Term
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Definition
| A "compartment" with its own enzymes and other specialized molecules |
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Definition
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Definition
| Site of DNA and RNA synthesis |
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Definition
| Surrounds nucleus. Contains organells and cytosol |
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Definition
| Makes up a little more than half of cell's volume. Site of protein synthesis and degradation. Performs cellular intermediate metabolism. |
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Definition
| Folded membrane. About half of the cells total membrane surface. |
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Definition
| Ribosomes bound to ER. Synthesizes soluble and integral membrane proteins. Produces lipid for cell. Stores Calcium Ions |
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Definition
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Definition
| Recieves proteins and lipids from ER. Sends them out to other destinations, usually modifying them. |
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Definition
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Definition
| Only in plants. Special version of a plastids, which generates ATP, Stores food and pigment. |
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Definition
| Contain digestive enzymes that break down molecules, defunct organelles, and particles that enter the cell through endocytosis. |
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Definition
| Material passes through this on the way to lysosomes. Actually a series of organelles. |
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Definition
| Small compartments thatcontain enzymes used in oxidation reactions |
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Definition
| Directs delivery of proteins outside the cytosol. |
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Definition
| Moves proteins between cytosol and nucleus through nuclear pores. |
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Term
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Definition
| Moves proteins from cytosol to mitochondria, ER, plastids, and peroxisomes. Protein unwinds to go through translocater |
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Term
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Definition
| Moves proteins from ER to Golgi, then from Golgi elsewhere. Uses spherical or large irregular tansport vesicles. |
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Definition
| Recognize the sorting signals and direct transportation |
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Term
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Definition
| Site of sorting signals, usually at the N terminus of a protein |
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Term
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Definition
| Remove signal sequence from finished protein once sorting is completed. |
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Term
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Definition
| Special sorting signals that form a 3-D arrangement on the proteins surface |
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Term
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Definition
| Encloses the DNA and defines the nuclear compartment. Two membranes, has pores. |
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Term
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Definition
| Contains anchor proteins for chromatin. |
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Term
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Definition
| Surrounds the inner. Continuous with the ER. Contains ribosomes. Proteins made on these ribosomes go to Perinuclear Space |
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Term
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Definition
| Space between inner and outer nuclear membrane |
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Term
| Nuclear Pore Complexes(NPCs) |
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Definition
| Perforate nuclear envelope of all eukaryotes. Composed of around 30 NPC proteins, or nucleoporins |
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Term
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Definition
| Huge. Can transport in both directions. Can transport up to 500 macromolecules per second. |
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Term
| Nuclear Localization Signals |
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Definition
| Rebuilds proteins after they are introduced into the nucleus. |
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Term
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Definition
| Initiates nuclear import. Binds to Nuclear Localization Signals and NPC Proteins |
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Term
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Definition
| Same as Import, but in reverse. Still binds to both. |
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Term
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Definition
| Internal subcompartment of mitochondria |
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Term
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Definition
| The other subcompartment of mitochondria |
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Term
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Definition
| Inner and outer, forms the two subcompartments |
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Term
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Definition
| Encloses the matrix and forms inVAJinations called cristae |
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Term
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Definition
| Is in contact with the cytosol |
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Term
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Definition
| Are first fully synthesized by ribosomes and then sent into mitochondria. These Precursor proteins use a post-translational mechanism |
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Term
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Definition
| Transfers proteins across outer membrane |
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Term
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Definition
| TIM 23 and TIM22. Transfers proteins across inner membrane. |
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Term
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Definition
| Helps Beta-Barrel proteins fold correctly |
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Term
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Definition
| Mediates the insertion of inner membrane proteins |
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Term
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Definition
| Completes protein import by binding and releasing the protein. |
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Term
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Definition
