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Organelles or Compartments in Bacteria and Eukaryotic Cells

Linda Crampton has an honors degree in biology and many years of teaching experience. She finds the study of microorganisms fascinating.

A bacterial cell (Some bacteria don't have a flagellum, capsule, or pilli. They may also have a different shape.)

A bacterial cell (Some bacteria don't have a flagellum, capsule, or pilli. They may also have a different shape.)

Bacterial Compartments

In animal and plant cells, organelles are compartments surrounded by membrane that have a particular function in the cell’s life. Until quite recently, it was thought that bacterial cells were much simpler and that they didn’t have any organelles or internal membranes. Recent research has shown that these ideas are wrong. At least some bacteria do have internal compartments surrounded by a boundary of some kind, including membrane. Some researchers are calling these compartments organelles.

Animal cells (including ours) and the cells of plants are said to be eukaryotic. Bacterial cells are prokaryotic. For a long time, bacteria were thought to have comparatively primitive cells. Researchers now know that the organisms are more complex than they realized. Studying the structure and behavior of bacteria is important for advancing scientific knowledge. It’s also important because it might indirectly benefit us.

A plant cell has a wall made of cellulose and chloroplasts that perform photosynthesis.(The true extent or number of some of the organelles isn't shown in the illustration.)

A plant cell has a wall made of cellulose and chloroplasts that perform photosynthesis.(The true extent or number of some of the organelles isn't shown in the illustration.)

Eukaryotic and Prokaryotic Cells

Eukaryotic Cells

Members of the five kingdoms of living things (with the exception of monerans) have eukaryotic cells. Eukaryotic cells are covered by a cell membrane, which is also called a plasma or a cytoplasmic membrane. Plant cells have a cell wall outside the membrane.

Eukaryotic cells also contain a nucleus that is covered by two membranes and contains the genetic material. In addition, they have other organelles surrounded by membrane and specialized for various tasks. The organelles are embedded in a fluid called cytosol. The entire contents of the cell—organelles plus cytosol—is referred to as cytoplasm.

Prokaryotic Cells

Monerans include bacteria and cyanobacteria (once known as blue-green algae). This article specifically refers to the features of bacteria. Bacteria have a cell membrane and a cell wall. Though they have genetic material, it’s not enclosed in a nucleus. They also contain fluid and the chemicals (including enzymes) needed to maintain life. As in eukaryotic cells, the cytosol moves and circulates the chemicals.

Enzymes are vital substances that control the reactions involving chemicals called substrates. In the past, bacteria were sometimes referred to as a "bag of enzymes" and were thought to contain very few specialized structures. This model of bacterial structure is now inaccurate because compartments with specific functions have been discovered in the organisms. The number of known compartments is increasing as more research is performed.

Organelles in Eukaryotic Cells

A brief overview of some major organelles in eukaryotic cells and their functions is given in the three sections below. Bacteria can perform similar jobs, but they may perform them in different ways from eukaryotes and with different structures or materials. Although bacteria lack some of the eukaryotic cell's structures, they have some unique ones of their own. I mention related bacterial structures in my description of the eukaryotic cell's organelles.

Some people restrict the definition of "organelle' to internal structures that are surrounded by membrane. Bacteria do contain these structures, as I describe below. The microbes appear to make use of pockets that were formed from their cell membrane instead of creating new membranes, however.

An animal cell doesn't have a cell wall or chloroplasts. Many animal cells don't have a flagellum, either.

An animal cell doesn't have a cell wall or chloroplasts. Many animal cells don't have a flagellum, either.

Four Eukaryotic Organelles or Structures


The nucleus contains the chromosomes of the cell. Human chromosomes are made of DNA (deoxyribonucleic acid) and protein. The DNA contains the genetic code, which depends on the order of chemicals called nitrogenous bases in the molecule. Humans have twenty-three pairs of chromosomes. The nucleus is surrounded by a double membrane.

