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.
What is influx?
Influx is the movement of substance into the cell.
What is efflux?
Efflux is the movement of substance out of the cell.
Diffusion
a spontaneous process in which a substance moves from a region of high concentration to a region of low concentration, eventually eliminating the concentration difference between the two regions
Delta G depends on…
how far away a state is from equilibrium
In diffusion, equilibrium occurs when…
the concentration is equal on both sides of the membrane
Concentration gradient
how different the concentration is on the two sides of the membrane
This equation describes the movement of a nonelectrolyte into the cell:
Where delta G is the free-energy change (Section 3.1), R is the gas constant, T is the absolute temperature, and [Ci]/[Co] is the ratio of the concentration of the solute on the inside (i) and outside (o) surfaces of the membrane. *KNOW BETTER HOW IT WORKS
What is an electrochemical gradient?
An electrochemical gradient is the combined effect of:
Chemical gradient – The concentration difference of an ion across a membrane.
Electrical gradient – The charge difference (voltage) between two compartments.
Both gradients influence the movement of electrolytes (charged solutes) across membranes.
How does charge affect ion movement?
Ions repel like charges → It is unfavorable for an ion to move into a compartment with the same charge.
Ions are attracted to opposite charges → Movement is favored when the ion enters a compartment with opposite charge.
The greater the voltage difference, the greater the free-energy change for ion movement.
What is the equation for electrochemical gradients?
The free-energy change for an electrolyte moving across a membrane is:
How does the electrochemical gradient influence Na+ movement?
Example: Na+ is 10 times more concentrated outside the cell than inside.
The cell membrane voltage is about -70mV.
This means Na+ has a strong drive to enter the cell due to both its chemical and electrical gradients.
The total free-energy change for Na+ entry = -3.1 kcal/mol, meaning Na+ diffusion is highly favorable.
How does the electrochemical gradient affect K+ movement?
K+ is more concentrated inside the cell.
The chemical gradient favors K+ leaving the cell.
However, as K+ leaves, the inside of the cell becomes more negative, creating an electrical gradient that pulls K+ back in.
This opposing effect is important in membrane potential and nerve impulses (discussed in Section 4.7).
What are the two requirements for a nonelectrolyte to diffuse passively across a plasma membrane?
- The substance must be present at higher concentration on one side of the membrane than on the other. 2. The membrane must be permeable to the substance.
What is the partition coefficient?
The partition coefficient is the ratio of a substance’s solubility in a nonpolar solvent to its solubility in water.
What factor determines the rate of penetration of a compound through a membrane?
The size of the compound; smaller compounds tend to penetrate quicker than larger ones.
What does it mean for membranes to be semipermeable?
Membranes are semipermeable because of the difference in penetrability of water vs solutes; water is more penetrable.
What is osmosis?
Osmosis is the process of moving from lower solute concentration to higher concentration.
-water undergoes this process
What is a hypertonic solution?
A hypertonic solution is a compartment with higher solute concentration.
What is a hypotonic solution?
A hypotonic solution is a compartment with lower solute concentration.
What happens to a cell placed in a hypotonic solution?
It rapidly gains water by osmosis and swells.
What happens to a cell placed in a hypertonic solution?
It rapidly loses water by osmosis and shrinks.
A cell’s volume is controlled by:
the difference between the solute concentrations inside the cell and in the extracellular medium
What is isotonic?
Isotonic refers to when the internal solute concentration equals the external solute concentration, resulting in no net movement of water into or out of the cells.
What is plasmolysis?
Plasmolysis is the shrinkage that occurs when a plant cell is placed into a hypertonic medium; its volume shrinks as the plasma membrane pulls away from the surrounding cell wall.
True or false: all cells are equally permeable to water
False
-is this the correct explanation? [:They are semi-permeable, which means that some molecules can diffuse across the lipid bilayer but others cannot. Small hydrophobic molecules and gases like oxygen and carbon dioxide cross membranes rapidly. Small polar molecules, such as water and ethanol, can also pass through membranes, but they do so more slowly.”]
What are aquaporins?
Aquaporins are a family of small integral proteins that allow the passive movement of water from one side of the plasma membrane to the other.
Do all cells have the same permeability to water?
No, some cells are much more permeable to water than can be explained by simple diffusion through the lipid bilayer.
What is the structure of an aquaporin?
Aquaporins are tetramers, with each subunit containing a hydrophobic-lined central channel that is highly specific for water molecules.
How fast do water molecules move through aquaporins?
Water molecules pass through in single file at a rate of about 1 billion molecules per second.
Can ions pass through aquaporins?