| Only have a single membrane |
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Term
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Definition
| the membranes of ER, Golgi, Mitochondria, and other membrane enclosed organelles maintain character diffs btwn contents of each organelle and the cytosol. |
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Term
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Definition
| encloses cell, defines boundaries, maintains diffs btwn cytosol and extracellular environment. |
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Term
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Definition
| can be used to synthesize ATP, drive transmembrane movement of selected solutes or produce/transmit electrical signals (as in nerve&muscle cells). |
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Term
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Definition
| plasma membrane has proteins that act as sensors of external signals which allow cell to change behavior in response to external cues (including signals from other cells) – protein sensors (receptors) transfer info across membrane. |
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Term
| General Membrane Structure |
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Definition
| thin lipid (fatty) film and protein molecules – held together by mainly noncovalent interactions |
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Term
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Definition
| continuous double layer ~ 5nm thick |
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Term
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Definition
| provides basic fluid structure of membrane and serves as impermeable barrier to passage of most H2O-soluble molecules. |
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Term
| Major Lipids in Cell Membrane |
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Definition
| Phosphoglycerides, sphingolipids and sterols |
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Term
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Definition
| important phospholipid built from sphingosine not glycerol – sphignosine is long acyl chain with NH2 (amino) group and 2 OH (hydroxyl) groups @ one end of molecule. |
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Term
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Definition
| a fatty acid tail attached to amino group and a phosphocholine group attached at the terminal OH group, leaving one OH group free – this free OH contributes to polar properties of the adjacent head group as it can form H bonds with head group of neighboring lipid, H2) molecule or with a membrane protein |
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Term
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Definition
| contains a rigid ring which is attached to a single polar OH group and a short nonpolar hydrocarbon chain – the cholesterols orient themselves in the bilayer with their OH group close to the polar head groups of adjacent phospholipid molecules |
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Term
| Phospholipids spontaneously form bilayers |
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Definition
| Shape and amphiphilic nature of phospholipids makes them spontaneously form in aqueous environments – do this to bury their hydrophobic tails in the interior and expose their hydrophilic heads to H2O – can be done in either of 2 ways depending on shape: form spherical micelles with tails inward or form dbl-layered sheets or bilayers with hydrophobic tails sandwiched btwn the hydrophilic head groups |
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Term
| Phospholipids spontaneously form bilayers pt.2 |
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Definition
| They are cylindrical which helps form spontaneously in aqueous environments – in this energetically most favorable arrangement, the heads face water at each surface of the bilayer and tails are shielded from water in interior |
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Term
| Phospholipids spontaneously form bilayers pt.3 |
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Definition
| These same forces also provide self-healing properties – a small tear in the bilayer creates a free edge with water; because this is energetically unfavorable, the lipids tend to rearrange spontaneously to eliminate the free edge – the only way for a bilayer to avoid having edges is by closing in on itself and forming a sealed compartment – this behavior is fundamental to the creation of a living cell and follows directly from shape and amphiphilic nature of the molecule |
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Term
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Definition
| Around 1970 it was found that indiv lipids are able to diffuse freely within LB’s – this first came about from studies w/2 preparations: 1. Bilayers made in form of spherical vesicles called liposomes, which can vary in size depending on how they are produced 2. Planar bilayers, called black membranes, formed across a hole in a partition btwn 2 aqueous compartments |
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Term
| Various ways to measure motion of indiv lipid molecules and components: |
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Definition
| add fluorescent dye or small gold particle attached to its polar head group and follow diffusion if even indiv molecules in membrane. |
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Term
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Definition
| Studies show that phospholipid molecules in synthetic bilayers very rarely migrate from the monolayer (leaflet) on one side to that on the other. |
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Term
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Definition
| – phospholipid translocators – catalyze the rapid flip-flop of phospholipids from one monolayer to the other |
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Term
| LB luidity has to be precisely regulated |
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Definition
| certain transport processes and activities cease when the bilayer viscosity is experimentally increased beyond a threshold level – fluidity depends on composition and temperature. |
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Term
| Cholesterol modulates the properties of LBs |
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Definition
| when mixed w/phospholipids, the permeability-barrier properties of the LB are enhanced – it inserts into the bilayer w/OH group close to polar head groups of phospholipids making its rigid & making platelike steroid rings interact & partly immobilize the regions of the hydrocarbon chains closest to polar head groups. |
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Term
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Definition
| lipids usually have 20-25 C long prenyl chains instead of fatty acids – both are similarly hydrophobic and flexible – thus LBs can be built from similar featires but diff molecular designs |
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Term
