The document discusses the three domain system of life - Archaea, Bacteria, and Eukarya. It provides background on how Archaea were identified as a unique third domain based on differences in ribosomal RNA from other prokaryotes. Key differences between the three domains are outlined, including cellular structure, genetics, metabolism, and environments inhabited. Archaea share some similarities with both bacteria and eukaryotes but are sufficiently distinct to be placed in their own domain.

1. Introduction To Three Domain System
Divya Chetnani
M.Sc BT, Department of Biotechnology
Shree M & N Virani Science College(Autonomous),
Rajkot - 360005, Gujarat, India.
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2. History Of Phylogenetic Classification
•Until the middle of the 20th century, biologists classified all living things as either a
plant or an animal. But this system failed to accommodate fungi, protists and
bacteria.
• In 1969., the classification system evolved to what was known as Five Kingdoms
— prokaryotes (bacteria) and eukaryotes (plants, animals, fungi,
protists).
•Eukaryotes are characterized by the presence of nuclei, cytoskeletons, and internal
membranes in their cells.
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3. • In the late 1970s, Dr. Carl Woese and his colleagues
at the University of Illinois identified a group of
microorganisms whose genetic makeup was vastly
different from other bacteria.
• So they divided prokaryotic life into what they called
archaeabacteria and eubacteria.
• However, they later concluded that "archaeabacteria"
were sufficiently different as to not be bacteria at all. So
the groups were renamed to archaea and bacteria.
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4. There are three domains of life: Bacteria (also known as Eubacteria), Archaea, and
Eukarya.
The Bacteria and Archaea are made up entirely of microorganisms; the
Eukarya contains plants, animals, and microorganisms such as fungi and
protists.
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5. • Archaea were split off as a third domain because of the large differences in their ribosomal
RNA structure. The particular RNA molecule sequenced, known as 16s rRNA, is present in all
organisms and always has the same vital function, the production of proteins.
• Because this function is so central to life, organisms with mutations of its 16s rRNA are
unlikely to survive, leading to great stability in the structure of this nucleotide over many
generations.
• Functions:
• Like the large (23S) ribosomal RNA, it has a structural role, acting as a scaffold defining the
positions of the ribosomal proteins.
• Interacts with 23S, aiding in the binding of the two ribosomal subunits (50S+30S)
• 16s rRNA is also large enough to retain organism-specific information, but small enough to
be sequenced in a manageable amount of time.
• In 1977, Carl Woese, a microbiologist studying the genetic sequencing of organisms,
developed a new sequencing method that involved splitting the RNA into fragments that
could be sorted and compared to other fragments from other organisms.
• The more similar the patterns between species were, the more closely related the organisms.
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6. • Archaea: Archaea is derived from the Greek word archaios, meaning
“ancient” or “primitive,” and indeed some archaea exhibit characteristics
worthy of that name.
• Members of the archaea include: Pyrolobus fumarii, which holds the upper
temperature limit for life at 113 °C (235 °F) and was found living in
hydrothermal vents.
• Species of Picrophilus, which were isolated from acidic soils in Japan and
are the most acid-tolerant organisms known—capable of growth at around
pH 0.
• And the methanogens, which produce methane gas as a metabolic by-
product and are found in anaerobic environments, such as in marshes, hot
springs, and the guts of animals, including humans.
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7. • Eubacteria:Eubacteria, known as "true bacteria," are
prokaryotic (lacking nucleus) cells that are very common in
human daily life kill thousands upon thousands of people
each year, but also serve as antibiotics producers and food
digesters in our stomachs.
• We use Eubacteria to produce drugs, wine, and cheese.
• They lacks a membrane-bound nucleus (karyon), mitochondria, or
any other membrane-bound organelle.
• Eukaryote: A eukaryote is any organism whose cells have
a nucleus and other organelles enclosed within membranes.
• Eukaryotes belong to the taxon Eucarya or Eukaryota.
• The defining feature that sets eukaryotic cells apart
from prokaryotic cells (Bacteria and Archaea) is that they have
membrane-bound organelles, especially the nucleus, which contains
the genetic material and is enclosed by the nuclear envelope.
