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Posted by Jim True on August 31, 2004 6:05 AM. Last Updated October 22, 2006 9:23 PM

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CH 27: Prokaryotes and the Origins of Genetic Diversity

Prokaryotes

• In terms of sheer numbers, prokaryotic organisms, almost all of which are single celled, are the predominant form of life on Earth.
• Most prokaryotes are benign (causing neither harm nor benefit) or are beneficial to other life forms, either directly or indirectly.
• Many types of bacteria are decomposers, organisms that convert organic matter from dead organisms back into component molecules. (Important function because they cause organic material to break down to molecular and elemental material: the great recyclers).
• Also, many bacteria live in constant association with (on or in) other living organism, E. coli.

Prokaryote Systematics

• Bacteria are relatively uniform in appearance and so are difficult to classify.
• However, more than 1,200 genera and over 5,000 species have been described.
• Estimates of actual extant (opposite of extinct) species numbers range from 400,000 to 4 million!
• Until recently, all bacteria were placed in a single kingdom, the Monera (also known as the Prokaryotae).
• However, recently discovered molecular differences, especially in ribosomal RNA has caused a major taxonomic reorganization of the largest groupings of living organisms from 5 to 6 kingdoms.
• These 6 kingdoms of life are now included in 3 domains, a taxonomic rank that was established above kingdoms as the most inclusive category.
• Even more recent molecular work has shown that the "six kingdom concept" will probably be dramatically changed within the next few years to perhaps as many as 15 to 18 separate kingdoms!
• Domain Bacteria, which includes most of our common bacteria and is the largest of the prokaryotic groups.
  • This domain originally was thought to contain a single kingdom, but scientists have differentiated at least 5 major groupings in the domain.
  • As of this time, these groupings have not yet been given a kingdom or phylum status.
• Domain Archaea - simple bacteria that live mainly in extreme environments similar to conditions on the primitive Earth. Two distinct groupings have been identified within this domain.
• Domain Eukarya -- contains the four familiar kingdms of eukaryotic organisms, the Protista, Fungi, Plantae and Animalia. Of these, the Protista at least will probably be split into numerous kingdoms.

Prokaryote Characters

• Typically small in size, usually 1-5 microns, although a few get quite large.
• All lack a membrane around the DNA (no nucleus).
• Virtually no organelles, although ribosomes (different than eukaryotic) are present, as are cytoplasmic granules that act as energy storage sites.
• There is little internal structure, although cell membrane may be highly folded.
• The infolding of membranes found in aerobic and photsynthetic bacteria are very reminiscent of the cristae and thylakoids of eukaryotic mitochondria and chloroplasts, respectively.
• This is one of the reasons that these eukaryotic organelles are thought to have once been independent cells.
• There are three common shapes to bacterial cells:
  1. Coccus (cocci) - Spherical cells.
     • If cells form chains, are referred to as streptococci, e.g. Streptococcus pyrogenesIf they form a cluster, they are called staphylococci, e.g Staphylococcus aureus (lives on skin, can cause "staph" infections).
  2. Bacillus (bacilli) -- Rod-like cells, e.g. Lactobacillus plantarum, used to produce lactic acid in the fermentation of cucumbers to produce pickles.
  3. Spirillum (spirilli) -- An elongate corkscrew shaped cell, e.g. Spirillum rubrum, a common saprobic bacterium. Other spiral shapes include:
     • Vibrio -- short, comma shaped cells e.g. Vibrio vulnificus, which produces shellfish poisoning (eating raw oysters!).
     • Spirochetes, which are short spiral cells, e.g. Treponema pallidum, which causes syphilis in humans.
• Most possess a cell wall that is structurally different than eukaryotes.
• The cell walls provide structural support and allow bacteria to be adapted to hypotonic environments, however, they do poorly in hypertonic environments.
• Peptidoglycans -- two special sugar groups crossed linked to polypeptides only in bacterial cell walls.
• Archean bacteria have cell walls but no peptidoglycan.
• Two groups of bacteria can be differentiated by the peptidoglycan content of their cell walls:
  • Gram-positive-- Bacteria with a thick layer of peptidoglycan outside the cell membrane.
  • Gram-negative -- Bacteria possess a very thin peptidoglycan layer sandwiched between a thick outer membrane and the inner cell membrane. Cell wall is thus more complex.
• The composition and structure of the gram-negative walls make these more pathogenic and resistant to antibiotics.
• Most antibiotics operate by inhibiting the construction of peptidoglycans, thus gram positive bacteria historically were more susceptible to antibiotic treatment.
• In addition to the cell wall, other extrenal structures may also be present:
  • Capsule -- a sticky slime layer that surrounds the cell wall in some bacteria.
    • May provide protection against phagocytosis, and also can serve to attach the bacteria to surfaces.
    • Presence of a capsule is found in many bacteria that form colonies, where cells are permanently aggregated together.
  • Pilus ("hair") (Pili) -- Hairlike appendages (usually 100's or more) on surface of cell.
    • Allow attachment to surfaces (e.g. Neisseria gonorrhoeae), other bacteria, and also exchange of genetic material.
• Many bacteria are motile ("mot" -- motion), capable of moving about in the environment.
• The most common means is by the use of a flagellum("whip") or multiple flagella -- One or more long hairlike extensions on the surface of the cell, used for locomotion.
• The structure and mechanism of movement differ from eukaryotic cells.
• A bacterial flagellum is a solid, three piece structure that spins like a propeller.
• Another form of motion occurs in some spirochetes, which possess dual spiral filaments beneath the cell wall.
• These rotate like corkscrews, moving the bacterium.
• Some filamentous (chain forming) bacteria use sticky threads that they can anchor to a substrate.
• They then slide over the sticky filaments.
• Flagellar motion produces the greatest speed -- some bacteria can move 100 times their body length per second!