| Despite Fluidity, LBs can form domains of diff compositions |
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Definition
| Bc a LB is 2-D fluid, might expect most types to be randomly distributed in own monolayer – van der waals forces btwn neighboring hydrocarbon tails are not selective enough to hold groups of phospholipid molecules together – but with certain lipid mixtures, diff lipids can come together transiently, making a dynamic patchwork of diff domains – in synthetic LBs composed of phosphatidylcholine, sphingomyelin, and cholesterol, VDW forces btwn long and saturated chains of sphingomyelin molecules can be just strong enough to hold adjacent molecules together transiently. |
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Term
| Despite Fluidity, LBs can form domains of diff compositions pt2 |
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Definition
| Been a long debate whether lipids in PM of animal cells can transiently assemble into specialized domains called lipid rafts- certain specialized regions of PM such as the caveolae involved in endocytosis, are enriched in sphingolipids and cholesterol, and its thought that specific proteins that assemble there help the rafts |
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Term
| Despite Fluidity, LBs can form domains of diff compositions pt3 |
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Definition
| Hydrocarbon chains of sphingomyelin longer/straighter than other membrane lipids, so raft domains are thicker than other parts of bilayer & better accommodate certain membrane proteins – thus the lateral segregation of proteins & of lipids into raft domains would be a mutually stabilizing process – in this way, rafts help organize membrane proteins, concentrating them for transport in membrane vesicles or for working together in protein assembly, as when they convert extracellular signals into intracellular ones. (all for organization) |
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Term
| Lipid droplets surrounded by a phospholipid monolayer |
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Definition
| Most cells store excess of lipids in droplets where they can ge retrieved as building blocks for membrane synthesis or as food source – fat cells, adipocytes, are specialized for lipid storage – they contain many droplets, from which fatty acids can be liberated and exported to other cells thru bloodstream – droplets store neutral lipids, such as triglycerides and cholesterol esters, which are synthesized from fatty acids and cholesterol by enzymes in the ER membrane. |
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Term
| Lipid droplets surrounded by a phospholipid monolayer |
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Definition
| Bc these lipids have no hydrophilic head groups, they are exclusively hydrophobic molecules which aggregate into 3-D droplets rather than into bilayers. |
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Term
| Lipid droplets surrounded by a phospholipid monolayer |
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Definition
| Lipid droplets are unique organelles bc surrounded by a single monolayer of phospholipids that have a variety of proteins – some proteins are enzymes involved in lipid metabolism, but the funcs of most are unknown – droplets form rapidly when cells exposed to high concentrations of fatty acids – form from discrete regions of ER membrane where many enzymes of lipid metabolism are concentrated. |
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Term
| Lipid compositions of 2 monolayers of LB in many membranes are diff – |
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Definition
| in human RBC membrane, for ex. almost all phospholipid molecules that have choline in head group (phosphatidylcholine and sphignomyelin) are in outer monolayer, whereas almost all that have a terminal primary amino group are in inner monolayer. |
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Term
| Lipid asymmetry is functionally imp, especially in converting extracellular signals into intracellular ones |
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Definition
| many cytosolic proteins bind to specific lipid head groups found in cytosolic monolayer of LB – enzyme protein kinase for ex. is activated in response to many extracellular sigs – it binds to cytosolic face of PM, where phosphatidylserine is concentrated, and requires this neg charged phospholipid for its activity. |
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Term
| the translocation of the phosphatidylserine in apoptotic cells is thought to occur byt 2 mechanisms: |
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Definition
| The phospholipid translocator that normally transports this lipid from the noncytosolic monolayer to the cytosolic monolayer is inactivated |
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Term
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Definition
| Perform most of the tasks of membrane, give each type of cell membrane its characteristic functional props – lipid molecules so small compared to protein molecules in CMs – about 50x as many lipids as proteins but proteins are 50% of the mass of CM |
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Term
| Membrane transport proteins: |
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Definition
| specialized proteins that transfer solutes, such as ions, sugars, amino acids, and nucleotides, across cell membranes. Each protein transports a particular class of molecule and often only certain molecular species of the class. |
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Term
| Transporters (carriers or permeases): |
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Definition
| bind the specific solute to be transported and undergo a series of conformation changes to transfer solute across membrane. |
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Term
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Definition
| interact with the solute to be transported. Weaker than transporters. Form pores, that when open allow transfer of solutes. |
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Term
| Passive transport/facilitated diffusion: |
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Definition
| Process by which solutes cross membrane passively. Powered by concentration gradient and electrical potential difference across membrane. (downhill) |
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Term
| Electrochemical gradient: |
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Definition
| Combination of concentration gradient and electrical gradient that form driving force. Inside of cell usually negative, favors positive entry. |
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Term
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Definition
| Transporters “pump” solutes across membrane. (uphill) |
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Term
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Definition
| Transporters that mediate the movement of a single solute from one side to another, determined by Vmax and Km. |
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Term
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Definition
