Biodiversity: Domains

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Biodiversity Domains

• There are three principal domains of living
  organisms in the universal phylogenetic tree of
  life.
• They are Archaea, Bacteria, and Eukarya.
• The phylogenetic tree is a theoretical
  representation of all living things, constructed
  on the basis of comparative ribosomal RNA
  sequencing and reflecting evolutionary
  relationships rather than structural
  similarities.

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Prokaryotes

• Domain Archaea
• Domain Bacteria
• All members of these two domains are without
  membrane-bound organelles
• They all do have DNA and ribosomes

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Domain Archaea

• Many scientists hypothesize that the Archaea are
  the closest modern relatives of Earth's first
  living cells.
• Called "universal ancestors," these are the cells
  from which all other life is believed to have
  evolved. This hypothesis is based on two types of
  evidence.

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Domain Archaea

• Genetic analyses indicate that the Archaea domain
  branches off of the phylogenetic tree at a point
  that is closest to the tree's root.
• Furthermore, it has been observed that many of
  the Archaea prefer to live in extremes of
  temperature, salt concentration, and
  pHenvironmental conditions thought to be similar
  to those found on Earth over 3.5 billion years
  ago, when life first originated.

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Domain Archaea

• The Archaea share certain characteristics with
  Bacteria, others with Eukarya, and have some
  characteristics that are unique.

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Domain Archaea

• Cell Walls
• Archaea cell walls do not contain the complex
  material called peptidoglycan that is a signature
  molecule of the Bacteria.
• The examples of Eukarya cell walls are composed
  of chitin or cellulose, neither of which occurs
  in cell walls of Archaea or Bacteria.
• Nucleus
• Like the Bacteria, the Archaea lack a
  membrane-enclosed nucleus.

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Domain Archaea

• DNA
• Exists in a circular form in both Archaea and
  Bacteria. Archaea DNA is associated with histones
  as seen in Eukarya, not in Bacteria.
• Translation/transcription
• Archaea uses eukaryotic-like initiation and
  elongation factors, and their transcription
  involves TATA-binding proteins as in eukaryotes.
• Cell Machinery (such as protein synthesizing
  enzymes and RNA polymerases)
• The Archaea machinery more closely resembles that
  found in the Eukarya.

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Domain Archaea

• Unique Traits
• The lipids that comprise Archaea membranes are
  unique, resembling neither the Bacteria nor the
  Eukarya.
• The introns found in Archaea are unique.
• Certain members of the Archaea are able to
  produce methane gas.
• They thrive in environmental conditions that we
  would find extreme (high salt, high pH (very
  alkaline), high temperatures (a number of
  species, in fact, require temperatures over 80 C
  in order to grow, and can live in temps up to 113
  C, well above boiling), and low temperatures
  (Archaea are among the few organisms found in the
  frigid waters of the Antarctic)).

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Domain Archaea

• Extremophiles live in extreme environments
• Methanogens live in marshes and swamps where O2
  is absent, produce methane (marsh gas) as a
  waste product
• Extreme halophiles live in high salt environments
  (Great Salt Lake, Dead Sea)
• Extreme thermophiles live in very hot
  environments (deep sea thermal vents)

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Orange and yellow colonies of heat-loving
prokaryotes in the hot water of a Nevada geyser
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Domain Bacteria

• Outside their cell membranes, Bacteria posses a
  cell wall containing peptidoglycans
• Gram-positive bacteria have simpler walls with
  more peptidoglycan
• Gram-negative bacteria have more complex walls
  with less peptidoglycan
• Pili are appendages used to adhere to other
  surfaces
• About ½ are motile due to the presence of
  flagella
• Remember prokaryote genetics plasmids, binary
  fission, operons, mutation rates, transformation,
  conjugation, and transduction
• Most prokaryotes are in Domain Bacteria (e.g., E.
  coli)
• The most common shapes are spheres, rods and
  helices, and most are 1-5um

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The most common shapes of Bacteria
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Prokaryote Metabolism

• Prokaryotes can be placed in four groups
  depending on how they take in carbon and obtain
  energy
• Photoautotrophs photosynthesize, use sunlight
  energy to convert CO2 into organic compounds
  (e.g., carbohydrates)
• Chemoautotrophs dont use sunlight as a source
  of energy, instead they use H2S, NH3 or other
  inorganic molecules to convert CO2 into organic
  compounds
• Photoheterotrophs use sunlight as the energy
  source, but must obtain their carbon in an
  organic form (i.e., they cant use CO2)
• Chemoheterotrophs get both carbon and energy
  from organic compounds (this is what humans do!)

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Metabolism

• Most prokaryotes are chemoheterotrophs
• Saprobes (decomposers) absorb nutrients from dead
  organic matter (important step in nutrient
  cycling in an ecosystem)
• Parasites absorb the nutrients from the body of a
  living host (may also participate in mutualism
  and commensalism)
• Some prokaryotes can use atmospheric nitrogen
  (N2) and convert it to NH4 in a process called
  nitrogen fixation
• Obligate aerobes require O2 to live
• Obligate anaerobes are poisoned by O2
• Facultative anaerobes use O2 when it is available
  and undergo fermentation when it is not
• Prokaryotes have specialized membranes for
  photosynthesis and respiration

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Specialized membranes of prokaryotes