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Flagella (singular is flagellum) are long, threadlike appendages which provide the mechanical means by which living single cells can move. Flagella can be present on prokaryotic cells (cells such as bacteria whose genetic material is not contained within a specialized nuclear membrane) and eukaryotic cells (whose nuclear material is contained within a nuclear membrane). Prokaryotic cells have flagella made up of the protein flagellin. Eukaryotic cells (such as sperm) which have a nucleus have flagella composed of a protein called tubulin.

Bacteria can have a single flagellum or multiple flagella in a number of patterns. A single flagellum is located at an end of a rod-shaped bacterium, similar to the position occupied by a propeller on a submarine. This orientation represents a monotrichous flagellum. Bacteria with multiple flagella may have one at each end (an amphitrichous arrangement), several at one end (a lophotrichous arrangment), or many all around their perimeter (a peritrichous arrangement).

Flagellar movement is chemically driven. Nutrients attract motile bacteria, while other substances repulse them. This reactive motility, which involves the comparison of the amount of the target compound by the bacteria at different times, is termed chemotaxis. The actual mechanism involves the entry of an atomic element called a proton into a bacterium. The flow of the protons powers the rotation of the base of a flagellum (an area called the hook) at about 150 revolutions per second. When the hook rotates counter-clockwise, a bacterium will move toward a chemical attractant. If the hook rotates clockwise the bacterium tumbles aimlessly until it senses a more favorable chemical environment, at which time the counterclock-wise rotation resumes.

Eukaryotic flagella are very different from bacterial flagella. The tubulins of eukaryotic flagella are arranged in a microtubule array of nine doublets surrounding two singlets along the length of the flagella, reminiscent of drinking straws standing up in a cylindrical container. These straws slide along each other to generate movement and are connected by protein spokes to regulate their interaction. This sliding motion generates the flagellar beat, which begins at the base (next to the cell) and is propagated away from the cell (distally) in a standing wave. This beat occurs in a single plane with a whiplike movement.

Flagellar movement can be visualized using specialized microscopic techniques. Flagella are usually 12-30 nanometers (nm) in diameter and much longer than the cell which they move. Because they are so thin, they cannot be seen with normal light microscopy. Instead scientists use staining techniques or phase-contrast microscopy to visualize them. Phase-contrast microscopy accentuates differences in how light bends as it passes through the specimen observed. Motile bacteria will appear oval, oblong or spiral; whereas sperm look triangular with rounded corners. Cells such as the photosynthetic protist Chlamydomonas reinhardtii, which have two flagella at one end, will appear as though they are doing the breaststroke.

A number of environmental factors greatly influence the stability of the flagellar structure. In both prokaryotes and eukaryotes, an acidic pH will cause flagella to fall off. In addition, very cold temperatures will lead to disassembly of the flagellar proteins. However, flagella will reassemble with a change to an environment with a neutral pH or normal temperature.

See also Eukaryotae.