unit 2 week 1 Flashcards
Plasma membrane
The outer boundary of a cell, protecting it from outer world
What are the functions of membranes?
- Compartmentalization
- Scaffold for biochemical activities
- Selectively permeable barrier
- Solute transport
- Response to external stimuli
- Cell-cell communication
- Energy transduction
What does membrane ‘sidedness’ refer to?
refers to the orientation and asymmetry of the membrane.
How can membrane proteins be grouped?
Into 3 distinct classes based on their intimacy of relationship to the lipid bilayer: Integral proteins, Peripheral proteins, Lipid-anchored proteins.
Integral proteins
Integral proteins are also known as transmembrane proteins. A membrane-associated protein that penetrates or spans the lipid bilayer
Peripheral proteins
A membrane-associated protein that is located entirely outside of the lipid bilayer and interacts with it through noncovalent bonds.
Lipid-anchored proteins
A membrane associated protein that is located outside the bilayer but is covalently linked to a lipid molecule within the bilayer.
What challenges exist in isolating integral membrane proteins?
Hydrophobic transmembrane domains make integral membrane proteins difficult to isolate in soluble forms.
[EXPLAINED: Integral membrane proteins are hard to isolate because they have hydrophobic (water-repelling) regions that interact with the lipid bilayer. These regions make them insoluble in water, causing them to clump together or stick to membranes. To extract them, scientists use detergents that mimic the membrane environment, but finding the right conditions is tricky. Some detergents can damage the protein, making it lose its function. Additionally, some proteins depend on lipids to stay stable, making isolation even more challenging.]
What are detergents used for in membrane protein isolation?
Detergents like SDS and Triton X-100 are used to remove integral membrane proteins from membranes and stabilize them in solution.
What is a key challenge in crystallizing membrane proteins?
1) Less than 1% of known high-resolution protein structures are integral membrane proteins.
2) Most crystallized structures are prokaryotic proteins (smaller and easier to obtain).
3)Technical difficulties in crystallizing membrane proteins include:
-Low protein abundance in cells.
-Instability in detergent solutions.
-Prone to aggregation.
-Heavy glycosylation modification.
What is Cryo-Electron Microscopy (Cryo-EM)?
Cryo-EM is a technique that allows for high-resolution membrane protein structure determination using low temperatures and averaging of images.
details:
[In cryo-EM, samples are rapidly frozen in a thin layer of ice to preserve their natural shape without needing crystals (unlike X-ray crystallography). An electron microscope then captures images of many individual molecules from different angles. Advanced computer software processes these images to reconstruct a detailed 3D model of the protein. Cryo-EM is especially useful for studying large, flexible, or membrane proteins that are difficult to crystallize.]
What are transmembrane domains?
-Segments of the protein embedded within the lipid bilayer, often forming an α helix.
-Structure: About 20 nonpolar amino acids form the helix, spanning the lipid bilayer’s core.
-Example: Glycophorin A, an integral protein in the erythrocyte plasma membrane, has a single transmembrane helix.
Most of the amino acids in the transmembrane domain are:
Hydrophobic
-Exceptions: Polar residues like serine and threonine, which may form hydrogen bonds, or charged residues at the ends of the helix that interact with the hydrophobic environment.
What is a hydropathy plot?
Hydropathy plots identify transmembrane segments by measuring the hydrophobicity of amino acids along the polypeptide chain.
-A “jagged peak” in the plot indicates a transmembrane segment.
-Hydrophobicity is determined by the amino acids’ lipid solubility or the energy required to transfer them into an aqueous medium.
Orientation of Transmembrane Segments
In many proteins, the cytoplasmic flanking residues of transmembrane segments tend to be positively charged, while the extracellular residues are more likely to be neutral or negatively charged.
Alternative Membrane Protein Structures
Not all membrane proteins have transmembrane α helices. Some contain β barrel structures (e.g., in bacterial, mitochondrial, and chloroplast outer membranes) that form aqueous channels.
What is site-directed mutagenesis?
Site-directed mutagenesis involves introducing specific mutations into the gene encoding a membrane protein to study accessibility of residues to aqueous environments and how their accessibility changes with the protein’s function.
-Ex: In lactose permease (a sugar-transporting protein), cysteine substitution and exposure to N-Ethylmaleimide (NEM) helps determine which residues are accessible to the aqueous environment. -
-In the absence of sugar: Some residues (shown as red spheres) are alkylated by NEM, indicating they are accessible to the aqueous medium.
-In the presence of sugar: Different residues (gold spheres) show increased reactivity to NEM, suggesting a conformational change in the protein that opens up new regions to the aqueous environment.
What does the Alternating Access Model describe?
The Alternating Access Model describes how lactose permease switches between two conformations to transport sugar across the membrane. [details: In one conformation, the sugar-binding site is open to the cytoplasm, and in the other, it’s open to the extracellular space. This alternation allows sugar transport across the membrane.]
What is EPR (Electron Paramagnetic Resonance) Spectroscopy used for?
EPR Spectroscopy is used to study conformational changes in membrane proteins by measuring the distance between labeled residues.
-EX: [In a bacterial K+ channel, EPR spectroscopy revealed how the distance between subunits changes when the channel opens in response to pH shifts:
-At pH 6.5 (closed state): The nitroxides are closer, resulting in a broader spectrum.
-At pH 3.5 (open state): The nitroxides are farther apart, indicating that the channel opening involves a separation of subunits, increasing the diameter of the channel to allow K+ ions to pass.]
What is FRET?
FRET (Fluorescence Resonance Energy Transfer) is a technique used to measure the distance between labeled groups within a protein.
What does NMR Spectroscopy measure?
NMR Spectroscopy measures distances between atoms in a protein and is important for studying membrane protein dynamics.
What is the plasma membrane?
The plasma membrane is a barrier that retains the dissolved materials of the cell so that they do not simply leak out into the environment, yet it must allow the necessary exchange of materials into and out of the cell.
What are the two means for substance movement through the membrane?
Substances move through the membrane passively by diffusion or actively by an energy-coupled transport process.
What is net flux?
Indicates that the movement of the substance into the cell (influx) and out of the cell (efflux) is not balanced, but that one exceeds the other.