What Can Pass Through the Phospholipid Bilayer?

Small, nonpolar molecules like oxygen, carbon dioxide, and nitrogen gas pass through the phospholipid bilayer with little resistance, while charged particles like sodium and potassium ions are almost completely blocked. Between those two extremes sits a spectrum of permeability that depends on a molecule’s size, charge, and how well it dissolves in fat. The bilayer is not a simple wall with fixed holes; its selectivity shifts with temperature, lipid composition, and even the physical shape of the membrane itself.

Gases Cross With Almost No Resistance

The phospholipid bilayer’s interior is essentially a thin sheet of oil, made up of the long hydrocarbon tails of the lipid molecules. Small nonpolar gases dissolve readily into that oily core and diffuse across it almost as easily as they move through open water. Oxygen and nitric oxide are small and hydrophobic enough that cellular membranes pose virtually no barrier to them.¹ Nitrogen dioxide and hydrogen sulfide meet a slightly higher barrier but still cross largely unimpeded. This free passage of respiratory gases is what allows your red blood cells to pick up oxygen in the lungs and dump carbon dioxide without needing dedicated protein channels for those molecules.

Carbon dioxide is a good illustration of how freely gases move. Researchers measuring CO₂ transport across lipid bilayers found that the membrane itself is rarely the bottleneck. Instead, the limiting step is usually how fast CO₂ diffuses through the water layers sitting on either side of the membrane. Only at very high pH, where nearly all the dissolved CO₂ has been converted to bicarbonate, does the membrane’s own resistance become the rate-limiting factor, yielding a permeability coefficient of about 0.35 cm/s.² That is fast. For comparison, bicarbonate ions, which carry a negative charge, do not cross the membrane at all under the same conditions.

Hydrogen sulfide, a signaling molecule the body produces in small quantities, also crosses with ease. Its hydrophobicity allows it to partition into the membrane’s oily interior readily, even though it diffuses somewhat more slowly than water once inside.³ The energy barrier it faces is negligible, which makes sense for a molecule that needs to reach neighboring cells quickly to act as a signal.

Engineered lipid vesicles designed to carry hemoglobin as artificial oxygen carriers confirm this picture from a practical angle: adding lipid-modifying compounds to fine-tune the membrane’s pH sensitivity did not limit gas diffusion, and the gas exchange rates matched those of natural red blood cells.⁴

Water and Small Uncharged Polar Molecules

Water is polar and forms hydrogen bonds, so you might expect the bilayer to block it outright. In reality, water does cross, just slowly compared to gases. The solubility-diffusion model explains this reasonably well: a molecule’s ability to enter and traverse the oily membrane core depends partly on how well it dissolves in that hydrophobic environment. Water’s permeability is modest but measurable, and it decreases in a roughly linear fashion as the membrane gets thicker, dropping about fivefold when lipid tail length increases from 14 to 24 carbons.⁵ In living cells, the bulk of water movement relies on aquaporin channels, but a baseline trickle of water gets through the lipids on its own.

Other small uncharged polar molecules like urea and glycerol follow the same pattern. They permeate the bilayer slowly by the same solubility-diffusion mechanism, and their permeability also drops with increasing membrane thickness.⁵ Larger polar molecules like glucose and sucrose are effectively excluded by simple diffusion. Their size and polarity create too high an energy cost to enter the membrane core, which is why cells need glucose transporter proteins to import sugar.

Why Ions Are Almost Completely Blocked

Ions carry a full electrical charge, and dragging that charge through the low-dielectric oily interior of the bilayer costs an enormous amount of energy. The result is that the lipid bilayer is the primary barrier to ion diffusion in biological membranes.⁶ Sodium, potassium, calcium, and chloride ions all depend on protein channels and pumps to get across. Without those proteins, ion flow would be vanishingly small.

There are some curious wrinkles, though. Negatively charged ions (anions) are measurably more permeable than positively charged ions (cations), and protons and hydroxide ions are orders of magnitude more permeable than other single-charge inorganic ions.⁶ Protons are special because they are so small they can hop along transient chains of water molecules that briefly span the membrane, rather than physically dissolving in the lipid core and swimming across. This anomalous proton permeability matters for energy production in mitochondria and bacteria, where maintaining a proton gradient is the whole point.

