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4.1: Unique Characteristics of Prokaryotic Cells

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    Learning Objectives

    • Explain the distinguishing characteristics of prokaryotic cells
    • Describe common cell morphologies and cellular arrangements typical of prokaryotic cells and explain how cells maintain their morphology
    • Describe internal and external structures of prokaryotic cells in terms of their physical structure, chemical structure, and function
    • Compare the distinguishing characteristics of bacterial and archaeal cells

    Cell theory states that the cell is the fundamental unit of life. However, cells vary significantly in size, shape, structure, and function. The two largest categories of cells—prokaryotic cells and eukaryotic cells—are defined by major differences in several cell structures. Prokaryotic cells lack a nucleus surrounded by a complex nuclear membrane and generally have a single, circular chromosome located in a nucleoid. Prokaryotic microorganisms are classified within the domains Archaea and Bacteria.

    The structures inside a cell are analogous to the organs inside a human body, with unique structures suited to specific functions. Some of the structures found in prokaryotic cells are similar to those found in some eukaryotic cells; others are unique to prokaryotes. Although there are some exceptions, eukaryotic cells tend to be larger than prokaryotic cells. The comparatively larger size of eukaryotic cells dictates the need to compartmentalize various chemical processes within different areas of the cell, using complex membrane-bound organelles. In contrast, prokaryotic cells generally lack membrane-bound organelles; however, they often contain inclusions that compartmentalize their cytoplasm. Figure \(\PageIndex{1}\) illustrates structures typically associated with prokaryotic cells. These structures are described in more detail in the next section.

    A diagram of a rod-shaped prokaryotic cell. The thick outer layer is called the capsule, inside of that is a thinner cell wall and inside of that is an even thinner plasma membrane. Inside of the plasma membrane is a fluid called the cytoplasm, little dots called ribosomes, small spheres called inclusions, a small loop of DNA called a plasmid, and a large folded loo of DNA called the nucleoid. Long projections start at the plasma membrane and extend out of the capsule; these are called flagella (singular: flagellum). A shorter projection is labeled pilus. And many very short projections are labeled fimbriae.
    Figure \(\PageIndex{1}\): A typical prokaryotic cell contains a cell membrane, chromosomal DNA that is concentrated in a nucleoid, ribosomes, and a cell wall. Some prokaryotic cells may also possess flagella, pili, fimbriae, and capsules.

    Common Cell Morphologies and Arrangements

    Individual cells of a particular prokaryotic organism are typically similar in shape, or cell morphology. Although thousands of prokaryotic organisms have been identified, only a handful of cell morphologies are commonly seen microscopically. Recall that cells are generally coccus (round/spherical), bacillus (rod/elongated), or spiral in shape (rigid spirillia or flexible spirochetes). However vibrio (curved rods) or coccobacillus (short rods) are also possible. In addition to cellular shape, prokaryotic cells of the same species may group together in certain distinctive arrangements depending on the plane of cell division. Some common arrangements are singles, diplo- (pairs), tetrads (set of four in a square), strepto- (chains) or staphylo- (clusters). (Check out Chapter 3, section 2 for reminders).

    Clinical Focus - part 1

    Marsha, a 20-year-old university student, recently returned to the United States from a trip to Nigeria, where she had interned as a medical assistant for an organization working to improve access to laboratory services for tuberculosis testing. When she returned, Marsha began to feel fatigue, which she initially attributed to jet lag. However, the fatigue persisted, and Marsha soon began to experience other bothersome symptoms, such as occasional coughing, night sweats, loss of appetite, and a low-grade fever of 37.4 °C (99.3 °F).

    Marsha expected her symptoms would subside in a few days, but instead, they gradually became more severe. About two weeks after returning home, she coughed up some sputum and noticed that it contained blood and small whitish clumps resembling cottage cheese. Her fever spiked to 38.2 °C (100.8 °F), and she began feeling sharp pains in her chest when breathing deeply. Concerned that she seemed to be getting worse, Marsha scheduled an appointment with her physician.

    Exercise \(\PageIndex{1}\)

    Could Marsha’s symptoms be related to her overseas travel, even several weeks after returning home?

    The Cellular Envelope: Between Outside and In

    Cell Wall

    In most prokaryotic cells, morphology is maintained by the cell wall in combination with cytoskeletal elements. The cell wall is a structure found in most prokaryotes and some eukaryotes; it envelopes the cell membrane, protecting the cell from changes in osmotic pressure. Osmotic pressure occurs because of differences in the concentration of solutes on opposing sides of a selectively or semi-permeable membrane. Water is able to pass through a membrane, but solutes (dissolved molecules like salts, sugars, and other compounds) cannot. When the concentration of solutes is greater on one side of the membrane, water diffuses across the membrane from the side with the lower concentration (more water) to the side with the higher concentration (less water) until the concentrations on both sides become equal. This diffusion of water is called osmosis, and it can cause extreme osmotic pressure on a cell when its external environment changes. This will be discussed further in chapter 8. When present, there are notable similarities and differences among the cell walls of archaea, bacteria, and eukaryotes.

