Module Notes PDF

Module Notes Module 13: - Main product: Citric Acid + CO₂ - Peroxisome: Contains a dense crystalline core of oxidative enzymes - Endomembrane system excludes mitochondria and peroxisomes - Mitochondrial proteins: Synthesized in microsomes - Cytochrome C: Stimulates apoptosis cascade - Intermediate s...

Module Notes Module 13: - Main product: Citric Acid + CO₂ - Peroxisome: Contains a dense crystalline core of oxidative enzymes - Endomembrane system excludes mitochondria and peroxisomes - Mitochondrial proteins: Synthesized in microsomes - Cytochrome C: Stimulates apoptosis cascade - Intermediate space: Impermeable to most membranes due to protein gradient maintenance for ATP synthesis - Peroxisome: Involved in bile acid and phospholipid synthesis - Inner Mitochondria Membrane: Forms cristae, involved in electron transport Module 14: - N-linked glycosylation: Rough ER - Cytosol and Nucleus: Gated transport - Translocon: Transfers peptide chain during protein synthesis - Steroid hormone synthesis: Smooth ER - Glucosidase I and II: Trim glucose residues and prevent misfolding (CNX and CRT) Module 15: - Proteasome: Degrades misfolding proteins in the ER pathway - CRTR (Cystic fibrosis transmembrane regulator): Not a stress sensor, but important for transmembrane signaling - Phosphorylation of N-linked oligosaccharides: Forms mannose-6-phosphate for lysosomal targeting - Synthesis of sphingomyelin and glycolipids: Occurs in the Smooth ER - Foldases: Bind to misfolded proteins (CNX and CRT) - Amyloid proteins: Aggregate into fibers causing misfolding-related disorders GDP and GTP Cycle: - GDI (Guanine Nucleotide Dissociation Inhibitor): Prevents anchorage of small GDP-bound proteins - GTP Hydrolysis: Occurs after vesicle fusion, converting GTP to GDP - GEF (Guanine Exchange Factor): Exchanges GDP for GTP, activating small GTPases - SOS: Acts as a GEF for Ras signaling in the RAS-GTP pathway - Rab Proteins: GTPases involved in intracellular vesicle targeting - Rab-GDP: Inactive form, returned to the cytoplasm after hydrolysis  - Rab-GTP: Active form, involved in vesicle fusion - ARF: Involved in vesicle fusion with acceptor membranes; activated by GTP binding, inactivated by GDP hydrolysis Quiz 4 (Key Concepts Review): - Topography: Configuration, arrangement, and position of cell components - Mitochondria: Does not participate in topographical arrangement during cell division; it mixes everything - ER lumen: Continuous with the nucleus - N-terminus signal peptide: In ER during protein synthesis - Default protein pathway: - If made in the nucleus, stays in the cytosol - If made in the RER, leaves the cell - Mitochondria: Can release cytochrome C for programmed cell death (apoptosis) - Contains circular, self-replicating, double-stranded mtDNA - Chaperones: Assist in protein folding (in the ER) - Signaling Sequence: Short stretch of amino acids that leave the cell Additional Notes on Protein Processing: - Biological membranes: Selectively permeable - Misfolding protein (selectively retained): Remains in the ER bound to chaperones like Bip or calnexin - Localization signals: Allow large proteins to enter the nucleus