Flagellum

# Overview
A flagellum (plural: flagella) is a long, slender projection from the cell body, composed of microtubules and surrounded by the plasma membrane. In small, single-cell organisms they may function to propel the cell by beating in a whip-like motion; in larger animals, they often serve to move fluids along mucous membranes such as the lining of the trachea.
Eukaryotic flagella are quite different from the flagella of prokaryotes and bacteria. They have an internal structure comprised of nine microtubule doublets, forming a cylinder around a central pair of microtubules. The nine peripheral doublets are linked to each other by proteins such as dynein, a molecular motor which can cause flagella to bend.
A eukaryotic cell usually has only one or two flagella. As in prokaryotes, the eukaryotic flagellum may be used in locomotion; one well known example of this is the sperm cell, in which the "tail" of the sperm (a flagellum) is used to propel the cell forward. However, all non-dividing eukaryotic cells contain a flagellum (or cilium), not only sperm cells. Stationary cells (such as kidney, intestine, and nerve cells) also contain flagella (cilia) which project from the cell body out into the extracellular environment. There, these flagella can serve in sensation or in the movement of extracellular fluid.
The main differences among bacterial, archaeal, and eukaryotic flagella are summarized below:
- Bacterial flagella are helical filaments that rotate like screws.
- Archaeal flagella are superficially similar to bacterial flagella, but are different in many details and considered non-homologous.
- Eukaryotic flagella - those of animal, plant, and protist cells - are complex cellular projections that lash back and forth.
Sometimes eukaryotic flagella are called cilia or undulipodia to emphasize their distinctiveness.

# Bacterial flagellum
The bacterial flagellum is composed of the protein flagellin.  Its shape is a 20 nanometer-thick hollow tube. It is helical and has a sharp bend just outside the outer membrane; this "hook" allows the helix to point directly away from the cell. A shaft runs between the hook and the basal body, passing through protein rings in the cell's membrane that act as bearings. Gram-positive organisms have 2 of these basal body rings, one in the peptidoglycan layer and one in the plasma membrane. Gram-negative organisms have 4 such rings: the L ring associates with the lipopolysaccharides, the P ring associates with peptidoglycan layer, the M ring is imbedded in the plasma membrane, and the S ring is directly attached to the plasma membrane. The filament ends with a capping protein.
The bacterial flagellum is driven by a rotary engine composed of protein, located at the flagellum's anchor point on the inner cell membrane. The engine is powered by proton motive force, i.e., by the flow of protons (e.g., hydrogen ions) across the bacterial cell membrane due to a concentration gradient set up by the cell's metabolism (in Vibrio species the motor is a sodium ion pump rather than a proton pump). The rotor transports protons across the membrane, and is turned in the process. The rotor alone can operate at 6,000 to 17,000 rpm, but with the flagellar filament attached usually only reaches 200 to 1000 rpm.
The components of the bacterial flagellum are capable of self-assembly  without the aid of enzymes or other factors. Both the basal body and the filament have a hollow core, through which the component proteins of the flagellum are able to move into their respective positions. During assembly, protein components are added at the flagellar tip rather than at the base.
The basal body has several traits in common with some types of secretory pores, such as the hollow rod-like "plug" in their centers extending out through the plasma membrane. Given the structural similarities, it was thought that bacterial flagella may have evolved from such pores; however, it is now known that these pores are derived from flagella.
Different species of bacteria have different numbers and arrangements of flagella. Monotrichous bacteria have a single flagellum (e.g., Vibrio cholerae). Lophotrichous bacteria have multiple flagella located at the same spot on the bacteria's surfaces which act in concert to drive the bacteria in a single direction. Amphitrichous bacteria have a single flagellum on each of two opposite ends (only one flagellum operates at a time, allowing the bacteria to reverse course rapidly by switching which flagellum is active). Peritrichous bacteria have flagella projecting in all directions (e.g., Escherichia coli).
Some species of bacteria (such as Spirochetes) have a specialized type of flagellum called an "axial filament" that is located in the periplasmic space, the rotation of which causes the entire bacterium to move forward in a corkscrew-like motion.
Counterclockwise rotation of monotrichous polar flagella thrust the cell forward with the flagella trailing behind. Periodically, the direction of rotation is briefly reversed, causing what is known as a "tumble" in which the cell seems to thrash about in place. This results in the reorientation of the cell. When moving in a favorable direction, "tumbles" are unlikely; however, when the cell's direction of motion is unfavorable (e.g., away from a chemical attractant), a tumble may occur, with the chance that the cell will be thus reoriented in the correct direction.

