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1.11: Prokaryotic Cells

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    Learning Objectives
    • Distinguish between prokaryotic cells and eukaryotic cells in terms of structure, size, and the types of organisms that have these cell types.
    • Identify structures of bacterial cells in models and diagrams, including details of Gram-positive and Gram-negative cell walls and flagella.
    • Describe the functions of the structures found in prokaryotic cells.
    • Define endospore.
    • Identify the structures and explain the functions of endospores.
    • Identify and name bacterial cell shapes and arrangements using correct terminologies.
    • Name the correct terms of flagellar arrangements from descriptions, illustrations, and images.


    Bacteria are Prokaryotic Cells

    Cells fall into one of two broad categories: prokaryotic and eukaryotic. Prokaryotic cells do not have a nucleus (membrane-bound structure that surrounds the cell's DNA). Only eukaryotic cells have a nucleus. Bacteria and archaea are the forms of life that are composed of prokaryotic cells, whereas plants, animals, fungi, and protists (including protozoa) are all composed of eukaryotic cells. In addition to prokaryotic and eukaryotic cells differing from each other based on absence or presence of a nucleus, prokaryotic cells are typically much smaller than eukaryotic cells and also have fewer organelle structures inside of their cells.

    relative size of bacteria, molecules, atoms



    Figure 1: This figure shows relative sizes of microbes on a logarithmic scale (recall that each unit of increase in a logarithmic scale represents a 10-fold increase in the quantity being measured). The smallest cells in the world are prokaryotic cells (including bacteria) that tend to be between 1 μm and 10 μm long. Eukaryotic cells are usually larger than prokaryotic cells (between 10 μm and 100 μm, but sometimes they can be much larger such as a frog egg that is 1 mm and can be viewed with the naked eye)


    All cells (both prokaryotic and eukaryotic) share four common components:

    1. a plasma membrane, an outer covering that separates the cell’s interior from its surrounding environment
    2. cytoplasm, consisting of a jelly-like cytosol within the cell in which other cellular components are found
    3. DNA, the genetic material of the cell
    4. ribosomes, which synthesize proteins (prokaryotic ribosomes differ from eukaryotic ribosomes in several ways)

    A prokaryote is a simple, mostly single-celled (unicellular) organism that lacks a nucleus, or any other membrane-bound organelle. Prokaryotic DNA is found in a central part of the cell: the nucleoid


    Prokaryotic cell with structures labeled


    Figure 2: This figure shows the generalized structure of a prokaryotic cell. Prokaryotes have chromosomal DNA localized in a nucleoid, ribosomes, a cell membrane, and a cell wall. The other structures shown are present in some, but not all, bacteria (flagellum, pili, capsule).

    prokaryotic cell structure function of this cell structure
    capsule enables the cell to attach to surfaces in its environment (including attachment to a host in pathogenic [disease-causing] species)
    cell wall acts as an extra layer of protection, helps the cell maintain its shape, and prevents dehydration
    cytoplasm semifluid inside of the cell that holds cell components and is the site of the cell's metabolism (its chemical reactions that keep it alive)
    flagellum (singular) / flagella (plural) a whip-like tail that rotates to move a cell; prokaryotic cells can have no flagella, one flagellum, or multiple flagella depending on the species
    nucleoid a central region within a prokaryotic cell composed of the cell's chromosome (its DNA); the chromosome is a single DNA molecule that is in a circular and comprises the genome of the cell; this chromosome wraps and twist onto itself to form the nucleoid
    plasma membrane a fluid membrane that separates the inside of the cell from the outside of the cell; this structure is semipermeable (some materials can pass through the membrane and others cannot)
    plasmid (not shown in the figure) a small DNA molecule (often circular) found in the cytoplasm; plasmids are much smaller than the DNA chromosome in the nucleoid; plasmids can be exchanged by cells or picked up by cells to acquire new traits; plasmids can carry antibiotic resistance genes and therefore create challenges for treating some infections when they are shared between cells; prokaryotic cells can survive without plasmids and do not always contain a plasmid, while some may contain multiple plasmids
    pilus (singular) / pili (plural) important for attachment to surfaces or other cells, including host cells for pathogenic (disease-causing) cells; some pili, called "sex pili," can be used to exchange genetic material (DNA) between cells during a process called conjugation
    ribosome (singular) / ribosomes (plural) small structures found in the cytoplasm that build proteins; proteins are needed to conduct a cell's metabolism, form structures, and do so many other things within a cell; instructions for building different types of proteins come through chemical messages originating in the DNA


    Bacterial Cell Shapes & Arrangements

    Bacterial cells can have a variety of cell shapes that differ for different species. Each cell shape has a specific terminology used to describe it:

    • cocci - round
    • bacilli - rods
    • vibrios - curved rods
    • spirochetes - long, thin, wavy, and helical/corkscrew
    • spirilla - long, thin wavy, and not helical/corkscrew

    Bacteria that are cocci can be found arranged as:

