Trafficking through the Endomembrane System

Proteins are routed from the ER lumen to the Golgi complex, secretory vesicles, or back to the ER.
Sorting begins in the ER and early Golgi, with final sorting occurring in the trans-Golgi network (TGN).
Protein Tags: Features like amino acid sequences, hydrophobic domains, or oligosaccharide side chains determine destination or exclusion from vesicles.

Retention Tags: The sequence $RXR$ ( $\text{Arg-X-Arg}$ ) is used to retain proteins in the ER until multi-subunit complexes (e.g., $NMDA$ receptors) are fully assembled.
Retrieval Tags: Short C-terminal sequences such as $KDEL$ ( $\text{Lys-Asp-Glu-Leu}$ ) or $KKXX$ in mammals, and $HDEL$ ( $\text{His-Asp-Glu-Leu}$ ) in yeast, trigger return from the Golgi via receptor-ligand complexes.
Golgi Sorting: Integral membrane proteins are sorted by the length of their hydrophobic membrane-spanning domains. Membrane thickness increases from the ER (5\text{nm}) to the plasma membrane (8\text{nm}).

Mannose-6-Phosphate (M6P) Tag: Soluble lysosomal enzymes are $N\text{-glycosylated}$ in the ER. In the Golgi, mannose residues are phosphorylated to form $M6P$ , ensuring delivery to lysosomes via late endosomes.
Acidification: Lysosomes maintain an acidic environment ( $\text{pH } 4.0\text{–}5.0$ ) using ATP-dependent proton pumps ( $V\text{-ATPases}$ ) to activate acid hydrolases.
Clinical Relevance: Defects in lysosomal proteins lead to Lysosomal Storage Diseases, such as $Type\text{ }II\text{ }glycogenosis$ , $Hurler\text{ }syndrome$ , and $Tay\text{-Sachs}\text{ }disease$ .

Stop-Transfer Sequences: Polypeptides with an N-terminal ER signal sequence are halted during translocation by a hydrophobic stop-transfer sequence, resulting in a Type I transmembrane protein.
Internal Start-Transfer Sequences: Proteins without an N-terminal signal use an internal sequence bound by $SRP$ to target the ER, resulting in a Type II transmembrane protein.
Multi-pass Proteins: Alternating start-transfer and stop-transfer sequences are used for proteins with multiple segments (e.g., $GPCRs$ with seven domains).
Posttranslational Import: Proteins synthesized in the cytosol avoid folding via $Hsp70$ chaperones and are pulled into the ER lumen by $BiP$ using $ATP$ hydrolysis through the $Sec61$ pore.

Exocytosis: * Constitutive: Unregulated, continuous fusion with the plasma membrane (e.g., mucus secretion). * Regulated: Vesicles fuse only in response to specific signals (e.g., neurotransmitter release). * Polarized: Secretion limited to a specific cell surface (e.g., intestinal cells).
Endocytosis: * Phagocytosis: Ingestion of solid particles. * Pinocytosis: Uptake of liquids. * Receptor-Mediated: Occurs at clathrin-coated pits (20\text{%} of surface area), involving ligands binding to surface receptors.

Coat Proteins: * Clathrin: Mediates transport from the TGN or plasma membrane to endosomes. Basic unit is a triskelion. * COPI: Involved in retrograde transport (Golgi to ER); uses $ARF$ ( $\text{ADP ribosylation factor 1}$ ). * COPII: Involved in anterograde transport (ER to Golgi); involves $Sar1$ , $Sec\text{ }13/31$ , and $Sec\text{ }23/24$ .
Dynamin: A cytosolic $GTPase$ that constricts and closes budding vesicles.
SNARE-Mediated Fusion: * $v\text{-SNAREs}$ (vesicle) and $t\text{-SNAREs}$ (target) provide recognition. * $Rab\text{ }GTPases$ stimulate $SNARE$ association. * $NSF$ and $SNAPs$ promote the dissociation of the $SNARE$ complex after fusion.

Peroxisomes: Bounded by a single membrane and characterized by catalase for degrading $H_2O_2$ . They function in fatty acid $(\beta\text{ oxidation})$ and detoxification.
Autophagy: The "self-eating" process for breaking down damaged cellular structures, recently linked to cancer.