Biomembrane Permeability and Transport Mechanisms (Channels, Carriers, and Pumps)

Exam logistics (transcript details)

• Exam: Jam 1, one week from today, starts at 03:30.
• Exams handed out a little before time; you’ll have until 04:45 (75 minutes total).
• Format: 40 questions, multiple choice; ~2 minutes per question.
• Covers material from the first lecture through Thursday.
• Pen color: red pen not allowed; blue or black preferred; avoid pink/fluorescent colors for visibility.

Biomembrane permeability: basic ideas

• The biomembrane is a lipid bilayer with a hydrophilic exterior surface and a hydrophobic core.
• Permeability of the lipid bilayer (no proteins): what can cross on its own?
  • Very small hydrophobic molecules (e.g., O$2$, CO$2$) can diffuse directly through the lipid bilayer because they can tolerate the hydrophobic interior.
  • Very small polar molecules with no net charge (e.g., water, urea) can diffuse, but diffusion is slower than for nonpolar molecules.
  • Larger polar molecules (e.g., sugars like glucose) diffuse poorly; they are largely impermeable without help.
  • Any molecule with a net charge (ions: Na$^+$, K$^+$, Cl$^-$, etc.) cannot cross the lipid bilayer unaided; these are effectively impermeable to the bare lipid bilayer.
• Therefore, crossing the membrane typically requires membrane transport proteins (channels, carriers, pores).

Roles of transport proteins and pores

• Pores: nonselective openings that allow aqueous passage depending mostly on size; environment on both sides of the pore is the same, so flow is largely nonselective except for size.
• Channels vs. carriers (the two main transport types):
  • Channel proteins form tunnels that allow rapid passage of specific solutes; they are highly selective by size/chemistry and can be gated (open/close).
  • Carrier proteins bind a solute, change conformation, and shuttle it across the membrane; this is typically slower and often energy-requiring (active transport).
• Some organelles have pores (e.g., nuclear pores) that are openings and are nonselective to a degree; selectivity depends on size and the environment.

Ion channels and basic design

• Ion channels: a major class of channels that conduct ions (Na$^+$, K$^+$, Ca$^{2+}$, Cl$^-$, etc.) and generate currents that contribute to membrane potential.
• Channel transport is usually considered passive (downhill) transport: movement from higher to lower ion concentration without direct energy input.
• Typical features:
  • High selectivity: channels discriminate ions (e.g., Na$^+$ channel vs K$^+$ channel).
  • Gates: channels are gated; once opened, they tend to close more slowly than they open (opening is fast; closing takes longer).
  • Open channels allow thousands of ions per second to pass, typically one (or a few) ions at a time.
• Channels create electrical currents when ions move, contributing to membrane potential.

Electrical consequences: membrane potential and ion movement

• Membrane potential (V$_m$): the net difference in charge across the membrane, typically measured outside vs inside the cell.
  • Outside is more positive; inside is more negative due to negative proteins and ions in the cytoplasm.
  • Resting potential in many neurons is around V_{rest} \,\approx\, -70\ \text{mV}.
• Ion distribution (typical resting state):
  • More Na$^+$ outside the cell than inside.
  • More K$^+$ inside the cell than outside.
• Equilibrium potentials (illustrative values from the lecture):
  • Potassium equilibrium potential: E_K \approx -94\ \text{mV}
  • Sodium equilibrium potential: E_{Na} \approx +60\ \text{mV}
• What happens when channels open:
  • K$^+$ channels: high intracellular K$^+$ moves to the outside (down its gradient); membrane potential tends toward E_K \approx -94\ \text{mV} if mostly K$^+$ moves.
  • Na$^+$ channels: Na$^+$ flows into the cell (down its gradient); membrane potential moves toward E_{Na} \approx +60\ \text{mV}.
• Conceptual depolarization/hyperpolarization/repolarization:
  • Depolarization: membrane potential becomes more positive (e.g., from $-70$ mV toward a less negative value).
  • Expressed as a move toward a higher potential: V_m\uparrow (e.g., from -70\ \text{mV} toward something closer to +60\ \text{mV}).
  • Hyperpolarization: membrane potential becomes more negative (V_m\downarrow; e.g., toward -90\,-100\ \text{mV}).
  • Repolarization: returning to resting potential after a depolarization event.

