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2.3: 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

    Related Chapter Learning Outcomes:

    • Recognize and apply the terms for common bacterial cell morphologies and arrangements.
    • Identify the group(s) of microbes which can have peptidoglycan in their cell wall.
    • Describe in words and sketch the important chemical and structural features of the bacterial peptidolycan (murein) incluing N-acetyl-muramic acid (NAM), N-acetyl-glucosamine (NAG), amino acids, and peptide crosslinks.
    • Explain the importance of peptide crosslinking in peptidoglycan structure.
    • Compare and contrast (in words and diagrammatically) Gram-positive and Gram-negative cell envelopes including: peptidoglycan structure, teichoic acid, Braun’s lipoprotein, lipopolysaccharide (and its components lipid A and O-side chains), outer membrane, plasma membrane, and porins.
    • Explain at the cellular/molecular level why Gram-positive cells stain purple and Gram-negatives pink in the Gram stain (discussed in lab).
    • Name a genus of bacteria that naturally lacks a cell wall.
    • Explain how the cell wall of acid-fast bacteria differs from other Gram-positive bacteria and name the most common example genus of acid-fast bacteria.
    • Describe structure and function bacterial appendages outside the cell wall including: flagella, pili, fimbrae, and glycocalyx (slime layer, capsule).
    • Explain how bacterial cellular structures aid in the pathogenicity of some organisms. Discuss specifically: LPS (a.k.a LOS), capsules, fimbrae/pili, and endospores.

    As mentioned in the previous section, prokaryotic cells lack a nucleus surrounded by a complex nuclear membrane and generally have a single, circular chromosome located in a nucleoid. Prokaryotes do not have membrane-bound organelles and are generally smaller than eukaryotic cells, but that does not mean they are simple.  Many prokaryotes have complex infoldings of the plasma membrane to aid in metabolism such as respiration or photosynthesis.  They also contain structures called inclusion bodies used for a variety of function such as energy storage.

    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 Prokaryotic 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. Figure \(\PageIndex{2}\) names and illustrates cell morphologies commonly found in prokaryotic cells. 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 shown in Figure \(\PageIndex{3}\).

    Common Prokaryotic Cell Shapes. The term Coccus (plural: cocci) is the name given to round, spherical shapes. The term bacillus (plural: bacilli) is the name given to rod shaped cells. These cells are shaped like long rounded rectangles. The term vibrio (plural vibrios) is the name given to curved rods, these cells have a shape like a long comma. The term coccobacillus (plural coccobacilli) is the name for short rods; these cells look like ovals. The term spirillum (plural spirilla) is the name for long spiral cells; these look like cork screws. The term spirochete (plural spirochetes) is the name for long, loose helical spiral shaped cells. These look similar to the spirillum but are more floppy.
    Figure \(\PageIndex{2}\): (credit “Coccus” micrograph: modification of work by Janice Haney Carr, Centers for Disease Control and Prevention; credit “Coccobacillus” micrograph: modification of work by Janice Carr, Centers for Disease Control and Prevention; credit “Spirochete” micrograph: modification of work by Centers for Disease Control and Prevention)
    Common prokaryotic cell arrangments. The term Coccus (plural cocci) is the name for a single coccus (a single round cell). The term diplococcus (plural diplococci) is the name for a pair of two cocci (two spheres attached together). The term tetrad (plural tetrads) is the name for a grouping of four cells arranged in a square. The term streptococcus (plural streptococci) is the name for a chain of cocci; the spheres are connected into a long chain. The term staphylococcus (plural staphylococci) is the name for a cluster of cocci; the spheres are connected into a bundle. The term bacillus (plural bacilli) is the name for a single rod. The term streptobacillus (plural streptobacilli) is the name for a chain of rods; the rectangles are connected into a long chain.
    Figure \(\PageIndex{3}\): Common cell arrangements.