The Meyer-Overton Rule and Its Limits

For over a century, the dominant framework for predicting whether something will cross a lipid membrane has been the Meyer-Overton rule. The idea is simple: measure how well a substance dissolves in oil versus water (its oil-water partition coefficient), and that number predicts how permeable the membrane will be to it. Hydrophobic molecules partition easily into the membrane and cross quickly; hydrophilic ones do not.⁷

This rule works well for many small molecules, and it remains the starting point for thinking about membrane permeability. But over 110 years of testing have revealed situations where it breaks down. Some small molecules cross faster than their oil-water partition would predict, and others cross more slowly. The proton anomaly mentioned above is one example: protons are extremely hydrophilic yet permeate the bilayer far more readily than other ions. Researchers continue to refine the model, but the core insight holds for most practical purposes: if a molecule is small, uncharged, and dissolves readily in fat, it will likely get through the bilayer on its own.

How Membrane Composition Changes Permeability

Not all bilayers are created equal. The specific lipids making up the membrane substantially change what can get through. Cholesterol is the single biggest modifier in animal cell membranes. It wedges itself between phospholipid molecules, increasing the order of lipid packing and lowering permeability.⁸ Experiments on intact cells and liposomes confirm that adding cholesterol reduces the permeability to uncharged solutes.⁹ This is one reason cholesterol-rich membranes, like those of animal cells, are tighter barriers than membranes lacking cholesterol.

The types of fatty acid tails in the phospholipids matter just as much. Membranes built from shorter-chain, branched, or unsaturated fatty acids are leakier than those with long, straight, saturated tails.⁹ Unsaturated tails have kinks that prevent tight packing, leaving transient gaps through which small polar molecules can slip. Organisms that need to maintain membrane function in cold environments often increase the proportion of unsaturated fatty acids in their membranes, accepting higher permeability in exchange for keeping the membrane fluid enough to function.

Even the physical shape of the membrane plays a role. Curved membranes, such as those found in small vesicles or at the tips of cellular projections, are more permeable than flat ones. The convex (outward-bulging) side of a curved bilayer has a larger area per lipid and looser packing, which lowers the barrier for ions, water, and even some drugs compared to a flat membrane.¹⁰

Temperature and Phase Transitions

Phospholipid bilayers exist in different physical states depending on temperature. Below a characteristic transition temperature, the lipids are packed tightly in a rigid gel phase. Above it, they loosen into a fluid phase with more space between molecules.¹¹ The transition zone between these two states is where things get interesting for permeability.

Right around the melting point, the membrane contains patches of gel-phase lipids next to patches of fluid-phase lipids, and the interfaces between these patches are especially leaky. A dramatic spike in permeability begins about two degrees below the transition peak and extends several degrees past it, with the maximum permeability coinciding exactly with the transition temperature itself.¹² The ion permeability during this transition tracks the same temperature pattern as the heat absorbed by the lipid mixture.¹³

This is more than a lab curiosity. Drug-delivery researchers exploit it by designing liposomes whose transition temperature sits just above normal body temperature. When mild heating is applied to a tumor, the liposomes pass through their transition and become leaky, releasing their drug payload right where it is needed. The phase-transition effect makes even ions, which are normally almost completely excluded, temporarily able to cross.

How Drugs Get Through

Most orally administered drugs need to cross cell membranes to be absorbed from the gut and reach their targets. The pharmaceutical industry’s rough guide for this is the Rule of Five, which predicts that a drug is likely to be poorly absorbed if it has too many hydrogen-bond donors, too many hydrogen-bond acceptors, too high a molecular weight, or too high a lipophilicity. In practice, the distribution coefficient at physiological pH turns out to be the single most useful predictor of both permeability and solubility.¹⁴

Drugs that are weak acids or weak bases add a layer of complexity. At any given pH, a fraction of the drug molecules will be in their uncharged (neutral) form and a fraction will be ionized. Only the neutral form crosses the bilayer easily. Once inside a compartment with a different pH, the drug re-ionizes and becomes trapped. This “ion trapping” mechanism can drive surprising accumulations of drug inside cells. Research on small acidic drugs has shown that passive influx followed by ion trapping in compartments like mitochondria and lysosomes is the dominant factor in how much drug accumulates inside a cell, more so than transporter proteins previously suspected of doing the heavy lifting.¹⁵

Predicting permeability computationally remains challenging, especially for larger or ionizable drugs that violate the Rule of Five. Simulations of the antibiotic tetracycline, which has six hydrogen-bond donors and breaks the Rule of Five, illustrate the difficulty: the molecule’s multiple protonation states and tautomeric forms all influence how it interacts with the bilayer, and uncertainties in their relative proportions at physiological pH ripple through the permeability estimate.¹⁶

Cell-Penetrating Peptides

Proteins and peptides are normally far too large and polar to slip through the bilayer by passive diffusion. Yet a family of short peptides, typically 5 to 30 amino acids long and often carrying a positive charge, can cross cell membranes without the help of any receptor or transporter. These cell-penetrating peptides (CPPs) use two routes into cells: active uptake by the cell’s own internalization machinery, and direct translocation straight through the lipid bilayer.¹⁷ The energy-independent translocation route is the more surprising one, and researchers are still working out exactly how it happens at the molecular level.¹⁸

