L7 membrane trafficking 2 Flashcards
what does acyl chain saturation determine?
unsaturated: disordered, loose packing, high lateral mobility, thinner LIQUID-DISORDERED PHASE (Ld) properties due to some of the vertical space taken up by kinks in the lipid tails.
saturated: ordered, tight packing, low lateral mobility, thicker SOLID ORDERED PHASE (So)
degree of saturation in acyl chains influences lipid shape and packing. Lipid packing changes the physical properties of the bilayer.
cholesterol and membrane microdomain formation?
Cholesterol helps form membrane microdomains, such as lipid rafts. A cholesterol-rich domain can stabilize the ordered phase of lipids, increasing membrane thickness by allowing acyl chains to extend. Cholesterol can also stabilize long transmembrane domains and create specialized membrane regions enriched in certain proteins. These lipid rafts are thought to form and function as platforms for cellular signaling and trafficking
*chatgpt
how do proteins embed in the membrane?
Alpha-helices typically embed in the lipid bilayer due to their hydrophobic nature. For example, bacteriorhodopsin, a membrane protein, is rich in alpha-helices. These helices have hydrophobic residues on the outside that interact with the hydrophobic interior of the lipid bilayer, stabilizing their position. This is similar to many membrane proteins with multi-pass helices. These proteins may have hydrophilic regions between the alpha-helices that help stabilize the structure, while the hydrophobic residues are oriented towards the membrane’s hydrophobic core.
For single-pass membrane proteins, the alpha-helix that spans the membrane will need to present hydrophobic residues along its entire length to interact with the lipid bilayer.
However, membrane association is not limited to alpha-helices. Some hydrophilic proteins can also associate with membranes through lipid modifications on their amino acids. For example, Ras GTPase is modified with acyl chains, allowing it to anchor to the inner or outer leaflet of the membrane. One type of lipid modification is glycosylphosphatidylinositol (GPI) anchoring, which also attaches proteins to membranes.
Another way proteins associate with membranes is through peripheral membrane proteins, which do not directly span the lipid bilayer but interact with proteins already embedded in the membrane.
crossing biological membranes: wht are transporters?
Conformational change accompanies transporter-mediated transport, where the transporter protein changes shape to move substrates across the membrane.
Transporters can be classified as uniporters, symporters, or antiporters depending on how they transport molecules:
Uniporters transport one molecule in one direction.
Symporters transport two molecules in the same direction.
Antiporters transport two molecules in opposite directions.
Channels need to be gated to prevent the dissipation of concentration gradients. Gating allows the channel to open and close at specific times, controlling the flow of ions or molecules.
Organelles need communication routes for the movement of substances across membranes. The hydrophobic nature of the lipid bilayer makes it difficult for most molecules to cross. Only small, hydrophobic, or lipid-soluble molecules (such as fatty acids) can diffuse across easily. Charged molecules or polar compounds prefer to stay in the aqueous environment of the cytoplasm and cannot diffuse across the membrane by simple diffusion.
To overcome this, membrane proteins facilitate the movement of substrates across the membrane, either passively (down their concentration gradient) or actively (against their concentration gradient). This includes:
Transporters, which bind a molecule, change shape, and release the molecule on the other side of the membrane.
Channels, which allow molecules to move through a pore, typically down the concentration gradient.
Passive transport allows the movement of solutes from high to low concentration and can occur through channel-mediated or transporter-mediated mechanisms.
For active transport, cells can use transporters that employ nucleotide hydrolysis (such as ATP hydrolysis) to release energy, allowing the solute to be moved against its concentration gradient (from low to high concentration).
transporter coupling?
transporter coupling allows for secondary active transport.
Transporters can work together to allow nutrients to move into cells, establishing concentration gradients (c.g.) across the cell membrane. This is critical in secondary active transport, where one transporter creates an ionic gradient (e.g., via active transport), which can be used by another transporter to pull molecules across the membrane in the opposite direction.
example of secondary active transport?
In the intestinal lumen, active transport occurs at the basolateral surface of enterocytes (intestinal cells). Here:
Sodium (Na+) is actively extruded out of the cell, and potassium (K+) is actively brought in via the Na+/K+ ATPase pump.
This creates a sodium deficit inside the cell, establishing a concentration gradient.
The Sodium-Glucose Cotransporter (SGLT) takes advantage of this gradient by pulling in sodium and glucose from the gut lumen at the same time into the cell.