    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 (Figure \(\PageIndex{4}\)). Osmotic pressure occurs because of differences in the concentration of solutes on opposing sides of a semipermeable membrane. Water is able to pass through a semipermeable 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.


    a) An isotonic solution is a solution that has the same solute concentration as another solution. There is no net movement of water particles, and the overall concentration on both sides of the cell membrane remains constant. The image shows a cell with 20% solute (80% water) in a beaker containing 20% solute (80% water). Arrows in and out indicate that water moves both into and out of the cell. b) A hypertonic solution is a solution that has a higher solute concentration than another solution. Water particles will move out of the cell, causing crenation. The cell in this image still has 20% solute concentration (80% water) but the cell is now in a beaker containing 40% solute concentration (60% water). An arrow shows water moving out of the cell and the cell shriveling. C) A hypotonic solution is a solution that has a lower solute concentration than another solution. Water particles will move into the cell, causing the cell to expand and eventually lyse. The cell in this diagram still has 20% solute concentration (80% water) but is now in a beaker containing 10% solute concentration (90% water). An arrow shows water mving into the cell and the cell swelling.
    Figure \(\PageIndex{4}\): In cells that lack a cell wall, changes in osmotic pressure can lead to plasmolysis (shriveling) in hypertonic environments or cell lysis in hypotonic environments.

    Exercise \(\PageIndex{1}\)

    1. Explain the difference between cell morphology and arrangement.
    2. What advantages do cell walls provide prokaryotic cells?

    Plasma Membrane

    Structures that enclose the cytoplasm and internal structures of the cell are known collectively as the cell envelope. In prokaryotic cells, the structures of the cell envelope vary depending on the type of cell and organism. Most (but not all) prokaryotic cells have a cell wall, but the makeup of this cell wall varies. All cells (prokaryotic and eukaryotic) have a plasma membrane (also called cytoplasmic membrane or cell membrane) that exhibits selective permeability, allowing some molecules to enter or leave the cell while restricting the passage of others.

    The structure of the plasma membrane is often described in terms of the fluid mosaic model, which refers to the ability of membrane components to move fluidly within the plane of the membrane, as well as the mosaic-like composition of the components, which include a diverse array of lipid and protein components (Figure \(\PageIndex{10}\)). The plasma membrane structure of most bacterial and eukaryotic cell types is a bilayer composed mainly of phospholipids formed with ester linkages and proteins. These phospholipids and proteins have the ability to move laterally within the plane of the membranes as well as between the two phospholipid layers.

    A drawing of the plasma membrane. The top of the diagram is labeled outside of cell, the bottom is labeled cytoplasm. Separating these two regions is the membrane which is made of mostly a phospholipid bilayer. Each phospholipid is drawn as a sphere with 2 tails. There are two layers of phospholipids making up the bilayer; each phospholipid layer has the sphere towards the outside of the bilayer and the two tails towards the inside of the bilayer. Embedded within the phospholipid bilayer are a variety of large proteins. Protein channels span the entire bilayer and have a pore in the center that connects the outside of the cell with the cytoplasm. Peripheral proteins sit on one side of the phospholipid bilayer. Transmembrane proteins span the bilayer. Glycolipids have long carbohydrate chains (shown as a chain of hexagons) attached to a single phospholipid; the carbohydrates are always on the outside of the membrane. Glycoproteins have a long carbohydrate chain attached to a protein; the carbohydrates are on the outside of the membrane. The cytoskeleton is shown as a thin layer of line just under the inside of the phospholipid bilayer.
    Figure \(\PageIndex{10}\): The bacterial plasma membrane is a phospholipid bilayer with a variety of embedded proteins that perform various functions for the cell. Note the presence of glycoproteins and glycolipids, whose carbohydrate components extend out from the surface of the cell. The abundance and arrangement of these proteins and lipids can vary greatly between species.

    Archaeal membranes are fundamentally different from bacterial and eukaryotic membranes in a few significant ways. First, archaeal membrane phospholipids are formed with ether linkages, in contrast to the ester linkages found in bacterial or eukaryotic cell membranes. Second, archaeal phospholipids have branched chains, whereas those of bacterial and eukaryotic cells are straight chained. Finally, although some archaeal membranes can be formed of bilayers like those found in bacteria and eukaryotes, other archaeal plasma membranes are lipid monolayers.

