Structural Biochemistry/Three Domains of Life/Archaea
Archaea are a branch of the three-domain system of life that contains single-celled microorganisms. In 1977, Carl Woese was studying recently discovered prokaryotes in hot springs. With much observations, he noticed that there was a unique sequencing of 16S rRNA genes from many of the organisms. He noticed that the sequencing of the prokaryotes were a distinct form of life in itself- he called them archaea. This transformed the previous 5-kingdom system (plantae, animalia, fungi, protists, and prokaryotes) drawn by Lynn Margulis into 3 equally distinct groups (bacteria, archaea, and eukarya).  Woese argued that the bacteria, archaea, and eukaryotes each represent a primary line of descent that diverged early on from an ancestral progenote with poorly developed genetic machinery. This hypothesis is reflected in the name archaea, from the Greek archae or ancient. Later he treated these groups formally as domains, each comprising several kingdoms. This division has become very popular, although the idea of the progenote itself is not generally supported. Some biologists, however, have argued that the archaebacteria and eukaryotes arose from specialized eubacteria and actually are from the same origin. Archaea are a class of prokaryotes.
Similarities and Differences to Bacteria and Eukarya 
It is thought that archaea and bacteria diverged early in their existence because of all the dissimilarities between the two groups. Archaea are similar to other prokaryotes in most aspects of cell structure and metabolism. Both bacteria and archaea are enclosed in cell membranes. But unlike most bacteria, they have a single cell membrane that lacks a peptidoglycan wall and their genetic transcription and translation - the two central processes in molecular biology - do not show the typical bacterial features, but are extremely similar to those of eukaryotes. Archaea are evolutionarily more related to eukaryotes than they are to eubacteria, even though eubacteria and archaea are both prokaryotic groups.
Eukarya and archaea are noted to have many similarities especially in regards to metabolic pathways. For example, enzymes present in transcription and translation of archaea are more closely related to those of Eukarya than bacteria. They both use elongation factors, and their transcription involves TATA-binding proteins and TFIIB as in eukaryotes.
Several other characteristics also set the archaea apart. Both bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids, whereas archaea have membranes composed of glycerol-ether lipids. These differences may be an adaptation on the part of archaea to hyperthermophily. Archaea also have flagella that are notably different in composition and development from the superficially similar flagella of bacteria. A phylogenetic tree based on rRNA data, showing the separation of bacteria, archaea, and eukaryotes.
The relationship between archaea and Eukarya remains an important problem. Aside from the similarities noted above, many genetic trees group the two together. Some place eukaryotes closer to Eurarchaeota than Crenarchaeota are, although the membrane chemistry suggests otherwise. However, the discovery of archaean-like genes in certain bacteria, such as Thermotoga, makes their relationship difficult to determine. Some have suggested that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm, which accounts for various genetic similarities but runs into difficulties explaining cell structure.
Individual archaeans range from 0.1 to over 15 μm in diameter. They occur in various shapes, such as spherical, rod-shaped, spiral, lobed, or rectangular. They also exhibit a variety of different types of metabolism. Of note, the halobacteria can use light to produce ATP, although no archaea conduct photosynthesis with an electron transport chain, as occurs in other groups.
Archaea are bound by a plasma membrane that is layered by pseudopeptidoglycans instead of peptidoglycans. So unlike for the latter, the membrane is resistent to antibiotics that target and prevent the synthesis of peptidoglycan wall. The pseudopeptidoglycans consist of polysaccharides that give the archaea a rigid structure. The archaeal membranes consist of a glycerol-1-phosphate backbone with either linkages between glycerol and fatty acids. The fatty acids are hydrocarbons that are strengthened due to branched terpenoids (polymeric structures derived from isoporene. This limits the movement of the chains).The membranes can exist as bilayers or monolayers. They contain cytosol, a nucleoid, metabolites, coenzymes, inorganic ions and enzymes. Archaea reproduce asexually; they divide by binary fission, fragmentation and budding. Unlike the other two branches, they do not spore. Unlike bacteria, no pathogenic archaea have ever been identified.
The most common cell wall type for archaea is the S-Layers. The S-Layers are made up of proteins and glycoproteins in a hexagonal symmetry. But archaea does not always have a wall. For example, thermoplasmas thrive at acidic environments lower than 2. These archaeas have a unique tetraether lipid monolayer membrane that is not acid labile. This unique membrane structure is what allows it to withstand extreme environments. 