The Na+/K+ ATPase pump activity on one membrane (basolateral surface) thus indirectly facilitates the secondary active transport of glucose from the apical membrane (lumen side), allowing nutrients to enter the cell.
why do you need ion channels and how are they gated?
ion channels are essential for balancing the flow of charged molecules (ions) across membranes, particularly when there are concentration gradients that need to be maintained.
Ion channels are typically composed of protein subunits arranged around a water-filled pore, which allows ions to flow through the channel in a single-file manner at a high rate (similar to diffusion).
These channels are characterized by the type of ion they pass (e.g., sodium channels) and their mechanism of gating.
Types of Ion Channel Gating:
Voltage-gated: Open or close in response to changes in membrane potential (e.g., sodium channels during action potential).
Ligand-gated: Open or close when a specific ligand (e.g., neurotransmitter) binds to the channel (e.g., NMDA receptors).
Mechanosensitive: Open when the membrane is stretched, allowing ions like calcium to flow into the cell (e.g., in muscle cells when they stretch).
Light-gated: Found in plants, these channels open in response to light.
Temperature-gated: Found in sensory systems, these channels open or close in response to temperature changes.
Some ion channels are rectifying, meaning they allow the flow of ions in only one direction.
aquaporins?
Aquaporins are specialized membrane channels that allow the movement of water molecules across cell membranes. They are critical in cells that need to transport water quickly, such as in the gut lining, kidney epithelial cells, and secretory cells.
Function: Aquaporins allow water to pass through while blocking ions, ensuring that only water molecules move across the membrane.
Structure: Aquaporins have a narrow pore lined with hydrophobic residues, which helps restrict the passage of ions and other molecules. There is also a single band of hydrophilic residues (often from the carbonyl groups of the pore lining), which interacts with the water molecules and stabilizes them as they pass through.
Water Flow: Aquaporins can allow up to 3 billion water molecules per second to pass through, facilitating rapid water transport.
Water Movement: Water doesn’t pass through the membrane freely due to the hydrophobic nature of the lipid bilayer. Therefore, aquaporins are necessary for water to flow into the cell along with ions, ensuring efficient water transport.
Aquaporins are designed to selectively allow single-file water movement, where a single water molecule can move through the pore at a time. The hydrophilic residues inside the pore help stabilize the water molecules, allowing them to move in an organized manner through the channel.
compartmental identity: phosphoinositides?
Compartmental identity refers to the unique molecular “code” that exists on the membranes of different organelles. This code helps direct effector proteins to bind to the correct membrane compartments. One of the key ways to establish this compartmental identity is through phosphoinositides—a specific class of lipids embedded in cellular membranes.
What are Phosphoinositides?
Phosphoinositides are phospholipids that feature an inositol head group.
Inositol is a 6-carbon molecule that can be phosphorylated at different positions on its ring. This phosphorylation creates distinct phosphoinositide species that act as signals for specific organelles.
Phosphoinositides can be phosphorylated at various positions, and the pattern of phosphorylation dictates the identity of the membrane where they are located.
Phosphorylation at position 3: Forms PI(3)P (phosphatidylinositol 3-phosphate), typically found on endosomes.
Phosphorylation at position 4: Forms PI4P, found on the Golgi apparatus.
Phosphorylation at positions 4 and 5: Forms PI(4,5)P2, found on the plasma membrane.
Phosphorylation at positions 3, 4, and 5: Forms PI(3,4,5)P3, found on subdomains of the plasma membrane—typically after stimulation.
How Phosphoinositides Contribute to Compartmental Identity:
Binding of Effector Proteins: Proteins that recognize and bind to these phosphorylated lipids often have specific domains that interact with them:
PH (Pleckstrin Homology) or PX domains: These domains bind to PI(3)P, which is found on endosomes.
C2 domains: These domains bind to PI(3,4,5)P3, found on certain subdomains of the plasma membrane.
Regulation of Phosphorylation: The phosphorylation state of these lipids can be dynamically regulated by lipid kinases (which add phosphate groups) and lipid phosphatases (which remove them). This process helps govern the identity of each membrane compartment.
Examples of Phosphoinositide Localization:
PI3P is found on endosomes, signaling endosomal identity.
PI4P is localized to the Golgi, signaling Golgi identity.
PI(4,5)P2 is found at the plasma membrane, crucial for signaling and cellular processes.
PI(3,4,5)P3 is found at subdomains of the plasma membrane, typically formed in response to cellular signaling.