A bacterium has no nucleus, but it has DNA. Most bacteria have a long chromosome that forms a looped structure in the cytosol. Linear chromosomes have been found in some types of bacteria, however. A bacterium may have one or more small, circular pieces of DNA that are separate from the main chromosome. These are known as plasmids.


Ribosomes are the site of protein synthesis in a cell. They are made of protein and ribosomal RNA, or rRNA. RNA stands for ribonucleic acid. The DNA code in the nucleus is copied by messenger RNA, or mRNA. The mRNA then travels through the pores in the nuclear membrane to the ribosomes. The code contains instructions for making specific proteins.

The ribosomes aren't surrounded by a membrane. This means that some people call them an organelle and others don't. Bacteria have ribosomes as well, though they aren't completely identical to the ones in eukaryotic cells.

Endoplasmic Reticulum

The endoplasmic reticulum or ER is a collection of membranous tubes that extend through the cell. It's classified as rough or smooth. Rough ER has ribosomes on its surface. (Ribosomes are also found unattached to ER.) The endoplasmic reticulum is involved in the manufacture, modification, and transport of substances. Rough ER focuses on proteins and smooth ER on lipids.

Golgi Body, Apparatus, or Complex

The Golgi body can be thought of as a packaging and secretion plant. It's composed of membranous sacs. It accepts substances from the endoplasmic reticulum and changes them into their final form. It then secretes them for use within the cell or outside it. At the moment, highly membranous structures such as the ER and Golgi body haven't been found in bacteria.


The mitochondria produce most of the energy needed by a eukaryotic cell. A cell may contain hundreds or even thousands of these organelles. Each mitochondrion contains a double membrane. The inner one forms folds called cristae. The organelle contains enzymes that break down complex molecules and release energy. The ultimate source of the energy is glucose molecules.

Energy released by mitochondrial reactions is stored in chemical bonds in ATP (adenosine triphosphate) molecules. These molecules can be quickly broken down to release energy when the cell needs it.

Anammoxosomes have been found in some bacteria. They have a different structure from mitochondria and perform different chemical reactions, but as in mitochondria, energy is released from complex molecules inside them and stored in ATP.

Chloroplasts, Vacuoles, and Vesicles


Chloroplasts carry out photosynthesis. In this process, plants turn light energy into chemical energy, which is stored in the chemical bonds in molecules. A chloroplast contains stacks of flattened sacs known as thylakoids, Each stack of thylakoids is called a granum. The fluid outside the grana is called the stroma.

Chlorophyll is located in the membrane of the thylakoids. The substance traps light energy. Other processes involved in photosynthesis occur in the stroma. Some bacteria contain chlorosomes that contain the bacterial version of chlorophyll and enable them to perform photosynthesis.

Vacuoles and Vesicles

Eukaryotic cells contain vacuoles and vesicles. Vacuoles are larger. These membranous sacs store substances and are the site of certain chemical reactions. Bacteria have gas vacuoles that have a wall made of protein molecules instead of membrane. They store air. They are found in aquatic bacteria and enable the microbes to adjust their buoyancy in the water.

Structures in Prokaryotic Cells

Bacteria are unicellular organisms and are generally smaller than animal and plant cells. Without the required equipment and techniques, it has been hard for biologists to explore their interior structure. The apparently unspecialized structure of bacteria meant they were regarded as lesser organisms in terms of evolution for a long time. Though bacteria could obviously perform the activities needed to keep themselves alive, it was thought that for the most part these activities happened in undifferentiated cytoplasm inside the cell instead of in specialized compartments.

The new equipment and techniques that are available today are showing that bacteria are different from eukaryotic cells, but they are not as different as we once thought. They have some interesting organelle-like structures that are reminiscent of eukaryotic organelles and other structures that seem to be unique. Some bacteria have structures that other ones lack.

A representation of the cell membrane of a eukaryotic cell

A representation of the cell membrane of a eukaryotic cell

Bacterial Cell Membrane and Wall

The Cell Membrane

Bacterial cells are covered by a cell membrane, The structure of the membrane is very similar but not identical in prokaryotes and eukaryotes. As in eukaryotic cells, the bacterial cell membrane is made of a double layer of phospholipids and contains scattered protein molecules.