    The major component of bacterial cell walls is called peptidoglycan (or murein); it is only found in bacteria. Structurally, peptidoglycan resembles a layer of meshwork or fabric (Figure \(\PageIndex{2}\)). Each layer is composed of long chains of alternating molecules of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). The structure of the long chains has significant two-dimensional tensile strength due to the formation of peptide bridges that connect NAG and NAM within each peptidoglycan layer. In gram-negative bacteria, tetrapeptide chains extending from each NAM unit are directly cross-linked, whereas in gram-positive bacteria, these tetrapeptide chains are linked by pentaglycine cross-bridges. Peptidoglycan subunits are made inside of the bacterial cell and then exported and assembled in layers, giving the cell its shape.

    Since peptidoglycan is unique to bacteria, many antibiotic drugs are designed to interfere with peptidoglycan synthesis, weakening the cell wall and making bacterial cells more susceptible to the effects of osmotic pressure. In addition, certain cells of the human immune system are able “recognize” bacterial pathogens by detecting peptidoglycan on the surface of a bacterial cell; these cells then engulf and destroy the bacterial cell, using enzymes such as lysozyme, which breaks down and digests the peptidoglycan in their cell walls.

    The diagram of the gram-positive cell wall shows alternative NAG (N-acetylglucosamine) and NAM (N-acetylmuramic acid) in a chain; these are shown as alternative red and blue spheres. The chains or red and blue spheres are connected to other chains with smaller yellow spheres in a chain labeled pentapeptide and smaller green spheres labeled tetrapeptide. Each NAG in the chain is connected to the NAG in the chains next to it by both a tetrapeptide connected to a pentapeptide. The diagram of the gram-negative cell wall has the same NAG and NAM chains. But this time they are linked with a kirect line to the chains next to them.
    Figure \(\PageIndex{2}\): Peptidoglycan is composed of polymers of alternating NAM and NAG subunits, which are cross-linked by peptide bridges linking NAM subunits from various glycan chains. This provides the cell wall with tensile strength in two dimensions.

    The Gram staining protocol is used to differentiate two most common types of cell wall structures (Figure \(\PageIndex{3}\)). Gram-positive cells have a cell wall consisting of many layers of peptidoglycan totaling 30–100 nm in thickness. These peptidoglycan layers are commonly embedded with teichoic acids (TAs), carbohydrate chains that extend through and beyond the peptidoglycan layer.4 TA is thought to stabilize peptidoglycan by increasing its rigidity. TA also plays a role in the ability of pathogenic gram-positive bacteria such as Streptococcus to bind to certain proteins on the surface of host cells, enhancing their ability to cause infection. In addition to peptidoglycan and TAs, bacteria of the family Mycobacteriaceae have an external layer of waxy mycolic acids in their cell wall; these bacteria are referred to as acid-fast, since acid-fast stains must be used to penetrate the mycolic acid layer for purposes of microscopy (Figure \(\PageIndex{4}\)).

    The gram-positive bacterial cell wall diagram shows a plasma membrane on top of the cytoplasm. The cell wall is shown as a thick layer of peptidoglycans connected to the plasma membrane by techoic acids. The gram-negative cell wall also has a plasma membrane on top of the cytoplasm. On top of the plasma membrane is a thin periplasmic space. On top of that is a thin peptidoglycan cell wall. On top of that is an outer membrane that contains murein lipoproteins that connect the outer membrane to the peptidoglycan cell wall. Lipid A, O antigens, and lipopolysaccharides sit on top of the outer membrane. Proins are tubes that connect the outside of the outer membrane with the region of the peptidoglycan cell wall.
    Figure \(\PageIndex{3}\): Bacteria contain two common cell wall structural types. Gram-positive cell walls are structurally simple, containing a thick layer of peptidoglycan with embedded teichoic acid external to the plasma membrane.5 Gram-negative cell walls are structurally more complex, containing three layers: the inner membrane, a thin layer of peptidoglycan, and an outer membrane containing lipopolysaccharide. (credit: modification of work by “Franciscosp2”/Wikimedia Commons)
    A) A diagram of gram-positive acid-fast bacteria. The plasma membrane is shown on top of the cytoplasm and a thick layer of peptidoglycan makes up the cell wall outside the plasma membrane. Teichoic acids connect the peptidoglycans to the plasma membrane. On top of the peptidoglycans are mycolic acids, lipomannan and arabinoglycans. B) A micrograph of red cells labeled acid fast bacteria.
    Figure \(\PageIndex{4}\): (a) Some gram-positive bacteria, including members of the Mycobacteriaceae, produce waxy mycolic acids found exterior to their structurally-distinct peptidoglycan. (b) The acid-fast staining protocol detects the presence of cell walls that are rich in mycolic acid. Acid-fast cells are stained red by carbolfuschin. (credit a: modification of work by “Franciscosp2”/Wikimedia Commons; credit b: modification of work by Centers for Disease Control and Prevention)