# Archaeal flagellum
The archaeal flagellum is superficially similar to the bacterial (or eubacterial) flagellum; in the 1980s they were thought to be homologous on the basis of gross morphology and behavior (Cavalier-Smith, 1987). Both flagella consist of filaments extending outside of the cell, and rotate to propel the cell.
However, discoveries in the 1990s have revealed numerous detailed differences between the archaeal and bacterial flagella; these include:
- Bacterial flagella are powered by a flow of H+ ions (or occasionally Na+ ions); archaeal flagella are almost certainly powered by ATP. The torque-generating motor that powers rotation of the archaeal flagellum has not been identified.
- While bacterial cells often have many flagellar filaments, each of which rotates independently, the archaeal flagellum is composed of a bundle of many filaments that rotate as a single assembly.
- Bacterial flagella grow by the addition of flagellin subunits at the tip; archaeal flagella grow by the addition of subunits to the base.
- Bacterial flagella are thicker than archaeal flagella, and the bacterial filament has a large enough hollow "tube" inside that the flagellin subunits can flow up the inside of the filament and get added at the tip; the archaeal flagellum is too thin to allow this.
- Many components of bacterial flagella share sequence similarity to components of the type III secretion systems, but the components of bacterial and archaeal flagella share no sequence similarity. Instead, some components of archaeal flagella share sequence and morphological similarity with components of type IV pili, which are assembled through the action of type II secretion systems (the nomenclature of pili and protein secretion systems is not consistent).
These differences mean that the bacterial and archaeal flagella are a classic case of biological analogy, or convergent evolution, rather than homology. However, in comparison to the decades of well-publicized study of bacterial flagella (e.g. by Berg), archaeal flagella have only recently begun to get serious scientific attention. Therefore, many assume erroneously that there is only one basic kind of prokaryotic flagellum, and that archaeal flagella are homologous to it. For example, Cavalier-Smith (2002) is aware of the differences between archaeal and bacterial flagellins, but retains the misconception that the basal bodies are homologous.

# Eukaryotic flagellum
The eukaryotic flagellum is completely different from the prokaryote flagellum in both structure and evolutionary origin. The only shared characteristics among bacterial, archaeal, and eukaryotic flagella are their superficial appearance; they are intracellular extensions used in creating movement. Along with cilia, they make up a group of organelles known as undulipodia.
A eukaryotic flagellum is a bundle of nine fused pairs of microtubule doublets surrounding two central single microtubules. The so-called "9+2" structure is characteristic of the core of the eukaryotic flagellum called an axoneme. At the base of a eukaryotic flagellum is a basal body, "blepharoplast" or kinetosome, which is the microtubule organizing center for flagellar microtubules and is about 500 nanometers long. Basal bodies are structurally identical to centrioles. The flagellum is encased within the cell's plasma membrane, so that the interior of the flagellum is accessible to the cell's cytoplasm. Each of the outer 9 doublet microtubules extends a pair of dynein arms (an "inner" and an "outer" arm) to the adjacent microtubule; these dynein arms are responsible for flagellar beating, as the force produced by the arms causes the microtubule doublets to slide against each other and the flagellum as a whole to bend. These dynein arms produce force through ATP hydrolysis. The flagellar axoneme also contains radial spokes, polypeptide complexes extending from each of the outer 9 mictrotubule doublets towards the central pair, with the "head" of the spoke facing inwards. The radial spoke is thought to be involved in the regulation of flagellar motion, although its exact function and method of action are not yet understood.
Motile flagella serve for the propulsion of single cells (e.g. swimming of protozoa and spermatozoa) and the transport of fluids (e.g. transport of mucus by stationary flagellated cells in the trachea).
Additionally, immotile flagella are vital organelles in sensation and signal transduction across a wide variety of cell types
(e.g. eye: rod photoreceptor cells, nose: olfactory receptor neurons, ear: kinocilium in cochlea).
Intraflagellar transport (IFT), the process by which axonemal subunits, transmembrane receptors, and other proteins are moved up and down the length of the flagellum, is essential for proper functioning of the flagellum, in both motility and signal transduction.
For information on biologists' ideas about how the various flagella may have evolved, see evolution of flagella.