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Prokaryotes II - Structure and Function

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Introduction and Goals

Figure 1. Vibrio cholerae.

Figure 1 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 metabolism, structure and movement.

By the end of this tutorial you should have a basic understanding of:

  • Prokaryotic cell structure
  • Prokaryotic movement and responses to the environment
  • The different nutritional modes of prokaryotes
  • The diversity of prokaryotic carbon sources
  • Bioremediation

Performance objectives:

  • Diagram the structure of bacterial cell walls and describe how this relates to virulence
  • Identify the nutritional modes seen in prokaryotes and the sources of carbon that they can use
  • Describe the structure of the prokaryotic flagella
  • Discuss the different types of taxis and why this response is important
  • Explain the advantage of sporulation to prokaryotes

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.  Most prokaryotes have cell walls, but they are structurally different than those of the plants, fungi, and protists (Archaea have unique molecules in their cell walls and cell membranes that we won’t discuss here).


Figure 2. Gram-positive versus gram-negative bacteria. (Click to enlarge)  Gram's stain is used to differentiate bacteria, based upon the amount of peptidoglycan in their cell walls.

The cell walls of Bacteria 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 (Figure 2)

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. In particular, 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 the host organism. 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.

Many pathogenic diseases are caused by gram-negative bacteria. Do a Web search on Yersinia pestis.  What disease does this bacterium cause in humans?


The Capsule and Pilus

Numerous adaptations have evolved in host organisms to fight bacterial infections, and the numerous 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 a bacterium, and they help 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 sexually transmitted disease (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 some can actually move quite quickly, up to 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 over 400 miles per hour!)


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 similar to the action of a corkscrew. The most common type of movement in prokaryotes is through 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 structurally 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 3.  Flagellum of a gram-negative bacterium. (Click to enlarge)

Figure 4. 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 an 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.

Prokaryotes (and eukaryotes) that exhibit taxis typically respond to some environmental cue. If the cue is a chemical, such as a carbon source, then the organism typically responds in a positive manner and moves toward the source in a response referred to as positive chemotaxis (Figure 4). Conversely, if the chemical is noxious, then the organism typically responds in a negative manner and moves away from the source in a process known as negative chemotaxis. Other environmental cues are also used (e.g., light, gravity, and magnetism). What type of taxis is a motile bacterium  displaying when it moves toward light?


Nutritional Modes of Prokaryotes

During the course of evolution, prokaryotes have adapted to a myriad of environments. Part of this adaptation involves different ways of obtaining energy and carbon. In looking at the diversity of prokaryotes, one observes many different nutritional modes. When considering nutritional modes, there are some general features that are commonly used to categorize the nutritional state of any life form.

All life can be categorized nutritionally, according to how an organism obtains its energy and from where it gets its carbon. The prefixes "chemo" and "photo" are used to describe whether the energy comes from a high-energy molecule (e.g., glucose) or from light, respectively. "Auto" and "hetero" are used to describe whether carbon dioxide or a more complex form of carbon is used as a carbon source, respectively. The prefixes are then affixed to the suffix "troph," meaning nourishment.


Diversity of Carbon Sources

Prokaryotes can use carbon in a variety of forms, both as an energy source and as a precursor for anabolic reactions. As you've learned, carbon dioxide is the simplest form of carbon used. Organisms that use this simple form of carbon are often called "carbon fixers." (You will learn more about this process in the photosynthesis tutorials 26 and 27)


Figure 5. The Exxon Valdez oil tanker. (Click to enlarge).  The Exxon Valdez ran aground in Alaska's Prince William Sound in the spring of 1989, dumping approximately 11-million gallons of oil.  Photo source: Office of Response and Restoration, National Ocean Service, National Oceanic and Atmospheric Administration

Most prokaryotes use sugars (monosaccharides and disaccharides) and complex carbohydrates (e.g., starch) as a carbon source. However, very unusual forms of carbon can also be used by some prokaryotes. For example, some prokaryotes can feed on oil. Although a bane to the oil fields, these oil-eating bacteria have been used to help clean oil spills (Figure 5).

