What Are Cilia & Flagella?

When it comes to the structure of living cells, no components are perhaps as vital to their continual thriving than the cilia and flagella. 

What Are Cilia & Flagella?

But what exactly are they, and what are their benefits to cell movement and growth? 

The Cilia

The Cilia 

One of the most commonly occurring cellular components, cilium can be found in most species of living organisms, and serves several internal purposes. 


The term cilium (the singular of cilia), is derived from the Latin word for “eyelash”, and as their name implies, they are a thin, whip-like appendage that occur on cellular levels. 

The History Of The Cilia

Despite being discovered in 1898, the cilia was, for a long time, thought to just be a useless appendage without any real function or role. 

It was only with further research and exploration that scientists now recognize the necessity of healthy cilia to the avoidance of heart disease, kidney disease, mitral valve prolapse, and retinal degeneration. 

The Formation Of Cilia

The formation of the cilia happens through a process called ciliogenesis. 

This genesis occurs through a series of steps, beginning with the attachment of basal bodies to the cortex, attaching to membrane vesicles along the way, and fusing with the plasma membrane of the cell. 

This fusion is likely the cause of the creation of the cilia, the alignment of which is then determined by the way the original basal bodies are positioned and distributed. 

After alignment has been secured, axonemal microtubules extend from basal bodies, burrowing beneath the developing cilia membrane, and forming a cilium. 

For these cilia to then be effective, specific proteins need to be produced in the cytoplasm, before being selected and allowed entry to the tip of the cilium with the help of intraflagellar transportation. 

Continued cilia length and extensions have to be preserved by other systems, as if these extensions lessen, cells can grow weak and die. 

The Structure Of Cilia

Within their whip-like, tendril form, there are many different elements to their structure. This consists of a basal body, ciliary rootlet, transition zone, and axoneme. 

Basal Body

The basal body of a cell forms the foundation for the cilium, and is formed of a barrel of nine triplet microtubules, subdistal appendages, and an additional nine structures, resembling struts. These are known as distal appendages, and their purpose is to attach the basal body to the thin membrane at the base of the cilium. 

Ciliary Rootlet

Ciliary rootlets are essentially a skeleton-like structure, and they form from the basal body at the proximal end of the cilium. 

Transition Zone

The transition zone is also called the ciliary gate, and this has the function of controlling the entry and exit of proteins to and from the cilium.

This employs a sieve-like structure, which allows appropriately proportioned proteins to pass through with ease, whilst stopping larger, denser proteins from entering the cilium. 

This is why the transition zone is an important tool for maintaining the overall composition of the cilium. 

Due to the importance of this function, the transition zone is a commonly found component within the cells of most living organisms, including certain vertebrates such as nematodes, certain flies, and some forms of alga. 


The cytoskeletal core of the cilium is known as the axoneme. This is connected to the ciliary rootlet, and has a ring of nine outer microtubule doublets, and two central microtubule singlets. 

These are used to form a scaffold for the inner and outer dynein arms, which are used to move the cilium and provide passage for motor proteins kinesin and dynein. 

They are also useful for the transportation of ciliary components, and are referred to as IFTs, or intraflagellar transports. Similar to the axonal transports in a nerve fiber, these offer bidirectional movement, helping to transport proteins to either end of the cilium. 

The Types Of Cilia

As with anything, cilia has different variants, all of which serve different functions. 

Non-Motile Cilia

In the animal kingdom, these can be found on almost every single cell, with the only notable exception being the blood cells. Most cells only possess one single non-motile cilia, which is in contract with motile cilia, which are more prevalent. 

Modified Non-motile Cilia

Certain cilia are categorized under this term, most notably the kinocilia, which are the small cilia found on hair cells in the inner ear. 

Whilst possessing the same 9+2 axoneme, they lack the dynein arms for movement, although they do move passively following the detection of sound. 

Motile Cilia

Motile cilia, or secondary cilia, can be found in almost all mammals, and can normally be found on the surface of the cells in large groups. 

Prominent in the lining of the respiratory tract, these multiciliac cells are vital in mucous removal, and in keeping debris and contaminants away from the lungs.

They can also be found in the reproductive tract, and are responsible for ushering the egg cell from the ovary to the uterus. Similar cells in the brain also circulate cerebrospinal fluid. 

Modified Motile Cilia

These can be found in early embryonic development, and can be seen by their lack of two singlets. 

Nodal Cilia

Featuring a single cilium called a monocillium, nodal cells are present in the very beginning of embryonic development, and the primitive node. 

These nodal cells are responsible for regulating the left-right asymmetry in bilateral animals, and are thus incredibly important. 

The Flagella

The Flagella

Flagella are hair-like tendrils which protrude from plant cells and are found on the sperm cells of animals. Important for motility in countless different living cells, these appendages are paramount to the continuation of healthy cells. 


Derived from the latin word flagellum, meaning “whip”, the flagella is described thusly to represent the lashing motion seen in the motility of the appendages. 

The History Of Flagella 

The differences between eukaryotic and prokaryotic cells were established in 1962 by microbiologists Roger Stanier and C. B Van Niel. 