    Gram-negative cells have a much thinner layer of peptidoglycan (no more than about 4 nm thick6) than gram-positive cells, and the overall structure of their cell envelope is more complex. In gram-negative cells, a gel-like matrix occupies the periplasmic space between the cell wall and the plasma membrane, and there is a second lipid bilayer called the outer membrane, which is external to the peptidoglycan layer (Figure \(\PageIndex{3}\)). This outer membrane is attached to the peptidoglycan by murein lipoprotein. The outer leaflet of the outer membrane contains the molecule lipopolysaccharide (LPS), which functions as an endotoxin in infections involving gram-negative bacteria, contributing to symptoms such as fever, hemorrhaging, and septic shock. Each LPS molecule is composed of Lipid A, a core polysaccharide, and an O side chain that is composed of sugar-like molecules that comprise the external face of the LPS (Figure \(\PageIndex{5}\)). The composition of the O side chain varies between different species and strains of bacteria. Parts of the O side chain called antigens can be detected using serological or immunological tests to identify specific pathogenic strains like Escherichia coli O157:H7, a deadly strain of bacteria that causes bloody diarrhea and kidney failure.

    A diagram of the outer membrane of gram-negative bacteria. At the top of the diagram is a long chain of structures labeled O antigen. Below that is a shorter chain labeled core. Below that are two spheres labeled lipid A. Attached to the lipid A are squiggly tails labeled fatty acids.
    Figure \(\PageIndex{5}\): The outer membrane of a gram-negative bacterial cell contains lipopolysaccharide (LPS), a toxin composed of Lipid A embedded in the outer membrane, a core polysaccharide, and the O side chain.

    Archaeal cell wall structure differs from that of bacteria in several significant ways. First, archaeal cell walls do not contain peptidoglycan; instead, they contain a similar polymer called pseudopeptidoglycan (pseudomurein) in which NAM is replaced with a different subunit. Other archaea may have a layer of glycoproteins or polysaccharides that serves as the cell wall instead of pseudopeptidoglycan. Last, as is the case with some bacterial species, there are a few archaea that appear to lack cell walls entirely.

    Plasma Membrane

    The plasma membrane structure of most bacterial and eukaryotic cell types is a bilayer composed mainly of phospholipids formed with ester linkages and proteins. Proteins on the cell’s surface are important for a variety of functions. (review chapter 3 section 3 for more detail, and this will be described more in chapter 8)

    Photosynthetic Membrane Structures

    Some prokaryotic cells, namely cyanobacteria and photosynthetic bacteria, have membrane structures that enable them to perform photosynthesis. These structures consist of an infolding of the plasma membrane that encloses photosynthetic pigments such as green chlorophylls and bacteriochlorophylls. In cyanobacteria, these membrane structures are called thylakoids; in photosynthetic bacteria, they are called chromatophores, lamellae, or chlorosomes. These membranes are still contiguous with the plasma membrane.

    Exercise \(\PageIndex{1}\)

    1. Explain the difference between cell morphology and arrangement.
    2. What advantages do cell walls provide prokaryotic cells?
    3. What parts are included in the cellular envelope?

    On the Inside

    The Nucleoid

    All cellular life has a DNA genome organized into one or more chromosomes. Prokaryotic chromosomes are typically circular, haploid (unpaired), and not bound by a complex nuclear membrane. Because the chromosome contains only one copy of each gene, prokaryotes are haploid. Prokaryotic DNA and DNA-associated proteins are concentrated within the nucleoid region of the cell (Figure \(\PageIndex{6}\)). In general, prokaryotic DNA interacts with nucleoid-associated proteins (NAPs) that assist in the organization and packaging of the chromosome, as it would be many times longer than the cell. In bacteria, NAPs function similar to histones, which are the DNA-organizing proteins found in eukaryotic cells. In archaea, the nucleoid is organized by either NAPs or histone-like DNA organizing proteins.

    A micrograph of an oval cell with a lighter region in the center of the cell. The lighter region takes up approximately one third of the volume of the cell and is labeled nucleoid.
    Figure \(\PageIndex{6}\): The nucleoid region (the area enclosed by the green dashed line) is a condensed area of DNA found within prokaryotic cells. Because of the density of the area, it does not readily stain and appears lighter in color when viewed with a transmission electron microscope.


    Prokaryotic cells may also contain extrachromosomal DNA, or DNA that is not part of the chromosome. This extrachromosomal DNA is found in plasmids, which are small, circular, double-stranded DNA molecules. Cells that have plasmids often have hundreds of them within a single cell. Plasmids are more commonly found in bacteria; however, plasmids have been found in archaea and eukaryotic organisms. Plasmids often carry genes that confer advantageous traits such as antibiotic resistance; thus, they are important to the survival of the organism.

    Lethal Plasmids

    Maria, a 20-year-old anthropology student from Texas, recently became ill in the African nation of Botswana, where she was conducting research as part of a study-abroad program. Maria’s research was focused on traditional African methods of tanning hides for the production of leather. Over a period of three weeks, she visited a tannery daily for several hours to observe and participate in the tanning process. One day, after returning from the tannery, Maria developed a fever, chills, and a headache, along with chest pain, muscle aches, nausea, and other flu-like symptoms. Initially, she was not concerned, but when her fever spiked and she began to cough up blood, her African host family became alarmed and rushed her to the hospital, where her condition continued to worsen.