    Proteins on the cell’s surface are important for a variety of functions, including cell-to-cell communication, and sensing environmental conditions and pathogenic virulence factors. Membrane proteins and phospholipids may have carbohydrates (sugars) associated with them and are called glycoproteins or glycolipids, respectively. These glycoprotein and glycolipid complexes extend out from the surface of the cell, allowing the cell to interact with the external environment (Figure \(\PageIndex{10}\)). Glycoproteins and glycolipids in the plasma membrane can vary considerably in chemical composition among archaea, bacteria, and eukaryotes, allowing scientists to use them to characterize unique species.

    Plasma membranes from different cells types also contain unique phospholipids, which contain fatty acids. As described in Using Biochemistry to Identify Microorganisms, phospholipid-derived fatty acid analysis (PLFA) profiles can be used to identify unique types of cells based on differences in fatty acids. Archaea, bacteria, and eukaryotes each have a unique PFLA profile.

    Membrane Transport Mechanisms

    One of the most important functions of the plasma membrane is to control the transport of molecules into and out of the cell. Internal conditions must be maintained within a certain range despite any changes in the external environment. The transport of substances across the plasma membrane allows cells to do so.

    Simple diffusion. A diagram with a phospholipid bilayer (plasma membrane) along the middle. Above the bilayer is the extracellular fluid and below is the cytoplasm. At the far left there are many hexagons in the extracellular fluid above the bilayer and none in the cytoplasm below. At a later time shown in the middle of the timeline there are a few hexagons in the cytoplasm and still many in the extracellular fluid. At the last timeframe shown on the right there are equal numbers of hexagons in the extracellular fluid as in the cytoplasm.
    Figure \(\PageIndex{11}\): Simple diffusion down a concentration gradient directly across the phospholipid bilayer. (credit: modification of work by Mariana Ruiz Villareal)

    Cells use various modes of transport across the plasma membrane. For example, molecules moving from a higher concentration to a lower concentration with the concentration gradient are transported by simple diffusion, also known as passive transport (Figure \(\PageIndex{11}\)). Some small molecules, like carbon dioxide, may cross the membrane bilayer directly by simple diffusion. However, charged molecules, as well as large molecules, need the help of carriers or channels in the membrane. These structures ferry molecules across the membrane, a process known as facilitated diffusion (Figure \(\PageIndex{12}\)).

    Facilitated diffusion. A diagram with a phospholipid bilayer (plasma membrane) in the middle of the image. There are many hexagons in the extracellular fluid above the membrane and few hexagons in the cytoplasm below the membrane. A protein channel is shown transporting the hexagons across the membrane from the extracellular fluid to the cytoplasm.
    Figure \(\PageIndex{12}\): Facilitated diffusion down a concentration gradient through a membrane protein. (credit: modification of work by Mariana Ruiz Villareal)

    Active transport occurs when cells move molecules across their membrane against concentration gradients (Figure \(\PageIndex{13}\)). A major difference between passive and active transport is that active transport requires adenosine triphosphate (ATP) or other forms of energy to move molecules “uphill.” Therefore, active transport structures are often called “pumps.”

    Active Transport. A diagram with a phospholipid bilayer (plasma membrane) along the middle. Above the bilayer is the extracellular fluid and below is the cytoplasm. There are more sodium ions in the extracellular fluid than in the cytoplasm. There are more potassium ions in the cytoplasm than in the extracellular fluid. A protein in the membrane is shown moving sodium from the cytoplasm to the extracellular fluid. The same membrane is shown moving potassium from the extracellular fluid to the cytoplasm. As the protein moves these ions, it also breaks down ATP to ADP.
    Figure \(\PageIndex{13}\): Active transport against a concentration gradient via a membrane pump that requires energy. (credit: modification of work by Mariana Ruiz Villareal)

    Group translocation also transports substances into bacterial cells. In this case, as a molecule moves into a cell against its concentration gradient, it is chemically modified so that it does not require transport against an unfavorable concentration gradient. A common example of this is the bacterial phosphotransferase system, a series of carriers that phosphorylates (i.e., adds phosphate ions to) glucose or other sugars upon entry into cells. Since the phosphorylation of sugars is required during the early stages of sugar metabolism, the phosphotransferase system is considered to be an energy neutral system.

