MCB 2000 Chapter 12

amphipathic lipid

• the head and tail behave like different molecules

  • the phosphate head is polar and charged. it hydrogen-bonds with water and sits comfortably on the surface

    • often with a charged amine attached

  • the fatty acid tails are pure hydrocarbons. no polar bonds, no H-bond capacity. water can’t accommodate them

  • that structural split is what makes everything else in this module possible

the hydrophobic effect

• entropy is the driver and the entropy belongs to water

• nonpolar tails cluster together to minimize ordered water, increasing the entropy (ΔS) of water

micelle vs bilayer

• same thermodynamics

• the lipid’s shape picks the structure

• micelles shaped from lipids shaped like a cone (big head, usually one tail)

  • detergents, lysophospholipids

• bilayer shaped from cylindrical lipids

  • phosphatidylcholine

  • pack into sheets — two layers, tails inward, head facing water

bilayer asymmetry

• two leaflets carry lipids, and the cell maintains that difference

• two faces, two compositions

  • the outer leaflet is rich in phosphatidylcholine and sphingomyelin, with neutral head groups and the occasional glycolipid for cell recognition

  • the inner leaflet is rich in phosphatidylserine and phosphatidylethanolamine. PS carries a negative charge that helps recruit cytoplasmic proteins

• flippases use ATP to maintain the difference. It doesn’t happen on its own

  • asymmetry is maintained because lipids don’t naturally stay on one side and diffusion would scramble the asymmetry

what the bilayer makes possible

• selective barrier

  • what crosses: water and small nonpolar gases (O2 and CO2) passes freely

  • what’s blocked: ions and large polar molecules. the hydration shell is too costly to strip

  • effect: foundation of cell chemistry

• self sealing

  • why: an exposed tail is the worst possible state (thermodynamically). the bilayer rearranges within microseconds

  • results: sealed vesicles form spontaneously. tear close without machinery

  • effect: robust, self-repairing

• dynamic, not static

  • lateral diffusion: lipids slide sideways within a leaflet at ≈2 μm per second

  • flip-flop: crossing between leaflets is much slower because it requires dragging a hydrophilic head group through hydrophobic region: minutes to days without enzymes

  • effects: fluid but ordered

three properties, one cause: tails dislike water, heads loves it

lipid rafts

• the membrane is more organized than a uniform sea

• fluid mosaic, revised

  • proteins float in a fluid sea has structure

  • Singer and Nicolson (1972) got the broad picture right. The membrane is a 2-D fluid with proteins floating in it

  • rafts: cholesterol-rich patches of tightly-packed saturated lipid form more-ordered microdomains. Specific membrane proteins, especially signaling receptors and GPO-anchored proteins, concentrate there

the Goldilocks principle

• fluidity has a sweet spot, and crossing into either extreme is bad news

• low temp — lipid tails packed tightly side by side, membrane= ordered and viscous, almost crystalline

  • gel- state (solid-like)

  • molecules can’t pass and membrane cracks under mechanical stress

• high temp — gain enough thermal energy to bend and rotate, packing starts breaking down and membrane becomes a true 2-D fluid

  • liquid state (fluid-like)

  • ions leak across, gradient collapse, cell loses membrane potential

• Tm — flip from too low too high = melting temperature

  • cooperative, so it is sharp rather than a gradual change

  • narrow sweet spot where membrane is flexible enough for proteins to function, but stable enough to hold the barrier

gel vs liquid-crystalline

• same lipid, two states. the difference is the order of the tails

Knob 1: fatty acid saturation

• straight chains pack tight

• Cis double bonds create kinds that don’t

• each cis double bond bends the chain by about 30 degrees. neighbors can’t pack as tightly and Tm drops

• the more cis double bonds, the lower the melting temps and the more fluid at any given temp

Knob 2: Acyl chain length

• more carbons mean more van der Waals contact, which means higher Tm

• why it matters:

  • each additional CH2 adds another point of van der Waals contact with neighboring tails. long chains have more total contact area, so they stay packed at higher temps