Prokaryote Genome

• the most extensive bacterial DNA found are only about 1/1000th as large as in eukaryotes.
• The DNA is found within two structures:
  • Nucleoid -- the larger of the two structures, it is a highly tangled single loop of double stranded DNA.
  • Plasmid -- Small rings of DNA, often numerous in bacterial cells, each of which contain only a few genes.
    • The cell can survive without plasmids, but the genes allow many specialized characteristics.
    • Examples include antibiotic resistance, and the ability to metabolize special nutrients.
    • Plasmids can be replicated without replication of the nucleoid, and can also be transferred between bacterial cells.

Prokaryote Reproduction

• All prokaryotes exhibit only asexual reproduction in binary fission.
• This is NOT mitosis, as there are no chromosomes, spindle fibers or other structures associated with nuclear division.
• As a result, the replication of the nucleoid and division of the cell into two cells can occur quite rapidly, as little as 15 minutes for many bacteria.
• Although there is NO sexual reproduction, there can be gene transfer among bacterial cells.
• This can occur through one of three mechanisms:
  1. Transformation -- fragments of DNA released from one bacterial cell during lysis can be absorbed and incorporated by another cell.
     • This can occur between unrelated species.
  2. Conjugation -- In this case, living cells make actual physical contact and transfer plasmids via their pili.
  3. Transduction -- Lytic prophage carries host DNA fragments to new host.
• Most alterations to the bacterial genome involve mutation.
• Mutational effects can be expressed very rapidly because of the short generation times of most bacteria.
• These rapid generation times and mutational effects allow bacterial populations to increase to phenomenal numbers quickly.
• This is how diseases caused by bacteria can quickly build and spread in host population.
• In addition, many bacteria are able to withstand unfavorable environmental conditions through the formation of an endospore, (endo means 'inside') e.g. Bacillus anthracis.
  • Endospores are dormant, highly resistant cells.
  • They form within an original cell when it is subjected to adverse conditions. The outer cell is destroyed by the environment, leaving the endospore.
  • Endospores can remain dormant for centuries or even MILLENIA until suitable conditions return!
  • These are not reproductive spores as are found in plants and fungi.

Prokaryote Nutrition & Metabolism

Bacteria are metabolically diverse in both energy acquisistion and energy production via cellular respiration.

