06 - Lysosomes, Protein Turnover, and Peroxisomes

lyosomes

membrane-bound organelles that function as cell’s recycling and digestive centers

• arise from Golgi

• contain many acid hydrolases, enzymes that work best in acidic pH to break down proteins, lipids, nucleic acids, and carbohydrates

• work in an optimal pH of 5.0, and degraded when pH is raised

  • acidification maintained by v-type H⁺-ATPases pump

• lysosomal membrane proteins (LAMPs) protect membrane from self-digestion

endolysosome

hybrid organelle formed when late endosome fuses with a lysosome

• functional lysosome that is actively digesting material

• acid hydrolase made in ER is transported to Golgi, where it is tagged by mannose-6-phosphate (N-link glycosylation)

• M6P receptors in Golgi bind enzyme and package them into vesicles to bud off and fuse with late endosomes

• late endosome becomes acidic and causes receptors to release enzymes for activation

• when late endosome containing cargo fuses with lysosome carrying endolyosome, endolysosome is formed

receptor-mediated endocytosis

highly selective way for cells to bring in specific molecules from outside by using cell-surface receptors and forming clathrin-coated vesicles

• extracellular molcule binds to its receptor on plasma membrane

• adaptins bind receptors on inner side of cell membrane

• clathrin proteins assemble into lattice by binding adaptins and pulling them, bending membrane inward

• dynamin pinches off, forming a clathrin-coated vesicle

LDL and cholesterol

• LDL is brought into the cell via reeptor-mediated endocytosis

  • binding of LDL to receptor recruits adaptins, clathrins, and dynamin to create clathrin-coated vesicle

• clathrin coat is removed, leaving vesicle naked

• vesicle fuses with early endosome, whose acidic pH causes the ligand to dissociate from the receptor

  • receptor is recycled back to plasma membrane

• ligand is sent to late endosomes and then lysosomes for degradation

• LDL is degraded by hydrolytic enzymes, releasing free cholesterol into cytosol

  • free cholesterol exhibits feedback inhibition, where it stops making more cholesterol once detected inside the cell

microautophagy

lysosome engulfs its cytoplasmic material directly by invagination of its own membrane

• receptor-mediated endocytosis from plasma membrane has ubiquitin signal that targets cargo for lysosomal degradation

• cargo captured by early endosome and then invaginates its membranes, creating vesicles within the vesicle

• multivesuclar body combines with lysosome and breaks down contents

macroautophagy

use of double-membrane vesicle called autophagosome

• small, cup-shaped membrane forms in cytoplasm to engulf bulk cytoplasm or specific cargo

• phagophore membrane expands and seals, forming a double-membrane vesicle called autophagosome

• autophagosome fuses with lyosome to create autolysosome

• acid hydrolases inside defgrade cargo and result in residual body

direct protein transfer/chaperone-mediated autophagy

selective pathway where individual proteins are directly transported across lysosomal membrane for degradation

• cytosolic proteins have a specific amino acid sequence that is recognized by Hsc70 chaperone protein (heat shock protein)

• Hsc70 escorts protein to lysosomal membrane to dock with LAMP-2A receptor (lysosome associated membrane protein)

• target is unfolded to pass through narrow channel, and protein is translocated across lysosomal membrane into lumen

• once inside, lyosomal hydrolases degrade protein into amino acids for recycling

proteasomes

large barrel-shaped protein complexes in cytoplasm and nucleus that degrade unwanted or damaged proteins into short peptides, handling proteins specifically tagged with ubiquitins

• 20S core (proteolytic chamber) and 19S caps (recognize ubiquitinated proteins and feed inside chamber)

• target proteins are tagged with ubiquitin molecules at lysine residues

• regulatory cap binds polyubiquitin chain

• protein is unfolded using ATP and threaded into 20S core, where protease cuts protein into peptides

• peptides are released into cytoplasm and further degraded into amino acids for reuse

peroxisomes

small, membrane-bound organelles found in eukaryotic cells that carry oxidative reactions to break down fatty acids, amino acids, and toxins, producing hydrogen peroxide as a byproduct

• beta oxidation of very long chain fatty acids (VLCFAs)

• detoxification of hydrogen peroxide

  • oxidases produce hydrogen peroxide, catalase breaks down hydrogen peroxide

• synthesis of plamalogen phospholipids in perixosomes

• formation of new peroxisomes by division of pre-existing peroxisomes

• import of matrix proteins requires perixsomal targeting signals (PTS1/PTS2) to get into perixosome

ubiquitin tagging

• ubiquitin: small protein covalently attached to substrates for degradation

• required cascade of enzymes

  • E1 → activating enzyme (ATP-dependent)

  • E2 → conjugating enzyme

  • E3 → ligase (specificity for substrates)

• polyubiquitin chains → signal for proteasome degradation