  • cells pair longer chains with unsaturation to keep Tm near physiological temps. the two knobs work together

most mammalian membrane lipids land in the C16 to C18 range for this reason

Knob 3: Cholesterol structure

• three parts and each does a different job in the bilayer

• polar head — a small hydroxyl group at C3. hydrogen bonds with phospholipid head groups at the bilayer surface

• rigid steroid core — four fused rings, planar and inflexible. no rotation possible. this rigidity is what lets cholesterol restrain neighboring tails

• flexible tail — a short, branched chains with 8 carbons. nestles in the hydrophobic core alongside the acyl tails. cholesterol is roughly as long as a 16-carbon chain

only in animals, but = hopanoids in bacteria

cholesterol as a composition buffer

• same molecules, opposite effects, depending in what’s already there

• the composition question: at a fixed temp, cholesterol pushes whichever composition is at hand toward intermediate fluidity

cholesterol as a temp buffer

• hold composition fixed. lets temp change. cholesterol still tunes both ways

• cholesterol buffers both directions: composition and temp

2 questions to determine category of membrane proteins

GO BACK TO VIDEO — M3 CH. 12

5 different protein placements

positions a and b

• how integral proteins survive inside the lipid tail region: the alpha-helical transmembrane domain

• why helices work: the helix hides it backbone

  • an alpha helix uses every backbone N-H and C=O in internal hydrogen bonds. the polar backbone is completely satisfied inside the helix

  • that lets the helix expose only its side chains. if those side chains are hydrophobic, the whole helix can sit comfortably in the lipid tail region

about 20 hydrophobic residues are enough to span a bilayer

multi-pass (a) and single pass (b) both use this trick. the bilayer never sees the polar peptide backbone

inside positions c and d

• how peripheral proteins stay attached without ever entering the lipid core

• peripheral logic: they never touch the tails

  • peripheral proteins (C,D) hold to the membrane by interacting with the polar head groups, not the hydrophobic tails. hydrogen bonds, salt bridges and electrostatic contacts do the work

  • some bind directly to phospholipid head (C). others, like D, hold onto the exposed surface of an integral protein (B)

change the pH or raise the salt and these interactions break. the protein comes off without disturbing the bilayer

if a salt wash takes a protein off the membrane, you were looking at a peripheral protein, but if it takes a detergent, it was an integral protein

inside position e: lipid-anchored

• the protein body stays out of the bilayer. a covalent lipid tail does the tethering

• how it works: the lipid is the anchor

  • a fatty acid or isoprenoid chain is covalently attached to the protein after translation. the chain inserts into one leaflet and the protein body sits in the aqueous space on that side

  • which leaflet? depends on the anchor. GPI anchors face out, into the extracellular space, like alkaline phosphatase. acyl and prenyl anchors face in, into the cytoplasm, like Ras

the protein never enters the bilayer. a single fatty chain or isoprenoid tethers it to one leaflet

the fluid mosaic in action

• proteins float in the bilayer, but they don’t all move at the same rate

• two rules of motion:

  • lateral diffusion is fast. flip-flop isn’t

  • lipids and proteins both diffuse sideways within their leaflets. lipids move quickly because they’re small. proteins move more slowly, scaling roughly with the size of their transmembrane footprint

  • crossing between leaflets requires dragging polar groups through the hydrophobic core (flip-flopping) . for lipids that takes minutes to days with enzymes. for proteins it doesn’t happen (dragging a folded protein through a tail region of the membrane with all its hydrophilic surfaces exposed is not energetically feasible)

that asymmetry is what lets the cell maintain leaflet-specific protein placement

sideways yes, across no. the cell uses that to keep its leaflet distinct.

permeability scale

• coefficient P spans 14 orders of magnitude

why ions can’t cross

• Na+ and K+ carry a shell of 6-8 water molecules ]

• stripping it to cross the hydrophobic core costs ~150 kJ/mol — prohibitive without a protein

why O2 and CO2 cross freely

• small, nonpolar, uncharged = no hydration shell

• the hydrocarbon core acts as a solvent so these gases dissolve in and diffuse across freely

simple diffusion

• down the gradient, through the bilayer, no protein

• rate law: rate is proportional to the gradient

  • more gradient, more flux

  • Fick’s law: rate scales linearly with the concentration difference across the membrane

