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Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
Biochem Lectures 36-39 Outline
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Biochem Lectures 36-39 Outline

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  • 1. Lecture 36: Membranes and Membrane Proteins 11/27/2011 10:24:00 PM Cell membranes act as selective barriers Prevent molecules from mixing Three roles of plasma membrane Receiving information (signaling) Import/export (transportation) Motility/cell growth Membranes enclose many different compartments in a eukaryotic cell: Nucleus (2x) Mitochondria (2x) ER, vesicles, golgi apparatus, lysosome, peroxisome The Lipid Bilayer Two-dimensional fluid Fluidity depends on composition Lipid bilayer is asymmetrical Lipid asymmetry is generated inside the cell Hydrophilic head, hydrophobic tail The more unsaturated the tails are, fluidity is increased Phosphatidylcholine is the most common phospholipid in cell membranes There are different types of membrane lipids and all are amphipathic Hydrophilic molecules attract water, like dissolves in like Hydrophobic molecules avoid water Fats are hydrophobic, phospholipids are amphipathic (and form a bilayer in water) Pure phospholipids can form closed, spherical liposomes Phospholipids can move o Lateral o Flexion o Rotation o Flip-flop Fluidity depends on composition o Cholesterol stiffens o Low temperature, less unsaturation, long tails all reduce fluidity. Phospho and glycolipids are distributed asymmetrically in the plasma membrane
  • 2. o Glycolipids found on outside o Phosphatidyl-serine, inositol, ethanolamine found on inside usually.Flippases transfer phospholipids to other side of membraneNew membranes are synthesized from ER. o Form vesicles which fuse with other membranes Membrane ProteinsPolypeptide chain usually crosses the bilayer as an α-helixProteins can be solubilized in detergents and purifiedPlasma membrane is reinforced by the cell cortexCell surface is coated with carbohydrateCells can restrict movement of membrane proteinsFunctions o Transporters (ie Na pump) o Anchors (integrins) o Receptors (platelet-derived growth factor receptor) o Enzymes (adenylcyclase)50% of mass of plasma membranes, 50 times more lipid than proteinmolecules.Different ways of associating with membrane: o Alpha helix, beta pleated sheets, transmembrane, lipid linked o Can be peripheral (protein attached)Folded up proteins traverse membrane easier because the polarbackbone is exposedMultiple alpha helixes form a hydrophilic porePorin proteins form water-filled channels in the outer membrane of abacterium o Formed by 16 strands of β-sheets o Allows passage of ions and nutrients across outer membranes of some bacteria and of mitochondriaMembranes are disrupted by detergents such as SDS and Triton X-100 o Have only one tailBacteriorhodopsin acts as a proton pump powered by light, drives ATPsynthase
  • 3. Plasma membrane reinforced by cell cortex – imparts shape andfunction o Spectrin meshwork forms the cell cortex in red blood cellsEukaryotic cells are sugar coated o Absorb water for lubrication o Cell-cell recognition o Protect cell from physical, chemical, enzymatic damage o Recognition of cell surface carb on neutrophils mediates migration in infectionMovement can be restricted by cells o Tethering to cell cortex, extracellular matrix, proteins on surface of another cell, or by barriers of diffusion like tight junctions.