No, aquaporins exclude ions, including protons (H+), from passing through the channel.
How do aquaporins prevent protons from passing through?
At the narrowest point of the channel, positively charged residues attract the oxygen atoms of passing water molecules, causing a reorientation that disrupts the hydrogen bond network.
Why is disrupting the hydrogen bond network important?
It prevents protons from hopping along water molecules, ensuring only water passes through the channel.
How was the mechanism of aquaporins discovered?
The exclusion of protons was explained through X-ray crystallography and molecular dynamics simulations, which helped model how the protein functions.
What is conductance?
Conductance is the rapid movement of ions.
What are ion channels?
Ion channels are openings in the membrane that are permeable to specific ions.
Are most ion channels selective?
Yes, most ion channels are selective; diffusion of ions is always downhill, meaning from higher to lower energies.
What is a gated ion channel?
A gated ion channel can change conformation between a form open to its solute ion and one closed to the ion.
What is a voltage-gated ion channel?
A voltage-gated ion channel’s conformational state depends on the difference in ionic charge on the two sides of the membrane.
What is a ligand-gated ion channel?
A ligand-gated ion channel’s conformational state depends on the binding of a specific molecule (the ligand).
What is a mechano-gated ion channel?
A mechano-gated ion channel’s conformational state depends on mechanical forces applied to the membrane.
What are the two distinct domains of eukaryotic Kv channel subunits?
The two distinct domains are the pore domain and the voltage-sensing domain.
What’s the pore domain?
The part of a voltage-gated ion channel that forms an ion-conducting channel through the membrane
What’s the voltage sensing domain?
The portion of a voltage-gated ion channel that allows it to respond to membrane voltage.
What is facilitated diffusion?
[UNSURE IF IT’S THE RIGHT DEFINITION] Facilitated diffusion occurs (in many cases) when substances bind selectively to a membrane-spanning protein (facilitative transporter), facilitating the diffusion process.
-important in mediating the entry and exit of polar solutes, such as sugars and amino acids, that do not penetrate the lipid bilayer
-[GOOGLE’S DEF.]: a type of passive transport where molecules move across a cell membrane down their concentration gradient, with the help of specific membrane proteins (channel or carrier proteins), without requiring energy input from the cell.
-
What is a facilitative transporter?
A facilitative transporter is a transmembrane protein that binds a specific substance and changes conformation to facilitate diffusion down its concentration gradient.
*know their features??
What are saturation-type kinetics?
Saturation-type kinetics is a condition in which every molecule of an enzyme or transporter is bound with its substrate molecule, so adding more substrate has no additional effect.
What is active transport?
Active transport is the energy-requiring process in which a substance binds to a specific transmembrane protein, changing its conformation to allow passage of the substance through the membrane against the electrochemical gradient.
-drives ions in 1 direction
What does active transport depend on?
Active transport depends on integral membrane proteins that selectively bind a particular solute and move it across the membrane.
How does active transport differ from facilitated diffusion?
Active transport moves solutes against their concentration gradient and requires an input of energy.
Why does active transport require energy?
Moving a solute against its concentration gradient is an endergonic process, meaning it requires energy input.
How is the energy for active transport supplied?
The energy comes from exergonic processes such as ATP hydrolysis, absorption of light, electron transport, or flow of other substances down their gradients.
What are pumps?
Pumps are proteins that carry out active transport.
What is the sodium-potassium pump?
The sodium-potassium pump is responsible for ATP hydrolysis and is active in transporting Na+ and K+ ions.
Who discovered the Na+/K+ -ATPase? (sodium-potassium pump)
Jens Skou discovered the Na+/K+ -ATPase in 1957. He found that this enzyme, later called the Na+/K+ -ATPase (sodium-potassium pump), was responsible for both ATP hydrolysis and ion transport.
How does active transport differ from facilitated diffusion?
Facilitated diffusion allows movement in either direction, depending on the concentration gradient, whereas active transport moves ions in only one direction using energy.
What role does the Na+/K+ -ATPase play in ion distribution?
It maintains a high concentration of Na+ outside the cell and a high concentration of K+ inside the cell.
How are charges balanced inside and outside the cell?
- Extracellular Na⁺ is balanced by Cl⁻ ions.
- Intracellular K⁺ is balanced by negatively charged proteins and nucleic acids.
What is the pumping ratio of Na+ to K+ in the Na+/K+ -ATPase?
The ratio is 3 Na+ ions out for every 2 K+ ions in per ATP hydrolyzed.
Why is the Na+/K+ -ATPase considered electrogenic?