The Cell Wall

Like plants, bacteria have a cell wall as well as a cell membrane. The wall is made of peptidoglycan instead of cellulose. In Gram-positive bacteria, the cell membrane is covered with a thick cell wall. In Gram-negative bacteria, the cell wall is thin and is covered by a second cell membrane.

The terms "Gram positive" and "Gram negative" refer to the different colors that appear after a special staining technique is used on the two types of cells. The technique was created by Hans Christian Gram, which is why the word "Gram" is often capitailzed.

Bacterial Microcompartments or BMCs

Structures involved in the metabolic processes that occur in bacteria are sometimes called bacterial microcompartments or BMCs. Microcompartments are useful because they concentrate the enzymes needed in a particular reaction or reactions. They also isolate any harmful chemicals made during a reaction so that they don't harm a cell.

The fate of any harmful chemicals made in microcompartments is still being investigated. Some appear to be transient—that is, they are made in one step of the overall reaction and then used up in another. The passage of materials into and out of the compartment is also being investigated. The protein shell or lipid envelope surrounding a bacterial microcompartment may not be a complete barrier. It often allows the passage of materials under specific conditions.

The names of the first four bacterial compartments described below end in "some," which is a suffix meaning body. The suffix rhymes with the word home. The similar names are related to the fact that the structures were once—and sometimes still are—known as inclusion bodies or inclusions.

By limiting diffusion to a confined space, concentrations of enzymes and substrates can be optimized to promote specific enzymatic reactions. In turn, sequestration of activities within compartments protects the cell from toxic byproducts of such reactions.

— Elias Cornejo, Nicole Abreu, and Arash Komeili, US National Library of Medicine

Carboxysomes in a bacterium named Halothiobacillus neopolitanus (A: within the cell and B: isolated from the cell)

Carboxysomes in a bacterium named Halothiobacillus neopolitanus (A: within the cell and B: isolated from the cell)

Carboxysomes and Anabolism

Carboxysomes were first discovered in cyanobacteria and then in bacteria. They are surrounded by a protein shell in a polyhedral or roughly icosahedral shape and contain enzymes. The illustration on the right below is a model based on discoveries made so far and is not intended to be completely biologically accurate. Some researchers have pointed out that protein shell of a carboxysome looks similar to the outer covering of some viruses.

Carboxysomes are involved in anabolism, or the process of making complex substances from simpler ones. They make compounds from carbon in a process called carbon fixation. The bacterial cell absorbs carbon dioxide from the environment and converts it into a usable form. Each tile of the protein shell of a carboxysome appears to have an opening to allow for the selective passages of materials.

Carboxysomes (on the left) and a representation of their structure (on the right)

Carboxysomes (on the left) and a representation of their structure (on the right)

Anammoxosomes and Catabolism

Anammoxosomes are compartments in which catabolism occurs. Catabolism is the breakdown of complex molecules into simpler ones and the release of energy during the process. Though they have a different structure and different reactions, both anammoxosomes and mitochondria in eukaryotic cells produce energy for the cell.

Anammoxosomes break down ammonia to obtain energy. The term "anammox" stands for anaerobic ammonia oxidation. An anaerobic process occurs without the presence of oxygen. As in mitochondria, the energy produced in anammoxosomes is stored in ATP molecules. Unlike carboxysomes, anammoxosomes are surrounded by a lipid bilayer membrane.

Magnetite magnetosomes in a bacterium

Magnetite magnetosomes in a bacterium

The open access image above appears in Pósfai M, Lefèvre CT, Trubitsyn D, Bazylinski DA, Frankel RB - Frontiers in Microbiology (2013)


Some bacteria contain magnetosomes. A magnetosome contains a magnetite (iron oxide) or a greigite (iron sulfide) crystal. Magnetite and greigite are magnetic minerals. Each crystal is enclosed by a lipid membrane produced from an invagination of the bacterium's cell membrane. The enclosed crystals are arranged in a chain that acts as a magnet.

