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Prokaryote structure

Overview of prokaryotes (bacteria and archaea). Structural features of prokaryotic cells.

Key points:

  • Prokaryotes are single-celled organisms belonging to the domains Bacteria and Archaea.
  • Prokaryotic cells are much smaller than eukaryotic cells, have no nucleus, and lack organelles.
  • All prokaryotic cells are encased by a cell wall. Many also have a capsule or slime layer made of polysaccharide.
  • Prokaryotes often have appendages (protrusions) on their surface. Flagella and some pili are used for locomotion, fimbriae help the cell stick to a surface, and sex pili are used for DNA exchange.
  • Most prokaryotic cells have a single circular chromosome. They may also have smaller pieces of circular DNA called plasmids.


Bacteria often get a bad rap: they’re described as unsafe “bugs” that cause disease. Although some types of bacteria do cause disease (as you know if you've ever been prescribed antibiotics), many other are harmless, or even beneficial.
Bacteria are classified as prokaryotes, along with another group of single-celled organisms, the archaea. Prokaryotes are tiny, but in a very real sense, they dominate the Earth. They live nearly everywhere – on every surface, on land and in water, and even inside of our bodies.
To emphasize that last point: you probably have about the same number of prokaryotic cells in your body as human cells1! That may sound gross, but many of our prokaryotic "sidekicks" play important roles in keeping us healthy.
In this article, we'll look at what prokaryotes are and what exactly makes them different from eukaryotes (such as you, a houseplant, or a fungus). Then, we'll take a closer look at the structures these efficient, omnipresent little organisms use to survive.

What are prokaryotes?

Prokaryotes are microscopic organisms belonging to the domains Bacteria and Archaea, which are two out of the three major domains of life. (Eukarya, the third, contains all eukaryotes, including animals, plants, and fungi.) Bacteria and archaea are single-celled, while most eukaryotes are multicellular.
Fossils show that prokaryotes were already here on Earth 3.5 billion years ago, and scientists think that prokaryotic ancestors gave rise to all of the life forms present on Earth today2,3.

Prokaryotes vs. eukaryotes

Prokaryotes and eukaryotes are similar in some fundamental ways, reflecting their shared evolutionary ancestry. For instance, both you and the bacteria in your gut decode genes into proteins through transcription and translation. Similarly, you and your prokaryotic inhabitants both pass genetic information on to your offspring in the form of DNA.
In other ways, prokaryotes and eukaryotes are quite different. That may be obvious when we're comparing humans to bacteria. But for me at least, it's less obvious when we're comparing a bacterium to a yeast (which is tiny and unicellular, but eukaryotic). What actually separates these categories of organisms?
The most fundamental differences between prokaryotes and eukaryotes relate to how their cells are set up. Specifically:
  • Eukaryotic cells have a nucleus, a membrane-bound chamber where DNA is stored, while prokaryotic cells don't. This is the feature that formally separates the two groups.
  • Eukaryotes usually have other membrane-bound organelles in addition to the nucleus, while prokaryotes don't.
  • Cells in general are small, but prokaryotic cells are really small. Typical prokaryotic cells range from 0.2 - 2 μm in diameter, while typical eukaryotic cells range from 10 - 100 μm in diameter4.
Many prokaryotic cells have sphere, rod, or spiral shapes (as shown below). In the following sections, we’ll walk through the structure of a prokaryotic cell, starting on the outside and moving towards the inside of the cell.
Prokaryotic cells are typically shaped as either spheres (called cocci), rods (called bacilli), or spirals.
_Image modified from "Bacterial morphology diagram," by Mariana Ruiz Villareal (public domain)._

The capsule

Many prokaryotes have a sticky outermost layer called the capsule, which is usually made of polysaccharides (sugar polymers).
The capsule helps prokaryotes cling to each other and to various surfaces in their environment, and also helps prevent the cell from drying out. In the case of disease-causing prokaryotes that have colonized the body of a host organism, the capsule or slime layer may also protect against the host’s immune system.
Remember Griffith's experiment, which demonstrated the existence of a "transforming principle" (DNA) that could turn rough, harmless bacteria into smooth, pathogenic bacteria? The smooth bacteria were smooth (and capable of causing disease) because they had a capsule!