| Transfer of one solute depends on transfer of a second. |
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Term
| Symporters (co-transporters): |
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Definition
| Coupled transporters that move solute in same direction. |
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Term
| Antiporters (exchangers): |
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Definition
| Coupled transporters that move solute in opposite direction. |
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Term
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Definition
| Hydrogen driven symporter that transports lactose across plasma membrane of E coli. |
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Term
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Definition
| Transporters in cells move solutes across epithelial cell layer into extracellular fluid then to blood. |
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Term
| ATP-driven pumps (transport ATPases): |
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Definition
| hydrolyze ATP to ADP and phosphate and use energy released to pump solutes across membrane. In prokaryotes and eukaryotes. |
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Term
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Definition
| 1. Multipass trans-membrane proteins. Phosphorylate themselves during the pumping cycle. Control Na+, K+, H+ and Ca2+. Contain 10 transmembrane alpha helices. Three create central channel that spans lipid bilayer. Moves bound ions across membrane through phosphrylation. |
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Term
| F-type pumps (ATP synthases): |
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Definition
| 1. turbine-like proteins from multiple subunits. Plasma membrane of bacteria, inner membrane of mitochondria, and thylakoid membrane of chloroplasts. Use H+ gradient to drive synthesis of ATP from ADP and phosphate. V-type ATPases pump H+ into organelles. |
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Term
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Definition
| 1. primarily pump small molecules across cell membranes, where P and F only transport ions. |
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Term
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Definition
| in sarcoplasmic reticulum membrane of skeletal muscle cells. Moves Ca2+ in and out of cell as a signaler to contract muscles. |
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Term
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Definition
| In plasma membrane. Maintains concentration differences. K+ concentration is 10-30 times high inside cells, vice versa with Na+. Hydrolyzes ATP to pump Na+ out of and K+ into cell. |
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Term
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Definition
| Tonicity of the cytosol. Maintained by Na+/K+ pump. |
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Term
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Definition
| Each member contains two highly conserved ATPase domains. Change structure of membrane to expose substrate-binding sites. Largest famiy of membrane transport proteins. |
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Term
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Definition
| Form hydrophilic pores across membranes. Create gap junctions which connects cytoplasm of two cells. Narrow, highly selective pores that open and close rapidly. |
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Term
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Definition
| Channel proteins that focus on inorganic, ion transport. Have ion selectivity through filter which limits rate of passage. Ion channels are gated, opening and closing. Change in voltage across membrane, mechanical stress, or binding of a ligand causes ion channels to open. |
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Term
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Definition
| Difference in electrical charge on two sides of a membrane. |
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Term
| Resting membrane potential: |
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Definition
| Equilibrium condition where there is no net flow of ions across the plasma membrane. Nernst equation quantifies equilibrium condition. |
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Term
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Definition
| Formed from short alpha helix and loop. Structure of filter explains selectivity of ion channel. |
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Term
| Water channels/aquaporins: |
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Definition
| protein complexes that allow water to move quickly across membrane. |
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Term
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Definition
| Receive, conduct and transmit signals. Made up of cell body, axon, dendrites and terminal branches of axon. |
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Term
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Definition
| Traveling wave of electrical excitation. Direct consequence of voltage-gated cation channels. |
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Term
| Voltage-gated cation channels: |
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Definition
| Responsible for generating action potentials. Depolarization opens channels. Na+ channels allow depolarization and K+ channels bring cell back to original negative potential. K+ channels are delayed, but regains negative state faster. |
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Term
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Definition
| Insulator of axon that greatly increases rate of action potential. Formed by glial cells that wrap themselves around the axon. |
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Term
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Definition
| Examine transport of molecule through channel in membrane that covers mouth of pipette. Helps to study ion channels of all types. Shows that channels open in all-or-nothing fashion. |
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Term
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Definition
| Sites where neuronal signals are transmitted from cell to cell. Presynaptic cell separated from postsynaptic cell by synaptic cleft. |
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Term
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Definition
| Signal molecules released when change of electrical potential in presynaptic cell occurs. Bind to transmitter-gated ion channels in postsynaptic cells. |
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Term
| Transmiiter-gated ion channels: |
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Definition
| Specialized channels for rapidly converting extracellular chemical signals into electrical signals at chemical synapses. |
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Term
| Excitatory neurotransmitters: |
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Definition
