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The First Organisms

What is the meaning of the word "prokaryote"?
pro =
karyon =

What is the meaning of the word "eukaryote"?
eu =
karyon =

At one time, all prokaryotes were lumped into "Kingdom Monera."
We now know that there are two distinct lineages of prokaryotic organisms:

This tree is based upon shared and derived rRNA sequences.

Or, simplified....

Note the recency of common descent. Not what one might expect. (Recall that the diagram can be swiveled at any node, and it would be just as correct to have Archaea and Eukarya on the left side of the phylogenetic tree).

The earliest known fossil organisms are nearly indistinguishable from archaebacteria. It is currently thought that Archaean-like prokaryotes were the first inhabitants of earth, and spent their first 2 billion years alone (taxonomically).


Both Archaea and Bacteria are considered to be pre-nuclear (from the Greek pro, meaning "before" and karyon, meaning "nut").

They lack membrane bounded organelles or nuclei, though many do have internal membrane systems.

NOTE: The term "prokaryote" descriptive, not phylogenetic: the lack of a characteristic (in this case, a membrane-bounded nucleus) usually is not a very good basis for classification.

The divergence of prokaryotic lineages happened so long ago that it may not be possible to determine exact evolutionary relationships.


Domain Archaea: Nature's Extremophiles

This Domain includes organisms that can withstand the most extreme environments of any living thing known. They are not classified on the basis of common descent (as far as we know), but rather are placed into form taxa that reflect their metabolic strategies (which do not necessarily represent physiological homologies).

Archaean Morphology (<--required link!)

  • DNA is a single, circular chromosome with a single copy of every gene (archaeans are haploid)
  • genome size ranges from just under 500,000 base pairs (537 protein-coding genes in Nanoarchaeum equitans) to nearly 6 million base pairs in Methanosarcina acetivorans.
  • some shapes are similar to those of Bacteria (spherical, rod-shaped)
  • cell wall is made of material unique to Archaeans
  • flagella are composed of multiple proteins (flagellins)--encoded by several genes--unique to Archaeans
  • Archaeans have tRNAs that are unique to them, different from all other tRNAs.
  • Archaean ribosomes are more similar to those of eukaryotes than to those of Bacteria.
  • cell membrane structure and composition is unique to Archaeans


    Domain Bacteria: They're Everywhere

    The beta taxonomy (The level of taxonomy concerned with arranging species into higher (and sometimes lower) taxa) of these organisms isn't complete, and their true evolutionary relationships may never be known. Modern classification changes as new data become available.

    Bacterial Structure and Function

  • Bacteria may be unicellular, aggregate or colonial.
  • More derived species may form colonies with a division of labor among cells.
  • The genome is contained in a single, circular chromosome with one copy of each gene (like archaeans, bacteria are haploid)
  • The average bacterial genome has about 1000 genes.
  • Bacteria may be categorized (but not classified) on the basis of shape: Bacterial shapes do not necessarily reflect phylogenetic relationships. There may be

    Still, shape is useful for grouping and identifying on a visual basis.


  • External to the cell wall, some species have a gel capsule that is often protective against predators (or a host's immune system).

  • Bacteria range in size from 1-5 micrometers--much smaller than most eukaryotic cells (100-1000 micrometers).

  • The circular chromosome of double-stranded DNA is organized in the nucleoid region of the cell.

  • The average bacterium has about 1000 genes.

  • some bacteria contain plasmids small, circular pieces of autonomously replicating DNA. A plasmid usually contains only a few genes, and is not considered part of the bacterium's genome. However, it may confer phenotypic traits (e.g., antibiotic resistance or the ability to produce toxins) on the host bacterium.
  • Many species have fimbriae (singular = fimbria extending from the cell surface that allow them to attach to substrates or to other bacteria.

  • A pilus (plural = pili) is type of fimbria used in exchange of genetic material during conjugation.

  • Most bacteria are motile (they can move); the means of locomotion is another way to identify them.