What makes CPP translocation especially interesting is that it depends heavily on the lipids present in the membrane. One peptide derived from a mitochondrial protein translocated far more efficiently across bilayers containing phosphatidic acid than across membranes made of other anionic or zwitterionic lipids.¹⁹ This lipid specificity matters because different cellular compartments have different lipid compositions, which could help explain why certain peptides accumulate in one organelle but not another. Drug designers are trying to exploit CPPs as vehicles to carry cargo molecules, like anticancer drugs or gene-editing tools, across membranes that would otherwise be impenetrable.

Forcing the Membrane Open With Electric Fields

Electroporation is a technique that uses brief pulses of electric field to punch transient holes in the bilayer. The process begins when the electric field reorganizes water molecules at the membrane’s surface, pulling thin wires of water into and across the lipid core.²⁰ Molecular dynamics simulations show that at field strengths on the order of 0.5 to 1.0 V per nanometer, these water wires expand into channels that span the entire membrane.²¹

Once those pores form, molecules that would normally be excluded, including DNA, RNA, proteins, and various drugs, can flow through. The pores are temporary: when the field is removed, the membrane reseals within seconds to minutes, depending on pulse duration and intensity. Electroporation is already used clinically to deliver chemotherapy drugs directly into tumor cells and is the basis for most laboratory transfection protocols that introduce foreign DNA into cells.

The energy barrier for pore formation depends on the membrane’s lipid makeup. Measurements across a full range of lipid compositions show that the electric field lowers the energy barrier to pore opening in a linear fashion, rather than the quadratic relationship that older theoretical models predicted.²² Lipid oxidation products, which accumulate naturally through aging and oxidative stress, further lower this barrier, meaning that damaged membranes are easier to electroporate than healthy ones.

Nanoplastics Getting Where They Should Not

A more recently studied category of uninvited membrane guests is nanoplastics. Molecular dynamics simulations of polyethylene nanoparticles show that they can dissolve into the hydrophobic core of lipid bilayers, with individual polymer chains disentangling from the particle and spreading through the membrane’s interior.²³ This happens spontaneously, without any external force, because polyethylene is hydrophobic enough to be welcomed into the oily core much like a lipid tail would be.

The consequences go beyond simple passive entry. Once embedded, nanoplastic chains alter the structural organization of the lipids around them and inhibit membrane fluidity in most cases.²⁴ This matters because fluidity is essential for virtually every membrane function: protein mobility, vesicle budding, signal reception, and all the transport processes discussed earlier. Short and medium-length polyethylene chains penetrate across diverse lipid bilayer compositions, adopting extended conformations inside the hydrophobic core, though their structural influence appears smaller than that of larger aggregates.²⁵

The interaction is not limited to the plasma membrane. Simulations show that polyethylene nanoplastics interact spontaneously with the membranes of the endoplasmic reticulum, Golgi apparatus, lysosomes, and endosomes as well.²⁴ If cells lack a mechanism to break down those embedded polymer chains, the disruption could be long-lasting. This is still a young field, mostly studied through simulations rather than live-cell experiments, but the basic physics of why it happens is consistent with everything known about the bilayer: hydrophobic materials dissolve into its core, and once there, they are hard to remove.

How Researchers Measure What Gets Through

Much of what we know about bilayer permeability comes from experiments with liposomes, which are artificial spheres of phospholipid bilayer that can be loaded with various substances. One widely used approach encapsulates a fluorescent dye and a quencher molecule together inside a liposome. When both are trapped inside, the quencher suppresses the dye’s fluorescence. If the membrane becomes leaky, the dye and quencher escape and separate, and the resulting increase in fluorescence provides a direct readout of how much leakage occurred.²⁶ Variations using self-quenching probes or dye-metal pairs are broadly employed to study how different chemicals, peptides, and physical forces alter membrane integrity.²⁷

These assays are the workhorses behind most of the findings described in this article, from quantifying the permeability spike at phase transitions to testing whether a candidate drug or peptide can cross a membrane unaided. Their simplicity is a strength, but they also have limits: a liposome is not a cell. Real cell membranes are studded with proteins, asymmetric in their lipid composition between the inner and outer leaflets, and connected to a cytoskeleton. Model membranes typically lack all of those features. This is why permeability measured in liposomes sets a baseline, but permeability in living cells can differ, often being higher because of the proteins embedded in the membrane that provide alternative crossing routes.