Summary:
The phosphoinositide code enables precise targeting of proteins to specific organelles by modifying the lipid composition of membranes. This lipid modification can recruit different effector proteins to these organelles, which helps maintain their function and identity.
comaprtmental identity: RAB GTPases
RAB GTPases: A Key Mechanism for Compartmental Identity
RAB GTPases are small GTP-binding proteins that play a crucial role in demarcating different organelles within the cell. They help establish compartmental identity by ensuring that specific effectors are recruited to regulate vital processes such as vesicle budding, motility, and fusion.
Function of RAB GTPases:
Compartmental Identity: RAB GTPases are embedded in the membranes of different intracellular organelles, marking the identity of each organelle.
Recruitment of Effectors: They recruit specific effector proteins that regulate key processes, including:
Motor proteins (for vesicle transport)
Tethering proteins (for vesicle docking)
SNARE proteins (for vesicle fusion)
Activation and Inactivation:
GEFs (Guanine nucleotide Exchange Factors) activate RAB GTPases by promoting the exchange of GDP for GTP.
GAPs (GTPase-Activating Proteins) inactivate RAB GTPases by accelerating the hydrolysis of GTP to GDP, turning off their signaling.
Subcellular Localization:
Endosomes: RAB5, RAB4, and RAB21 are enriched in early endosomes, marked by the presence of PI3P (phosphatidylinositol 3-phosphate).
Golgi Apparatus: RAB6 is specifically enriched in the Golgi membrane.
Late Endosomes: RAB7 and RAB9 are localized to late endosomes.
By ensuring that these RAB GTPases are localized to specific organelles, cells can impose another layer of compartmental identity, allowing for precise regulation of intracellular trafficking.
Summary:
RAB GTPases act as molecular markers for different organelles, ensuring that the right effector proteins are recruited for essential processes like vesicle transport, fusion, and motility. This localized activation and inactivation of RAB GTPases through GEFs and GAPs contributes significantly to membrane identity and the proper functioning of the cell.
transport between intracellular compartments?
Transport Between Intracellular Compartments
Intracellular transport is essential for moving materials between different organelles within the cell. This process involves several steps to ensure the cargo reaches its correct destination. Here’s how it works:
- Selection of Cargo
The first step in intracellular transport is the selection of cargo. This involves identifying which proteins, lipids, or other molecules need to be transported from one organelle to another. The cargo is recognized by specific proteins that help package it into transport intermediates (e.g., vesicles). - Formation of Transport Intermediate
Once the cargo is selected, it must be packaged into transport intermediates. This typically involves the formation of vesicles at the donor compartment’s membrane. Special proteins help shape the membrane to form a vesicle that is capable of containing and concentrating the selected cargo.
During this process, the membrane also needs to be separated from the donor organelle. This is achieved through vesicle scission, a process where the vesicle buds off and detaches from the donor membrane, allowing it to be transported through the cytoplasm.
- Movement Through the Cell
Once the vesicle is formed, it is moved within the cell. Molecular motors (such as kinesins or dyneins) move the vesicles along microtubules to the target compartment. - Fusion with Target Organelle
When the vesicle reaches its target compartment, it must fuse with the membrane of the organelle. This fusion event ensures that the contents of the vesicle (including proteins and lipids) are delivered to the target organelle. This step also allows the vesicle’s membrane to become integrated into the target membrane, contributing to the exchange of membrane proteins and lipids.
lipid exchange between organelles?
Lipid Exchange Between Organelles
In addition to vesicular transport, lipids can also be exchanged between organelles through membrane contact sites.
Membrane Contact Sites: These are regions where two organelles are in close proximity, allowing for lipid exchange without the need for vesicles. Specialized proteins at these sites help extract lipids from one organelle, flip them, and insert them into another organelle’s membrane. This is a form of non-vesicular transport, which is crucial for maintaining membrane composition and function across different organelles.
transport vesicle formation?
Coat Proteins Assemble on Donor Membranes: Coat proteins, such as clathrin or COP proteins, first assemble on the donor membrane. This is the first step in vesicle formation, where the coat proteins help determine the shape of the vesicle.
Concentration of Cargo: The coat proteins assist in concentrating the cargo (proteins, lipids, or other materials) that needs to be packaged into the vesicle. The concentration of cargo helps ensure that the materials are effectively transported to the next destination.
Membrane Shaping Proteins Form the Vesicle: Membrane-shaping proteins, like dynamin, assist in bending the membrane into the characteristic shape of a vesicle. These proteins help the membrane adopt a curvature that is necessary for vesicle formation.
Membrane Fission Proteins Sever the Vesicle: Once the vesicle is fully formed, fission proteins (such as dynamin) help “cut” the neck of the budding vesicle. This process physically separates the vesicle from the donor membrane.