  • 4. Lecture 37I. General Principles of Cell Signaling Can act over long or short range Each cell responds to limited set of signals Signals relayed via intracellular signaling pathways Nitric oxide crosses plasma membrane and activates intracellular enzymes directly Some hormones cross plasma membrane and bind to intracellular receptors There are three classes of cell surface receptors Ion channel-linked receptors convert chemical into electrical signals Intracellular signaling proteins act as molecular switches Origins in unicellular organisms o Yeast shows single cell-cell communication o Two mating types, a and α plus a secreted mating factor signal Signals transduction: conversion of one type of signal into another o Extracellular -> intracellular 4 ways animal cells signal o Endocrine o Paracrine o Neuronal o Contact-dependent  Lateral inhibition: Unspecified epithelial cells, one cell is dedicated to becoming a nerve cell and inhibits surrounding cells by Delta-Notch signaling. One signal molecule can induce different responses in different cells o ie: acetylcholine: (time scale is seconds to minutes)  In heart muscle cells, causes decreased rate and force of contraction.  In salivary gland cells, causes secretion.  In skeletal muscle cells, causes contraction. An animal cell depends on multiple extracellular signals Extracellular signal molecules can alter activity of diverse cell proteins which in turn alter cellular behavior
  • 5. o The intracellular signaling proteins are involved in a signaling cascade which ultimately reach the target proteins for altered behavior like metabolism, gene expression, and cell shape or movement.Cellular signaling cascades can follow a complex path o Primary transduction, relay, amplification, or branching to different targets.Extracellular signal molecules can either bind to cell surface receptorsor to intracellular enzymes or receptors (like nitric oxide) o Nitric oxide is a product of nitroglycerin which is taken to relax smooth muscle cells.  Triggers smooth muscle relaxation in blood-vessel wallSteroid hormones bind intracellular receptors that act as generegulatory proteins o Cross plasma membrane, like NO o Cholesterol does not cross membrane, rather inserts IN membrane. o Cortisol acts by activating a gene regulatory proteinMost signal molecules bind to receptor proteins on the target cellsurface o Extracellular domains are the cell surface receptor o Three basic classes:  Ion channel linked -> nervous system, muscle  G-protein linked -> all cells  Enzyme-linked -> all cellsMany intracellular signaling proteins act as molecular switches o Signaling by phosphorylation  Signal in by phosphorylation, off by phosphatase inactivation. o Signaling by GTP-binding protein  GTP binds to G-protein, turning it on.  GTP hydrolysis inactivates by removing P.II. G-protein-linked ReceptorsStimulation of G-protein linked receptorsG proteins can regulate ion channels
  • 6. G proteins can activate membrane bound enzymesCyclic AMP pathway can activate downstream genesInositol phospholipid pathway triggers rise in CaCa signal triggers many biological processesIntracellular signaling cascades can achieve astonishing speed (iephotoreceptors in the eye)All G-protein linked receptors possess a similar structure o 7 transmembrane protein o Ligand binds to extracellular binding domain o Cytoplasmic domain which binds to G-protein o Tetramer is active, GDP can dissociate, GTP can bind, and then complex dissociates into two activated parts. o The alpha subunit switches itself off by hydrolyzing bound GTPG proteins couple receptor activation to opening of cardiomyocyte Kchannels o Acetylcholine binds to G protein linked receptor o Beta gamma complex binds to closed K channel to open it o Alpha subunit is inactivated (by hydrolysis) and inactive complex reassociates with betta gamma complex to close K channel.Enzymes activated by G proteins catalyze synthesis of intracellularsecond messengers o Alpha subunit activates adenylyl cyclase which makes lots of cylic AMP. o Cyclic AMP concentration rises rapidly in response to neurotransmitter serotonin o Cyclic AMP is synthesized by adenylyl cyclase, degraded by cAMPphosphodiesteraseExtracellular signals can act rapidly or slowlyRise in intracellular cyclic AMP can activate gene transcription throughprotein kinase A o Translocates through nuclear pore, into nucleus, phosphorylates gene regulatory protein to activate target gene.
