Cilia and Flagella- Definition, Structure, Functions and Diagram

Cilia and Flagella Definition

  • Cilia and Flagella are complex filamentous cytoplasmic structures protruding through a cell wall.
  • They are minute, especially differentiated appendices of the cell.
  • Flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and are used to move an entire cell.
  • Cilia (singular = cilium) are short, hair-like structures that are used to move entire cells (such as paramecia) or substances along the outer surface of the cell (for example, the cilia of cells lining the Fallopian tubes that move the ovum toward the uterus, or cilia lining the cells of the respiratory tract that trap particulate matter and move it toward the nostrils).
  • The terms cilium (meaning an eyelash) and flagellum (meaning a whip) are often used arbitrarily.
  • Generally, cilia are shorter than flagella (<10 μm compared to >40μm).
  • Cilia are present on the surface of the cell in much greater numbers (ciliated cells often have hundreds of cilia but flagellated cells usually have a single flagellum).
  • The real difference, however, lies in the nature of their movement. Cilia row like oars. The movement is biphasic, consisting of an effective stroke in which the cilium is held rigid and bends only at its base and a recovery stroke in which the bend formed at the base passes out to the tip.
  • Flagella wriggle like eels. They generate waves that pass along their length, usually from base to tip at constant amplitude.
  • Thus the movement of water by a flagellum is parallel to its axis while a cilium moves water perpendicular to its axis and, hence, perpendicular to the surface of the cell.

Cilia and Flagella- Structure and Functions

Figure: Diagram of Cilia and Flagella

Structure of cilia and flagella

Despite their different pattern of beating, cilia and flagella are indistinguishable structurally.

All cilia and flagella are built on a common fundamental plan:

  1. A bundle of microtubules called the axoneme (1 to 2 nm in length and 0.2 μm in diameter) is surrounded by a membrane that is part of the plasma membrane.
  2. The axoneme is connected with the basal body which is an intracellular granule lying in the cell cortex and which originates from the centrioles.
  3. Each axoneme is filled with ciliary matrix, in which are embedded two central singlet microtubules, each with the 13 protofilaments and nine outer pairs of microtubules, called doublets. This recurring motif is known as the 9 + 2 array.
  4. Each doublet contains one complete microtubule, called the A sub fiber, containing all the 13 protofilaments. Attached to each A sub fiber is a B sub fiber with 10 protofilaments.
  5. Subfibre A has two dynein arms which are oriented in a clockwise direction. Doublets are linked together by nexin links.
  6. Dynein is an ATPase that converts the energy released by ATP hydrolysis into the mechanical work of ciliary and flagellar beating.
  7. Each sub fiber A is also connected to the central microtubules by radial spokes terminating in fork-like structures, called spoke knobs or heads.

This regular arrangement of microtubules and associated proteins with the nine-way pattern is also seen in centrioles. But unlike centrioles, cilia and flagella have a central pair of microtubules, so that the overall structure is called the 9 + 2 axoneme. 

Note: Eukaryotic flagella diverge from prokaryotes in composition. Flagella in eukaryotes contain far more proteins and bear some similarity to motile cilia, with the same general motion and control patterns. 

Working of Cilia and Flagella

In eukaryotes

Using ATP produced by mitochondria near the base of the cilium or flagellum as fuel, the dynein arms push on the adjacent outer doublets, forcing a sliding movement to occur between adjacent outer doublets. Because the arms are activated in a strict sequence both around and along the axoneme and because the amount of sliding is restricted by the radial spokes and inter-doublet links, sliding is converted into bending.

In prokaryotes

Bacterial flagella use a fundamentally different mechanism. Like the propeller of a boat, the motion of the bacterial flagellum is entirely driven by the rotary motor at its base. The bacterial flagellum itself is a specialized piece of extracellular cell wall, made of one protein (flagellin) that has no similarity to tubulin or dynein. Cilia and flagella are full of cytosol all the way to their tips and use the ATP in that cytosol to generate force all the way along their length.

Functions of Cilia

  • Cilia are used for locomotion in isolated cells, such as certain protozoans (e.g., Paramecium).
  • Motile cilia use their rhythmic undulation to sweep away substances, as in clearing dirt, dust, micro-organisms and mucus, to prevent disease. 
  • Cilia play roles in the cell cycle as well as animal development, such as in the heart.
  • Cilia selectively allow certain proteins to function properly.
  • Cilia also play a role in cellular communication and molecular trafficking.
  • Non-motile cilia serve as sensory apparatus for cells, detecting signals. They play crucial roles in sensory neurons. Non-motile cilia can be found in the kidneys to sense urine flow, as well as in the eyes of the photoreceptors of the retina.
  • They also provide habitats or recruitment areas for symbiotic microbiomes in animals. 
  • Cilia have also been discovered to participate in vesicular secretion of ectosomes.

Functions of Flagella

  • Flagella are generally used for locomotion of cells, such as the spermatozoon and Euglena (protozoan).
  • Flagella have an active role in aiding cell feeding and eukaryotic reproduction.
  • In prokaryotes such as bacteria, flagella serve as propulsion mechanisms; they’re the chief way for bacteria to swim through fluids.
  • It also provides a mechanism for pathogenic bacteria to aid in colonizing hosts and therefore transmitting diseases.
  • Flagella also function as bridges or scaffolds for adhesion to host tissue.


  1. Verma, P. S., & Agrawal, V. K. (2006). Cell Biology, Genetics, Molecular Biology, Evolution & Ecology (1 ed.). S .Chand and company Ltd.
  2. Stephen R. BolsoverElizabeth A. ShephardHugh A. WhiteJeremy S. Hyams (2011). Cell Biology: A short Course (3 ed.).Hoboken,NJ: John Wiley and Sons.
  3. Alberts, B. (2004). Essential cell biology. New York, NY: Garland Science Pub.

Cilia and Flagella- Definition, Structure, Functions and Diagram

About Author

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Sagar Aryal

Sagar Aryal is a microbiologist and a scientific blogger. He attended St. Xavier’s College, Maitighar, Kathmandu, Nepal, to complete his Master of Science in Microbiology. He worked as a Lecturer at St. Xavier’s College, Maitighar, Kathmandu, Nepal, from Feb 2015 to June 2019. After teaching microbiology for more than four years, he joined the Central Department of Microbiology, Tribhuvan University, to pursue his Ph.D. in collaboration with Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarbrucken, Germany. He is interested in research on actinobacteria, myxobacteria, and natural products. He has published more than 15 research articles and book chapters in international journals and well-renowned publishers.

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