    After learning about her recent work at the tannery, the physician suspected that Maria had been exposed to anthrax. He ordered a chest X-ray, a blood sample, and a spinal tap, and immediately started her on a course of intravenous penicillin. Unfortunately, lab tests confirmed the physician’s presumptive diagnosis. Maria’s chest X-ray exhibited pleural effusion, the accumulation of fluid in the space between the pleural membranes, and a Gram stain of her blood revealed the presence of gram-positive, rod-shaped bacteria in short chains, consistent with Bacillus anthracis. Blood and bacteria were also shown to be present in her cerebrospinal fluid, indicating that the infection had progressed to meningitis. Despite supportive treatment and aggressive antibiotic therapy, Maria slipped into an unresponsive state and died three days later.

    Anthrax is a disease caused by the introduction of endospores from the gram-positive bacterium B. anthracis into the body. Once infected, patients typically develop meningitis, often with fatal results. In Maria’s case, she inhaled the endospores while handling the hides of animals that had been infected.

    The genome of B. anthracis illustrates how small structural differences can lead to major differences in virulence. In 2003, the genomes of B. anthracis and Bacillus cereus, a similar but less pathogenic bacterium of the same genus, were sequenced and compared.4 Researchers discovered that the 16S rRNA gene sequences of these bacteria are more than 99% identical, meaning that they are actually members of the same species despite their traditional classification as separate species. Although their chromosomal sequences also revealed a great deal of similarity, several virulence factors of B. anthracis were found to be encoded on two large plasmids not found in B. cereus. The plasmid pX01 encodes a three-part toxin that suppresses the host immune system, whereas the plasmid pX02 encodes a capsular polysaccharide that further protects the bacterium from the host immune system (Figure \(\PageIndex{7}\)). Since B. cereus lacks these plasmids, it does not produce these virulence factors, and although it is still pathogenic, it is typically associated with mild cases of diarrhea from which the body can quickly recover. Unfortunately for Maria, the presence of these toxin-encoding plasmids in B. anthracis gives it its lethal virulence.

    A diagram of Bacillus cereus showing an oval cell with a folded loop of a chromosome. The second diagram of this cell has two small loops, one labeled px01 encoding toxin and the other labeled px02 encoding toxin.
    Figure \(\PageIndex{7}\): Genome sequencing of Bacillus anthracis and its close relative B. cereus reveals that the pathogenicity of B. anthracis is due to the maintenance of two plasmids, pX01 and pX02, which encode virulence factors.

    Exercise \(\PageIndex{2}\)

    What do you think would happen to the pathogenicity of B. anthracis if it lost one or both of its plasmids?


    All cellular life synthesizes proteins, and organisms in all three domains of life possess ribosomes, structures responsible protein synthesis. However, ribosomes in each of the three domains are structurally different. Ribosomes, themselves, are constructed from proteins, along with ribosomal RNA (rRNA). Prokaryotic ribosomes are found in the cytoplasm. They are called 70S ribosomes because they have a total size of 70S (Figure \(\PageIndex{8}\)). This is built up from two subunits, a large 50S subunit and a small 30S subunit. The S stands for Svedberg unit, a measure of sedimentation in an ultracentrifuge, which is based on size, shape, and surface qualities of the structure being analyzed. Although they are the same size, bacterial and archaeal ribosomes have different proteins and rRNA molecules, and the archaeal versions are more similar to their eukaryotic counterparts than to those found in bacteria.

    A drawing showing that the complete ribosome is made of a small subunit and a large subunit. The small subunit is about half the size of the large one. The small subunit has a size of 30S, the large subunit has a size of 50S and the complete ribosome (containing both the small and large subunit) has a size of 70S.
    Figure \(\PageIndex{8}\): Prokaryotic ribosomes (70S) are composed of two subunits: the 30S (small subunit) and the 50S (large subunit), each of which are composed of protein and rRNA components.


    As single-celled organisms living in unstable environments, some prokaryotic cells have the ability to store excess nutrients within cytoplasmic areas called inclusions. Storing nutrients in a polymerized form is advantageous because it reduces the buildup of osmotic pressure that occurs as a cell accumulates solutes. Various types of inclusions store glycogen and starches, which contain carbon that cells can access for energy. Volutin granules, also called metachromatic granules because of their staining characteristics, are inclusions that store polymerized inorganic phosphate that can be used in metabolism and assist in the formation of biofilms. Microbes known to contain volutin granules include the archaea Methanosarcina, the bacterium Corynebacterium diphtheriae, and the unicellular eukaryotic alga Chlamydomonas. Sulfur granules, another type of inclusion, are found in sulfur bacteria of the genus Thiobacillus; these granules store elemental sulfur, which the bacteria use for metabolism.