The magnetic crystals are produced inside the bacteria. Fe(lll) ions and other required substances move into a magnetosome and contribute to the growing particle. The process is intriguing for researchers not only because the bacteria can make magnetic particles but also because they are able to control the size and shape of the particles.

Bacteria that contain magnetosomes are said to be magnetotactic. They live in aquatic environments or in the sediments at the bottom of a body of water. Magnetosomes enable the bacteria to orient themselves in a magnetic field in their environment, which is believed to benefit them in some way. The benefit may be related to a suitable concentration of oxygen or the presence of suitable food.

A cartoon representation of a chlorosome

A cartoon representation of a chlorosome

Chlorosome illustration from "Chlorophylls, Symmetry, Chirality, and Photosynthesis" by Mathias O. Senge, Aoife A. Ryan, Kristie A. Letchford, Stuart A. MacGowan, and Tamara Mielke, via MDPI Open Access

Chlorosomes for Photosynthesis

Like plants, some bacteria perform photosynthesis. The process occurs in structures called chlorosomes and their attached reaction center. It involves the capture of light energy and its conversion into chemical energy. Researchers who are exploring the chlorosome say that it's an impressive light-harvesting structure.

The pigment that absorbs the light energy is called bacteriochlorophyll. It exists in different varieties. The energy that it absorbs is passed to other substances. The specific reactions that occur during bacterial photosynthesis are still being studied.

The rod model and the lamellar model for the internal structure of the chlorosome are depicted in the illustration above. Some evidence suggests that the bacteriochlorophyll is arranged in a group of rod elements. Other evidence suggests that it's arranged in parallel sheets, or lamellae. It's possible that the arrangement is different in different groups of bacteria.

The chlorosome has a wall made of a single layer of lipid molecules. As the illustration shows, the cell membrane is made of a lipid bilayer. The chlorosome is attached to the reaction center in the cell membrane by a protein base plate and FMO protein. The FMO protein isn't present in all types of photosynthetic bacteria. In addition, the chlorosome isn't necessarily oblong in shape. It's often ellipsoidal, conical, or irregularly-shaped.

The PDU Microcompartment

Bacteria contain other interesting compartments/organelles. One of these can be found in some strains of Escherichia coli (or E. coli). The bacterium uses the compartment to break down a molecule called 1,2 propanediol in order to obtain carbon (a vital chemical) and perhaps energy.

The picture on the left above shows an E.coli cell expressing PDU (propanediol utilization) genes. "Expressing" means the genes are active and triggering protein production. The cell is making PDU microcompartments, which have walls of protein. They are visible as dark shapes in the bacterium and in a purified form in the right picture.

The microcompartment encapsulates the enzymes required for the breakdown of 1,2 propanediol. The compartment also isolates those chemicals made during the breakdown process that could be harmful for the cell.

Researchers have also found PDU microcompartments in a bacterium named Listeria monocytogenes. This microbe can cause foodborne illness. It sometimes causes serious symptoms and even death. Understanding its biology is therefore very important. The study of its microcompartments may lead to better ways to prevent or treat infections by the living bacterium or to prevent harm from the bacterium's chemicals.

Listeria monocytogenes has multiple flagella on its body..

Listeria monocytogenes has multiple flagella on its body..

Increasing Our Knowledge of Bacteria

Many questions surround the bacterial structures that have been discovered. For example, were some of them forerunners to eukaryotic organelles or did they evolve along their own line? The questions become more tantalizing as more organelle-like structures are found.

Another interesting point is the wide variety of organelles that are present in bacteria. Illustrators can create a picture that represents all animal cells or all plant cells because each group has organelles and structures in common. Though some animal and plant cells are specialized and have differences from other ones, their basic structure is the same. This doesn't seem to be true for bacteria because of the apparent variation in their structure.