Potassium and sodium channels: simple walkthrough

• Potassium current during resting/perhaps depolarizing step:
  • Potassium is more concentrated inside; opening a K$^+$ channel causes K$^+$ to exit (down its gradient) and the inside becomes more negative, moving toward E_K \,\approx\, -94\ \text{mV}.
  • The flow continues until equilibrium is reached for the ionic species involved.
• Sodium current during depolarization:
  • Sodium outside is higher; opening a Na$^+$ channel causes inward flow of Na$^+$, decreasing membrane negativity and contributing to depolarization toward E_{Na} \approx +60\ \text{mV}.
• Propagation concept (stepwise):
  • Opening of Na$^+$ channels in a region causes local depolarization; this depolarization triggers neighboring Na$^+$ channels to open, propagating the wave along the cell.
  • Concurrently, K$^+$ channels open in response to changing voltage to repolarize and restore resting potential.
• A note on timing: these events occur on the order of milliseconds; fast opening of channels vs slower closing/inactivation steps.

Voltage-gated ion channels: structure and gating

• General structure: voltage-gated channels typically have four to six alpha-helical bundles that form the ion-conducting pore.
• Voltage sensor: one of the transmembrane helices acts as a voltage sensor; movement of this helix in response to changes in membrane potential opens/closes the channel.
• Open-closed-inactivated cycle (example for a Na$^+$ channel):
  • Closed state: channel is nonconductive.
  • Open state: channel conducts ions; many ions pass through quickly.
  • Inactivated state: a tether (drain plug) blocks the pore to stop conduction even though the channel is still activated.
  • Recovery to closed state: channel returns to closed state after inactivation is removed.
• Inactivation and gating times: opening is very fast (sub-millisecond range); closing and inactivation can take longer (milliseconds), contributing to the timing of action potentials.
• Other types of gating:
  • Ligand-gated channels (e.g., acetylcholine receptor) open in response to ligand binding (not voltage changes).
  • Multiple ligand-gated channel designs exist; acetylcholine binding often occurs at a specific site (e.g., M2 helix region) leading to a conformational change and pore opening.

Selectivity at the channel selectivity filter

• The selectivity filter determines which ions can pass through a given channel.
• Potassium vs sodium selectivity (classic example with K$^+$ channel):
  • The filter is lined with carbonyl oxygens that interact with ions as they pass.
  • Ions have hydration shells; dehydration costs energy. The carbonyls can effectively replace hydration water for certain ions.
  • Size and hydration differences matter: Na$^+$ is smaller (diameter ~ 0.96\ \text{Å}) but has a larger hydration shell; K$^+$ is larger (diameter ~ 1.33\ \text{Å}) but has a less tightly held hydration shell.
  • In the potassium channel, the selectivity filter coordinates the hydrated ion after dehydration with carbonyl oxygens, matching the K$^+$ size well and allowing passage, whereas Na$^+$ does not navigate the dehydration/coordination as favorably in the same pore.
• Historical context: Rod McKinnon crystallized a potassium channel in 1998, revealing the selectivity filter region and how the carbonyls coordinate ions to permit selective flow.
• Visual cue (conceptual, not needed for exam): the selectivity filter (often the narrowest part of the pore) is tuned to the preferred ion; different channels have different filters to distinguish Na$^+$, K$^+$, Ca$^{2+}$, Cl$^-$, etc.

Membrane potential: a quick recap of mechanism

• Baseline idea: membrane potential is the net difference in charge inside vs outside the cell; typically measured with microelectrodes inserted near the membrane.
• For neurons in the resting state:
  • Inside is more negative due to intracellular proteins and ion distributions.
  • Outside is more positive.
• Why resting potential is negative: concentration gradients and selective permeability set by channels determine the resting current; major players include Na$^+$ and K$^+$ currents and the activity of pumps that maintain gradients.

Primary active transport: Na$^+$/K$^+$-ATPase and friends

• Primary (direct) active transport uses energy (usually ATP hydrolysis) to move substances against their gradients.
• Na$^+$/K$^+$-ATPase example (classic pump):
  • Mechanism (illustrative steps):
  • The pump binds Na$^+$ on the cytoplasmic side (inside, E1 conformation).
  • ATP binds and phosphorylates the pump; this triggers a conformational change to the E2 state (open to outside).
  • Na$^+$ is released to the extracellular space (outside).
  • The pump binds K$^+$ on the outside; dephosphorylation returns the pump to the E1 conformation (open to inside).
  • K$^+$ is released inside; the cycle restarts.
  • The ATPase activity is the energy source; the cycle moves ions against their gradients: Na$^+$ out, K$^+$ in.
  • Conceptual note: the process is bidirectional across the cycle, but the net effect per cycle moves ions in opposing directions to restore the resting gradients.
• Some proteins have specific binding-site stoichiometries that vary by transporter; examples discussed include varying numbers of Na$^+$ and K$^+$ binding sites (the transcript notes multiple possibilities and emphasizes variability between transporters).
• ABC (ATP-binding cassette) transporters: another family of primary active transporters
  • Structure: exist as dimers with two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs).
  • Function: ATP binding/hydrolysis drives conformational changes to move a wide variety of substrates (amino acids, sugars, ions, drugs).
  • Example: the MDR (multidrug resistance) protein discovered in cancer cells, which exports chemotherapy drugs out of cells to promote survival.
  • Characteristic: typically unidirectional (one-way transport) per cycle, powered by ATP hydrolysis; each cycle often requires two ATP molecules (one per NBD) per substrate translocation.