The cell wall

All prokaryotic cells have a stiff cell wall, located underneath the capsule (if there is one). This structure maintains the cell’s shape, protects the cell interior, and prevents the cell from bursting when it takes up water.
The cell wall of most bacteria contains peptidoglycan, a polymer of linked sugars and polypeptides. Peptidoglycan is unusual in that it contains not only L-amino acids, the type normally used to make proteins, but also D-amino acids ("mirror images" of the L-amino acids). Archaeal cell walls don't contain peptidoglycan, but some include a similar molecule called pseudopeptidoglycan, while others are composed of proteins or other types of polymers5,6.
The external structures of the prokaryotic cell include a plasma membrane, cell wall, and capsule (or slime layer).
_Image modified from "Structure of Prokaryotes: Figure 2," by OpenStax College, Biology (CC BY 3.0)._
Some of the antibiotics used to treat bacterial infections in humans and other animals act by targeting the bacterial cell wall. For instance, some antibiotics contain D-amino acids similar to those used in peptidoglycan synthesis, "faking out" the enzymes that build the bacterial cell wall (but not affecting human cells, which don't have a cell wall or utilize D-amino acids to make polypeptides)5,7.

The plasma membrane

Underneath the cell wall lies the plasma membrane. The basic building block of the plasma membrane is the phospholipid, a lipid composed of a glycerol molecule attached a hydrophilic (water-attracting) phosphate head and to two hydrophobic (water-repelling) fatty acid tails. The phospholipids of a eukaryotic or bacterial membrane are organized into two layers, forming a structure called a phospholipid bilayer.
The plasma membranes of archaea have some unique properties, different from those of both bacteria and eukaryotes. For instance, in some species, the opposing phospholipid tails are joined into a single tail, forming a monolayer instead of a bilayer (as shown below). This modification may stabilize the membrane at high temperatures, allowing the archaea to live happily in boiling hot springs.
The plasma membrane of bacterial and eukaryotic (and some archael) cells is composed of a phospholipid bilayer. The tails of opposite-facing phospholipids remain separated, forming two separate layers.
The plasma membrane of some archaeal cells is composed of a phospholipid monolayer. The tails of opposite-facing phospholipids become united, forming a single layer.
_Image modified from "Archaea membrane," by Fransciscosp2 (public domain)._


Prokaryotic cells often have appendages (protrusions from the cell surface) that allow the cell to stick to surfaces, move around, or transfer DNA to other cells.
Thin filaments called fimbriae (singular: fimbria), like those shown in the picture below, are used for adhesion—that is, they help cells stick to objects and surfaces in their environment.
A fimbria (plural: fimbriae) is a type of appendage of prokaryotic cells. These hair-like protrusions allow prokaryotes to stick to surfaces in their environment and to each other.
_Image modified from "E. coli fimbriae.png," by Manu Forero (CC BY 2.5)._
Longer appendages, called pili (singular: pilus), come in several types that have different roles. For instance, a sex pilus holds two bacterial cells together and allows DNA to be transferred between them in a process called conjugation. Another class of bacterial pili, called type IV pili, help the bacterium move around its environment10.
The most common appendages used for getting around, however, are flagella (singular: flagellum). These tail-like structures whip around like propellers to move cells through watery environments.
Bacteria may have various types of surface structures. These include fimbriae, short protrusions found all over the surface of the bacterium; a flagellum, found at the back of the bacterium and used for propulsion; and a sex pilus, used to grab on to other bacteria for exchange of genetic material.