In their paper, they cite the 1932 work of Edouard Chatton, Titres et Travaux Scientifiques, who allegedly originated the terms and theorized this very distinction. 

The Types Of Flagella

In biology, there are three known types of flagella: bacterial, archaeal, and eukaryotic. 

These have some differences, for example, whilst eukaryotic flagella have both dynein and microtubules, allowing them to move with a bending mechanism, bacterial and archaeal flagella do not, instead using a rotary technique to achieve movement. 

Bacterial Flagella

These are helical filaments, and can move via clockwise and counterclockwise thanks to a rotary motor at their base. 

Archaeal Flagella

Similar to bacterial flagella, archaeal flagella also has a rotary motor, but are differently classified due to their wide variety of differences and status as non-homogenous, or uncommon

Eukaryotic Flagella

These are complex cellular appendages that lash back and forth, and are nearly identical to motile cilia, albeit with different lengths, waveforms, and functions.

The Structure Of Flagella

Structurally, there are several differences between flagella and cilia that should be recognized. 

Specific Structural Components

As with cilia, flagella also are formed from basal bodies, although this is only in prokaryotic flagella. 

These basal bodies are generally composed of: protein rings (C, MS, P, and L), connecting rods capable of burrowing, and sleeves to protect the rods. 

They also have specially designed hooks, which are composed of 120 different strands of a single protein. These are essentially a universal joint tool, which attaches the basal body to the filament. 

Whilst not embedding themselves in the plasma membrane like the basal bodies themselves, the hooks play an important role in moving the bacteria to the filament using their transmittable motor torque. 

The filament is the long part of the flagella, or the main part of the “tendril” shape. This is a tube shape, and consists of 11 protofilaments, resembling those found in the rod and hook components. 

Flagella can be found in eukaryotic and prokaryotic cells, and the two have distinct differences. 


These flagella tend to be smaller, and less complex. 

They are driven by protons, are characterized by a rotary movement, and lack a plasma membrane. 


They are larger, more complex, and possess a plasma membrane, setting them apart from their prokaryotic counterparts. 

They are also powered by ATP, and travel in a bending movement style. 

The Reproduction Of Flagella

When it comes to reproduction, flagella use assexual reproduction, namely binary fission, which involves the separation of one cell into two identical cells. 

Genetic exchange still occurs, as does recombination, but this is by horizontal gene transfer, as opposed to the transfer of DNA between two cells. 

Prokaryotic Cells: Differences

There are several different shapes and forms that prokaryotic cells can take. 

The first is cocci, which are a spherical bacteria and can be called a coccus

They can also be a bacilli, which is a bacteria with a cylindrical shape called a bacillus

Another form is spiral bacteria. These are rods which have twisted into spiral shapes, and are generally called spirilla

They can also be called vibrio, which are comma-shaped, and the archaeon haloquadratum, which has flat, square shaped cells. 

Eukaryotic Cells: Differences

On a structural level, eukaryotic cells differ greatly between plants and animals. 

Animal Cells

Whilst all animal cells are eukaryotic, they are distinctly different from those of other eukaryotic cells. They lack the cell walls that plants have, as well as chloroplasts, and large vacuoles. 

They also have a phagocytic cell that has the potential to engulf entire structures as a means of protecting the health and integrity of the host body. 

Plant Cells

Plant cells are also distinctly different from other, generalized eukaryotic cells. 

Firstly, they have a large centralized vacuole, which is enclosed by a membrane called a tonoplast. This maintains the cell’s “turgor” (internal cellular pressure) and controls the to and fro of molecules from the cytosol and the sap. 

They have a primary cell wall which is used to contain cellulose, hemicellulose, and pectin. These are deposited by protoplasts on the exterior cell membrane, something which contrasts with fungi cell walls. 

They have pores in their cell walls called plasmodesmata, and are used to link adjacent cells to allow intercellular communication. Whilst animals do have adjacent cells, they have a more analogous structure composed of gap junctions. 

Plant cells also have plastids, such as chloroplasts and organelles. Chloroplasts contain chlorophyll, a chemical pigment that creates the signature green color of plants.

And are essential for the function of photosynthesis – the method by which plants use sunlight to turn inorganic chemicals into usable substances for food and energy. 

Certain plants also have individualistic compositions. Bryophytes and seedless vascular plants (such as ferns) only have flagella and centrioles in their sperm cells.

Similarly, conifers, and flowering plants do not possess any of the flagella or centrioles found in the cells of animals

Fungal Cells

The cells in fungi are somewhat similar to the cells of animals. However, understandably, they do have their unique characteristics. 

They have cell walls containing chitin, and have less compartmentation between cells. For example, the hyphae of higher fungi use porous membranes called septa. These allow the passage of cytoplasm, organelles, and even nuclei. 

Also, unlike plants and animals, only the most primitive of fungi have flagella. This is a species known as chytrids. 

The Function Of Cilia & Flagella

When it comes to both types of appendages, there are three main functions shared by each: mobility, sensory purposes, and transporting material. 


With the help of cilia or flagella, cells are able to propel themselves around moist or underwater environments. This is usually in distinct patterns which match and correlate with the amount and formation of cilia/flagella that they have. 