| Open cation channels, causing influx of Na+ that depolarizes membrane. Readies firing an action potential. Acetylocholine, glutamate, and serotonin. |
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Term
| Inhibitory neurotransmitters: |
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Definition
| Open Cl- or K+ channels, suppresses firing of action potential. Acetylocholine can excite or inhibit. GABA and glycine. |
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Term
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Definition
| Specialized chemical synapse between motor neuron and skeletal muscle. |
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Term
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Definition
| First ion channel to be purified, first to have complete amino acid sequence determined, first to be functionally reconstituted in synthetic lipid bilayers and first where electrical signal of single open channel was recorded. |
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Term
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Definition
| Unique region of each neuron with plentiful voltage-gated Na+ channels. Where action potentials are initiated. Contain delayed K+ channels, rapidly inactivating K+ channels and Ca2+ activated channels. |
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Term
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Definition
| Short burst of repetitive firing. Activated by high levels of Ca2+ |
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Term
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Definition
| Activated by modest levels of Ca2+. |
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Term
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Definition
| Protein synthesis begins in the ribosomes in the cytosol. Sometimes ribosomes on mitochondria and plastids |
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Term
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Definition
| Some proteins do not have sorting signals and stay inside the cytosol. |
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Term
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Definition
| Proteins with sorting signals go from cytosol to the nucleus, ER, mitochondria, plastids, or peroxisomes |
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Term
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Definition
| Sorting signals can direct proteins from ER to other parts of the cell |
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Term
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Definition
| When a cell divides it must make a duplicate organelle for the new cell |
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Term
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Definition
| Usually by pumpoing new molecules to the organelles making them larger |
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Term
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Definition
| The organelle can then divide and the new organelle goes to the new daugher cell. |
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Term
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Definition
| A new organelle cannot be made from scratch. You have to have a parent organelle |
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Term
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Definition
| Transport between Cytosol and Nucleus (Gated Transport) |
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Term
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Definition
| Import and export both require Ran GTPase. It provides free energy and directionality for transport. |
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Term
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Definition
| The nuclear envelope breaks apart in mitosis. |
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Term
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Definition
| The nuclear lamina falls apart at the onset of mitosis due to a presence oh kinase Cdk. |
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Term
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Definition
| The nuclear lamina holds the nuclear envelope in its specific shape and keeps it stable. |
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Term
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Definition
| Nuclear localization signals are not removed after the envelope breaks so proteins can be repeatedly imported. |
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Term
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Definition
| This happens each time after the envelope breaks. |
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Term
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Definition
| Tranport of Proteins into Mitochondria and Chloroplasts (Transmembrane Transport) |
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Term
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Definition
| Chloroplasts have the same two subcompartments, plus a third called the thylakoid space, surrounded by the thylakkoid membrane |
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Term
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Definition
| Each subcompartment contains a specific set of proteins |
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Term
| Major Lipids in Cell Membrane |
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Definition
| Lipid molecules about 50% of mass of most animal cell membranes, rest is protein – about 5x10^9 lipid molecules in plasma membrane of small animal cell – all lipid molecules in cell membranes are amphiphilic (hydrophilic, polar head & hydrophobic, non polar tail) |
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Term
| Major Lipids in Cell Membrane |
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Definition
| Most abundant membrane lipids – phospholipids. In animal, plant and bacterial cells, tails usually fatty acids and can differ in length (btwn 14-24 C’s) – one tail usually one or more cis-dbl bonds (unsaturated) while other doesn’t (saturated) à cis-dbl bonds cause the kink in tail |
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Term
| Major Lipids in Cell Membrane |
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Definition
| Main phospholipids in animal cell membranes are phosphoglycerides – 3 C glycerol backbone – two long-chain fatty acids linked through ester bonds to adjacent C atoms of the glycerol and third is attached to a phosphate group which in turn is linked to one of several diff types of head group – doing this, cells make diff phosphoglycerides (main in mammalian CM’s are phosphatidylethanolamine, phosphatidylserine, and phosphatidylcholine |
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Term
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Definition
| lipid molecules exchange places with neighbors within a monolayer readily – gives rise to rapid lateral diffusion, with a diffusion coefficient (D) of about 10^-8 cm^2/sec, which means that avg lipid molecule diffuses the length of a large bacterial cell in about 1 second. |
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Term