    Cell Wall

    The primary function of the cell wall is to protect the cell from harsh conditions in the outside environment. 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 (more specifically murein, to distinguish it from a similar structure in some archaea).  Peptidoglycan is only found in bacteria. Structurally, peptidoglycan resembles a layer of meshwork or fabric (Figure \(\PageIndex{14}\)). 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 \(\PageIndex{14}\): 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 (see Staining Microscopic Specimens) is used to differentiate two common types of cell wall structures (Figure \(\PageIndex{15}\)). Gram-positive cells have a cell wall consisting of many layers of peptidoglycan totaling 30–100 nm in thickness. This thick layer of peptidoglycan traps the crystal violet used in the Gram stain resulting in the purple color of Gram-positive bacteria when this stain procedure is used. In Gram-positive bacteria, these peptidoglycan layers are commonly embedded with teichoic acids, carbohydrate chains that extend through and beyond the peptidoglycan layer.4 Teichoic acids are thought to stabilize peptidoglycan by increasing its rigidity. They also play 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 teichoic acids, bacteria of the family Mycobacteriaceae, such as the pathogenic bacterium Mycobacterium tuberculosis, 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 \(\PageIndex{16}\)).



    Figure \(\PageIndex{15}\): 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 \(\PageIndex{16}\): (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. When stained using the Gram stain method, these thinner layers of peptidoglycan cannot trap the crystal violet and only the pink safranin counterstain remains.  The overall structure of the Gram-negative cell envelope is more complex than Gram-positive. 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 \(\PageIndex{15}\)). This outer membrane is attached to the peptidoglycan by Braun's lipoprotein.

    Protein channels, called porins, allow molecules to cross the outer membrane (Figure \(\PageIndex{17}\)).  Porins are size-selective: only molecules of approximately 600 Da (about the size of a trisaccharide) or smaller can travel through them.  Any molecules that are larger require a specialized transport system to cross the outer membrane and enter the cell.  In this way, the outer membrane acts as a barrier to the entry of many molecules, including some larger antibiotics such as vancomycin.


    Figure \(\PageIndex{17}\): Porins are protein channels found in the outer membrane of Gram-negative bacteria (left). The proteins fold into a common structure called a beta-barrel, which forms an opening surrounded by beta-pleated sheets (right).  (Adapted from Left:  "File:Gram negative cell wall-de.svg" by Gram_negative_cell_wall.svg: Jeff Dahl derivative work: Matthias M. is licensed under CC BY-SA 3.0 Right: "File:Sucrose porin 1a0s.png" by Opabinia regalis is licensed under CC BY-SA 3.0)

    Although the inner leaf of the outer membrane is phospholipid similar to plasma membrane, the outer leaf of the outer membrane contains the molecule lipopolysaccharide (LPS), sometimes referred to as endotoxin.  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 \(\PageIndex{18}\)). 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. When LPS (more specifically lipid A) enters the bloodstream, the immune reaction can trigger endotoxic shock.  This is a dangerous condition with symptoms such as fever, hemorrhaging, and shock.

    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 \(\PageIndex{18}\): The outer membrane of a Gram-negative bacterial cell contains lipopolysaccharide (LPS), also referred to as endotoxin, composed of Lipid A embedded in the outer membrane, a core polysaccharide, and the O side chain.

    Some bacteria, most notably the mycoplasmas, do not have a cell wall at all.  Mycoplasmas almost exclusively live within other organisms where the osmotic pressure remains stable.  This stable environment, in addition to a strengthened plasma membrane, prevents mycoplasmas from lysing.


    The two groups of bacteria with cell envelopes that vary from the typical Gram-positive an Gram-negative are Mycobacteria (acid-fast) and Mycoplasma (no cell wall), which are frustratingly similar names.  Remember that Mycoplasma only has a plasma membrane as its cell envelope.