Some bacteria are capable of using synthetically produced carbon compounds such as TNT (used as an industrial and military explosive) and PCBs (banned substances which are persistent organic pollutants in the environment) as a carbon source. These bacteria metabolize these compounds and produce nontoxic by-products. Humans have exploited this ability by using various species of bacteria for the removal of toxins from the environment; a process known as bioremediation. There is an emerging field of civil engineering that utilizes bacteria (along with other eukaryotic microorganisms) for the purpose of cleaning contaminated soils, wells, and river sediments.

The Sporulation Advantage

Figure 6. Endospore within the prokaryote Bacillus.

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, necessitating the use of higher pressures and temperatures in an autoclave.


This tutorial continued our discussion of prokaryotes by introducing their cell walls, various means of locomotion, and nutritional modes. 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.

This tutorial presented the diversity of prokaryotic nutritional modes and carbon sources. Bacteria can use simple sugars, as well as complex sources of carbon. Some bacteria can live off oil, and some can decompose cellulose. The ability to breakdown complex carbon sources has been utilized for a variety of purposes. The field of bioremediation is based, to a large extent, on the use of bacteria that can breakdown harmful compounds that have been introduced into the environment from various industrial and agricultural sources. For example, bacteria are capable of breaking down TNT and PCBs.

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.

The next tutorial will discuss the ecological significance of various types of prokaryotes and the evolution of this group.



After reading this tutorial, you should have a working knowledge of the following terms:

  • bioremediation
  • capsule
  • cell wall
  • endospore
  • endotoxin
  • exotoxin
  • flagellin
  • flagellum (pl. flagella)
  • gram-positive
  • gram-negative
  • Gram's stain
  • lipopolysaccharide
  • peptidoglycan
  • plasma membrane
  • sporulation
  • taxis

Case Study for Prokaryotes II

The bacterium Clostridium botulinum produces one of the most potent human toxins known – the botulism toxin. This toxin has the effect of inhibiting the neurotransmitter acetylcholine which is required for a nerve to stimulate a muscle. As a result, a person who has ingested the botulism toxin suffers from flaccid paralysis which can lead to death. (Cosmetic surgeons have taken advantage of the actions of this toxin to use in the control of wrinkles. The toxin, at low concentrations, interferes with the underlying muscles' ability to contract which smoothes out wrinkles, particularly between the eyes and on the forehead).

Clostridium botulinum is an anaerobic gram positive bacterium. The actively growing cells are intolerant of oxygen (in other words, exposure to too much oxygen is lethal to these bacteria) but they can form resistant spores that withstand exposure to O2.  Sporulation can only occur in anaerobic environments and the neurotoxin is only produced during sporulation.   This bacterium is widely distributed in soil, sediments of lakes and ponds, and decaying vegetation. Illness and death due to Clostridium is not due to an infection but rather intoxication as a result of consuming the toxin (the bacterium itself does not cause illness but the neurotoxin it produces does).

In the United States, one of the most common routes of exposure to the botulism toxin is due to the consumption of improperly canned foods. Some people have expressed concern that Clostridium botulinum could be used in a terrorist attack.

Clostridium botulinum bacteria up close. 
Image courtesy of the US Centers for Disease Control.

  • What advantage does sporulation provide the Clostridium botulinum bacterium?
  • What conditions would be necessary for a canned food product to become tainted with botulism?
  • How is botulism poisoning prevented?
  • Why would a large scale release of Clostridium botulinum be an ineffective way to poison a large number of people?

Now that you have read this tutorial and worked through the case study, go to ANGEL and take the tutorial quiz to test your understanding.  Questions?  Either send your instructor a message through ANGEL or attend instructor office hours (the times and places are posted on ANGEL).