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Prokaryotes II - Structure and Function

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You should have a working knowledge of the following terms:

  • antibiotic
  • capsule
  • cell wall
  • commensalism
  • endospore
  • endotoxin
  • exotoxin
  • flagellum (pl. flagella)
  • gram-positive
  • gram-negative
  • Gram's stain
  • host
  • lipopolysaccharide
  • microsymbiont
  • mutualism
  • opportunistic infection
  • osmosis
  • parasitism
  • peptidoglycan
  • plasma membrane
  • sporulation
  • symbiont
  • symbiosis
  • taxis

Introduction and Goals

This is a magnification of Vibrio cholerae, the organism responsible for cholera. Note the tail-like flagellum on one end; many prokaryotes are propelled by rotating flagella. The cellular and genetic organization of prokaryotes was introduced in our last tutorial. Recall that we also introduced their morphologies by discussing three basic shape categories of prokaryotes: cocci, bacilli, and spirilla. We will continue our discussion by exploring their structure and movement, and by describing some interactions between prokaryotes and other life forms. By the end of this tutorial you should have a basic understanding of:

  • Prokaryotic structure
  • Relationships between prokaryotes and other life forms
  • Diversity of carbon sources
  • Beneficial bacteria

The Prokaryotic Cell Wall and Peptidoglycan

The cells of all organisms (including prokaryotes) are encased in a plasma membrane, which consists of a phospholipid bilayer that is selectively permeable. This bilayer keeps salts and liquids in balance inside the cell by engulfing needed particles and ridding the cell of wastes. In addition to a plasma membrane, many organisms (including plants, fungi, and some protists) also have cell walls. These walls are involved in maintaining cell shape and protection.

Figure 1. Gram-positive versus gram-negative bacteria. (Click to enlarge)  Gram's stain is used to differentiate bacteria, based on the amount of peptidoglycan in their cell walls.

Most prokaryotes also have cell walls, but they are structurally different than those of the plants, fungi, and protists. For example, bacterial cell walls contain some amount of peptidoglycan, which is a polymer consisting of sugar and polypeptides. If one were attempting to identify bacteria, one might first examine them under a microscope to detect whether the specimens were rod-shaped, round, or spiral. Then one might analyze the amount of peptidoglycan in the cell walls of the unknown organisms by using a technique known as Gram's stain.

Bacteria containing a lot of peptidoglycan in their cell walls also tend to have less complex cell walls, and are called gram-positive bacteria. Conversely, gram-negative bacteria have less peptidoglycan, but have more complex cell walls overall. The gram-negative bacteria have an additional outer membrane with attached lipopolysaccharides.

Some of these lipopolysaccharides are toxic, serving to counteract the natural defenses of host organisms. Also, the additional membrane of gram-negative bacteria can make them more resistant to antibacterial medications (antibiotics). For these two reasons, a gram-negative bacterial infection can be far more severe than a gram-positive infection.

The Capsule and Pilus

Numerous adaptations by host organisms to fight bacterial infection, and counter adaptations by bacteria to evade these adaptive defenses, have resulted in bacteria that are skilled at survival in inhospitable conditions. In addition to cell walls and cell membranes, many bacteria have an additional layer outside the cell wall termed the capsule. Capsules are sticky substances made and secreted by the bacteria, and they help the bacteria adhere to surfaces or to each other. Capsules also provide an additional layer of protection to the encapsulated organism.

Recall from the last tutorial that pili can provide an avenue for exchange of genetic information. Some prokaryotes also use these surface appendages for attachment to a variety of substrates. For example, Neisseria gonorrhoeae attaches to the epithelium within the reproductive tract via pili, where they can inflict individuals with the STD that carries the species name. Mutant strains that lack pili are nonpathogenic.

How Do Prokaryotes Get Around?

Many prokaryotes are capable of directional movement, and they can actually move quite quickly. Some motile prokaryotes can move 100 times their body length in one second. (Think about this in terms of human movement; if a running person has a six-foot stride, this translates to 600 feet/second!)

Some prokaryotes can secrete slimy chemicals and then glide around on them. Some helical bacteria, the spirochetes, have internal filaments that are arranged so that the whole organism rotates axially; because the organism is helical in shape, the resulting movement is analogous to the action of a corkscrew. The most common type of movement in prokaryotes is via flagellar action. A flagellum (plural, flagella) is a long appendage specialized for locomotion, and while both eukaryotes and prokaryotes may exhibit flagellar motion, the flagella of prokaryotes are quite different from those of eukaryotes. Prokaryotic flagella consist of tightly wound chains of the protein flagellin attached to a molecular motor complex located within the cell wall.