    Taxis means "movement. Bacteria exhibit various forms of positive or negative taxis, depending on species and specific environmental conditions (e.g. phototaxis, chemotaxis, etc.). Bacteria may move by means of


    Gram Stain

  • Another diagnostic character is the nature of the cell wall, which is present in most bacteria.
    (Exception: mycoplasmas, all of which are intracellular parasites; they are not classified via Gram Staining, as they have no cell wall.)

    Two main types of cell wall can be distinguished with Gram Staining.


    Bacterial Reproduction

    Bacterial cells can be grown in culture on appropriate nutrient media (e.g., agar with broth). A bacterial colony on an agar plate is called a lawn, and various species have characteristic lawn phenotypes, which make them useful in the study of bacterial genetics.

    Bacteria may reproduce via:

    Endospore: Dormant Phase

    Some species can form a tough, environment-resistant structure called an endospore that can survive extremes of temperature and drought.

    An endospore is little more than the DNA surrounded by a thick wall. It's nearly impossible to kill an endospore, so pathogens that can form them (e.g. Clostridium tetani, the cause of tetanus) can be particularly pernicious.


    Metabolic Diversity of Prokaryotes

    Three basic types of organisms re: oxygen tolerance/metabolism

    In the Krebs Cycle, the terminal electron acceptor can be


    Four Main Categories of Prokaryotic Energy Transduction

    How did it all begin?

  • Early hypotheses about the origin of bacterial metabolism suggested that the earliest cells used ATP from the "primordial soup".

  • Problem: it's not likely there was enough ATP out there to fuel those newly made cells. ATP is highly unstable, and won't remain in solution for long.

  • More plausible is the idea that CO2 was the first Carbon source, and that early cells had plasma-membrane anchored enzymes that could oxidize inorganic compounds to make the energy needed to drive synthesis of carbon compounds.


    Ecological Importance of Prokaryotes

  • Along with fungi, they are the biosphere's main decomposers.
  • Many are symbiotic

    The Importance of Nitrogen Metabolism

    Let's have a look at the Nitrogen Cycle

    And here are some of our pals who perform this marvel:


    Nitrogen-fixing bacteria in the roots of a leguminous plant

  • Nitrogen fixation - conversion of atmospheric nitrogen to nitrogen compounds (ammonia, nitrite or nitrate) that are usable by plants

  • Denitrification - nitrate-->nitrite-->ammonia-->N2

  • Nitrosomonas spp. - converts ammonia to nitrite

  • Pseudomonas spp. - converts nitrite or nitrate into N2 (denitrification)

    Although Pseudomonas bacteria are ubiquitous in the environment, they usually do not cause disease. However, in an immunocompromised animal, they can proliferate and cause infection. Hence, they are considered opportunistic pathogens.


    Prokaryotes as Pathogens

    A pathogen is a disease-causing agent.
    The vast majority of bacteria are non-pathogenic, or even beneficial.
    However, a number of bacteria can cause disease in plants and animals.

    Koch's Postulates

    In order for a microorganism to be declared the cause of a particular disease it must meet four criteria (Koch's Postulates): Some pathogens don't meet the postulates, so clinicians must be a little bit flexible when trying to determine how to treat difficult-to-culture pathogens.

    How do bacteria cause diseases?

  • Vocabulary Word of the Day: An iatrogenic infection - one that is caused by the place of healing or the healer (iatros is Greek for "healer").

    Antibiotics: Fighting Back

    Competition exists at even the microscopic level. Antibiotics are substances that inhibit the growth of prokaryotic cells. They are manufactured not only by plants and fungi, but also by some bacteria.

    Humans can use and modify naturally produced antibiotics for their own use and protection against bacteria.

    Antibiotics are not effective against viruses, and generally not against most eukaryotes. Their are primarily effective against bacteria, though they can have side effects in eukaryotes.

  • A bacteriostatic substance inhibits the growth of bacterial culture.

  • A bacteriocidal substance kills bacteria outright.

    Different antibiotics attack different aspects of the bacterial life cycle, and most fall into one of four main categories, in terms of their mechanism of action:


    Bacteria can be our competitors, our enemies, or our allies, but they form vital, ubiquitous threads in the Web of Life.