block 5-membrane transport Flashcards

Question

dehyration energy in potassium

Answer 1

Potassium ions (K⁺) in solution are surrounded by water molecules—this is called a hydration shell. To pass through the narrow selectivity filter of a K⁺ channel, the ion must lose its water shell—this process requires energy and is called dehydration energy. The selectivity filter mimics the shape and electrostatic properties of water molecules using carbonyl oxygen atoms. These carbonyls stabilize the "bare" K⁺ ion, replacing the water shell without energy loss. This precise match explains why K⁺ passes easily, but smaller ions like Na⁺ can't—they don't fit the filter well and can't be stabilized enough after dehydration.

Answer 2

Many ion channels share a similar structure: Made of 4 subunits (often a tetramer) Each subunit has transmembrane helices and contributes to a central pore Have a selectivity filter for ion specificity Use conserved structural motifs (e.g., TVGYG in K⁺ channels) Reflect a shared evolutionary origin

Answer 3

Help maintain osmotic balance by allowing controlled water transport across cell membranes Form tetramers, but each monomer has its own functional pore Highly selective: transport water in single file, excluding ions Contain positively charged residues that repel protons (H⁺), preventing pH disruption

Answer 4

Aquaporins are selective for water, but protons (H⁺) can sometimes pass through, especially in non-ideal conditions. Aquaporins typically have positively charged residues near their pore, which repel protons and prevent proton conduction by blocking the Grotian mechanism. This ensures selective water transport while preventing proton movement, maintaining osmotic balance. In short, the Grotian mechanism helps protons move through water, but aquaporins are designed to restrict this movement, allowing only water to pass

Answer 5

- transports sodium in potassium out and uses 1 molecule of ATP to do so Part of a superfamily of related proteins. ATP provides the energy for active transport. Pump cycle involves two major conformational states: Phosphorylated intermediate: critical step in the cycle. Mg²⁺ plays a crucial role in facilitating the pump's function.

Answer 6

Tetrameric protein consisting of two main subunits: α Subunit: Catalytic subunit with four key domains: A Domain: Binds ATP and mediates phosphorylation. P Domain: Gets phosphorylated during the cycle, facilitating ion transport. N Domain: Binds ATP for hydrolysis to drive the pump. M Domain: Forms the membrane-spanning pore for ion transport (Na⁺/K⁺). β Subunit: Provides structural support to the α subunit, assisting with folding. γ Subunit (optional): Modulates pump activity in some isoforms. Function: Pumps 3 Na⁺ ions out and 2 K⁺ ions in per ATP, maintaining ionic gradients across the cell membrane.

Answer 7

A pump is a type of membrane protein that uses energy (usually from ATP hydrolysis) to transport ions or molecules against their concentration gradient (from low to high concentration). Pumps are involved in active transport, requiring energy to move substances across the cell membrane. Example: Na⁺/K⁺ ATPase pump, which moves Na⁺ out of the cell and K⁺ into the cell.

Answer 8

Part of one super-family: Symporters and antiporters belong to the same protein super-family of transporters, meaning they share a similar structural and functional framework. Often employ the Na⁺ gradient: Both types use the Na⁺ gradient (created by the Na⁺/K⁺ ATPase pump) as a source of energy to drive active transport. This helps move other ions or molecules against their gradient. Have two pseudo-repeats: Their structure includes two similar or repeated domains (pseudo-repeats) that help with the transport of ions or molecules across the membrane. This is a characteristic feature in their design. Operate via the Rocker-Switch mechanism: They use the Rocker-Switch mechanism, where the transporter protein undergoes conformational changes to allow the movement of ions or molecules in one direction at a time.

Answer 9

This antiport mechanism relies on the Na⁺ gradient, which is maintained by the Na⁺/K⁺ ATPase pump. NCX operates passively in terms of Na⁺ transport (moving down its gradient), but it actively transports Ca²⁺ against its gradient, helping to keep intracellular Ca²⁺ levels low.

Answer 10

Structural biology concerns the study of biomolecules and their interactions in time and space, in order to explain cellular functioning

Answer 11

Structural biology central premisses and their caveats →wwPDB Electrophysiology Experimental techniques in structural biology: X-ray crystallography, NMR, cryo-Electron Microscopy →AlphaFold, Structural BioInformatics Molecular Dynamics

Answer 12

Structure is encoded by sequence: A protein’s 3D structure (secondary, tertiary, quaternary) is determined by its amino acid sequence. ⚠️ Exceptions: Intrinsically disordered proteins (IDPs), amyloids, and proteins with multiple conformations. Structure defines function: A protein’s function is linked to its structure. ⚠️ Exceptions: Some similar structures may have different functions. Structure and function are dynamic: Protein function depends on structural flexibility and dynamics. ⚠️ Influenced by: Environment — solutes, pH, temperature, and binding partners

Answer 13

Stores atomic-level 3D structures of proteins. Growing database from 2007 to 2020.