1. Energy Acquisition(Table 27.1) -- Includes two main groups:
   1. Autotrophs ("self feeder") -- bacteria that manufacture their own food supply. Two types:
      • Photoautotroph -- use energy from light to make food.
        • Cyanobacteria (or "blue-green algae") photosynthesize much like green plants, exacept that the pigements are in the cell membrane.
        • Other photosynthetic bacteria use near-infrared wavelengths to energize pigments and do not produce O₂ as a final product.
      • Chemoautotrophs -- use engergy from inorganic molecules such as H₂S or nitrogen to produce ATP which is then used to produce food.
   2. Heterotrophs ("other feeders") -- obtain energy from outside sources:
      • Photoheterotrophs -- in some prokaryotes that can generate ATP from light, but must obtain carbon from organic molecules.
      • Chemoheterotrophs -- must consume organic molecules in order to make ATP and provide carbon.
        • Chemoheterotrophs may be saprobes, which feed on dead organic matter, or may feed on living tissue (may or may not be pathogens).

   Because of their small size, many bacteria live on or in other living organisms, a relationship known as symbiosis ("process of life together"). (An intimate or physical relationship between two unrelated organisms where one lives on or inside the other).

   • Sybioses are quite common among all kingdoms of living organisms.
   • There are a number of patterns of sybiotic patterns but the three most common are:
     1. Mutualism -- both individuals beneft from the relationship, e.g., humans and Escherichia coli.
     2. Commensalism -- one organism benefits, the other is neither harmed nor benefitted, e.g. certain staph bacteria on human skin.
     3. Parasitism -- one organism (parasite) benefits, the other (host) is harmed, e.g. all pathogenic bacteria.
2. Energy Production (Cellular Respiration) - Two main patterns:
   1. Aerobic -- Require O₂ as final electron acceptor for respiration. Most bacteria are aerobes.
   2. Anaerobic -- Cellular respiration in the absence of oxygen, using inorganic molecules such as SO₄, NO₃ or Fe as final electron acceptors. Most archaeans are anaerobes.
   • Some anaerobic bacteria are facultative, meaning that they can perform cellular respiration in either the presence or absence of O₂.
   • Other are obligate anaerobes to whom O₂, even at low concentrations, is deadly. Many of the Archaea are obligate anaerobes.
   • Most aerobes are obligate.

Prokaryotic Types

1. Archaea ("Ancient") - There are three main groups, all of which live in conditions very similar to that found on ancient Earth.
• because these environments represent various extreme conditions, archaeans are collectively referred to as "extremeophiles" ("phil" -- love).
• Interestingly, the lack of peptidoglycan in the cell walls makes archaeans more closely related to eukaryotes than the other more common bacteria!
1. Methanogens ("methane generators") -- Obligate anaerobes found in anoxic sediments, swamps and digestive tracts of many animals (including humans). They produce methane (swamp gas), CH₄, from CO₂ and H₂.
• Methanogens are used in the bacterial decomposition of human sewage.
2. Extreme Halophiles ("salt lover") -- live in hypersaline environments such as brine pools.
• The typical salinity of seawater is about 3.5%. Extreme halophiles thrive in waters of 15-20% salinity!
• These are purplish-red bacteria and typicially stain their environment that color.
3. Thermoacidophiles ("temperature acid lover"), AKA thermophiles -- these bacteria typically live in very hot (45-110 degrees C) and often acid (pH of 1-2) environments. an example of such an environment is hot sulfur springs such as is found in Yellowstone Park.
• Currently, the methanogens and halophiles are included in one taxonomic subdivision of the Archae, while the thermophiles are placed in a separate group.
2. Bacteria -- Most identified prokaryotes are in this domain. They are found virtually everywhere on Earth and on and in many organisms as well.
• Table 27.3 on pages 538-539 lists the major groups of bacteria. Some taxonomists have already given these five major groupings kingdom status.
• As already mentioned, many bacteria are harmless or quite helpful to humans and other organisms.
• However, many are pathogenic.
• Pathogens cause disease by one of two means:
1. Secretion of exotoxins -- Toxic compounds that are secreted externally so the pathogen does not need to be present to cause disease symptoms. Examples include:
   • prophage infected Clostridium botulinium (botulism);
   • Vibrio cholerae (cholera).
   • In both diseases, individuals can be infected by eating substances or drinking fluids containing the toxins.
2. Secretion of endotoxins -- These are toxins that are components of the cell wall.
• Examples include various species of Salmonella.
• Antiobiotic treatments used to be very effective against many bacteria, especially gram positive types.
• However, indiscriminate use of antibiotics over the past few decades has resulted in many antiobiotic resistant strains of bacteria.

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