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Definition
| Studies show that indiv lipid molecules rotate rapidly about their long axis and have flexible hydrocarbon chains |
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Term
| LB luidity has to be precisely regulated |
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Definition
| A synthetic bilayer made from a single type of phospholipid changes from a liquid state to a 2-D gel at a certain freezing point – called a phase transition and temp @ which it occurs is lower (more difficult to freeze) if the hydrocarbon chains are short or have dbl bonds. |
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Term
| LB luidity has to be precisely regulated |
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Definition
| Shorter chain length reduces tendency of tails to interact with one another, in both the same and opposite monolayer, and cis-dbl bonds produce kinks in the chains that make then harder to pack together, so the membrane remains fluid @ lower temps. |
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Term
| LB luidity has to be precisely regulated |
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Definition
| Bacteria, yeasts, and other organisms whose temp changes w/environment adjust fatty acid composition of membrane lipids to maintain a constant fluidity – as temp falls, cells of organisms synthesize fatty acids with more cis-dbl bond and avoid decrease in bilayer fluidity that would otherwise happen due to temp drop. |
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Term
| Cholesterol modulates the properties of LBs |
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Definition
| Cholesterol decreases the first CH2 groups of chain of phospholipid molecules and makes the LB less deformable in this region and thus decreases the permeability of the bilayer to small, H2O soluble molecules |
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Term
| Cholesterol modulates the properties of LBs |
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Definition
| cholesterol does tighten the packing of lipids in bilayer but does not make membranes less fluid - @ high concentrations found in euk plasma membranes, cholesterol also prevents hydrocarbon chains from coming together and crystallizing. |
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Term
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Definition
| PMs of most euks more varied than those of proks and archaea, bc they not only have a lot of cholesterol but a mixture of diff phospholipids |
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Term
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Definition
| Studies of mass spectrometry show that membranes are composed of 500-1000 diff lipid species – they contain many structurally distinct minor lipids, some of which have imp funcs |
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Term
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Definition
| Inositol phospholipids, ex. are present in small numbers but have critical funcs in guiding membrane traffic and in cell signaling – their local synthesis and destruction are regulated by large # of enzymes, that create both small intracellular signaling and lipid docking sites on membranes that recruit specific proteins from cytosol |
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Term
| Lipid compositions of 2 monolayers of LB in many membranes are diff – |
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Definition
| Bc negatively charged phosphatidylserine is located in inner monolayer, significant diff in charge btwn two halves of the bilayer |
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Term
| Lipid asymmetry is functionally imp, especially in converting extracellular signals into intracellular ones |
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Definition
| In other cases, specific head groups must first be modified to create protein-binding sites @ a particular time/place. |
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Term
| Lipid asymmetry is functionally imp, especially in converting extracellular signals into intracellular ones |
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Definition
| Animals exploit the asymmetry of their PMs to distinguish btwn live and dead cells – when animal cells undergo apoptosis (form of cell death), phosphatidylserine, which is normally confined to the cytosolic monolayer of the plasma membrane LB, rapidly translocates to the extracellular monolayer – the phosphatidylserine exposed on the cell surface signals neighboring cells, such as macrophages, to phagocytose the dead cell and digest it |
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Term
| the translocation of the phosphatidylserine in apoptotic cells is thought to occur byt 2 mechanisms: |
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Definition
| A “scramblase” that transfers phospholipids nonspecifically in both directions btwn the 2 monolayers is activated. (all cell death) |
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Term
| the translocation of the phosphatidylserine in apoptotic cells is thought to occur byt 2 mechanisms: |
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Definition
| Glycolipids contain sugar, are found in noncytosolic monolayer of LB – have most extreme asymmetry in their membrane distribution – in animal cells they are made from sphingosine – they tend to self associate, partly through H bonds btwn sugars and partly thru VDW forces btwn long and straigt hydrocarbon chains, and may partition into lipid rafts. |
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Term
| the translocation of the phosphatidylserine in apoptotic cells is thought to occur byt 2 mechanisms: |
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Definition
| The asymmetric distribution of glycolipids in bilayer results from addn of sugar groups to lipid molecules in lumen of Golgi – thus the compartment in which theyre made is topologically equivalent to exterior of cell. |
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Term
| the translocation of the phosphatidylserine in apoptotic cells is thought to occur byt 2 mechanisms: |
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Definition
| As theyre delivered to PM, sugar groups are exposed @ cell surface where they have important roles in interactions of cell w/its surroundings |
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Term
| the translocation of the phosphatidylserine in apoptotic cells is thought to occur byt 2 mechanisms: |
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Definition
| Most complex glycolipids – gangliosides which contain oligosaccharides with one or more sialic acid residues – give a neg net charge – most abundant of these are in PM of nerve cells. |
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Term
| the translocation of the phosphatidylserine in apoptotic cells is thought to occur byt 2 mechanisms: |
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Definition
| Functions of these – protect against harsh conditions, can affect ion transport and binding, can affect solute diffusion, can affect membrane charge – some provide entry points for certain bacterial toxins |