Chromosome and plasmids

Most prokaryotes have a single circular chromosome, and thus a single copy of their genetic material. Eukaryotes like humans, in contrast, tend to have multiple rod-shaped chromosomes and two copies of their genetic material (on homologous chromosomes).
Also, prokaryotic genomes are generally much smaller than eukaryotic genomes. For instance, the E. coli genome is less than half the size of the genome of yeast (a simple, single-celled eukaryote), and almost 700 times smaller than the human genome13!
By definition, prokaryotes lack a membrane-bound nucleus to hold their chromosomes. Instead, the chromosome of a prokaryote is found in a part of the cytoplasm called a nucleoid.
Prokaryotes generally have a single circular chromosome that occupies a region of the cytoplasm called a nucleoid. They also may contain small rings of double-stranded extra-chromosomal DNA called plasmids.
In addition to the chromosome, many prokaryotes have plasmids, which are small rings of double-stranded extra-chromosomal ("outside the chromosome") DNA. Plasmids carry a small number of non-essential genes and are copied independently of the chromosome inside the cell. They can be transferred to other prokaryotes in a population, sometimes spreading genes that are beneficial to survival.
For instance, some plasmids carry genes that make bacteria resistant to antibiotics. (These genes are called R genes.) When the plasmids carrying R genes are exchanged in a population, they can quickly make the population resistant to antibiotic drugs. While beneficial to the bacteria, this process can make it difficult for doctors to treat harmful bacterial infections.

Internal compartments

Prokaryotes aren't "supposed" to have internal compartments like the organelles of eukaryotes, and for the most part, they don't. However, prokaryotic cells sometimes need to increase membrane surface area for reactions or concentrate a substrate around its enzyme, just like eukaryotic cells. Because of this, some prokaryotes have membrane folds or compartments functionally similar to those of eukaryotes.
For example, photosynthetic bacteria often have extensive membrane folds to increase surface area for the light-dependent reactions, similar to the thylakoid membranes of a plant cell. These bacteria may also have carboxysomes, protein-enclosed cellular compartments where carbon dioxide is concentrated for fixation in the Calvin cycle14.

Check your understanding!

  1. You are looking at a recently discovered unicellular organism using a powerful microscope.
    How can you determine if the organism is a prokaryote or eukaryote?
    Choose 1 answer:

Want to join the conversation?

  • leaf green style avatar for user Junsang
    does bacteria have a Hayflick limit (limit of division) like normal human cells do?
    (21 votes)
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    • starky ultimate style avatar for user ++§ Αλεκσανδαρ
      Okay, so this is very complicated question to answer and it requires a lot of molecular biology. If any part of my answer is incomprehensible, please let me know.

      The main difference between our genome and bacterial genome is that our DNA molecules are packed into structures we called chromosomes and they are linear, meaning they have a starting point and an end point. Bacteria don't have chromosomes and their DNA is circular.

      Due to the mechanism of DNA replication, our DNA isn't completely replicated. That is, "the mother" DNA and "the daughter" DNA (those are not official terms) aren't identical. "The daughter" DNA will always be a bit shorter.

      What does that mean for us? How much of DNA do we use per one cell division? Well, on the both ends of our linear DNA there are what we call telomeric regions, or telomeres. Those are long repeated sequences that don't code for any protein. Their only purpose (as far as we know) is to save the important part of DNA from being lost during the replication process. Instead of losing important genes, we lose a small part of telomeres in every cell division. After 40 - 60 divisions telomeres reach critical length and they can't be sacrificed anymore. This is where DNA replication and hence cell division stop happening.

      Because bacteria have circular DNA, they don't have those problems. Their polymerase can replicate an entire genome without losing one single part of it. They don't need telomerases and therefore they don't have any limits in cell division. If a bacterial specie had Hayflick limit they would stop reproducing after some number of divisions and that would be the end of the specie.

      What you should ask now is: what about cancer cells? They seem to be immortal and divide without any limits. What about single celled eukaryotes, like amoeba? They have chromosomes too (linear DNA) but they don't have Hayflick limit. The answer to those questions is very interesting and rises a lot of possibilities for us. There is an enzyme called telomerase. This enzyme extends telomerases and prevents them from being lost after a number of replication cycles. It works forever in cancer cells, but for some reason it stops working in "normal" cells. Why? We don't know yet, but we're on our way to find that out. This means we could treat cancers with telomerase inhibitors - if we prevent telomerase from extending their telomeres, cancer cells will stop multiplying after reaching Hayflick limit. Could we treat our normal body cells with telomerase and prevent them from reaching the limit? The answer might be yes. Would that mean we could become immortal in such a way? We don't know yet, but we're certainly going to dig deeper into the problem.