Figure 2.  Flagellum of a gram-negative bacterium. (Click to enlarge)

Figure 3. Chemotaxis in bacteria.  (Click to enlarge)

Bacterial flagella can rotate either clockwise or counterclockwise. When rotating clockwise, the flagella fly apart, causing the bacteria to tumble randomly. When rotating counterclockwise, the flagella are drawn together into a bundle that results in directional movement. Bacteria with flagella alternate between tumbling and directional movement. In some cases the movement is random, but in other cases there is a net oriented movement (taxis) toward or away from a stimulus. Thus, the directed movement of these bacteria resembles the walk of a drunken sailor heading back to the ship.

The Social Life of Prokaryotes

From some of the previous examples, you might have concluded that bacteria are simply pathogens that cause diseases. However, this generalization would be wrong. In fact, the myriad of bacteria around us are either essential or benign to the life of other organisms(including ourselves). Humans are covered with bacteria (both inside and out). You may find this fact unsettling, but right now there are approximately 400 different species of bacteria living in your gastrointestinal system.

Only a relatively small percentage of the bacterial species that colonize on us (and all other multicellular organisms) are pathogenic. The vast majority of bacteria are ecologically significant and extremely beneficial. In most instances, bacteria colonize on and live harmoniously with other species.

The state of any two species having an extended and intimate association is termed symbiosis. You might have heard other definitions for this term, but researchers in the field agree that this is the best definition.

The interacting organisms (symbionts) have varying relationships with one another. The host (the larger of two species) and the microsymbiont (the smaller of the two species) may derive mutual benefit from the association, in which case the symbiosis is termed mutualism. At the other end of the symbiotic spectrum is a relationship whereby one member of the symbiosis derives benefit at the expense of the other, which is termed parasitism. In the middle of this spectrum are associations which appear benign (are neither of benefit nor harm) to either or both species; this form of symbiosis is termed commensalism. These are not static relationships, and the association between the symbionts is not constant and can change, depending on conditions. For example, a relationship may be commensalistic (or even mutualistic)
most of the time, but under certain conditions the association can turn parasitic.

Mutualistic Symbioses

Quite a few mutualistic symbioses are known, but unfortunately they don't get nearly the attention they deserve. Without their existence, however, life as we know it would not exist. Let's consider a few examples.

Nitrogen is essential to all life. It is required for the synthesis of nucleic acids, proteins, and a host of other important biomolecules. However, without the action of certain prokaryotes, little nitrogen would be available to the biosphere. There are several species of bacteria that can convert atmospheric nitrogen  (N2) into a form (e.g., ammonium) that can be used by other life. One of the most important groups are those bacteria that form a symbiosis with certain plants. For example, Rhizobium colonize on the roots of pea plants, where they fix nitrogen. The plant provides carbon to the bacteria, and the bacteria provide nitrogen to the plant; a classic and extremely important example of a mutualistic symbiosis. Tutorial 20 will examine, in greater detail, the role that bacteria play in the cycling of nitrogen in the biosphere.

Humans serve as a host for a number of mutualistic symbioses with prokaryotes. Researchers have studied them to varying degrees. For example, one (or more) of the bacteria species that colonize our lower gastrointestinal tract has the ability to synthesize vitamin K (which humans cannot produce). Vitamin K is taken up by your intestines and used in the blood-clotting reaction (and possibly other reactions). In this symbiosis, we get an essential vitamin and the bacteria get a source of carbon from the food we do not completely digest. (The majority of bacteria in our GI tract are located past the major nutritive absorbing areas of the intestine.)

The mutualistic symbioses between prokaryotes and humans may also play a more general and important role. Go to the site that discusses the role of germ exposure during early infant development, and when you return be prepared to answer a question concerning a role that symbiotic bacteria may play in the development of specific cells involved in the human immune system.  Click here to read about Good Bugs.


In a parasitic symbiosis, one member of the symbiosis benefits at the expense of another. Parasitic bacteria that cause disease in their hosts are called pathogens. These pathogenic bacteria cause disease by either invading healthy host tissue or by producing toxins that poison the host. Exotoxins are proteins secreted by prokaryotes, whereas endotoxins are protein components of the outer cell membrane in some gram-negative bacteria. Clostridium botulinum (the causative agent of botulism) is a notorious exotoxin-secreter, as is Vibrio cholerae, which causes cholera. The causative agent of typhoid fever, Salmonella typhi, produces endotoxins that counteract the human host's natural defenses.