    • solitary - single cells unattached to other cells (may still be seen attached to another cell during division process)
    • diplococci - cells attached as pairs
    • tetrads - cells are grouped as four attached cells
    • sarcina - cells are grouped as eight attached cells
    • streptococci - cells are arranged in long chains resembling a string of pearls
    • staphylococci - cells are arranged in large bunches

    Bacteria that are bacilli can be found arranged as:

    • solitary - single cells unattached to other cells (may still be seen attached to another cell during division process)
    • diplobacilli - cells attached as pairs
    • streptobacilli - cells are arranged in long chains end-to-end
    • palisades - cells arranged lined up next to each other long-ways and resembles pickets in a picket fence

    To see illustrations and images of cell shapes and cell arrangements as well as more details see Bacterial Cell Morphology & Arrangement in the Simple Stain chapter.


    Bacterial Cell Wall Structures

    Most bacteria are divided into two major groups: Gram-positive bacteria and Gram-negative bacteria based on the cell wall composition (can be differentiated by using the Gram stain procedure on the bacteria). Knowing the Gram reaction of a clinical isolate (isolated bacterial species from a patient) can help the health care professional make a diagnosis and choose the appropriate antibiotic for treatment.

    Gram stain cell walls diagram


    Figure 3: (Top) Microscopic images of bacteria stained with the Gram stain. (Top right) Gram-positive bacterial species stain purple with the Gram stain. (Top left) Gram-negative bacterial species stain pink with the Gram stain. (Bottom) Diagrams illustrating major structural components of Gram-positive bacterial cell walls and Gram-negative bacterial cell walls. (Bottom right) Gram-positive bacterial species have a thick layer of peptidoglycan outside of the plasma membrane and a layer of periplasm. (Bottom left) Gram-negative bacterial species have a thin layer of peptidoglycan outside of the plasma membrane surrounded by periplasm with an outer membrane outside of the peptidoglycan layer. Embedded in the outer membrane of Gram-negative cell walls are lipopolysaccharides (LPS) that are not shown in this diagram.


    The results of the Gram stain reflect differences in cell wall composition. Gram-positive cells have thick layers of peptidoglycan (a substance composed of carbohydrates and protein subunits) in their cell walls. Gram-negative bacteria have very little peptidoglycan. Gram-positive bacteria also have teichoic acids, whereas Gram-negative bacteria do not. Gram-negative cells have an outer membrane that resembles the phospholipid bilayer of the plasma membrane. The outer membrane contains lipopolysaccharides (LPS), which are released as endotoxins when Gram-negative cells die. This can be of concern to a person with an infection caused by a Gram-negative organism.


    Gram stain cell walls diagram details

    Figure 4: Detailed view of the structure of bacterial cell walls for Gram-positive species and for Gram-negative species. (Left) Gram-positive cell walls consist of a thick layer of peptidoglycan (PG) outside of the cell's plasma membrane (PM) with teichoic acid (TA) and lipoteichoic acid embedded across the peptidoglycan layer. (Right) Gram-negative cell walls consist of a thin layer of peptidoglycan (PG) outside of the cell's plasma membrane (PM). Gram-negative cell walls have an outer membrane (OM) beyond the peptidoglycan layer containing lipopolysaccharide (LPS) as well as porin channels that enable some materials to pass across the outer membrane. In Gram-positive and Gram-negative cell wall types lipoprotein (LP) is also found.


    Some species are known as Gram-variable, and so both Gram-positive and Gram-negative reactions may occur when a Gram-variable species is stained using the Gram stain. The vast majority of bacteria are either Gram-positive or Gram-negative. However, not all bacteria can be stained with the Gram stain (for example, Mycoplasma sp., which have no cell wall, stains poorly with the Gram stain).


    Bacterial Endospores

    An endospore is a form of a bacterial cell. Only some species of bacteria can produce endospores. Endospores are made so the cell can survive poor growth or poor survival conditions. An endospore is a mainly inactive version of a cell that is analagous to a survival bunker. When environmental conditions are poor, or even deadly, bacteria that are able to will produce endospores to survive. When environmental conditions improve, endospores can produce the active cells again (active cells are called vegetative cells.) Bacterial endospores are the most resistant structures of all living organisms, and they can live in this dormant dehydrated state for hundreds of years (even some documented at thousands of years). The stimulus that triggers sporulation (formatio of spores) can vary and may include nutrient depletion, desiccation, chemicals, heat, etc.


    Endospores are not for reproduction. One spore forms inside of one vegetative cell (vegetative = metabolically active cell). When environmental conditions improve, one spore germinates to produce one vegetative cell.