    Occasionally, certain types of inclusions are surrounded by a phospholipid monolayer embedded with protein. Polyhydroxybutyrate (PHB), which can be produced by species of Bacillus and Pseudomonas, is an example of an inclusion that displays this type of monolayer structure. Industrially, PHB has also been used as a source of biodegradable polymers for bioplastics. Several different types of inclusions are shown in Figure \(\PageIndex{9}\).

    Some prokaryotic cells have other types of inclusions that serve purposes other than nutrient storage. For example, some prokaryotic cells produce gas globules, accumulations of small, protein-lined globs of gas. These gas globs allow the prokaryotic cells that synthesize them to alter their buoyancy so that they can adjust their location in the water column. Magnetotactic bacteria, such as Magnetospirillum magnetotacticum, contain magnetosomes, which are inclusions of magnetic iron oxide or iron sulfide surrounded by a lipid layer. These allow cells to align along a magnetic field, aiding their movement (Figure \(\PageIndex{9}\)). Cyanobacteria such as Anabaena cylindrica and bacteria such as Halothiobacillus neapolitanus produce carboxysome inclusions. Carboxysomes are composed of outer shells of thousands of protein subunits. Their interior is filled with ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and carbonic anhydrase. Both of these compounds are used for carbon metabolism. Some prokaryotic cells also possess carboxysomes that sequester functionally related enzymes in one location. These structures are considered proto-organelles because they compartmentalize important compounds or chemical reactions, much like many eukaryotic organelles.

    a) A micrograph showing gray spheres each containing 2-8 smaller white spheres. The gray spheres are approximately 600 nm in diameter B) A micrograph showing thin ribbons of approximately 100 µm length; each ribbon contains many dark spots in a line down the center of the ribbon. C) A micrograph showing a gray sphere of approximately 4 µm diameter with a cluster of smaller white spheres at the bottom of the larger sphere. D) A micrograph showing a larger sphere of approximately 10 µm diameter with many smaller spheres of approximately 1 µm diameter inside of the larger sphere. 3) a micrograph showing a long ribbon over 500 nm in length with small dots in the center. A closeup shows the dots to be a chain of spheres approximately 20 nm in diameter.
    Figure \(\PageIndex{9}\): Prokaryotic cells may have various types of inclusions. (a) A transmission electron micrograph of polyhydroxybutryrate lipid droplets. (b) A light micrograph of volutin granules. (c) A phase-contrast micrograph of sulfur granules. (d) A transmission electron micrograph of magnetosomes. (e) A transmission electron micrograph of gas vacuoles. (credit b, c, d: modification of work by American Society for Microbiology)


    Bacterial cells are generally observed as vegetative cells, but some genera of bacteria have the ability to form endospores, structures that essentially protect the bacterial genome in a dormant state when environmental conditions are unfavorable. Endospores (not to be confused with the reproductive spores formed by fungi) allow some bacterial cells to survive long periods without food or water, as well as exposure to chemicals, extreme temperatures, and even radiation. Table \(\PageIndex{1}\) compares the characteristics of vegetative cells and endospores.

    Table \(\PageIndex{1}\): Characteristics of Vegetative Cells versus Endospores
    Vegetative Cells Endospores
    Sensitive to extreme temperatures and radiation Resistant to extreme temperatures and radiation
    Gram-positive Do not absorb Gram stain, only special endospore stains
    Normal water content and enzymatic activity Dehydrated; no metabolic activity
    Capable of active growth and metabolism Dormant; no growth or metabolic activity

    The process by which vegetative cells transform into endospores is called sporulation, and it generally begins when nutrients become depleted or environmental conditions become otherwise unfavorable (Figure \(\PageIndex{10}\)). The process begins with the formation of a septum in the vegetative bacterial cell. The septum divides the cell asymmetrically, separating a DNA forespore from the mother cell. The forespore, which will form the core of the endospore, is essentially a copy of the cell’s chromosomes, and is separated from the mother cell by a second membrane. A cortex gradually forms around the forespore by laying down layers of calcium and dipicolinic acid between membranes. A protein spore coat then forms around the cortex while the DNA of the mother cell disintegrates. Further maturation of the endospore occurs with the formation of an outermost exosporium. The endospore is released upon disintegration of the mother cell, completing sporulation.

    a) A diagram showing the process of sporulation. Step 1 – the DNA replicates. The image shows a rod shaped cell with 2 loops of DNA; one in the center and one towards the end of the cell. Step 2 – Membranes form around the DNA. The drawing shows lines encircling the loop of DNA at the end of the cell. Step 3 – Forespore forms additional membranes. The lines around the loop of DNA are thickened. Step 4 – Protective cortex forms around the spore. The lines around the loop of DNA are thickened even more. Step 5 – protein coat forma around the cortex. The lines around the loop of DNA are thickened even more and the outer cell lyses. Step 6 – the spore is released. A small spherical structure with DNA inside of many thick layers is shown. B) A micrograph of an endospore shows a dark central core inside a lighter region; these are surrounded by thick layers on the outside. C) a micrograph showing red rods in chains; many of the rods have a green dot in their center.

