, and protein complexes.

Cytoplasmic Dynein

An ATP-driven motor protein that moves inward toward the minus (-) end of microtubules, driving retrograde transport of endocytic vesicles, worn-out organelles, and cargo toward the MTOC near the cell center.

Myosins

A superfamily of actin-dependent motor proteins that hydrolyze ATP to walk toward the plus (+) end of microfilaments; includes conventional Type II (muscle contraction and cell motility) and unconventional types (organelle and vesicle transport).

Nuclear Envelope

A dual phospholipid bilayer boundary comprising an outer nuclear membrane continuous with the rough ER and an inner nuclear membrane supported by the nuclear lamina, segregating transcription from cytoplasmic translation.

Nuclear Lamina

A dense fibrillar meshwork of intermediate filaments (lamins and keratins) lining the inner nuclear membrane that provides mechanical support to the nuclear envelope and anchors chromatin.

Nuclear Pore Complex (NPC)

An octagonal, basket-like supramolecular gateway composed of nucleoporins (NUPs) that fuses the inner and outer nuclear membranes to permit passive diffusion ($\le 40\,\text{kDa}$) and regulated nucleocytoplasmic exchange.

Nuclear Localization Signal (NLS)

A peptide sequence enriched in positively charged amino acids within a protein that directs its selective, regulated import from the cytoplasm through the nuclear pore complex into the nucleoplasm.

Nucleolus

The dense, non-membrane-bound structure inside the nucleus responsible for the transcription of ribosomal RNA (rRNA), rRNA processing, and the assembly of the $40\text{S}$ and $60\text{S}$ ribosomal subunits.