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Animals are multicellular organisms with eukaryotic cellular organization. A representative animal cell has a cell membrane, cell nucleus and mitochondria, but no cell wall or chloroplasts. A neuron illustrates how this common plan can acquire a specialized shape and signaling function. See OpenStax Biology 2e, 4.3: animal cell organization.

Archaea are a major evolutionary lineage distinct from bacteria. The cellular comparison here concerns the prokaryotic members of archaea; see two-domain system for broader clade usage. Their biological cells have a nucleoid rather than a membrane-bounded cell nucleus, yet aspects of DNA replication, transcription and biological translation resemble those of eukaryotes. Their characteristic lipids differ chemically from the usual bacterial membrane lipids, and their cell walls, when present, lack peptidoglycan. See OpenStax Biology 2e, 22.2: archaeal distinctions.

Some archaea perform methanogenesis, producing methane as part of their metabolism. Archaea also inhabit ordinary soils and oceans: extreme habitats do not define the lineage. See OpenStax Biology 2e, 22.1: moderate and extreme environments. Woese and Fox's 1977 analysis of ribosomal RNA distinguished the methanogenic group they called archaebacteria from typical bacteria. Their proposed three primary lines of descent were a historical interpretation, rather than the final resolution of deep phylogenetics. See Woese and Fox, 1977: Phylogenetic structure of the prokaryotic domain.

Bacteria are a major evolutionary lineage of organisms with prokaryotic cellular organization. Escherichia coli and cyanobacteria illustrate its variety: the same broad cellular plan supports different kinds of metabolism. Most bacteria have a cell wall containing peptidoglycan; archaea do not have peptidoglycan walls. A cell wall and a cell membrane are distinct structures, and some bacteria lack a cell wall. See OpenStax Biology 2e, 22.2: bacterial envelopes.

The usefulness of recognizing bacteria extends beyond naming: it identifies a shared evolutionary background for comparing genes, proteins and cellular mechanisms. A familiar shape or the absence of a cell nucleus alone cannot distinguish bacteria from archaea; molecular comparisons, including ribosomal RNA, supply additional evidence.

Carbohydrates are a family of chemical substances encompassing monosaccharides, combinations of monosaccharides, and their derivatives. Glucose is a small carbohydrate; cellulose is a long-chain polysaccharide. Deoxyribose illustrates why composition alone does not define the family: replacing a hydroxy group in ribose by hydrogen still leaves a carbohydrate. See IUPAC Gold Book: carbohydrates.

Many familiar monosaccharides have a molecular formula of the form ${\mathrm{C}}_n{\mathrm{H}}_{2n}{\mathrm{O}}_n$, equivalently ${\mathrm{C}}_n({\mathrm{H}}_2\mathrm{O}{)}_n$. This explains the historical name, “hydrate of carbon”, but does not mean the molecule consists of carbon mixed with intact water molecules. Nor is it a universal formula: deoxyribose has ${\mathrm{C}}_5{\mathrm{H}}_{10}{\mathrm{O}}_4$. The family is defined through chemical structure and relationships, not that ratio. See IUPAC's definition and origin of the name carbohydrate.

The useful surprise is the variety of roles obtainable from related building blocks. Glucose participates in metabolism, ribose forms part of RNA, and linked glucose units make structural cellulose in a plant cell wall. Understanding carbohydrates therefore connects cellular energy, molecular information, and material structure. See Alberts et al., Molecular Biology of the Cell: the chemical components of a cell.

The cell envelope comprises a biological cell's surrounding boundary layers, including its cell membrane and a cell wall or additional outer structures when present. The term is especially useful when discussing bacteria, where the layers must be distinguished.

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.