  • 7. Membrane bound phospholipase C activates two small messengermolecules: IP3, DAG o Phospholipase C activated by alpha subunit, splits inositol phospholipid into IP3 and DAG o IP3 opens Ca channel in ER, Ca is released and works with DAG to activate Protein Kinase C.Fertilization of an egg by sperm triggers a rapid increase in cytosolic Ca o Other processes triggered by Ca signal:  Sperm entry -> embryonic development  Skeletal muscle -> contraction  Nerve cells -> secretionCalcium/Calmodulin complex are what bind to proteins.A rod photoreceptor cell from the retina is exquisitely sensitive to light o G protein linked light receptor activates G protein transducing, activated alpha subunit causes Na channels to close. o Light induced signaling cascade in rod photoreceptors greatly amplifies light signals. III. Enzyme linked receptorsActivated receptor tyrosine kinases assemble a complex of intracellularsignaling proteins o Ligand brings two tyrosine kinase domains together, phosphorylated to activate. Intracellular signaling proteins bind to phosphorylated tyrosines. o Activated complex includes Ras-activating protein, which is anchored in membrane, transmits signal downstream.  Ras is monomeric GTP-binding protein, not a trimeric G protein, but resembles the alpha subunit and functions as a molecular switch.  30% of cancers arise from mutations in Ras.  Ras activates a MAP-kinase phosphorylation cascadeSome enzyme-linked receptors activate a fast track to the nucleusProtein kinase networks integrate info to control complex cell behaviorsMulticellularity and cell communication evolved independently in plantsand animals
  • 8. Cytokine receptors are associated with cytoplasmic tyrosine kinases o JAK kinases phosphorylate receptor which recruits cytoplasmic proteins.TGF-beta/BMP receptors activate gene regulatory proteins directly atthe plasma membraneSignaling pathways can be highly interconnected: cross-talkLecture 38 General introduction:Membrane enclosed organelles are distributed throughout thecytoplasm o Thousands of different reactions occur simultaneously, are partitioned o Cytosol is 54% of cell o Mitochondria is 22% of cells o ER is 12% of cell (1 per cell)Nuclear membrane and ER may have evolved at the same time throughinvagination of plasma membrane.Mitochondria are thought to have originated from aerobic prokaryotebeing engulfed by a larger anaerobic eukaryotic cell -> has it’s owngenome.Nucleus is a double membrane organelle o Encloses nuclear DNA, defines nuclear compartment and contains most of the genetic information. o Export, import through nuclear pore complex  Contains about 100 proteins, two way gate, export of mRNA, and ribosome subunits.  Import of proteins requires a signal sequence called the nuclear localization signal  Requires energy (GTP) and special chaperone proteins  Export of RNA from nucleus – RNA molecules are made in the nucleus and exported to the cytoplasm as processed mRNAOne Endoplasmic Reticulum
  • 9. o System of interconnected sacs and tubes of membrane o Extend throughout most of cell o Major site of new membrane (lipid) synthesis o With ribosomes on cytosolic side = rough ER o Without ribosomes = smooth ER o Most extensive network membrane in eukaryotic cellsGolgi apparatus o Flattened sacs called cisternae which are piled like stacks of plates o Usually near nucleus o Two faces:  Cis face adjacent to ER  Trans face towards plasma membrane (where post translational modification occurs) o Receives proteins and lipids o Site of modification of proteins and lipids o Dispatches proteins and lipids to final destinations o Transport vesicles bud offOther membrane enclosed organelles o Endosomes – small membrane enclosed organelles that sort ingested molecules in endocytosed materials. Passed to lysosomes or recycled back to the plasma membrane. o Lysosomes – small sacs containing digestive enzymes that degrade organelles, macromolecules, and particles taken in by endocytosis. “garbage disposal of the cell.” Ph about 7.2 o Peroxisomes – small membrane enclosed organelle containing oxidative enzymes that break down lipids and destroy toxic moleculesProtein transport o Multiple modes of protein transport (import and export) o Three mechanisms  Transport through nuclear pores: protein with nuclear localization signal enter through pores  Across membranes: proteins moving from cytosol into ER, mitochondria and peroxisomes transported across organelle membrane by protein translocators
  • 10.  By vesicles: from ER onward and from one endomembrane compartment to another ferried by transport vesiclesProtein sorting signals o Specific amino acid sequence o Directs protein to organelle o Proteins without signals remain in cytosol o Signal sequences direct proteins to different compoartments  Continuous stretch of AA usually 15-20 residues in length  Usually removed after the protein reaches destination  Organelles and signal sequences:  ER import rich in V A L I and retendtion KDEL  Mitochondria rich in R  Nucleus PPKKKRKV  Peroxisomes SKL o Signal sequences are both necessary and sufficient to direct protein to organellesER: entry point for protein distribution o Proteins destined for golgi, lysosomes, endosomes and cell surfaces first enter ER from cytosol o Once inside ER or membrane, proteins do not reenter cytosol o Water soluble proteins are completely translocated across ER membrane and released into ER lumen o Transmembrane proteins only partially translocated across ER membrane and become embeddedVesicular transport o Entry into ER o To golgi apparatus o From er ->golgi -> other by continuous budding, fusion of transport vesicles o Vesicle transport provides routes of communicationProtein transport: quality control o Most proteins that enter ER are destined for other locations