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Term
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Definition
| Many diff proteins extend thru LB with part of mass on either side – transmembrane proteins are amphipilic; their hydrophobic regions pass thru the membrane and interact w/hydrophobic tails of lipid molecules in interior of bilayer where they are kept from away from water; hydrophilic regions exposed to water on either side of membrane – the covalent attachment of a fatty acid chain that inserts into the cytosolic monolayer of the LB increases hydrophobicity of some transmembrane proteins. |
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| Other proteins are located entirely inside cytosol and are associated with cytosolic monolayer of LB by an amphiphilic alpha helix exposed on surface of the protein or by one or more covalently attached lipid chains – yet some other proteins attached at external surface of cell, being attached to LB only by a covalent linkage to phosphatidylinosital in outer lipid monolayer of PM |
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| Some proteins are bound only to one side of the LB and don’t insert into it – they are bound by noncovalent interactions – many of these proteins can be released from membrane by gentle extraction procedures (exposure to soln’s of high or low ionic strength or extreme PH, which interfere with protein-protein interactions but leave LB intact) – these are referred to as, peripheral membrane proteins. |
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| Transmembrane proteins and many proteins held together by lipid groups or hydrophobic polypeptide regions that insert into the hydrophobic core of the lipid bilayer cant be released in these ways – they are known as integral membrane proteins. |
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| o Lipid anchors control the membrane localization of some signaling proteins |
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| § Only transmembrane proteins can func on both sides of LB or transport molecules across it |
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| § Some func only on one side of LB, often associated with either lipid monolayer or a protein domain on that side – some intracellular signal proteins involved in converting extracellular sigs into intracellular ones are bound to cytosolic half of PM by one or more covalently attached lipid groups which can be fatty acid chains or prenyl groups |
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| § Some cases – myristic acid is added to N-terminal amino group of the protein by during its synthesis on the ribosome – membrane attachment thru a single lipid anchor not very strong so a 2nd is often added to anchor proteins better to membrane – the 2nd lipid modification is attachment of palmitic acid to a cysteine side chain of the protein – this occurs in response to an extracellular signal and helps recruit kinases to the plasma membrane - when signaling pathway is turned off, palmitic acid is removed, allowing kinase to return to cytosol |
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Definition
| o In most transmembrane proteins the polypeptide chain crosses LB in an alpha-helical conformation |
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| § A transmembrane protein always has a unique orientation in the membrane – reflects both assymetrical manner in which it is inserted into LB in ER during its biosynthesis and the diff funcs of its cytosolic/noncytosolic domains – these domains separated by membrane-spanning segments of polypep chain which touch the hydrophobic environment of the LB & are composed of a.a.’s w/nonpolar side chains. |
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| · Because the peptide bonds are polar and water is absent, all peptide bonds in bilayer are driven to form H bonds w/one another – this h-bonding is maximized if polypep chain forms a regular alpha-helix as it crosses the bilayer, and this is how most membrane-spanning segments of polypep chains traverse the bilayer |
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| § In single pass transmembrane proteins, polypep chain crosses only once but multipass it crosses multiple times – an alternative way for peptide bonds in LB to satisfy their H-bonding requirements is for multiple transmembrane strands of a polypep chain to be arranged in a B barrel – seen in porin proteins – segments of about 20-30 a.a.’s w/high degree of hydrophobicity needed to span LB as an alpha helix, can be ID’d in hydropathy plots, these cannot ID the membrane spanning segments of a B barrel |
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| o Transmembrane alpha helices often interact w/one another |
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| § These do not contribute to the folding of the protein domains on either side of the membrane – it is often possible to engineer cells to produce the cytosolic or extracellular domains of these proteins as water-soluble protein. |
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| § A transmembrane a-helix often does more than just anchor the protein to the LB – many single pass protein membranes form heterodimers, held together by strong, highly specific interactions btwn the 2 transmembrane a-helices; the sequence of the hydrophobic AA’s of these helices contains info that directs protein-protein interaction. |
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| § Similarly, the transmembrane a-helices in multipass membrane proteins occupy specific positions in the folded protein structure that are determined by interactions btwn neighboring helices – these interactions crucial for the structure & func of many channels and transporters that move molecules across LBs. |
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| · Loops can be cut by proteases and the helices stay together and keep functioning |
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| § Transmembrane a-helices inserted into LB sequentially by a protein translocator – after leaving this, each helix is transiently surrounded by lipids in bilayer, which means helix must be hydrophobic – it is only as the protein folds into final structure that contacts are made btwn adjacent helices and protein-protein contacts replace some of the protein-lipid contacts. |
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| o Some B barrels form large transmembrane channels |
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| § Multipass transmembrane proteins arranged a B barrel rather than an a helix are rigid and tend to crystallize readily – so some of them were among first multipass membrane protein structures to be determined by x-ray crystallography – number of strands varies from 8-22 |
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| § These proteins are abundant in outer membrane of mitochodria, chloroplasts, and many bacteria – some are pore forming proteins that create water-filled channels that allow selected small hydrophilic molecules to cross LB of bacterial outer membrane |
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| § Loops of the polypep chain often protrude into lumen of the channel, narrowing it so only certain solutes can pass – determines specificity, so some porins are highly selective |