Sensory Purposes

Certain cilia and flagella allow cells to sense changes within the host environment. This can be in the case of an infection, or the presence of foreign material, and can allow the cells to react accordingly. 


Whilst some cells can limit and regulate certain materials, others can also transport them throughout their host environment. 

An example of this is in mammalian reproductive systems, where cilia can transport the egg cells from the ovary to the uterus. 

Primary Cilia: The Functions

Primary cilia plays an important role in the sending and receiving of signals within the cells. As they are on the exterior of the cells, they are privy to various signals, environmental changes, and other stimuli that can affect the cells, and thus can act accordingly. 

They can also detect changes in chemical composition, morphogens, and growth in the extracellular matrix, as well as monitoring changes in pressure and fluid changes on the cell’s surface. 

Their main role is as an alert function, and instances where cilia are defective or damaged have been linked as contributing factors to undiagnosed degenerative diseases. 

Cilium Vs Flagellum

There are of course many noticeable differences between these two cellular appendages, not least in terms of movement, and reproductive origins. 


Whilst structurally, both cilia and flagella each have a basal body with an protruding appendage, the way they move are entirely different. 

Cilia use a distinct and widely studied beating movement, which goes back and forth rapidly with a wide range of movement. 

Flagella on the other hand, uses a propeller like motion, wherein the appendage spirals to create torque and thus movement. 

Reproductive Origins

In reproductive terms, cilia use a process called ciliogenesis, whilst flagella use binary fission to expand their numbers. 

This is quite a distinct difference, and whilst both methods involve assexual reproductive methods, they are still distinctly unique from one another. 

Cilia & Flagella: The Importance

Both of these appendages have incredible importance to their coinciding cells, and thus of the hosts the cells belong to. 

This importance can be reflected in the presence of diseases within human beings, and the defective or damaged cellular material that seems to be linked. 

Cilia and flagella which are not functioning properly can result in several troublesome ailments, ranging from the upsetting to the life threatening. 

Ectopic Pregnancies

For example, if the cilia within the fallopian tubes does not function correctly, then the fertilized ovum won’t reach the uterus. This will result in an ectopic pregnancy, something that can be both harmful and incredibly upsetting to the people involved. 

An ectopic pregnancy is essentially where the fertilized egg attaches itself to somewhere outside the uterus, and results in bleeding which can be life threatening if left untreated. 

Polycystic Kidney Disease

Another important function is the prevention of polycystic kidney disease. 

This is a genetic disorder where numerous sacks filled with fluid form in the kidneys. The effects of this if untreated can be high blood pressure, back pain, headaches, blood in urine, kidney stones, and urinary tract infections (UTIs). 

This can be caused by a defect in the primary cilium within the renal tube cells, and can be fatal if left untreated. 

Male Infertility

Defects or flaws within the flagellum of the sperm cells can also cause infertility in men. This is caused by flagellum dysfunction, and can mean that the mobility of the sperm is reduced to such a degree that the sperm cannot swim to the ovum and carry out fertilization. 

Alstrom Syndrome

This is a rare, genetically inherited syndrome which can cause several severe ailments within the human body. 

These can include: 

  • Retinal degeneration – This is the deterioration of the retinas, leading to blurred vision and poor eyesight. 
  • Hearing loss – in young people. 
  • Cardiomyopathy – the heart doesn’t pump blood as it should. 
  • Obesity – in children and young people especially. 
  • Renal failure – the failure of the kidneys. 
  • Orthopedic & rheumatological problems – spondylitis, arthritis, joint pain, and short stature. 


This is a disease that affects the kidneys, and can cause inflammation and scarring, impairing kidney function, impeding the production of urine, and can cause excess thirst and weakness. 

This can also cause a shortage of red blood cells, also known as anemia. 

Meckel-Gruber Syndrome

This is another kidney syndrome, and similar to PKD, sees the kidneys fill with numerous fluid filled sacs, which can limit and harm kidney function.


Dyskinesia is a syndrome where you cannot control how your body moves, or, more specifically, how your body moves in ways you haven’t told it to. 

This can present itself with the following symptoms: fidgeting, wriggling, swaying of the body, bobbing of the head, twitching and restlessness. 

There are several causes of this, however, one major cause seems to be the extended use of a medication called Levodopa, commonly used in treating Parkinsons’ Disease. 

With regards to dysfunctions of the cilia, this causes a similar problem called primary ciliary dyskinesia, wherein lungs lose some of their basic functions.

Such as mucus flushing, stopping foreign materials from entering the lungs, and increased susceptibility to chronic bronchial infections, such as bronchitis, sinusitis, pneumonia, and otitis media – a bacterial infection that affects the inner ear. 

Final Thoughts

And there we have it, everything you need to know about cilia, flagella, and the functions and differences therein. 

As you can see, what stands out from this article is the sheer amazingness of their being, and the greater importance they hold with regards to cell health and integrity, cellular movement, and the sending and receiving of signals within the host environment. 

Just goes to show that even the smallest things can make a big difference!

Jennifer Dawkins

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