  • 11. o Exit from the ER is highly selective: improperly modified and or folded proteins are retained in lumen; dimeric or multimeric proteins that fail to assemble are also retainedExocytosis o Constitutive: newly synthesized proteins, lipids, and carbs delivered from ER via golgi to subcellular locations, extracellularly to ECM via transport vesicles.  Lipids and proteins supplied to plasma membrane  Proteins secreted into ECM or onto the cell surface o Regulated  Specialized secretory cells synthesize high levels of proteins such as hormones or digestive enzymes that are stored in secretory vesicles for subsequent release  Vesicles bud off from trans golgi network and accumulate adjacent to plasma membrane until mobilized by extracellular signalEndocytosis o Pinocytosis (drinking)  Internalizes plasma membrane: as much membrane is added to cell surface by exocytosis as is removed by endocytosis – total surface area and volume remain unchanged.  Mainly carried out by transport vesicles: deliver extracellular fluid and solutes to endosomes; fluid intake is balanced by fluid loss during exocytosis o Phagocytosis (eating)  Specialized cells only
  • 12. o
  • 13. Lecture 39: CytoskeletonRoles of cytoskeletal filaments: Intermediate – cell structure against mechanical stress Microtubules – intracellular transport, railroad of cell Actin – membrane mobility; cell movement Intermediate filaments: 10 nm in diameter Rope like structure composed of long polypeptides twisted together Associated with cell junctions Mechanical strength, cell shape, cell-cell contacts, and structure for nuclear envelope Monomers -> dimer -> tetramer -> 8 tetramers make one ropelike filament Different proteins: o Epithelia – keratins o Connective tissue, muscles, neuroglial cells – vimentin o Nerve cells – neurofilaments o Nuclear envelope in animal cells – nuclear lamins Mutation in keratin genes = epidermolysisbullosa simplex Networks of filaments connect across desmosomes in epithelia Microtubules: 25 nm wide Hollow, made of α and β tubulin anchored to γ tubulin Have polarity – gives directionality “Dynamic instability”: built or disassembled as needed o Zip up to grow o Unravel and tubulin molecules fall off if not needed o This is done by GTP since tubulin are GTPases  GTPases are the cell’s timers  High energy phosphate bond. Molecules with GTPases hydrolyze that bond, leaving GDP  GTP between α and β tubulin molecules makes them straighter, so they pack better. GTP hydrolysis makes them kinked, so they fall off.
  • 14. Organize cell organelles and control traffic of vesiclesRoles in interphase cell, dividing cell, ciliated cells, flagella.The centrosome o Centriles inside of centrosome, nobody knows what they do o Centrosome is an envelope of tubulin where microtubules extend out with plus end out.Structure: o α and β tubulin strandsStabilizing or destabilizing MTs o Microtubule associated proteins (MAPs)  Bind to free ends of MTs and stabilize ends selectively to polarize a cell o Drugs can be used to change MT stability  Colchicine binds free tubulin to prevent polymerization; MTs disintegrate and mitosis stops  Taxol prevents loss of subunits from MTs; MTs become “frozen” in place and mitosis stops.MT organized transport o Anterograde transport, retrograde transport.Motor proteins use ATP to power transport along the MT railroad o Kinesin and dynein are dimers that walk along microtubule. o One ATP is used per step.Cilia and flagella are made of MTs Actin Filaments:Control cell movementFound in: o Epithelial cell microvilli o Stress fibers in cultured cells o Leading edge lamellipodia o Contractile ring in dividing cells – cytokinesisActin polymerization requires ATP o Free G-actin monomers use ATP to become F-actin to form filaments. To uncoil, hydrolyze ATP and fall apart.Actin dynamics provide force for membrane movement o ARP complex create branches
  • 15. o Depolymerizing protein promotes ATP hydrolysis o Capping proteins cap the ends and stabilize ATP bound monomer, stabilizing leading edge.Actin binding proteins link actin fibers to the membrane and othercellular componentsIntegrins link actin to focal adhesions o Binds to extracellular structures, messages to actin.Cells move by actin crawling (dynamics)Axon growth cone crawlingRho family GTPases control actin dynamics o RhoA causes stress fibers  Stabilize actin filaments  Induces myosin phosphorylation and thus contractility o Cdc432 causes filopodia extension  Promotes actin nucleating by ARP complexes o Rac promotes lamellipodia extension  Promotes actin nucleation, but also uncapping to allow more sites of nucleation o Cell surface receptors modulate Rho family activity  Attractive cues activate Rac and Cdc42 on area of growth cone  Repulsive cues activate RhoA  Growth cone turnsMyosins: actin motor proteins o Head, neck, tail o Tails link up together o Work as dimers o Moves membranes or cell componentsMuscle contraction by actin and myosin o Myosin heads climb up actin filament o Z disks move together, muscle contracts

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