Bacterial organelles are useful for them and could be useful for us if we make use of the microbes in some way. Understanding how certain organelles work may enable us to create antibiotics that attack harmful bacteria more effectively than current medications. That would be an excellent development because antibiotic resistance is increasing in bacteria. In a few cases, however, the presence of the bacterial organelles might be harmful for us. The quote below gives one example.

The deadly pathogen that causes tuberculosis, for example, scavenges fatty molecules from our own bodies and stores them as energy reserves in organelles, helping the pathogen to persist for years in our lungs, compromising treatment and making the emergence of drug resistance likely

— Chris Greening, Monash University

Organelles, Compartments, or Inclusions

At the moment, some researchers appear to have no problem referring to certain bacterial structures as organelles and do it frequently. Others use the word compartment or microcompartment instead of or sometimes alternating with the word organelle. The term "organelle analog" is also used. Some documents that are older but still available use the terms inclusion bodies or inclusions for the structures in bacteria.

The terminology can be confusing. In addition, it may suggest to casual readers that one structure is less important or less complex than another based on its name. Whatever terminology is used, the structures and their nature are fascinating and potentially important for us. I'm looking forward to seeing what else scientists discover about the structures inside bacteria.


This content is accurate and true to the best of the author’s knowledge and is not meant to substitute for formal and individualized advice from a qualified professional.

© 2020 Linda Crampton


Linda Crampton (author) from British Columbia, Canada on August 18, 2020:

Thank you, Jeremiah. I appreciate your visit.

Jeremiah on August 18, 2020:

Good work! The article is detailed.

Linda Crampton (author) from British Columbia, Canada on August 18, 2020:

Thank you very much, Umesh.

Umesh Chandra Bhatt from Kharghar, Navi Mumbai, India on August 18, 2020:

It is a great resource to refer anytime. Well explained.

Linda Crampton (author) from British Columbia, Canada on August 12, 2020:

Hi, Denise. I think there's a high probability that the discoveries will help us fight harmful bacteria. I'm not so sure about viruses. It's possible that the studies will be indirectly useful in increasing our understanding of viruses, though.

Blessings to you as well, Denise.

Denise McGill from Fresno CA on August 12, 2020:

I feel like a biology student. These studies will help us better understand and combat bacterial infections and maybe even fight viruses, yes? I think we have come a long way since I was in school last. So many new things to study and new words to learn.



Linda Crampton (author) from British Columbia, Canada on August 12, 2020:

Thank you for the visit and the comment, Nell.

Nell Rose from England on August 12, 2020:

Really interesting. I could have done with studying your articles back in college. Really useful for schools etc.

Linda Crampton (author) from British Columbia, Canada on August 12, 2020:

Thank you very much, Moondot. I appreciate your kindness.

EK Jadoon from Abbottabad Pakistan on August 12, 2020:

Alicia, this is a very informative article. I think your articles are the best source of scientific knowledge for students. You reminded me of my college days. Thank you for sharing your knowledge.

Linda Crampton (author) from British Columbia, Canada on August 11, 2020:

Hi, Lisa. I learned about bacteria in school, too. I think it's very interesting how much more has been discovered about them since then. Thank you for the comment.

Liza from USA on August 11, 2020:

A very detailed and informative article. I remember when I was in a biology class in high school learning about bacteria and how I have to answer the question in the exam. Reading the article brings back the memory, and I certainly learned a lot from it! Thanks for sharing, Linda.

Linda Crampton (author) from British Columbia, Canada on August 11, 2020:

Hi, Liz. The discoveries are amazing. Researchers are still exploring bacterial (and other) cells, so some new observations may be reported soon. Thanks for the comments about the article.

Liz Westwood from UK on August 11, 2020:

I am amazed at how much has been discovered not only about these cells, but about the compartments of the cells. Your article gives a detailed description of the compartments in a very structured and interesting manner. I especially appreciate the detailed diagrams that you have included to illustrate the points you make.

Linda Crampton (author) from British Columbia, Canada on August 11, 2020:

That's a good way to describe bacteria and their structure! Thanks for the visit, Mary.