    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.

    Glycocalyces and Capsules

    Although most prokaryotic cells have cell walls, some may have additional cell envelope structures exterior to the cell wall, such as glycocalyces. A glycocalyx is a coating over the cell envelope, 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 \(\PageIndex{19}\)). 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 generally hold water like a sponge, preventing desiccation. They also protect cells from predation and hinder the action of antibiotics and disinfectants. 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.

    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 \(\PageIndex{19}\): (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)

    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. Because capsules cover the cell envelope many of the features recognized by phagocytic cells of the immune system, such as teichoic acids and peptidoglycan, these bacteria are hidden from the immune system and can proliferate in the body.  Streptococcus pneumoniae, for example, produces a capsule that is well known to aid in this bacterium’s pathogenicity. As explained in Staining Microscopic Specimens, capsules are difficult to stain for microscopy; negative staining techniques are typically used.


    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. 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. 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. We will discuss plasmids in more detail in Bacterial Genetics.


    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 size of 70S (Figure \(\PageIndex{7}\)), whereas eukaryotic cytoplasmic ribosomes have a size of 80S. (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 \(\PageIndex{7}\): 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 structures 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 \(\PageIndex{8}\).

    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 \(\PageIndex{8}\): 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)

    Some prokaryotic cells have other types of inclusions that serve purposes other than nutrient storage. For example, some prokaryotic cells produce gas vacuoles, accumulations of small, protein-lined vesicles of gas. These gas vacuoles 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 \(\PageIndex{8}\)). 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.


    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 (see Staining Microscopic Specimens)
    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 \(\PageIndex{9}\)). 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 \(\PageIndex{9}\): (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.

    The ability to form endospores is restricted to a few genera of Gram-positive bacteria; 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 Control of Microbial Growth.

    Exercise \(\PageIndex{2}\)

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

    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

    Fimbriae and pili are structurally similar and, because differentiation between the two is problematic, these terms are often used interchangeably.7 8 The term fimbriae commonly 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, less numerous protein appendages that aid in attachment to surfaces (Figure \(\PageIndex{20}\)). A specific type of pilus, called the F pilus or sex pilus, 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.  In addition to sex pili, some pathogens, rely on pili for attachment to host tissues or transfer of toxins or other virulence factors to host cells.  One such example is enterohemorrhagic E. coli.

    A micrograph of two cells connected by two long strings labeled pilli.
    Figure \(\PageIndex{20}\): 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 \(\PageIndex{21}\)). 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 \(\PageIndex{22}\)). 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 \(\PageIndex{21}\): 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 \(\PageIndex{22}\): Flagellated bacteria may exhibit multiple arrangements of their flagella. Common arrangements include monotrichous, amphitrichous, lophotrichous, or peritrichous.


    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.
    • 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.
    • In prokaryotic cells, the cell envelope includes a plasma membrane and usually a cell wall.
    • Bacterial membranes are composed of phospholipids with integral or peripheral proteins. The fatty acid components of these phospholipids are ester-linked and are often used to identify specific types of bacteria. The proteins 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.
    • Some molecules can move across the bacterial membrane by simple diffusion, but most large molecules must be actively transported through membrane structures using cellular energy.
    • 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.
    • 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 that aid in attachment to surfaces. Pili are also 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.


    1. 1 Y.-H.M. Chan, W.F. Marshall. “Scaling Properties of Cell and Organelle Size.” Organogenesis 6 no. 2 (2010):88–96.
    2. 2 F. Rothfuss, M Bender, R Conrad. “Survival and Activity of Bacteria in a Deep, Aged Lake Sediment (Lake Constance).” Microbial Ecology 33 no. 1 (1997):69–77.
    3. 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. 4 T.J. Silhavy, D. Kahne, S. Walker. “The Bacterial Cell Envelope.” Cold Spring Harbor Perspectives in Biology 2 no. 5 (2010):a000414.
    5. 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. 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. 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. 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 2.3: Unique Characteristics of Prokaryotic Cells is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.