    Figure \(\PageIndex{10}\): (a) Sporulation begins following asymmetric cell division. The forespore becomes surrounded by a double layer of membrane, a cortex, and a protein spore coat, before being released as a mature endospore upon disintegration of the mother cell. (b) An electron micrograph of a Carboxydothermus hydrogenoformans endospore. (c) These Bacillus spp. cells are undergoing sporulation. The endospores have been visualized using Malachite Green spore stain. (credit b: modification of work by Jonathan Eisen)

    Endospores of certain species have been shown to persist in a dormant state for extended periods of time, up to thousands of years.2 However, when living conditions improve, endospores undergo germination, reentering a vegetative state. After germination, the cell becomes metabolically active again and is able to carry out all of its normal functions, including growth and cell division.

    Not all bacteria have the ability to form endospores; however, there are a number of clinically significant endospore-forming gram-positive bacteria of the genera Bacillus and Clostridium. These include B. anthracis, the causative agent of anthrax, which produces endospores capable of survive for many decades3; C. tetani (causes tetanus); C. difficile (causes pseudomembranous colitis); C. perfringens (causes gas gangrene); and C. botulinum (causes botulism). Pathogens such as these are particularly difficult to combat because their endospores are so hard to kill. Special sterilization methods for endospore-forming bacteria are discussed in later chapters.

    Exercise \(\PageIndex{3}\)

    1. What is an inclusion?
    2. What is the function of an endospore?

    On the Outside

    Glycocalyces and S-Layers

    Although most prokaryotic cells have cell walls, some may have additional cell envelope structures exterior to the cell wall, such as glycocalyces and S-layers. A glycocalyx is a sugar coat, of which there are two important types: capsules and slime layers. A capsule is an organized layer located outside of the cell wall and usually composed of polysaccharides or proteins (Figure \(\PageIndex{11}\)). A slime layer is a less tightly organized layer that is only loosely attached to the cell wall and can be more easily washed off. Slime layers may be composed of polysaccharides, glycoproteins, or glycolipids.

    Glycocalyces allows cells to adhere to surfaces, aiding in the formation of biofilms (colonies of microbes that form in layers on surfaces). In nature, most microbes live in mixed communities within biofilms, partly because the biofilm affords them some level of protection. Biofilms are abundant and frequently occupy complex niches within ecosystems. In medicine, biofilms can coat medical devices and exist within the body. Because they possess unique characteristics, such as increased resistance against the immune system, disinfectants, predation and to antimicrobial drugs, biofilms are of particular interest to microbiologists and clinicians alike. Biofilms generally hold water like a sponge, preventing desiccation.

    All of these properties are advantageous to the microbes living in a biofilm, but they present challenges in a clinical setting, where the goal is often to eliminate microbes. The ability to produce a capsule can contribute to a microbe’s pathogenicity (ability to cause disease) because the capsule can make it more difficult for phagocytic cells (such as white blood cells) to engulf and kill the microorganism. Streptococcus pneumoniae, for example, produces a capsule that is well known to aid in this bacterium’s pathogenicity. Capsules are difficult to stain for microscopy; negative staining techniques are typically used.

    a) A diagram showing the outer structures of bacterial cells. The thick outer layer is labeled capsule. Below that is a thinner cell wall and below that is an even thinner plasma membrane. B) A micrograph showing capsules as clearings outside of red stained cells; the background of the micrograph is a pale pink.

    Figure \(\PageIndex{11}\): (a) Capsules are a type of glycocalyx composed of an organized layer of polysaccharides. (b) A capsule stain of Pseudomonas aeruginosa, a bacterial pathogen capable of causing many different types of infections in humans. (credit b: modification of work by American Society for Microbiology)


    Figure \(\PageIndex{12}\): A biofilm forms when planktonic (free-floating) bacteria of one or more species adhere to a surface, produce slime, and form a colony. This diagram shows the five stages of biofilm development of Pseudomonas aeruginosa. All photomicrographs are shown to the same scale. (credit: Public Library of Science).

    An S-layer is another type of cell envelope structure; it is composed of a mixture of structural proteins and glycoproteins. In bacteria, S-layers are found outside the cell wall, but in some archaea, the S-layer serves as the cell wall. The exact function of S-layers is not entirely understood, and they are difficult to study; but available evidence suggests that they may play a variety of functions in different prokaryotic cells, such as helping the cell withstand osmotic pressure and, for certain pathogens, interacting with the host immune system.

    Filamentous Appendages

    Many bacterial cells have protein appendages embedded within their cell envelopes that extend outward, allowing interaction with the environment. These appendages can attach to other surfaces, transfer DNA, or provide movement. Filamentous appendages include fimbriae, pili, and flagella.


    Fimbriae and pili are structurally similar and, because differentiation between the two is problematic, these terms are often used interchangeably.7 8 However, common use it that the term fimbriae refers to short bristle-like proteins projecting from the cell surface by the hundreds. Fimbriae enable a cell to attach to surfaces and to other cells. For pathogenic bacteria, adherence to host cells is important for colonization, infectivity, and virulence. Adherence to surfaces is also important in biofilm formation.