It creates a charge separation across the membrane by pumping more positive charges (Na+) out than it brings in (K+).
What type of ion pump is the Na+/K+ -ATPase?
It is a P-type ion pump, meaning ATP hydrolysis phosphorylates the pump.
How does the Na+/K+ -ATPase change ion affinity during transport?
It binds Na+ or K+ from areas of low concentration (high affinity), ATP hydrolysis triggers a conformational change, and it releases ions into areas of high concentration (low affinity)
What is the proposed scheme for the pumping cycle of the Na+/K+ -ATPase?
The cycle follows a sequence of conformational changes from E1 to E2, binding and releasing Na+ and K+ ions. details:
[1. E1 conformation – The binding sites are open to the inside of the cell, allowing the protein to bind three Na⁺ ions and ATP.
2. A gate closes, preventing Na⁺ from flowing back into the cytosol.
3. ATP hydrolysis and ADP release trigger a conformational change from E1 to E2, exposing the binding site to the extracellular space.
4. The protein loses affinity for Na⁺, releasing the three Na⁺ ions outside the cell.
5. The protein then binds two K⁺ ions from the extracellular space.
6. Another gate closes, preventing K⁺ from leaking back out.
7. Dephosphorylation and ATP binding return the protein to its E1 conformation, opening the binding site to the inside of the cell and releasing K⁺ into the cytosol.
8. The cycle repeats.]
How does the rate of active transport through the Na+/K+ -ATPase compare to ion channels?
The Na+/K+ -ATPase moves ions across membranes at much lower rates than ion channels.
Where is the Na+/K+ pump found?
The sodium-potassium pump is found only in animal cells.
How much energy does the Na+/K+ pump consume?
It consumes one-third of the energy produced by most animal cells and two-thirds of the energy produced by nerve cells.
What is digitalis?
Digitalis is a steroid from the foxglove plant that binds to and inhibits the Na+/K+ -ATPase.
What are some other primary ion transport systems besides the Na+/K+ -ATPase?
Other important P-type ion pumps include Ca2+-ATPase and H+-ATPase in plants.
How do acid-blocking medications work?
Prilosec inhibits the H+/K+-ATPase directly, while Zantac and similar drugs block receptors on parietal cells.
What are V-type pumps?
V-type pumps use ATP without forming a phosphorylated protein intermediate and actively transport H+ ions.
What are ATP-binding cassette (ABC) transporters?
ABC transporters are a diverse group of ion transport proteins that all share a homologous ATP-binding domain.
How can light energy be used to actively transport ions?
Some organisms use light-driven proton pumps to transport ions across membranes.
What is bacteriorhodopsin?
Bacteriorhodopsin is a light-driven proton pump found in Halobacterium salinarium (an archaebacterium that lives in salty environments like the Great Salt Lake).
What happens to the protons after they are pumped out?
The movement of protons creates a steep proton gradient across the plasma membrane. This gradient is then used by an ATP-synthesizing enzyme to phosphorylate ADP, producing ATP for cellular energy.
What is secondary active transport (cotransport)?
Secondary active transport is the process of using the energy stored in ion gradients to transport other molecules across a membrane.
What is secondary active transport (cotransport)?
Secondary active transport (or cotransport) is the process of using the energy stored in ion gradients (such as Na+, K+, or H+) to transport other molecules across a membrane.
How does cotransport work in the intestine?
In the intestine, glucose absorption relies on the Na+/glucose cotransporter. Primary active transport by the Na+/K+-ATPase keeps Na+ concentrations low inside epithelial cells. This creates a Na+ gradient, where Na+ wants to diffuse back into the cell. The Na+/glucose cotransporter uses this gradient to bring in two Na+ ions and one glucose molecule, allowing glucose to enter against its concentration gradient. Once inside, glucose moves out of the cell through facilitated diffusion.
How efficient is the Na+/glucose cotransporter?
It can transport glucose against a 20,000-fold concentration gradient, making it extremely powerful.
How do plants use secondary active transport?
Instead of Na+, plant cells use H+ gradients to uptake nutrients like sucrose, amino acids, and nitrate. This process is also symport, where H+ and sucrose move in the same direction into the cell.
What is the difference between symport and antiport?
Symport: Both molecules move in the same direction (e.g., Na+ and glucose or H+ and sucrose). Antiport: Molecules move in opposite directions (e.g., Na+ moves in, while H+ moves out to regulate pH). Antiport proteins are also called exchangers.
What do secondary transporters have in common?
Like the Na+/K+-ATPase, secondary transporters work through a transport cycle, where the protein’s binding sites alternately face the cytoplasm and extracellular space.