      Thanks for asking such an interesting question!

      (79 votes)
  • winston default style avatar for user Izack
    Can bacteria get cancer if so what happens?
    (2 votes)
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  • leaf green style avatar for user jennifer sterling
    can eukaryotes have flagella and pilli? or is that only for prokaryotes?
    (2 votes)
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  • piceratops ultimate style avatar for user Ray
    how were the fossil of the prokaryotes found?
    Here it says that fossils of prokaryotic were found, how was it understood that it was a prokaryotic?
    i dont think that something so small like a bacteria could actually leave a imprint like a fossil.
    thank you
    (2 votes)
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    • piceratops ultimate style avatar for user Hecretary Bird
      Bacteria generally don't leave fossils, and at most we can infer their existence based on evidence of their effects on other fossilized creatures, such as infections. However, some bacteria have been known to create iron or clay sort of shells that survive after the bacteria has died, creating a sort of model of the bacteria. Bacteria have also been found in fossilized amber, and some cyanobacteria can create stromatolites, which are rocks created by cyanobacteria, calcium carbonate, and the surrounding sediments. Stromatolites can be fossilized, and when cut open, there are sometimes layers or fossilized cyanobacteria inside, protected by the stromatolite.
      (5 votes)
  • leafers seed style avatar for user sonya
    What is the difference between the flagella of eukaryotes and prokaryotes?
    (4 votes)
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  • blobby green style avatar for user nadyeol61
    what is the advantages of prokaryote with absence nucleus
    (3 votes)
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    • piceratops ultimate style avatar for user Hecretary Bird
      Essentially, prokaryotes are simpler than eukaryotes. This may not sound like an advantage, but it means that it's really easy to make new prokaryotes, which means that prokaryotic cells reproduce much faster than do eukaryotes. Also, this faster reproduction means that these cells can adapt faster as there are faster generations, which can be an advantage.
      (3 votes)
  • blobby green style avatar for user fire55force
    are the chromosomes in bacterial cells well developed ?
    (3 votes)
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    • mr pants teal style avatar for user Hannah W.
      Chromosomes are the genetic material of the cell, and they contain genes that are transcribed into RNA and translated into proteins. Bacterial chromosomes are one long, single molecule of double stranded, helical, supercoiled DNA. They are usually circular and covalently bonded at the ends1. They are not surrounded by a nuclear membrane, but are located in a region called the nucleoid. Bacterial chromosomes are different from human chromosomes, which are linear, arranged in pairs, and enclosed in a nucleus. Bacterial chromosomes do not undergo mitosis or meiosis, but they can exchange genetic material with other bacteria through processes such as conjugation, transformation, and transduction. Therefore, it depends on how you define “well developed”, but bacterial chromosomes are certainly adapted to their environment and function.
      (2 votes)
  • blobby green style avatar for user marvyayoub2
    where the DNA and the protein is present in the prokaryotic cells?
    (3 votes)
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  • blobby green style avatar for user estherbaffour101
    Is nucleoid considered to be an organelle?
    (2 votes)
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    • piceratops tree style avatar for user Cadmium Antimony
      Organelles perform a specific, specialized function and are membrane-bound. Nucleoid is an irregularly shaped organelle. Nucleoplasm and Nucleolus are present in the nucleus. Nucleoplasm and Nucleolus are not found in a nucleoid. It is composed of DNA, RNA, enzymes, dissolved ions, histones and other subnuclear bodies. Hope this helps.
      (3 votes)
  • blobby green style avatar for user owar padilla
    Why do eukaryotic cells need organelles, while prokaryotic cells don't?
    (2 votes)
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