MTG Past Paper, Intracellular Compartments and Protein Transport (2019)

Chapter 15 Intracellular Compartments and Protein Transport continuation April 03 (W) – April 08 (M) - MTG 24 from April 01 continues April 03 Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company PROTEINS ENTER PEROXISOMES FROM BOTH THE CYTOSOL AND THE ENDOPLASMIC RETICULUM...

Chapter 15 Intracellular Compartments and Protein Transport continuation April 03 (W) – April 08 (M) - MTG 24 from April 01 continues April 03 Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company PROTEINS ENTER PEROXISOMES FROM BOTH THE CYTOSOL AND THE ENDOPLASMIC RETICULUM Peroxisome produces enzymes that breakdown toxins, alcohols and fatty acids synthesis certain phospholipids Peroxisome produces enzymes that produces hydrogen peroxide bulk of proteins come from the cytosol some proteins arrive via vesicles that bud from the ER PROTEINS ENTER PEROXISOMES FROM BOTH THE CYTOSOL AND THE ENDOPLASMIC RETICULUM bulk of proteins come from the cytosol the import signal: SKL (ser-lys-leu) peroxisomal membrane contains protein translocator Proteins do not need to unfold when entering the peroxisomes. Zellweger syndrome- mutations that block peroxisomal protein import -affects liver, kidney, brain -affected individuals usually do not survive 6 months PROTEIN SORTING Proteins enter peroxisomes from both the cytosol and the endoplasmic reticulum. bulk of proteins come from the cytosol Signal sequences, protein receptors and protein translocators are required for protein transport from cytosol to organelles such as the peroxisomes. Protein does not need to unfold to enter the peroxisome via translocator. Proteins Are Transported into Organelles by Three Mechanisms Nuclear Pores Protein Translocators Transport Vesicles THE ENDOPLASMIC RETICULUM IS THE MOST EXTENSIVE MEMBRANE NETWORK IN EUKARYOTIC CELLS. Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company PROTEINS TRANSPORTED TO THE GOLGI APPARATUS, ENDOSOMES, LYSOSOMES, AND THE CELL SURFACE, FIRST ENTER THE ER FROM THE CYTOSOL. Protein trafficking is used to describe the process of moving proteins from the rough ER, through the Golgi apparatus, where they are modified and packaged into vesicles. Some proteins are retained the GOLGI APPARATUS ER , in they send signals LYSOSOMES ENDOSOMES THE CELL SURFACE https://www.youtube.com/watch?v=rvfvRgk0MfA Protein Trafficking Endomembrane System Proteins transported to the Golgi apparatus, endosomes, lysosomes, and the cell surface, all must first enter the ER from the cytosol. PROTEIN SORTING Proteins Enter the Endoplasmic Reticulum While Being Synthesized A COMMON POOL OF RIBOSOMES SYNTHESIZES ALL THE PROTEINS ENCODED BY THE NUCLEAR GENOME. Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Proteins Entry Through The ER Water-soluble proteins cross the ER membrane completely and are released into the lumen. Soluble proteins made in the ER are released into the ER lumen. KDEL at C-terminal acuous Transmembrane proteins only partially cross the ER and become embedded in the membrane. All these proteins are directed to the ER by a signal sequence of small hydrophobic amino acids. Entry of Proteins in the ER signal recognizes peptide- Signal SRP-Protein that will recognize SRP translocate Translocater SRP receptor Translocator proteins Start signal; stop signals- , the proteins Proteins Entry Through The ER Proteins Entry Through The ER The signal sequence is guided to the ER membrane with a signal-recognition particle (or SRP) which binds the ER signal sequence in the new protein as it emerges from the ribosome. AN ER SIGNAL SEQUENCE AND AN SRP DIRECT A RIBOSOME TO THE ER MEMBRANE. it Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company receives SRP PROTEINS ENTER THE ENDOPLASMIC RETICULUM WHILE BEING SYNTHESIZED PROTEINS ENTER THE ENDOPLASMIC RETICULUM WHILE BEING SYNTHESIZED In addition to directing proteins to the ER, the signal sequence functions to open the translocation channel. Glowing protein is be starting to translocated to ER the A SOLUBLE PROTEIN CROSSES THE ER MEMBRANE AND ENTERS THE LUMEN. Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company PROTEIN SORTING Start and Stop Signals Determine the Arrangement of a Transmembrane Protein in the Lipid Bilayer A Single-Pass Transmembrane Protein Is Retained In The Lipid Bilayer. not all will be lumen in the released Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company A Double-Pass Transmembrane Protein Has An Internal ER Signal Sequence. Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company PROTEINS ENTER THE ENDOPLASMIC RETICULUM WHILE BEING SYNTHESIZED PROTEIN SORTING Proteins Are Transported into Organelles by Three Mechanisms Signal Sequences Direct Proteins to the Correct Compartment Proteins Enter the Nucleus Through Nuclear Pores Proteins Unfold to Enter Mitochondria and Chloroplasts Proteins Enter Peroxisomes from both the Cytosol and the Endoplasmic Reticulum PROTEIN SORTING Proteins Enter the Endoplasmic Reticulum While Being Synthesized Soluble Proteins Made on the ER Are Released into the ER Lumen Start and Stop Signals Determine the Arrangement of a Transmembrane Protein in the Lipid Bilayer PROTEINS ARE TRANSPORTED INTO ORGANELLES BY THREE MECHANISMS Nuclear Pores Protein Translocators Sorting signal or signal sequence Transport Vesicles Example: hydrophobic signal sequence, KDEL Vesicular Transport Allows Materials To Exit Or Enter The Cell. Exocytosis versus Endocytosis a vesicle fuses with the plasma membrane, releasing its content to the cell’s surroundings extracellular materials are captured by vesicles that bud inward from the plasma membrane Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company VESICULAR TRANSPORT For some proteins delivered to the ER, this is just their first “stop”; they are still destined for another location. Transport Vesicles Carry Soluble Proteins And Membrane Between Compartments Transport vesicles bud from one membrane and fuse with another, carrying membrane components and soluble proteins between compartments of the endomembrane system and the plasma membrane. VESICULAR TRANSPORT Transport Vesicles Vesicle Budding Protein Coat Vesicle Budding is Driven by the Assembly of a Protein Coat Vesicles coated on the cytosolic side Examples: clathrin-coated vesicles COP (coat protein)- coated vesicles Clathrin molecules form basketlike cages that help shape membranes into vesicles. (A) Electron micrographs showing the sequence of events in the formation of a clathrin-coated vesicle from a clathrin-coated pit. (B) Electron micrograph showing numerous clathrin-coated pits and vesicles budding from the inner surface of the plasma membrane of cultured skin cells. (C) In a test tube, clathrin molecules sometimes selfassemble into basketlike cages Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Vesicle Budding is Driven by the Assembly of a Protein Coat cargo receptor adaptin clathrin coat dynamin- VESICLE IS DRIVEN BY THEby ASSEMBLY OF A PROTEIN VesicleBUDDING Budding is Driven the Assembly of COAT a Protein Coat VESICLE BUDDING IS DRIVEN BY THE ASSEMBLY OF A PROTEIN COAT cargo receptor- receives a specific molecule to be delivered adaptin- recognizes a specific cargo receptor clathrin coat- shapes the membrane into a vesicle dynamin- together with other proteins causes pinching off of the vesicle Clathrin-coated vesicles transport selected cargo molecules. cargo receptoradaptinclathrin coatdynamin- Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Clathrin-coated vesicles transport selected cargo molecules. dynamin is recruited around the neck of budding vesicles but fail to pinch them off Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Types of Coated Vesicle Coat Proteins origin Destination Clathrin-coated clathrin + adaptin 1 Golgi apparatus lysosome (via endosomes) Clathrin-coated clathrin + adaptin 2 plasma membrane endosomes COPII-coated COPII proteins ER Golgi cisterna COPI-coated COPI proteins Golgi cisterna ER Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company VESICULAR TRANSPORT Transport Vesicles Vesicle Budding Protein Coat Vesicle Docking Depends on Tethers and SNAREs After the vesicle has been formed, it has to be delivered to the target organelle. Rab proteins V-SNARES How do vesicles match up with the correct target organelle? Tethering proteins T-SNARES Vesicle Docking Depends on Tethers and SNAREs Proteins for initial recognition? Rab proteins, tethering proteins, and SNAREs help direct transport vesicles to their target membranes. SNAREs roles? Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company VESICLE DOCKING DEPENDS ON TETHERS AND SNARES Snare proteins aid in docking vesicles as well as catalyzing the membrane fusion process https://www.youtube.com/watch?v=V2FrQB6rX34 VESICULAR TRANSPORT Transport Vesicles Carry Soluble Proteins and Membrane Between Compartments Vesicle Budding Is Driven by the Assembly of a Protein Coat Vesicle Docking Depends on Tethers and SNAREs LEARNING OUTCOMES to outline the sequence of events in the travel of proteins in the secretory pathway to discuss the different modifications occurring as proteins travel in the secretory pathway to discuss fundamental concepts of the endocytic pathway -pinocytosis, phacytosis, receptor-mediated SECRETORY PATHWAYS Molecules travel through a fixed sequence of membrane-enclosed compartments and are often modified en route. Example: They travel from ER to Golgi to the plasma membrane. If proteins are not folded properly and assembled with their appropriate partners, these proteins are degraded. Most proteins are covalently modified in the ER. ❖ disulfide bond formation The formation of disulfide bonds between cysteine residues occurs during the folding of many proteins that enter the secretory pathway. Most proteins are covalently modified in the ER. ✓ disulfide bond formation ✓ proteins are glycosylated on asparagines Most proteins are covalently modified in the ER ✓ proteins are glycosylated on asparagines When an appropriate asparagine in a growing polypeptide chain enters the ER lumen, it is glycosylated by adding a branched oligosaccharide side chain. Most proteins are covalently modified in the ER Glycosylation: The sugar chain is linked to Asn serve for protection of the proteins from degradation help guide it to the proper organelle oligosaccharide chain added Most proteins are covalently modified in the ER Oligosaccharides are usually further modified by enzymes in the ER and the Golgi before the glycoprotein is inserted into the plasma membrane. Exit from the ER is controlled to ensure protein quality Proteins must be properly folded. proteins need appropriate , if to be folded not it cannot function Chaperone Protein folded its sure makes properly If misfolded proteins accumulate in the ER, it triggers unfolded protein response (UPR) Accumulation of misfolded proteins in the ER lumen triggers an unfolded protein response (UPR). The misfolded proteins are recognized by several types of transmembrane sensor proteins in the ER membrane, each of which activates a different component of the UPR. Effect? Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company THE SIZE OF THE ER IS CONTROLLED BY THE DEMAND FOR PROTEIN UPR prompts cells to produce more chaperones and other proteins concerned with quality control. SECRETORY PATHWAYS Exit from the ER is controlled to ensure protein quality The size of the ER is controlled by the demand for protein folding SECRETORY PATHWAYS Exit from the ER is controlled to ensure protein quality The demand for protein folding controls the size of the ER. Proteins are further modified and sorted in the Golgi apparatus Golgi apparatus- collection of flattened membrane sacs called cisternae Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Cis closer to ER seane closer Trans to Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company PROTEINS ARE FURTHER MODIFIED AND SORTED IN THE GOLGI APPARATUS additional glycosylation and sorting occurs in the Golgi Electron micrograph of a Golgi stack from a plant cell, where the Golgi apparatus is especially distinct Secretory proteins are released from the cell by exocytosis O Vesicles bud from the trans face of the Golgi and fuse with the plasma membrane Constitutive exocytosis pathway operates continually in all eukaryotic cells Regulated exocytosis pathway operates only in cells specialized for secretion in cells that produce large quantities of a particular product Hormones, mucus, digestive enzymes contents of the vesicles are released via a signaling mechanism acidic pH and high calcium concentration in the trans- golgi Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Secretory vesicles store and release concentrated proteins. The process, which takes place through vesicle docking and fusion requires a signal to initiate. Example? Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company The cryoelectron micrograph shows the release of concentrated neurotransmitter from a cultured mouse hippocampal neuron. Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company SELECTIVE AGGREGATION OF PROTEINS DESTINED FOR REGULATED EXOCYTOSIS Allows for the release of large amounts of proteins acidic pH and high calcium concentration in the trans- golgi SECRETORY PATHWAYS Most proteins are covalently modified in the ER Exit from the ER is controlled to ensure protein quality The demand for protein controls the size of the ER Proteins are further modified and sorted in the Golgi apparatus Secretory proteins are released from the cell by exocytosis LEARNING OUTCOMES to outline the sequence of events in the travel of proteins in the secretory pathway to discuss the different modifications occurring as proteins travel in the secretory pathway to discuss fundamental concepts of the endocytic pathway -pinocytosis, phagocytosis, receptor-mediated endocytosis ENDOCYTIC PATHWAYS Endocytosis- the process of taking up fluid, as well as large and small molecules Material to be ingested is enclosed by a portion of the plasma membrane, pinching off to form an endocytic vesicle. Main types: Pinocytosis Phagocytosis Receptor-mediated endocytosis SPECIALIZED PHAGOCYTIC CELLS INGEST LARGE PARTICLES Example: macrophage- WBC binding, activating receptors, extending sheet-like projections of the plasma membrane called pseudopods Engulfing, tips fused to form a phagosome Phagocytosis: WBC engulfing RBCs; Pseudopods extending to envelope or engulf the RBC. On the other hand, fluid and small molecules are taken up by pinocytosis. MAIN TYPES OF ENDOCYTOSIS RECEPTOR-MEDIATED ENDOCYTOSIS PROVIDES A SPECIFIC ROUTE INTO ANIMAL CELLS molecules bind to specific receptors selective concentrating mechanisms This pathway of cholesterol uptake is disrupted in individuals with a defective gene encoding LDL receptors as a result cholesterol accumulates in the blood and predisposes the individual to clogging of the arteries or atherosclerosis Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Viruses can enter cells via receptor-mediated endocytosis. Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company A pair of viruses have been taken up by receptor-mediated endocytosis. These vesicles will fuse with lysosomes, where the low pH will allow the release of the viral genome into the Essential Cell Biology, Fifth Edition cytoplasm—a necessary step in viral replication. Copyright © 2019 W. W. Norton & Company Endocytosed macromolecules are sorted in endosomes The “fate” of the vesicle membrane (1), (2), (3) The fate of receptor proteins following their endocytosis depends on the type of receptor. LYSOSOMES ARE THE PRINCIPAL SITES OF INTRACELLULAR DIGESTION Most of lysosomal membrane proteins are glycosylated. The lumen of the lysosome is maintained at an acidic pH by an ATP-driven H+ pump in the membrane that hydrolyzes ATP to pump H+ into the lumen. AUTOPHAGY- THE PATHWAY TO DEGRADE OBSOLETE PARTS OF THE CELL Autophagosomes carry the junk cell pieces to a part of the cell called a lysosome. “Autophagy in a nutshell: make the garbage bag, transport the garbage to waste management facility, disposal/recycling of garbage” ENDOCYTIC PATHWAYS Specialized phagocytic cells ingest large particles Pinocytosis takes up fluid and small molecules Receptor-mediated endocytosis provides a specific route into animal cells Endocytosed macromolecules are sorted in endosomes Lysosomes are the principal sites of intracellular digestion END OF CHAPTER 15 LECTURES