  • there is no saturation. the bilayer itself is the medium and it doesn’t run out of capacity

  • double the gradient, double the rate

  • works for anything that crosses the bare bilayer, but only at modest rates

facilitated diffusion

• still down the gradient, but now through a protein. the kinetics give it away

• channels: open pore, fast flow

  • substrate flows through without binding

  • up to 10^8 ions per second

  • gated open or closed by signals

• carriers: bind, switch, release

  • substrate binds, the protein changes conformation, the substrate is released on the other side

  • slower (10³ per seconds) but more specific

  • GLUT transporters move glucose this way

Ion channels

• selective, fast, gated. The K+ channels shows how all three work together

• selective:

  • the filter is sized for K+ and lined with carbonyl oxygens that mimic the hydration shell

  • Na+ is smaller and is rejected because it cannot afford to leave its hydration shell

• fast:

  • ions pass at up to 10^8 per second, near the diffusion limit

  • mutual repulsion in the file keeps them moving

• gated:

  • conformational changes open or close the channel in response to voltage, ligands, or mechanical force

aquaporins

• a specialized channel that does one thing very well: move water fast

• water, only water:

  • 10^9 molecules per second per channel

  • the pore is narrow enough that water passes single file

  • a precise electrostatic arrangement passes neutral H2O but blocks even a single proton

  • found wherever water flux is high; kidney tubules, red blood cells, plant root cells

drug absorption: you computed the charge before, membranes explain why it decides crossing

• stomach: pH 1.5

  • Aspirin pKa = 3.5 → mostly protonated (uncharged)

  • neutral and small: no hydration shell. it sits in the “crosses freely” zone and is absorbed here

• small intestine: pH = 6.5

  • Aspirin pKa = 3.5 → mostly deprotonated (charged)

  • now charged: a hydration shell forms. shedding it costs ~150 kJ/mol, so the bilayer rejects it

the charge was the easy half. the membrane is the point; only the neutral form sheds its water shell and crosses

why active transport exists

• cells must move things in the wrong direction, which passive transport can’t do

• gradients are useful but costly:

  • the cells uses gradients of Na+, K+, Ca2+, and H+ to drive nerve impulses, muscle contraction, secondary transport and signaling

  • those gradients dissipate as ions leak back across. without pumps, replenishing them, every gradient in the cell would equilibrate within minutes

  • pumps don’t move bulk material. they maintain the difference that everything else uses

Na+/K+ pump

• primary active transport

• 3 Na+ out, 2K+ in, 1 ATP — repeated billions of times per cell per second

• why it matters: the cell’s most expensive habit

  • use this pump constantly, using roughly 30% of all the ATP the cell produces

  • the gradient it builds is the energy source for nerve impulses, muscle contraction, secondary transporters and Ca2+ regulations

  • almost everything electrical or absorptive in animal physiology runs on this pump

  • P-type ATPase: the protein phosphorylates itself on asp residue with each cycle

Na+/K+ pump’s conformational cycle

• E1 binds Na+

  • pump open to cytoplasm. 3 Na+ bind

• phosphorylation

  • ATP transfers phosphate to as aspartate

  • conformational switch

• E2 releases Na+, binds K+

  • now open to outside. Na+ out, 2 K+ in

  • low affinity for Na, so Na leaves easily

• dephosphorylation

  • phosphate hydrolyzes off

  • protein flips back, K+ releases inside

  • K affinity drops

the cycle is irreversible. each step has a built-in direction: bind on one side, release on the other

secondary active transport

• use on ion’s downhill flow to drag another molecule uphill

• primary pumps build the Na+ gradient

• secondary transporters spend it to do other work

clinicals: digitalis and the heart

• inhibits one pump and strengthens heart contractions. a 200-year-old drug is still in use

• therapeutic uses: treats heart failure by increasing contractile force

• narrow therapeutic window: too much causes arrhythmia. from the foxglove plant, in use since the 1700s

same pump biology from S4-S6 in reverse: breaks the gradient deliberately and downstream transport flips

Chapter Overview