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| § Not all B barrel proteins are transport proteins – some form smaller barrels that are filled with AA side chains – these proteins func as receptors or enzymes and the barrel serves as a rigid anchor that holds the protein in the membrane and orients the cytosolic loops that form binding sites for specific intracellular molecules |
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| § B barrel proteins have many funcs, but they are restricted to bacterial, mitochondrial and chloroplast outer membranes – most multipass transmembrane proteins in euk cells and in bacterial PMs made of a-helices that can slide against each other, causing conformational changes in the protein that can open/close ion channels, transport solutes or transduce extracellular signals into intracellular ones – in B barrel proteins, by contrast, H bonds bind each B strand rigidly to its neighbors, making conformational changes w/in wall of barrel unlikely. |
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| o Many membrane proteins are glycosylated |
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| § Most in animals cells glycosylated – as in glycolipids, sugar residues added in lumen of ER & Golgi – thus, the oligosaccharide chains are always present on the noncytosolic side of the membrane – another imp diff btwn proteins on either side of membrane comes from the reducing environment of the cytosol – it decreases chances that intrachain or interchain disulfide (S-S) bonds will form btwn cysteines on cytosolic side of membranes, they form on the noncytosolic side where they help stabilize the folded structure of the polypep chain or its association with other polypep chains |
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| § Because most PM proteins are glycosylated, carbs coat the surface of akk euk cells – cell coat or glycocalyx used to describe the carb-rich zone on cell surface – one of the many funcs of the carb layer is to protect cells @ a distance against mechanical and chemical damage; it also keeps various other cells at a distance, preventing unwanted protein-protein interactions |
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| § Polysac side chains of glycoproteins/glycolipids are diverse in arrangement of sugars – often branched and sugars can be bonded together by various covalent linkages – unlike AAs in a polypep chain, which are linked by identical peptide bonds – even 3 sugars can be put together to form hundreds of diff polysacs. |
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| § First membrane transport protein to have structure determined – prototype of many multipass membrane proteins w/a similar structure – “the purple membrane” of Halobacterium salinarum ins a patch in plasma membrane that has a single species of protein molecule – each of these molecules has a single light absorbing group or chromophere called retinal that gives protein its purple color – retinal covalently linked to a lysine side chain of the bacteriorhodopsin protein – when activated by light, the excited chromophere changes shape and causes small conformational changes in the protein, resulting in transfer of one H+ from the inside to outside of cell – pumps H+ ions across membrane – it is a retinal cofactor – built from seven transmembrane a-helices that function as signal transducers instead of transporters – forms 2-D planar crystal in membrane. |
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| § Rotate and move laterally – do not flip flop or tumble across the LB but they do rotate about an axis perpendicular to the plane of the bilayer (rotational diffusion)– can form multiprotein complexes – arranged in large complexes not only for harvesting various forms of energy but also for transducing extracellular sigs into intracellular ones – many membrane proteins are able to move laterally within the membrane (lateral diffusion) |
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| · Lateral diffusion rates of membrane proteins measured using fluorescent recovery after photobleaching (FRAP) – this uses marking the protein of interest with a specific fluorescent group done with a ligand that binds to the protein or with recombinant DNA technology to express the protein fused to green fluorescent protein (GFP) – fluorescent group then bleached in a small area of membrane by a laser beam and the time take for the adjacent membrane proteins carrying unbleached ligand of GFP to diffuse into the bleached area is measured. |
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| Complementary technique is fluorscent loss in photobleaching (FLIP) – laser beam irradiates a small area of membrane to bleach all the fluorescent molecules that diffuse into it, thereby gradually depleting the surrounding membrane of fluorescently labeled molecules |
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| o From such FLIP/FRAP measurements, we can calculate the diffusion coefficient for the marked cell-surface protein – values are highly variable bc interactions w/other proteins impede the diffusion of the proteins to varying degrees – if measurements are minimally impeded it means that the cell membranes have a viscosity comparable to olive oil. |
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| · One drawback to FLIP/FRAP is that they monitor the movement of large populations of molecules in a large area of membrane so one cant follow indiv protein molecules – if a protein does not migrate in bleached area, for ex. one cant tell if the molecule is truly immobile or just restricted in its movement to a very small region of membrane, maybe by cytoskeletal proteins. |
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| § Many cells confine membrane proteins to specific regions in a continuous LB – in epithelial cells (those that line the gut or tubules of kidney), certain PM enzymes and transport proteins are confined to the apical surface of the cells, whereas others are confined to the basal and lateral surfaces – this assymetrical distribution of membrane proteins is often essential for func of the epithelium – the lipid compositions of these two membrane domains are diff showing that epithelial cells can prevent the diffusion of lipid as well as protein molecules btwn domains – experiments show that only lipid molecules in the outer monolayer of the membrane are confined this way – the barriers set up by a specific type of intercellular junction (tight junction) maintain separation of both protein and lipid molecules so the membrane proteins that form these intercellular junctions cant be allowed to diffuse laterally in the interacting membranes. |
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| § A cell can also create membrane domains w/out using intercellular junctions – some of the membrane molecules are able to diffuse freely within the confines of their own domain – the molecular nature of the “fence” that prevents the molecules from leaving their domain is not known |
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| § Read pages 646-648 for more info on protein confinement |
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