    Endospore production is a very important characteristic of some bacteria, allowing them to resist adverse environmental conditions such as desiccation, chemical exposure, extreme heat, etc. Endospores were first identified in the 1800s (John Tyndall developed a process for destroying them with an intermittent heating procedure), although the stain procedures to identify them did not develop until the early twentieth century.


    endospore formation and how endospores appear in the microscope

    Figure 5: (A) Endospores form from bacterial cells. Diagram shows the process how bacterial cells experiencing poor growth conditions can form endospores in the following steps: 1. DNA is replicated, 2. cellular division of cytoplasmic membrane, 3. prespore formation begins, 4. cortex forms, 5. spore coat formation begins, 6. maturation of exosporium formation, 7. mother cell releases mature spore. (B) Microscopic image prepared with an endospore stain shows bacterial cells (pink) with forming spore inside of them (green). (C) Microscopic image showing endospores.


    The identification of endospores is very important for the clinical microbiologist who is analyzing a patient's body fluid or tissue since there are not that many spore-forming genera. Knowing if the species of bacteria causing an infection forms spores or not helps to narrow down the possible bacterial species causing the infection. In fact, there are two major pathogenic (disease-causing) spore-forming genera: Bacillus and Clostridium. Bacillus and Clostridium species cause a number of dangerous and lethal diseases such as botulism, gangrene, tetanus, c-diff, and anthrax, to name a few.

    Some bacteria have to be put into unfavorable situations (high cell density and starvation are two key triggers) to go into sporulation. Other species will make spores easily without much provocation (e.g. Bacillus subtilis). Vegetative cells that have not yet made spores may be in the process of making the spore or will not make them at all. The vegetative cell is metabolically active, whereas the spore is not. The location where an endospore is within a vegetative cell is also useful for distinguishing bacterial species. Endospores may be located in a terminal (end of the cell), subterminal (near the end of the cell), or central (middle of the cell) position. A particular species of the genus will form spores in a specific area, producing another useful taxonomic identification tool and therefore useful in identifying the species of bacteria.


    Bacterial Flagella

    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. 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.


    flagellum structures

    Figure 6: 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)


    Different types of motile bacteria exhibit different arrangements of flagella. 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 or both ends 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.


    flagellar arrangments

    Figure 7: Flagellated bacteria may exhibit multiple arrangements of their flagella. Common arrangements include monotrichous, amphitrichous, lophotrichous, or peritrichous.


    Laboratory Instructions

    Identify Prokaryotic Cell Model Structures

    bacterial cell model

    bacterial cell wall model 1

    bacterial cell wall model 2

    1. Carefully examine cell models of bacterial cells.
    2. Identify the following structures on the cell models:
      • Prokaryotic structure

        Diagram letter

        basal body (of flagellum)




        cell wall




        filament (of flagellum)




        Gram-negative cell wall


        Gram-positive cell wall


        hook (of flagellum)





        outer membrane  
        peptidoglycan (thick layer)  
        peptidoglycan (thin layer)  
        periplasm (2 places)  
        plasma membrane (3 places)  
        teichoic acid  


    Collaboratively Study Prokaryotic Cell Structures

    1. Work with your group. You will point to each structure on the prokaryotic cell model to ask each member of your group its name. Wait for the person who you are asking to come up with the correct name of the structure on the model.
    2. Your group members will conduct the same process in step 1 so you and the rest of the group get practice recalling the prokaryotic cell structures on the model.
    3. Continue this practice until everyone in the group can make the cell structures without looking at the handout (i.e. from memory).
    4. You will be quizzed on the prokaryotic cell model by your instructor. They will initial the checkpoint below when you and your group successfully identify structures on the prokaryotic cell model from memory.

    Checkpoint: __________

    If you are waiting for assistance from your instructor, move on to the next section(s) until they are available.


    Prokaryotic Cell Shapes

    1. Use a microscope to examine the three different bacterial types on the Bacteria: Three Types slide (there are three different sections to the slide – move the slide around to see all three).
    2. Make detailed and clear illustrations of all three types of bacteria in the spaces provided below clearly showing the cell shapes/arrangements.
    3. In the spaces provided, indicate the appropriate term or terms that describe the cell shapes (and arrangements if appropriate).

    Bacterial Type #1

    location for microscopic illustrations

    Bacterial shape/arrangement term(s) appropriate for this bacterial species: ______________________

    Bacterial Type #2

    location for microscopic illustrations

    Bacterial shape/arrangement term(s) appropriate for this bacterial species: ______________________

    Bacterial Type #3

    location for microscopic illustrations

    Bacterial shape/arrangement term(s) appropriate for this bacterial species: ______________________



    1. Examine a slide that shows bacterial endospores.
    2. Make a clear illustration of the sample.
    3. In the illustration, label an endospore that is forming inside of a vegetative cell as “endospore forming inside vegetative cell”
    4. In the illustration, label a free spore as “endospore.”

    location for microscopic illustrations


    Flagellar Arrangements

    Some bacterial species do not have any flagella. Those bacterial species that do have flagella exhibit flagella in different arrangements. Make illustrations in each box below to show what the terms describing flagellar arrangements look like. If you are uncertain, use the lab manual for help.




    (draw two different types of arrangements)



    This page titled 1.11: Prokaryotic Cells is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Rosanna Hartline.

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