Cilia and flagella range in length from a few micrometers to more than 2 mm for some insect sperm flagella. They possess a central bundle of microtubules, called the axoneme, which consists of a so-called 9 + 2 arrangement of nine doublet microtubules surrounding a central pair of singlet, yet ultrastructurally distinct, microtubules (Figure 18-31a, b). Each of the nine outer doublets consists of an A microtubule with 13 protofilaments and a B microtubule with 10 protofilaments (see Figure 18-4). All the microtubules in cilia and flagella have the same polarity: the (+) ends are located at the distal tip. At its point of attachment in the cell, the axoneme connects with the basal body, a complicated structure containing nine triplet microtubules (Figure 18-31a).

The axoneme is held together by three sets of protein cross-links (Figure 18-31b). The two central singlet microtubules are connected to each other by periodic bridges, like rungs on a ladder. A second set of linkers, composed of the protein nexin, joins adjacent outer doublet microtubules to each other. Radial spokes project from each A tubule of the outer doublets toward the central pair.

The major motor protein present in cilia and flagella is axonemal dynein, a large, multisubunit protein related to cytoplasmic dynein. Two rows of axonemal dynein motors are attached periodically down the length of each A tubule of the outer doublet microtubules; these motors are called the inner-arm and outer-arm dyneins (see Figure 18-31b). It is the interaction of these dynein motors with the B tubule in the adjacent doublet that brings about ciliary and flagellar bending.