Cholera and the Importance of Water Balance

Cholera is a disease caused by Vibrio cholerae. This bacteria is spread via contaminated water supplies, and people who drink water tainted with this organism can succumb to the disease. The mortality rate of untreated, symptomatic individuals can be quite high; afflicted individuals can die within 24 hours. The bacteria itself does not cause the disease, rather it is the exotoxin it secretes.

To understand how cholera kills, one needs to know about osmosis (the net movement of water across a selectively permeable membrane, from lower solute concentrations to higher solute concentrations). So, what does osmosis have to do with cholera? Everything.

Vibrio cholera colonizes the intestines. The exotoxin (cholera toxin) stimulates the cells that line the lower GI tract (the intestinal epithelium) to secrete massive amounts of excessive ions into the lumen (the cavity) of the intestine. This creates an extremely hypertonic state within the intestinal lumen, relative to the epithelium. Think about the consequences of this in terms of osmosis and be prepared to make a prediction regarding the most severe symptoms of cholera.

The Body As a Community

Remember that our own bodies are teeming with bacteria, as are virtually all eukaryotes. At birth we were devoid of bacteria, but as we acquired bacteria through feeding, and simply by being around other humans, our bodies became colonized with hundreds of different species of bacteria. The relative proportions of these species are variable. As you should have learned on your Web tour about opportunistic infections, some of our commensalistic bacteria can become parasitic when our natural defense mechanisms become depressed.

The relationship between host and symbiont can be quite complex. Termites are a good example of this complexity. We normally think of these insects as wood eaters, and indeed they can dine on our homes. However, they themselves cannot directly digest the wood. Inside the termite gut is a menagerie of protozoa (a protist; to be discussed in future tutorials) that ingest the wood particles consumed by the termite. But even these protozoa cannot directly digest the cellulose. Rather, living in and around the protozoa are bacteria that can degrade the wood. So it is the microsymbiont living within the microsymbiont of the termite host that actually degrades the wood. Life is interrelated in surprising ways.

The Sporulation Advantage

This Bacillus is able to form endospores (boxed area in photograph) that are resistant to harsh conditions.
By now you should understand why bacteria dominate the globe. They divide rapidly, produce toxins, live just about anywhere, and are metabolically diverse. In addition, some bacteria can adopt an alternative form that allows them to survive extreme conditions. More specifically, many bacteria are able to form endospores (thickly coated, resistant cells) during harsh conditions (see image). Typically, sporulation (the formation of endospores) is triggered by a decline in key nutrients in the environment surrounding the bacteria. Some endospores can survive drying, freezing, or boiling. For this reason, it is not always sufficient to boil water to destroy all bacteria.


This tutorial continued our discussion of prokaryotes by introducing their cell walls and various means of locomotion. Prokaryotes have a number of modifications to their walls. The gram-positive bacteria have walls rich in peptidoglycans (a class of molecule derived from sugars and proteins). Gram-negative bacteria have a double-walled character and do not have a great deal of peptidoglycans (which is why they do not stain well with Gram's stain). On the other hand, the gram-negative bacteria are often rich in lipopolysaccharides (a class of molecules derived from lipids and sugars), which can be toxic to other life forms; many bacterial toxins belong to this class of molecules. An additional sticky capsule (and/or pili) may be present, which help some bacteria adhere to various substrates.

In addition to modifications to their walls, a variety of prokaryotes have the capability of moving about their environment. This movement is not random, but rather, can be governed by the presence of various molecules in the environment. Some bacteria can detect the presence of nutrients, and they move toward a high concentration of a particular carbon source in a process generally referred to as chemotaxis.

Most prokaryotes are very sensitive to their environment and can alter their behavior in response to changing conditions. For example, most species of Bacillus can form hardy spores in response to stressful conditions. These spores have low metabolic activity, can survive extreme conditions (e.g., boiling water) and are long-lived.

A great deal of life on the planet depends on prokaryotes, either directly or indirectly. Nitrogen fixation is one example of how bacteria can be beneficial. Many prokaryotes form intimate associations with other species. These symbiotic relationships can take on a variety of forms. At one extreme are the mutualistic relationships. In a mutualistic symbiosis, both species derive benefit from the association; the bacteria that live in our lower digestive tract provide us with a number of vitamins and, in turn, we provide them with a source of carbon from the food we do not digest ourselves. At the other extreme is a parasitic symbiosis, in which the symbiont benefits at the expense of the host. Such parasitic bacteria are usually termed pathogenic because they can cause serious diseases. Microbiologists have provided us with an appreciation for prokaryotes, and their discoveries have led to new opportunities for using prokaryotes to better humanity and to combat diseases caused by pathogenic bacteria.

The next tutorial will discuss the ecological significance of various types of prokaryotes (e.g., those used to clean up oil spills and fix nitrogen).