Classifications of the 1800's

     IN THE BEGINNING.... all life forms were thought to be either plants or animals. Accordingly, in the 1700's, Carolus Linnaeus designed 2 kingdoms into which all known organisms could be categorized. These 2 kingdoms were...

1. Vegetalia, and
2. Animalia. 

Classifications of the 1800's

   As microorganisms were discovered and studied by the pioneers of microbiology, it soon became clear that the "two-kingdom" system could not accommodate these new single-celled life-forms. Ernst Haeckel combined these tiny microorganisms into a separate third kingdom, called the Protista. 

   As the field of microscopy continued to advance with increasingly more powerful light microscopes, and eventually the electron microscope, the differences between bacteria and other microorganisms became more clear. 

The 5 kingdom system was in place for while as one of the more successful classifications of the 20th century. 

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    Then... There Were 3

   In 1977, evolutionary biologist Carl Woese, discovered a new type of cell that existed as a single-celled organism. Carl Woese made this discovery during his work comparing the nucleotide sequences of different types of cells, to uncover phylogenic relationships. 

Phylogeny is a diagrammatic hypothesis (giving us our phylogenic tree) about the history of the evolutionary relationships of a group of organisms, based on DNA evidence, morphological and physiological characteristics. 

The English Spelling for Eukaryotic and Prokaryotic is "Eucaryotic" and "Procaryotic"

    The nucleotide sequences that Carl Woese examined were those that formed the gene that codes for the ribosomal RNA (rRNA) which forms the small ribosomal subunit. Woese's work not only found a fundamental difference between prokaryotic cells and eukaryotic cells, but he also found that prokaryotic cells were divided into 2 distinct groups possessing unique morphological and physiological characteristics. ​​

Small subunit ribosomal RNA, 5' domain taken from the Rfam database. This example is RF00177

   Bacteria cells were known at the time, but there was another type of cell that was distinctly unique from both the eukaryotic cells and the bacteria cells. Carl Woese originally called this newly discovered group of single-celled organisms archaebacteria, which translates to "ancient bacteria". There was a campaign to change the taxonomic structure of the day to include a third domain for the archaebacteria.   

Taxonomy the word taxonomy comes from the Greeks words meaning "method" and "arrangement".  It is the science of categorizing, defining and naming groups of organisms based on common genetic, morphological, and/or physiological characteristics. 

Bacteria

Archaea

    Following the initial discovery of different ribosomal subunit found in archaeal cells, more differences were soon discovered as well.  These discoveries confirmed that these cells were indeed in a category ALL THEIR OWN! Some of these differences include...

1. differences in cell wall composition
2. differences in lipids that form the cell membrane
3. differences in sensitivities to antibiotics
4. lipids, and sensitivity

   Eventually, in light of the overwhelming scientific evidence, the taxonomic structure was finally reorganized into the 3-domain system we know today. To further distinguish the archaebacteria as a separate domain from bacteria, the name was changed to simply, "archaea". 

Comparisons

   ​Archaea have the same general appearance as bacteria, but upon further examination, archaeal cells have more in common with eukaryotic cells than bacteria cells. Despite their differences, all of the organisms in both the domain bacteria and the domain archaea are entirely made up of prokaryotic organisms. The names given to the two cell types derive from Greek words: ProKaryotic = ‘before nucleus’ EuKaryotic = ‘true nucleus’

Prokaryotic Cell

Most bacterial cells contain a single, circular chromosome that exists in the nucleoid region of the cytoplasm.

Eukaryotic Cell

Eukaryotic cells contain multiple linear chromosomes that are housed within the nucleus of the cell.

Compartmentalization

   Eukaryotic cells are compartmentalized. They have a nucleus which is separated from the cytoplasm by a nuclear membrane or nuclear envelope. Eukaryotic cells also contain many membrane-bound organelles.
​
   Prokaryotic cells do not have a nucleus, nor do they have membrane-bound organelles. ​

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The Cell Membrane of Bacteria and Eukaryotic Cells

    The cell theory states the following:
all life is composed of one or more cells
cells arise from other cells

 ​The cell membrane protects the cell by creating a barrier between what is inside the cell and what is outside the cell. 