Secondary active transport: coupling to primary transport

• Secondary (indirect) active transport uses the gradient created by a primary transporter to drive the movement of other solutes.
• Analogy: skiing up the hill (primary) vs dragging a sled uphill (secondary).
• Mechanisms described:
  • Symport (co-transport): X and Na$^+$ (or another driving ion) move in the same direction into the cell; they share the inward movement.
  • Antiport (exchange): X moves in one direction while Na$^+$ (or another ion) moves in the opposite direction (outward), i.e., opposite directions.
• In cotransport, the driving ion(s) can be charged; the overall charge movement can be electrogenic (net charge moved) or electroneutral (no net charge moved) depending on what moves in/out together with the solute.
• The transporter types (and stoichiometries) vary widely; specific numbers are transporter-specific (e.g., some transports couple Na$^+$ and glucose; others couple different ions with different substrates).

Key concepts and takeaways

• The lipid bilayer alone is permeable to very small nonpolar molecules and, to a lesser extent, to tiny uncharged polar molecules; charged species require transport proteins.
• Channel proteins provide fast, selective, gated pathways; carriers provide slower, conformational-change–driven transport and can be energy-requiring (active transport).
• Ion channels are usually gated (voltage-gated or ligand-gated) and create currents that underlie membrane potential and action potentials.
• The selectivity of ion channels arises from structural features such as the selectivity filter and hydration dynamics; this explains why channels discriminate Na$^+$ vs K$^+$ even when ions differ only slightly in size.
• The resting membrane potential and the dynamics of depolarization, repolarization, and hyperpolarization depend on the coordinated activity of Na$^+$ and K$^+$ channels and pump activity (Na$^+$/K$^+$-ATPase).
• The discovery and structural elucidation of channels (e.g., Na$^+$, K$^+$ channels) enabled by crystallography (e.g., Rod McKinnon, 1998) revealed the critical role of the selectivity filter and voltage-sensing domains in gating.
• Beyond ion channels, ABC transporters expand the transport repertoire by using ATP hydrolysis to move a wide range of substrates, often in a unidirectional manner; MDR is a key example with clinical relevance.
• Secondary active transport allows cells to couple the movement of essential solutes with ion gradients established by primary transporters; this enables diverse uptake and export strategies essential for metabolism and homeostasis.

Quick reference: selected numerical and conceptual anchors

• Exam duration and format anchors: 75-minute exam; 40 questions; ~2 minutes per question.
• Resting membrane potential: V_{rest} \approx -70\ \text{mV} (neurons, baseline).
• Ion equilibrium potentials (typical references):
  • E_{K} \approx -94\ \text{mV}
  • E_{Na} \approx +60\ \text{mV}
• Ion radii (size cues relevant to selectivity):
  • d_{Na^+} \approx 0.96\ \text{Å}
  • d_{K^+} \approx 1.33\ \text{Å}
• Structural features of voltage-gated channels: four-to-six alpha-helical bundles; one helix acts as the voltage sensor; gating involves movement of helices.
• Na$^+$/K$^+$-ATPase stoichiometry (typical ATPase example mentioned): cycle involves Na$^+$ release outside and K$^+$ uptake inside; energy from ATP hydrolysis drives the conformational changes (exact binding-site counts vary by transporter).
• ABC transporter general features: dimer with two NBDs and two TMDs; ATP binding and hydrolysis drive conformational changes; transports a broad range of substrates.

Connections and broader relevance

• The principles discussed tie to foundational bioelectricity concepts (resting membrane potential, action potentials, neuronal signaling) and to cellular homeostasis (ion gradients, nutrient uptake, and waste removal).
• Understanding selectivity explains how neurons maintain ionic gradients essential for signaling and how drugs, toxins, or mutations affecting channels and pumps can disrupt nervous system function.
• The interplay between passive diffusion, channel-mediated transport, and active transport illustrates how cells regulate energy expenditure to achieve selective and directional transport across membranes.