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9. • Archaea and bacteria are generally similar in size and
shape, although a few archaea have very strange shapes, such
as the flat and square-shaped cells of Haloquadratum
walsbyi.
• The RNA polymerase in archaea is similar to RNA polymerase II in
eukaryotes.
• Archaea resembles eukaryotes more than bacteria. Their ribosomes work
more like eukaryotic ribosomes than bacterial ribosomes.
• Lipids in membranes from Archaea are unique, containing ether linkages
between the glycerol backbone and the fatty acids, instead of ester
linkages.
• The cells walls of Archaea are chemically and structurally diverse and do not
contain peptidoglycan.
Haloquadratum walsbyi.
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10. • Despite this morphological similarity to bacteria, archeae
possess genes and several metabolic pathways that are
more closely related to those of eukaryotes, notably
the enzymes involved in transcription and translation. .
• Archaea reproduce asexually by binary fission, fragmentation,
or budding; unlike bacteria and eukaryotes, no known
species forms spores.
• Although Archaea are prokaryotic, they are more
closely related to Eukarya and thus cannot be placed
within either the Bacteria or Eukarya domains.
• Here are other major differences between the three domains.
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11. Characteristic Eubacteria Archeae Eukaryotes
Cell Type Prokaryote Prokaryote Eukaryote
Cell size Usually 0.5-4µ Usually 0.5-4µ >5µ
Cell wall Made of
peptidoglycan
Does not contain
peptidoglycan
In plants and
fungi, composed of
polysaccharides
First amino acid
during protein
synthesis
Formylmethionine Methionine Methionine
DNA Mostly circular
chromosome and
plasmids
Circular
chromosome and
plasmids
Linear
chromosome,
rarely plasmids
Histones No Yes Yes
Organelles No No Yes
Ribosomes 70S 70S 80S
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12. Predominantly
multicellular
no no yes
Membrane lipids
ester-linked*
yes
No (Archaea
membrane lipids
are ether-linked)
yes
Photosynthesis with
chlorophyll
yes no yes
Growth above 80o C yes yes no
Operons yes yes no
Capping and poly-A
tailing of mRNA
no no yes
Transcription
factors required
yes no yes
Methanogenesis no yes no
Nitrification yes no no
Introns in t-RNA absent present present
Introns in m-RNA absent absent present
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13. Capping and poly-
A tailing of mRNA
no no yes
Transcription
factors required
yes no yes
Methanogenesis no yes no
Nitrification yes no no
Denitrification yes yes no
Nitrogen Fixation yes yes no
Chemolithotrophy yes yes no
Gas vesicles
present
yes yes no
Sensitive to
chloramphenicol,
kanamycin and
streptomycin
yes no no
Sensitive to
anisomysin
no yes yes
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14. Cytological
features
Eubacteria Archeae Eukaryotes
Nucleus No No Yes
Cytoskeleton No No Yes
Organelles
(mitochondria,chlo
roplasts, Golgi
apparatus, endopla
smic reticulum)
No No Yes
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15. Molecular
features
DNA topology
Negatively
supercoiled
Relaxed or
positively
supercoiled (in
hyperthermophilic
Archaea that
contain reverse
gyrase)
Negatively
supercoiled
Promoterstructure
Two conserved
boxes at - 10
(TATAAT) and - 35
(TTGACA) from
transcription start
site
TATA box and/or
initiator element
TATA box and/or
initiator element
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16. RNA polymerase
One type;
relatively simple
subunit
composition; binds
directly to
promoter (can be
footprinted)
One type; complex
subunit structure
(subunit pattern,
genes, and
serological
properties similar
to eukaryal RNA
polymerase II)
Three types;
complex subunit
compositions
Poly(A) tails
in RNA
Short
Short (avg. 12
bases in length)
Long
Typical Organisms
Entric bacteria and
cyanobacteria
Methanogens,halo
philes,extremophil
es
Algae, Protozoa,
Fungi, Plants and
Animals
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