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Ch. 12 - Compartments & Protein Sorting Summary of chapter and lecture notes on compartments and protein sorting. Includes illustrations and graphics from the textbook.

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BIOL 2021
Julie Clark

BIOL 2021- March24 2009 CHAPTER 12: COMPARTEMENTS AND PROTEIN SORTING Organelles Figure 1-18b- Bacterial cell through micrograph  Only have plasma membrane; so one compartment only -Organelle: membrane bound compartment - lumen: interior of an organelle - cell = nucleus + cytoplasm - cytoplasm: cytosol + extra nuclear organelles - Cytoplasm includes organelles (mitochondrion) found in cytosol - Ribosome: found in cytosol and attached to ER Functions of organelles - 1. Increase surface area of membranes - 2. Divide cytoplasm into specialized compartments  Function depends on proteins Families of organelles Figure 1 The major intracellular compartments of an animal cell. The cytosol (gray), endoplasmic recticulum, Golgi apparatus, nucleus, mitochondrion, endosome, lysosome, and peroxisome are distinct compartments isolated from the rest of the cell by at least one selectively permeable membrane. 1) Nucleus and cytosol: connected by nuclear pores 2) Secretory and exocytotic: dump stuff outside of cell  ER, Golgi, endosomes, lysosomes 3) Mitochondria 4) Plastids (in plants only)  Chloroplasts (and other related)  Derived from bacteria - Mito and plastids have own DNA and do some protein synthesis and protein import - Endosymbiotic bacteria is ancestor Topology: study of mathematics of holes and maps - If things have to make a hole to get out of cell then things are topologically different  Topologically equivalent spaces shown in red  Lumen of the ER= outside of cell (same space)  So must be connected by vesicle traffic  All organelles come from pre existing organelles  Animation 12-1 - Proteins made in cytosol on free ribosomes: HOW DO YOU GET PROTEINS IN THE ORGANELLES?  NO SIGNAL= proteins stay in cytosol on free ribosomes  WITH SIGNAL= proteins are directed to the right organelle - Proteins are imported with a sorting receptor (on organelles); the sorting signal recognized by receptor sorting receptor SORTING SIGNALS 1) Signal sequence: continuous amino acid sequence - By looking at amino acid sequence we can predict where protein will be imported - Sequence can be at the end or middle of protein - Sometimes removed after they are imported - Usually found at the N terminus but can be at C terminus 2) Signal patch: discontinuous amino acid sequence (not all in one stretch) - Formed by 3D structure of protein - Sequence linked by tertiary structure of protein - Amino acids are separated in linear form but are together when the protein is folded TYPES OF PROTEIN SORTING (DISTRIBUTION) 1. Gated transport: proteins move between the cytosol and the nucleus (which are topologically equivalent) through nuclear pore complexes in the nuclear envelope. The nuclear pore complexes function as selective gates that actively transport specific macromolecules and macromolecular assemblies, although they also allow free diffusion of smaller molecules - Uses nuclear pores to get larger molecules in and out of nucleus. 2. Transmembrane transport: transmembrane protein translocators directly transport proteins across a membrane from the cytosol into a space topologically distinct. The transported protein molecule usually must unfold to snake through the translocator. The initial transport of selected proteins from the cytosol into the ER lumen or mitochondria. - across membranes; from one topological space to another - uses protein translocators 3. Vesicle transport: membrane enclosed transport intermediates- which may be small, spherical transport vesicles or larger irregularly shaped organelle fragments- ferry proteins from one compartment to another. The transport vesicles and fragments become loaded with a cargo of molecules derived from the lumen of one compartment as they bud and pinch off from its membrane; they discharge their cargo into a second compartment by fusing with the membrane enclosing that compartment. The transfer of soluble proteins from the ER to the Golgi apparatus, for example, occurs in this way. Because the transported proteins do not cross a membrane, vesicular transport can move proteins only between compartments that are topologically equivalent - Uses membrane budding and fusion - Proteins never cross membranes - Some topological spaces I. NUCLEUS AND CYTOSOL- GATED TRANSPORT - Bidirectional transport - Cytoplasm into nucleus: histone, enzyme (DN, RNA polymerase), transcription factors, proteins for RNA processing, ribosomal proteins need to be transported from cytosol to nucleus - Trna, mRNA, ribosomal proteins + RNA (ribosomal subunit) needs to be transported from nucleus to cytosol  Uses nuclear pores (connects with cytosol_ - Nuclear pores mediate gated transport  Regulates proteins that go through (so its not an empty hole, its filled with proteins)  Complex structure - NPC (nuclear pore complex) - Protein: nuclear porins (proteins in nuclear pore complex) TRANSPORT THROUGH NUCLEAR PORE COMPLEX a) Passive diffusion  Water soluble, small molecules transported through the channel (water filled)  No regulation b) Active transport  For macromolecules (i.e. RNA and protein)  Go through gated pore  Regulated (gate can open and close) - Active transport is gated transport Gated transport - Requires sorting signal: - 1) nuclear localization signal (NLS) : used to get things in (import) - 2) Nuclear export signal: for export  Found on proteins and RNA  Can be signal sequence or patch Nuclear transport receptors - To initiate nuclear import, most nuclear localization signals must be recognized by nuclear import receptors. - Nuclear transport receptors are soluble proteins in cytosol that bind to nuclear localizations signal (NLS) of cargo and bind to nucleo porins.  2 binding sites ( 1 on cargo, 1 on nucleo porin)  Different receptors for different signals - Also called nuclear import receptor shuttle in and out of nucleus to pick up more cargo - Requires energy source -> hydrolysis of GTP - Protein that uses energy is Ran GTPase Figure 2the compartmentalization of Ran GDP and Ran GTP. Localization of the nucleus, results from the localization of two Ran regulatory proteins. *2 conformational states of ran: one when GDP is bound and one where GTP is bound. Two specific regulatory proteins trigger the conversion between the two states, GAP triggers GTP hydrolysis and thus converts Ran GTP to Ran GDP and, GEF promotes the exchange of GDP for GTP and thus converts Ran- GDP to Ran GTP Ran GTP ase- binds and hydrolysis of GTP then moves out of the nucleus - Conformational change (twice in one cycle) - Hydrolyses GTP to GDP and moves into nucleus - Exchanges GDP for GTP and moves out - Ran gtp ase binds the nuclear import receptor - Conformational change when it binds to Ran GTP - Export= import in reverse REGULATION - Some proteins can shuttle in and out constantly Ex. Gene regulatory proteins, transcription factors -> respond to signals and change conformation of NLS Ex. NF AT - Responds to Ca - When concentrations of Ca are low, it goes out of the nucleus - Animation 12-2 - In cytosol, when Ca concentration goes into nucleus uses ionophore for transport MITOCHONDRIA AND CHLOROPLASTS (from cytosol) - Proteins made in cytosol to be transported to organelles - Transmembrane transport (protein in translocation) - Mitochondria has lots of membranes (compartments) - Two subcompartments in mitochondria: internal matrix space and intermembrane space.  4 places to put proteins: outer membrane, inner membrane, inside matrix, and intermembrane space. - Protein translocation: process of protein movement across membranes - To get into the inner membrane space, the protein must cross 2 membranes. IMPORT INTO MITCHONDRIA - Requires; 1) Signal sequence at N terminal 2) Protein translocators 3) Energy source - Different signal sequences bring proteins to different locations Mitochondrial protein translocators - Protein complexes in membranes - Embedded in membrane (integral membrane proteins) TOM= translocase o
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