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I know that dynein arms and microtubules are involved in the contraction of certain parts of the flagella to produce a wave motion, but I don't understand they are related to the 9+2 structure of the basal body.

How do flagella work in prokaryotes and eukaryotes?

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Flagella in prokaryotets is very different from that of eukaryotes.

The main structural protein in a prokaryotic flagellum is flagellin. The flagellar motion is caused by a molecular motor similar to Mitochondrial ATP-synthase; molecular motion generated by the chemiosmotic energy.

Eukaryotic flagella or cilia are made of microtubules with dynein attached on to them and cause the movement by the energy generated by ATP hydrolysis.

See the wikipedia article. It is clear enough.

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