    The term pili (singular: pilus) commonly refers to longer, hollow, less numerous protein appendages (Figure \(\PageIndex{13}\)). More specifically called the F pilus or sex pilus, it is important in the transfer of DNA between bacterial cells, which occurs between members of the same generation when two cells physically transfer or exchange parts of their respective genomes.

    A micrograph of two cells connected by two long strings labeled pilli.
    Figure \(\PageIndex{13}\): Bacteria may produce two different types of protein appendages that aid in surface attachment. Fimbriae typically are more numerous and shorter, whereas pili (shown here) are longer and less numerous per cell. (credit: modification of work by American Society for Microbiology)


    Flagella are structures used by cells to move in aqueous environments. Bacterial flagella act like propellers. They are stiff spiral filaments composed of flagellin protein subunits that extend outward from the cell and spin in solution. The basal body is the motor for the flagellum and is embedded in the plasma membrane (Figure \(\PageIndex{14}\)). A hook region connects the basal body to the filament. Gram-positive and gram-negative bacteria have different basal body configurations due to differences in cell wall structure.

    Different types of motile bacteria exhibit different arrangements of flagella (Figure \(\PageIndex{14}\)). A bacterium with a singular flagellum, typically located at one end of the cell (polar), is said to have a monotrichous flagellum. An example of a monotrichously flagellated bacterial pathogen is Vibrio cholerae, the gram-negative bacterium that causes cholera. Cells with amphitrichous flagella have a flagellum or tufts of flagella at each end. An example is Spirillum minor, the cause of spirillary (Asian) rat-bite fever or sodoku. Cells with lophotrichous flagella have a tuft at one end of the cell. The gram-negative bacillus Pseudomonas aeruginosa, an opportunistic pathogen known for causing many infections, including “swimmer’s ear” and burn wound infections, has lophotrichous flagella. Flagella that cover the entire surface of a bacterial cell are called peritrichous flagella. The gram-negative bacterium E. coli shows a peritrichous arrangement of flagella.

    A diagram showing the attachment point of flagella in gram-positive and gram-negative bacteria. The gram-positive diagram shows the filament on the outside of the cell wall; a bent elbow labeled hook connects the filament to the cell wall. A thin line between the filament and hook is labeled junction. The hook connects to a rod which connects to a basal body in the inner membrane. The basal body is a complex structure with a C-ring on the bottom. In the center of this ring is a sphere labeled type III secretion protein. Outside of this are oval structures labeled stator. On top of the secretion protein is a ring labeled MS-ring. The gram-negative flagellum is similar. There is a filament attached to a  junction attached to hook. In the outer membrane is a ring labeled L-ring that connects to a rod in the periplasmic space. A P-ring sits in the cell wall. In the inner membrane is the C-ring, type III secretion system, MS ring and stator.
    Figure \(\PageIndex{14}\): The basic structure of a bacterial flagellum consists of a basal body, hook, and filament. The basal body composition and arrangement differ between gram-positive and gram-negative bacteria. (credit: modification of work by “LadyofHats”/Mariana Ruiz Villareal)

    Diagrams of flagellar arrangements. Monotrichous bacteria have a single flagellum at one end. Amphitrichouls bacteria have one flagellum at each end. Lophotrichous bacteria have a tuft of flagella at one end. Peritrichous bacteria have flagella all the way around the outside of the cell.

    Figure \(\PageIndex{15}\): Flagellated bacteria may exhibit multiple arrangements of their flagella. Common arrangements include monotrichous, amphitrichous, lophotrichous, or peritrichous.


    Directional movement depends on the configuration of the flagella. Bacteria can move in response to a variety of environmental signals, including light (phototaxis), magnetic fields (magnetotaxis) using magnetosomes, and, most commonly, chemical gradients (chemotaxis). Purposeful movement toward a chemical attractant, like a food source, or away from a repellent, like a poisonous chemical, is achieved by increasing the length of runs and decreasing the length of tumbles. When running, flagella rotate in a counterclockwise direction, allowing the bacterial cell to move forward. In a peritrichous bacterium, the flagella are all bundled together in a very streamlined way (Figure \(\PageIndex{16}\)), allowing for efficient movement. When tumbling, flagella are splayed out while rotating in a clockwise direction, creating a looping motion and preventing meaningful forward movement but reorienting the cell toward the direction of the attractant. When an attractant exists, runs and tumbles still occur; however, the length of runs is longer, while the length of the tumbles is reduced, allowing overall movement toward the higher concentration of the attractant. When no chemical gradient exists, the lengths of runs and tumbles are more equal, and overall movement is more random (Figure \(\PageIndex{17}\)).