Vesicle Budding and Release: The vesicle “buds” inward, and the neck connecting the vesicle to the donor membrane gets thinner. Eventually, the neck is severed, and the transport vesicle is released into the cytoplasm, ready to deliver its cargo to other locations within the cell.
membrane coats?
Membrane Shaping Proteins (BAR domains):
BAR domains help curve membranes to facilitate vesicle budding.
N-BAR, F-BAR, and I-BAR bend the membrane in different directions, altering the lipid bilayer structure.
Coat Proteins:
Coat proteins often contain BAR domains to induce membrane curvature.
Clathrin, COPI, and COPII are the three major coat proteins.
Functions of Different Coat Proteins:
Clathrin: Works at the plasma membrane and trans-Golgi network to select cargo for internalization or Golgi budding.
COPI: Operates in the retrograde pathway, from the Golgi to the ER.
COPII: Operates in the anterograde pathway, from the ER to the Golgi.
COP (Coatomer Protein):
COP proteins form the coat for vesicle budding in various trafficking pathways.
RAB proteins?
RAB Proteins:
RAB proteins play a key role in membrane trafficking by cycling between GTP and GDP states.
They recruit different organellar effectors and bind tethering factors, which help vesicles approach and capture transport intermediates at specific membranes and place them for action by SNAREs.
Functions of RAB Proteins:
Organelle Maturation/Cascades: RAB proteins are involved in the maturation of organelles and help coordinate vesicle trafficking through cascades.
Interaction with Tethering Factors: They bind tethering factors that help bring vesicles to their target membranes.
Formation of Organellar Microdomains: For example, Rab5 and PI 3-kinase create a microdomain that aids in vesicle capture.
SNAREs?
vSNAREs are present in the transport vesicle (from donor compartments), while tSNAREs are present in the target membrane.
SNARE pairing (vSNARE + tSNARE) helps the vesicle fuse with the target membrane.
How Vesicles Fuse with Target Membranes:
SNAREs displace water from hydrophilic surfaces, promoting membrane fusion.
They overcome the ionic repulsion between charged membranes.
4 SNAREs form a trans-SNARE bundle during fusion.
More than 30 SNAREs are found in distinct compartments, providing specificity for membrane fusion.
Specificity of SNARE Pairings:
Only certain vSNAREs will bind to and fuse with specific tSNAREs, ensuring vesicles fuse with the correct target compartments.
Fusion Mechanism:
When the vesicle approaches the target membrane, SNAREs from both the vesicle and target membrane bind and wrap around each other.
This trans-SNARE bundle brings the vesicle closer to the membrane, leading to hemifusion (when the lipid bilayers start to mix) and then full fusion, allowing contents to be delivered across the membrane.
After fusion, a single target membrane contains the bundled SNARE complexes.
recycling SNARE complexes?
Recycling SNARE Complexes:
After docking, SNARE complexes form, and fusion occurs, with SNAREs bundled in the same membrane.
NSF (N-ethylmaleimide-sensitive factor) is an ATPase that disassembles the SNARE complexes, separating vSNAREs and tSNAREs.
vSNAREs are recycled back to the donor compartment for further use.
Role of NSF:
NSF uses ATP hydrolysis to pry apart the SNAREs, enabling multiple rounds of vesicle fusion.
vesicle fusion and neurotransmitter release?
Vesicle Fusion and Neurotransmitter Release:
Vesicle fusion through SNAREs is crucial for moving contents between compartments and for neurotransmitter (NT) release.
NT-containing vesicles move from internal compartments to the plasma membrane in the synapse.
SNARE pairing facilitates the fusion of these vesicles with the plasma membrane, releasing NT into the synaptic cleft.
The NT then acts on the postsynaptic density to initiate signaling.
This process is essential for neurotransmission between neurons, axons, dendrites, and muscle cells.
SNAREs and bacteria neurotoxins?
BoNT and TeNT Mechanism:
Botulinum toxin (BoNT) and Tetanus toxin (TeNT) cleave SNARE proteins, preventing vesicle fusion and neurotransmitter (NT) release.
By blocking SNARE pairing, these toxins stop NT transmission, causing paralysis, muscle spasms, and death.
BoNT also reduces wrinkles as it affects acetylcholine (ACh) release, which is involved in muscle contraction.
Role of SNAREs in Acetylcholine Release:
vSNAREs in synaptic vesicles and tSNAREs in the plasma membrane of neurons fuse to release ACh into the synaptic cleft.
BoNT and TeNT cleave SNAREs to prevent vesicle fusion, blocking NT release and disrupting normal communication between neurons and muscle cells.