A cell wall is a supporting structure outside a cell membrane. It helps preserve shape and bears the load when osmosis raises internal pressure. The cell membrane supplies the selective permeability described in its own article; the cell wall supplies mechanical reinforcement. These functions cooperate: a porous supporting layer can restrain expansion without being the boundary that retains dissolved solutes. Turgor pressure makes this cooperation visible in a firm leaf; plasmolysis and a lysozyme wall-removal experiment separate the two functions experimentally.^[ref]

The material is not universal. Most bacteria use peptidoglycan, whose linked sugar chains and amino acid cross-links are explained below. A plant cell wall uses cellulose; a fungal cell wall contains chitin and glucans. Animals lack a cell wall, some bacteria are naturally wall-free, and archaea have different wall chemistry. Thus a cell wall is neither a universal cellular component nor one chemical recipe.^{[ref][ref][ref]}

The bacterial outer membrane in typical Gram-negative bacteria is an additional membrane outside the peptidoglycan, not another name for that supporting mesh. The cell envelope includes the boundary layers together. An extra barrier can change access to the peptidoglycan, so response to lysozyme cannot be inferred from the mere presence of a cell wall.^[ref]

A eukaryote is an organism belonging to the lineage characterized by a membrane-bounded cell nucleus and extensive cellular compartmentalization. A nuclear envelope surrounds the nuclear genome; nuclear chromosomes are typically linear. Ribosomes perform biological translation outside the cell nucleus. See OpenStax Microbiology, 3.4: nuclear organization and protein synthesis. Specialized biological cells can lose their cell nucleus, as mature mammalian red blood cells do, while remaining parts of eukaryotic organisms; see OpenStax Biology 2e, 40.2: mature red blood cells.

Yeasts, plants and animals are all eukaryotes. Typical cells in these groups have mitochondria, but chloroplasts belong to photosynthetic plant and algae lineages, not to every eukaryote. A cell wall occurs in typical plant and fungus cells but is absent from animal cells. These are comparisons of representative cells, not a checklist every specialized cell must satisfy. See OpenStax Biology 2e, 4.3: nucleus, organelles and representative cells.

The interesting feature is controlled separation: cell membranes and organelle membranes let different cellular processes occupy distinct compartments while membrane transport connects them. The evolution of eukaryotes also involved partnership: mitochondria descend from a bacterial endosymbiosis. Modern phylogenetics supports an archaeal ancestry for the nuclear lineage, alongside this bacterial contribution; see two-domain system. Thus the history of a whole eukaryote cannot be read as the history of just one of its genes.

A fungal cell wall contains structural polysaccharides including chitin and glucans. Its composition and organization vary among fungi; the diagram illustrates a composite rather than a pure chitin shell. A fungus sharing a cell wall with a plant does not imply shared wall chemistry.^[ref]

A fungus is a eukaryote that obtains nutrients by absorption rather than photosynthesis. Fungi include unicellular yeasts and multicellular forms. Their cell walls differ from bacterial peptidoglycan walls; having a cell wall does not make a fungus a plant. See OpenStax Biology 2e, 24.1: fungal nutrition and organization.

Lysozyme is a protein enzyme that attacks the peptidoglycan of bacterial cell walls. Its active site is a cleft in the folded protein structure, where a suitable substrate can interact with positioned chemical groups. This illustrates why possessing the right amino acid residues is insufficient if their spatial arrangement is lost. See Alberts et al.: lysozyme as a worked example of protein binding and enzyme function.

A concrete structural example is Cheetham, Artymiuk and Phillips's 1992 study of hen egg-white lysozyme bound to a short carbohydrate that inhibits its action. The bound carbohydrate occupies part of the active site; it is not a reacting substrate in this complex. The study describes specific interactions and changes of shape accompanying binding. Thus a real binding site has chemical interactions and flexibility as well as a geometric outline. See Cheetham, Artymiuk and Phillips, 1992: structure of a lysozyme complex with bound inhibitor and RCSB PDB entry 1HEW: the authors' structure and bound three-unit carbohydrate. The diagrams above illustrate the idea; their twelve-residue strings are not lysozyme sequences or coordinates.

Peptidoglycan is a mesh of linked sugar chains cross-linked by short chains of amino acids in the cell walls of most bacteria. Its absence from the cell walls of archaea helps distinguish envelope chemistry without confusing either cell wall with a cell membrane. See OpenStax Microbiology, 3.3: cell walls and peptidoglycan.