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A bacterial outer membrane is an additional membrane outside the peptidoglycan in typical Gram-negative bacteria. It adds a barrier while the inner cell membrane remains the boundary of the cytoplasm.

A biological cell is a membrane-bounded basic unit of living organization. In a cell-level experiment it can be an experimental unit, provided that treatment assignment and relevant interactions are handled at that level.

The shared architecture of cellular life combines a selective cell membrane, internal cytoplasm, inherited information in DNA, and ribosomes that assemble proteins. Metabolism supplies transformations of matter and energy needed for maintenance and growth. These components form a coupled system: a boundary retains useful molecules, enzymes organize chemical reactions, and inherited information supports rebuilding the machinery. See Clark, Douglas and Choi, Biology 2e: prokaryotic cells.

A worked structural comparison: in a typical prokaryote, DNA occupies a region without a surrounding cell nucleus; in a typical nucleated eukaryote, much of the DNA lies inside a membrane-bounded cell nucleus. Both still have a cell membrane, cytoplasm and ribosomes. The extra boundary compartmentalizes processes; it does not create a different basic principle of living organization. See Clark, Douglas and Choi, Biology 2e: eukaryotic cells.

Shared architecture describes cellular life and its developmental machinery, rather than requiring every specialized biological cell to retain every component. A mature mammalian red blood cell, for example, lacks a cell nucleus, although it develops from nucleated precursors. See Clark, Douglas and Choi, Biology 2e: components of blood. This distinction makes cellular unity compatible with striking specialization.

The cell membrane, also called the plasma membrane, is the selective boundary separating a biological cell's cytoplasm from its surroundings. Both prokaryotes and eukaryotes have a cell membrane. Where a cell wall is present, it is a distinct structure outside the cell membrane; the two names are not synonyms. This separation lets a biological cell maintain internal conditions while exchanging material through membrane transport. See NHGRI: cell membrane.

The familiar architecture is a lipid bilayer containing membrane proteins. In a phospholipid-based lipid bilayer, two membrane leaflets face opposite ways: hydrophilic heads face the water on each side, while hydrophobic tails face one another in the interior. The heads are therefore exposed both outside and inside the biological cell. This arrangement combines a water-facing surface with a barrier to many water-soluble solutes; the schematic represents organization rather than an atomistic structure. See Alberts et al., Molecular Biology of the Cell: the lipid bilayer.

Selective permeability means that different substances cross at different rates under comparable conditions. Small nonpolar molecules can pass through a lipid bilayer by diffusion, while ions encounter a strong barrier without a suitable route. An ion channel supplies a selective water-filled pathway when open; a carrier protein binds a solute and changes shape to expose it to the other side. These membrane proteins therefore add specific routes to the barrier. An open ion channel permits passive transport, whereas a carrier protein can mediate either passive transport or active transport. See Alberts et al.: principles of membrane transport.

The useful combination is retention plus controlled exchange: a completely impermeable boundary would prevent uptake, whereas unrestricted mixing would erase differences in concentration and membrane potential. The fluid mosaic model connects these functions to an organized but mobile lipid bilayer containing proteins.

The cell nucleus is a membrane-bounded compartment characteristic of eukaryotic biological cells, containing most of the cellular DNA in a typical nucleated biological cell. Its double nuclear envelope separates this DNA from the surrounding cytoplasm. Most does not mean all: mitochondria and chloroplasts retain their own DNA. Nor does every specialized eukaryotic biological cell retain a cell nucleus: mature mammalian red blood cells have lost theirs. Prokaryotes organize their DNA in a nucleoid without a nuclear envelope, and still have ribosomes. See NHGRI: nucleus, ^[ref] and Clark, Douglas and Choi, Biology 2e, 40.2: mature mammalian red blood cells.

Follow one nuclear protein-coding gene: its DNA is used in transcription to make RNA; after the appropriate processing, messenger RNA is exported through a nuclear pore complex; a ribosome in the cytoplasm then uses it in biological translation to build an amino acid chain. The DNA remains in the cell nucleus. The RNA is a template, not the material converted into a protein. The ribosome diagram below follows this route; gene expression gives a complementary nucleotide sequence example. See Alberts et al.: selective RNA export and protein import.

This architecture makes gene expression interesting in a spatial way: nuclear transcription and cytoplasmic biological translation are separated by a selective boundary. A messenger RNA can be processed before export and use, while proteins needed for nuclear functions travel inward. Inside the cell nucleus, the cell nucleolus helps assemble ribosome subunits for export. Thus the compartment housing most DNA also helps build the machinery that interprets its messages elsewhere.