    A diagram showing the run and tumble of bacterial motion. The tumble is when a clockwise rotation of flagella cause the bacterial cell to tumble about. The run is when a counter-clockwise rotation of the flagella cause the bacterial cell to move in a linear direction.
    Figure \(\PageIndex{16}\): Bacteria achieve directional movement by changing the rotation of their flagella. In a cell with peritrichous flagella, the flagella bundle when they rotate in a counterclockwise direction, resulting in a run. However, when the flagella rotate in a clockwise direction, the flagella are no longer bundled, resulting in tumbles.
    A diagram showing the run and tumble motion of bacteria. In the run, the bundeled flagella move in a counter clockwise rotation and the cell moves in a straight line. In the tumble, the flagella separate due to a clockwise rotation and the bacterial cell floats with no particular direction. This is followed by another run. If there is an attractant (a chemical gradient) the bacterial cell moves towards the attractant and the length of the run is extended.
    Figure \(\PageIndex{17}\): Without a chemical gradient, flagellar rotation cycles between counterclockwise (run) and clockwise (tumble) with no overall directional movement. However, when a chemical gradient of an attractant exists, the length of runs is extended, while the length of tumbles is decreased. This leads to chemotaxis: an overall directional movement toward the higher concentration of the attractant.

    Exercise \(\PageIndex{4}\)

    1. What is the peptidoglycan layer and how does it differ between gram-positive and gram-negative bacteria?
    2. Compare and contrast monotrichous, amphitrichous, lophotrichous, and peritrichous flagella.


    • Prokaryotic cells differ from eukaryotic cells in that their genetic material is contained in a nucleoid rather than a membrane-bound nucleus. In addition, prokaryotic cells generally lack membrane-bound organelles.
    • Prokaryotic cells of the same species typically share a similar cell morphology and cellular arrangement.
    • Most prokaryotic cells have a cell wall that helps the organism maintain cellular morphology and protects it against changes in osmotic pressure.
    • In prokaryotic cells, the cell envelope always includes a plasma membrane and usually includes a cell wall. The proteins in the membrane serve a variety of functions, including transport, cell-to-cell communication, and sensing environmental conditions. Archaeal membranes are distinct in that they are composed of fatty acids that are ether-linked to phospholipids.
    • Prokaryotic cell walls may be composed of peptidoglycan (bacteria) or pseudopeptidoglycan (archaea).
    • Gram-positive bacterial cells are characterized by a thick peptidoglycan layer, whereas gram-negative bacterial cells are characterized by a thin peptidoglycan layer surrounded by an outer membrane.
    • Prokaryote DNA is generally found in the nucleoid. Outside of the nucleoid, prokaryotic cells may contain extrachromosomal DNA in plasmids.
    • Prokaryotic ribosomes that are found in the cytoplasm have a size of 70S.
    • Some prokaryotic cells have inclusions that store nutrients or chemicals for other uses.
    • Some prokaryotic cells are able to form endospores through sporulation to survive in a dormant state when conditions are unfavorable. Endospores can germinate, transforming back into vegetative cells when conditions improve.
    • Some prokaryotic cells produce glycocalyx coatings, such as capsules and slime layers, that aid in attachment to surfaces and/or evasion of the host immune system.
    • Some prokaryotic cells have fimbriae or pili, filamentous appendages. Fimbriae aid in attachment. Pili are used in the transfer of genetic material between cells.
    • Some prokaryotic cells use one or more flagella to move through water. Peritrichous bacteria, which have numerous flagella, use runs and tumbles to move purposefully in the direction of a chemical attractant.


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    3. R. Sinclair et al. “Persistence of Category A Select Agents in the Environment.” Applied and Environmental Microbiology 74 no. 3 (2008):555–563.
    4. T.J. Silhavy, D. Kahne, S. Walker. “The Bacterial Cell Envelope.” Cold Spring Harbor Perspectives in Biology 2 no. 5 (2010):a000414.
    5. B. Zuber et al. “Granular Layer in the Periplasmic Space of Gram-Positive Bacteria and Fine Structures of Enterococcus gallinarum and Streptococcus gordonii Septa Revealed by Cryo-Electron Microscopy of Vitreous Sections.” Journal of Bacteriology 188 no. 18 (2006):6652–6660
    6. L. Gana, S. Chena, G.J. Jensena. “Molecular Organization of Gram-Negative Peptidoglycan.” Proceedings of the National Academy of Sciences of the United States of America 105 no. 48 (2008):18953–18957.
    7. J.A. Garnetta et al. “Structural Insights Into the Biogenesis and Biofilm Formation by the Escherichia coli Common Pilus.” Proceedings of the National Academy of Sciences of the United States of America 109 no. 10 (2012):3950–3955.
    8. T. Proft, E.N. Baker. “Pili in Gram-Negative and Gram-Positive Bacteria—Structure, Assembly and Their Role in Disease.” Cellular and Molecular Life Sciences 66 (2009):613.


    • Nina Parker, (Shenandoah University), Mark Schneegurt (Wichita State University), Anh-Hue Thi Tu (Georgia Southwestern State University), Philip Lister (Central New Mexico Community College), and Brian M. Forster (Saint Joseph’s University) with many contributing authors. Original content via Openstax (CC BY 4.0; Access for free at

    This page titled 4.1: Unique Characteristics of Prokaryotic Cells is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.