Answer 14

AI tool that accurately predicts protein 3D structures from their primary sequence. Published in Nature (2021); major breakthrough in structural biology. Recognized with the 2024 Nobel Prize in Chemistry.

Answer 15

Lets scientists determine the structure of most proteins, even if they’ve never been crystallized. Especially useful in studying biochemical pathways.

Answer 16

Predicts the most likely structure — not always the biologically active or correct one. May be less accurate for membrane proteins or proteins with multiple conformations. Still unclear exactly what “rules” AlphaFold learned to make its predictions.

Answer 17

-lipid head = fully hydrated -lipid tail=fully dehydrated -charged residue = high energy barrier -hydrobic residues= favourable -polar residues mix depends on the type -aromatic side chain residues= mix as well look like its mostly high

Answer 18

1. Transmembrane (TM) Helices A TM helix typically has: ~20 amino acids Each residue spans ~0.15 nm → total helix spans ~3 nm (or 30 Å) Enough to span the membrane completely Forms ~6 turns of an α-helix 2. Hydropathy Plots Used to predict TM regions in a protein sequence. Detect stretches of hydrophobic amino acids (which prefer lipid membranes). Scoring algorithms include: Kyte-Doolittle Goldman-Engelman-Steitz Wimley-White TM helices show up as peaks in hydrophobicity plots (e.g., in bacteriorhodopsin). 3. Features of TM Helices Hydrophobic core of 20 residues Charged residues (e.g., Arg, Lys) often found outside the membrane at the ends of helices These charged residues help anchor and orient the helix

Answer 19

4. Positive-Inside Rule (Von Heijne Rule) TM proteins tend to have more positively charged residues (Arg/Lys) on the cytoplasmic side. Helps predict the orientation of helices (which side faces in/out).

Answer 20

Function: Porin is a membrane protein allowing passage of small molecules through the membrane Structure: Trimer Each subunit: 16 β-strand barrel

Answer 21

Residue distributions: In β-barrels, hydrophobic residues face the lipid bilayer, while hydrophilic residues face the pore interior. This alternating pattern helps predict barrel formation. Structure prediction + hydrophobicity: By combining known structural rules (like β-sheet patterns) with hydrophobicity plots, we can predict which sequences form β-barrels. β-Hairpin prediction: β-barrels are made of β-hairpins — pairs of β-strands connected by loops. Tools can predict these based on the sequence to map out the full barrel.

Answer 22

-equations on lecture slides What MD gives you: MD simulations are used to explore the dynamics of biomolecules like proteins, DNA, or complexes. It simulates the movement of atoms and molecules by solving the equations that describe their motion over time. How it works: In MD simulations, the forces acting on each atom in the system are calculated. These forces arise from the interactions between atoms and are used to update the positions of the atoms over time, allowing us to simulate how the molecules move and change. Simulated Annealing: This is a technique used in MD simulations where the system is slowly cooled to find its lowest energy state, similar to how a protein folds into its functional form. For example, the PAH2-Mad13 complex is a result of MD simulations predicting how two molecules interact. Purpose of MD: MD simulations provide valuable insights into how biomolecules move, how they interact, and how their structures change under different conditions. This helps us understand processes like protein folding, molecular binding, and function.

Answer 23

Purpose: Used to measure ion currents through single ion channels. Time-dependent behavior: The technique can track the probability of a channel being open (popen) vs. closed (pclosed) over time. Excised-patch mode: In this mode, a small patch of the membrane with a single ion channel is removed and studied to analyze its function.

Answer 24

Bacteriorhodopsin is a light-driven proton pump found in certain bacteria, such as Halobacterium salinarum. It absorbs light and uses the energy to pump protons (H⁺) across the membrane, creating a proton gradient. Structural States: 1AP9: Represents the ground state of bacteriorhodopsin (bR), also known as the dark state. 1BM1: This structure corresponds to the light-excited state of bacteriorhodopsin, where the protein absorbs light and undergoes a conformational change. 1DZE: This structure is of the M-intermediate state, an intermediate phase between the dark and light states. 1E0P: Represents the L-intermediate state, another intermediate phase in the process of proton pumping.

Answer 25

ock and Key Model: The enzyme's active site has a specific shape that exactly fits the substrate, like a key fitting into a lock. No change in enzyme structure is needed for binding. Induced Fit Model: The enzyme’s active site changes shape when the substrate binds to it. The binding induces a conformational change in the enzyme, optimizing the fit. Conformational Selection Model: The enzyme exists in multiple conformations, and the substrate selects the conformation that best fits. The enzyme preexists in multiple shapes, and binding stabilizes the specific one

block 5-membrane transport Flashcards

(49 cards)