Mary Norton from Ontario, Canada on August 11, 2020:

I can't believe how complicated bacterial structures are. It is mind-boggling how they behave and affect us.

Linda Crampton (author) from British Columbia, Canada on August 11, 2020:

Thank you for the visit, Ankita. I appreciate your comment.

Linda Crampton (author) from British Columbia, Canada on August 11, 2020:

Thank you very much, Flourish. I'm looking forward to seeing what else researchers discover about the structure of bacteria.

Linda Crampton (author) from British Columbia, Canada on August 11, 2020:

Hi, Devika. I think it's a very interesting topic. Thank you for the comment.

Ankita B on August 11, 2020:

This was greatly informative. You have detailed out so well. A wonderful read indeed.

FlourishAnyway from USA on August 11, 2020:

A detailed and thorough review of the topic. It definitely takes me back to biology class (and updates me as well). You do such a fine job with your research and plain-language explanations.

Devika Primić from Dubrovnik, Croatia on August 11, 2020:

Hi Linda this is a well-researched hub. Your time to create this hub shows me that you have a great interest on this topic. Informative and most useful indeed!

Linda Crampton (author) from British Columbia, Canada on August 10, 2020:

I agree, Heidi. The microscopic world is complex and fascinating. Thanks for the kind comment.

Heidi Thorne from Chicago Area on August 10, 2020:

One thing's for sure. The microscopic world is way bigger and more complex than we can imagine. I read this stuff and just marvel at how this all comes together to make the world as we know it.

Thanks, as always, for sharing your seemingly bottomless depth of knowledge on biology!

Linda Crampton (author) from British Columbia, Canada on August 10, 2020:

Thanks, Nithya. I think that biology is a very interesting topic.

Nithya Venkat from Dubai on August 10, 2020:

Interesting and informative article, detailed, and well-researched. This article brought back memories of my college days. I got to know a lot more through your article, thank you for sharing.

Linda Crampton (author) from British Columbia, Canada on August 10, 2020:

Thank you very much for the comment, Pamela. I appreciate your visit.

Pamela Oglesby from Sunny Florida on August 10, 2020:

This is a fascinating, well-written and very detailed article I need to read this article more than once. I do have more understanding now thanks to the way you explained everything. Thank you, Linda.

Linda Crampton (author) from British Columbia, Canada on August 10, 2020:

I appreciate your comment, Peggy. I find the topic very interesting. The research could be helpful for us.

Linda Crampton (author) from British Columbia, Canada on August 10, 2020:

Thanks for the kind and interesting comment, Bill. I hope you have a great week.

Linda Crampton (author) from British Columbia, Canada on August 10, 2020:

I appreciate your comment, Maren. I think it would be interesting to coexist with some of the dinosaurs!

Linda Crampton (author) from British Columbia, Canada on August 10, 2020:

Thanks, Eric. The conditions in the cell stimulate the mitochondria.

Linda Crampton (author) from British Columbia, Canada on August 10, 2020:

Thank you, Emmanuel.

Peggy Woods from Houston, Texas on August 10, 2020:

Continuing research into microbiology can be a cause to celebrate if scientists can figure out how to put this knowledge to good use when it comes to fighting disease. You have surely put a lot of work into creating this informative article.

Bill Holland from Olympia, WA on August 10, 2020:

Sign me up for your science class. Perfectly organized article, like your mind, I suspect.

Have a brilliant week, my friend!

Maren Elizabeth Morgan from Pennsylvania on August 10, 2020:

Wow - much more interesting than the "2 Kingdom and a few outliers" system I was taught back when dinosaurs roamed the earth (just kidding about the dinosaurs.) Thanks for the plain language explanations.

Eric Dierker from Spring Valley, CA. U.S.A. on August 10, 2020:

Wow this is really interesting. It will take coming back to finish up.

I am interested in mitochondria. Is there something that stimulates them?

Emmanuel Ekwunife from Abuja on August 10, 2020:


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