  The structure of the cell membrane in bacteria cells and eukaryotic cells is very similar.  

   The cell membrane in eukaryotic cells and bacteria cell is made up of a double layer of phospholipids. Proteins, sugars and lipids are also incorporated into the cell membrane. 

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   The fatty acid tails orient themselves toward each other, to get away from the water.  This provides a barrier between the inside of the cell and the outside of the cell. 

  The components of phospholipids include  2 hydrophobic fatty acid tails and a hydrophilic head. The tails consists of UNBRANCHED fatty acid chains that consist of hydrocarbons (H-C). The fatty acids give a hydrophobic barrier that orients itself away from the intracellular fluid and the extracellular fluid. 

Phospholipids spontaneously form lipid bilayers in any aqueous environment due this amphipathic nature of lipid molecules.

  The hydrophilic heads are in contact with the inner and outer liquid medium. The hydrophilic heads consist of choline, phosphate, and glycerol. 

Comparing the Phospholipids of
​Archaea to Bacteria Cells

   The type of fatty acids found in the phospholipids of bacteria and eukaryotic cells are UNBRANCHED fatty acid chains.​

   The phosphate groups of the phospholipids in bacteria and eukaryotic cells are bonded to the fatty acid chains using ESTER BONDS. 

​   In contrast, the phospholipids in archaeal cells contain BRANCHED ISOPRENE CHAINS instead of the unbranched fatty acid chains we see in bacteria and eukaryotic cells. In archaeal cells, the phospholipids contain ether bonds instead of ester bonds. 

    Archaea are extremely diverse and have adapted to many extreme habitats. Some forms have evolved to survive off of odd forms of nutrition such as sulfur and cyanide. Many members of the Archaea are found in extreme environments and are called "extremophiles". Some species of archaea can be found inside glacial ice in freezing temperatures. Others are found in deep-sea thermal vents feasting on sulfur bubbling up from the Earth, in a habitat where sunlight never reaches. Some species called thermophiles love the heat and are able to grow at temperatures well over 100 ◦C, that would boil water. There are examples of archaeal organisms that can survive or even prefer extreme levels of salinity, pH, or pressure. 

The Cell Wall

Peptidoglycan (cell wall) Provides bacterial shape and rigidity. The cell wall consists of alternating units of N-acetylglucosamine and N-acetylmuramic acid. The polysaccharide chains are cross-linked by a peptide bridge. It is a primary target of antimicrobial therapy – because it is specific to prokaryotes. 

BACTERIA

If they have a cell wall, it will contain some amount (either thick or thin) of peptidoglycan.

​Slime (extracellular polysaccharide): This is extracellular material, loosely associated with the bacteria, that is elaborated by some bacterial species that facilitates colonization of smooth, prosthetic surfaces such as intravascular catheters. Binary Fission MID 1 2) 

Capsule: This polysaccharide outer coating of the bacterial surface often plays a role in preventing phagocytosis of bacteria.

ARCHAEA

Like bacteria, archaeans have no internal membranes and their DNA exists as a single loop.

As with other living things, archaeal cells have an outer cell membrane that serves as a barrier between the cell and its environment. Within the membrane is the cytoplasm, where the living functions of the archeon take place and where the DNA is located. Around the outside of nearly all archaeal cells is a cell wall, a semi-rigid layer that helps the cell maintain its shape and chemical equilibrium. All three of these regions may be distinguished in the cells of bacteria and most other living things, but when you take a closer look at each region, you find that the similarities are merely structural, not chemical.
In other words, Archaea build the same structures as other organisms, but they build them from different chemical components. For instance, the cell walls of all bacteria contain the chemical peptidoglycan. Archaeal cell walls do not contain this compound, though some species contain a similar one. Likewise, archaea do not produce walls of cellulose (as do plants) or chitin (as do fungi). The cell wall of archaeans is chemically distinct.