Robert Brown described and named the cell nucleus in his account of plant biological cells, read to the Linnean Society in 1831 and published in its Transactions in 1833. This historical observation identified a recurring structure, without establishing its later-understood role in DNA storage or gene expression. See Brown, On the Organs and Mode of Fecundation in Orchideæ and Asclepiadeæ, Transactions 16, 685–738 (1833). This is a documented contribution rather than a claim that no one had observed the structure earlier.

Cellular reprogramming changes an established cell state so that a different developmental program becomes accessible. Experimentally induced cellular reprogramming must be distinguished from the ordinary progression of cell differentiation. An ovum's cytoplasm can reset aspects of a transferred cell nucleus; this does not mean that a specialized donor normally returns to an early developmental state in its original surroundings. ^[ref]

A molecular chaperone is a protein that assists other proteins in reaching or maintaining useful arrangements, for example by limiting unwanted association during protein folding. Assistance does not rewrite the client's protein primary structure. In a crowded cytoplasm, reducing protein aggregation can make successful protein folding more reliable. See Cooper: molecular chaperones and folding assistance.

Cytokinesis partitions the cytoplasm. Without cytokinesis, two cell nuclei can share one biological cell. ^[ref]

The cytoplasm is the material inside a cell membrane but outside the cell nucleus, when one is present. It includes the cytosol, the organelles suspended in it, and other structures; it is not just a name for the liquid. In a prokaryote, which has no cell nucleus, the nucleoid and ribosomes are within the cytoplasm. See Clark, Douglas and Choi, Biology 2e, 4.3: cytoplasm and cytosol and Clark, Douglas and Choi, Biology 2e, 4.2: prokaryotic organization.

Try classifying four positions in the diagram. A point in the pale blue region belongs to both cytosol and cytoplasm. A point inside the mitochondrion belongs to an organelle included in the cytoplasm, but not to the surrounding cytosol. A point on a free ribosome belongs to the cytoplasm, but the ribosome itself is not cytosol. A point inside the cell nucleus belongs to neither cytoplasm nor cytosol. These distinctions prevent the misleading inference that everything outside the cell nucleus shares one undivided liquid environment.

The usefulness of the cytoplasm is this combination of shared surroundings and specialized structures: enzymes in the cytosol carry out many steps of metabolism, while organelles maintain their own internal conditions. A soluble protein made by a free ribosome may work in the cytosol or be transported elsewhere, including into the cell nucleus. Cellular organization therefore combines separation with exchange, rather than assigning each protein permanently to its place of synthesis. See Alberts et al., Molecular Biology of the Cell (2002): traffic between nucleus and cytosol.

The cytosol is the aqueous part of the cytoplasm surrounding its structures, including organelles. It contains water, ions and dissolved molecules, including many proteins; it is a crowded working environment rather than pure water. The liquid inside a cell nucleus or a membrane-bounded organelle is not the surrounding cytosol.

An electrical synapse passes ionic electric current directly between neurons through gap junctions, whose paired channels connect the two cytoplasms. It does not require synaptic vesicle release and postsynaptic neurotransmitter binding. Transmission across the junction is very fast; the receiving cell membrane's capacitance and other conductances still determine its voltage response. Electrical coupling can coordinate the timing of activity across neurons. See Purves and colleagues: electrical synapses and gap junctions.

For a passive junction with constant conductance $g_j$, the inward electric current into cell 2 iswhere each $V_k$ is the cell's membrane potential, measured against a common extracellular reference. Taking $g_j=2\mathrm{nS}$, $V_1=-55\mathrm{mV}$ and $V_2=-65\mathrm{mV}$ gives $20\mathrm{pA}$ into cell 2 and the equal opposite electric current into cell 1. Exchanging the voltages reverses the electric current. Both depolarization and hyperpolarization can therefore be transmitted; an electrical synapse is not inherently an excitatory connection.

Many electrical synapses conduct in both directions, but this does not guarantee equal voltage responses: the cells can have different effective electrical resistance and capacitance. Some junctions rectify, meaning they conduct preferentially in one direction, so the constant-$g_j$ formula is insufficient. A concrete molecular example is the original study ^[ref]. Bidirectionality is thus a common property with important qualifications, rather than part of the definition.