Unlike bacteria that have their cell walls made of peptidoglycan, archaea, mostly methanogens, have cell walls made of pseudopeptidoglycan. The difference is in the sugars that make up the peptidoglycan backbone. In peptidoglycan, the two sugars are N-acetylglucosamine (NAG) and N-acetylmuramic (NAM) acid. While in pseudopeptidoglycan, the NAM is replaced by N-acetyltalosaminuronic acid (NAT). NAG and NAT are bonded by a β (1,3) sugar linkage instead of a β (1,4) linkage.
This is significant, because it makes these archaea resistant to the enzyme, lysozyme, which only breaks down β (1,4) sugar linkages like those found in peptidoglycan.
Pseudopeptidoglycan also has different amino acids used for their peptide cross links. The order of the attached amino acids is D-glutamine, L-alanine, L-lysine, and D-glutamine. The peptide bond that forms is between the L-lysine a of one NAT and the second D-glutamine of a parallel NAT. These different amino acids make it so antibiotics such as vancomycin and penicillin have no effect on these cell walls.
Archaea are commonly known as "extremeophiles", prevailing in extreme environments for they love to live under extreme, harsh environments of pH, temperature and salinity. Certain Archaea are called thermophiles because they are found in extremely high temperature environments, such as in the hot springs of volcanoes. There are psychrophiles that thrive in low temperatures, such as Antarctica. Others can live under highly acidic conditions (acidophiles), as well as highly saline environments (halophiles). This characteristic is very specific to Archaea. Out of the three domains, they are generally the only ones known to live and thrive under these extreme conditions. However, a large number of them also live in non-extreme environments, with the plankton community among the ocean waters.
Archaea can survive in both aerobic and anaerobic environments. Aerobic means in the presence of oxygen, while anaerobic means very a very small amount of oxygen available. In the past they have been known to inhabit extreme environments such as high-acidity bogs and ocean depths. However, it is now known that they inhabit soils, ocean and marshland, and might be one of the most abundant organisms on Earth. Under the archaea group, there are four phyla based on rRNA trees: Crenarchaeota, Euryarchaeota, Korarchaeota, and Nanoarchaeota. Crenarchaeota and Euryarchaeota are the only two that have been heavily researched. The other two other groups have been tentatively created for certain environmental samples and the peculiar species Nanoarchaeum equitans, discovered in 2002 by Karl Stetter, but their affinities are uncertain.
Crenarchaeota consists of these following divisions:
a. Hyperthermophiles: are thermophilic (love hot weather) and acidophillic ( can live under low pH environment)...organisms in this type are usually found in hot sulfur spring, can even live in pH 0.9...example : Sulfobus, Pyrolobus fumarii, etc..
b. Extreme halophiles: include organisms living in highly salty environments...example: halococcus,
c. Thermoplasma: similar to hyperthermophiles type (love high temperature and low pH environments) but they lack cell wall... They were found in coal deposits.
Methanogens is single division under this clade. As its name implies, methanogens release CH4 (methane) as waste product by reducing CO2 (carbon dioxide)...Methanogens are obligate anaerobes which are poisoned by Oxygen. Examples of methanogens are Methanobacterium bryantii, Methanopyrus, etc...
Groups of Archaeabacteria 
There are 3 groups of archaebacteria, such as methanogens, halophiles and thermoacidophiles. Methanogens produce energy by converting H2 and CO2 into methane gas. They are found in the intestinal areas of humans and some animals such as cows and in the marshes. Halophiles live in a high salt atmosphere. Therefore, they are found in the Great Salt Lake, Dead Sea and other areas with a high salt concentration. Thermoacidophiles are found in the areas with a very high temperature and very acidic circumstances. They can be found in hydrothermal vents and volcanic vents.
Characteristics of Archaebacteria 
Archaebacteria are force anaerobes and they live only in oxygen-free circumstances. They are known as extremophiles, as they are capable to live in a variety of atmosphere. Some species can live in the temperatures over boiling point at 100 degree Celsius. They can also live in acidic, alkaline or saline aquatic surroundings. Some can endure the pressures of more than 200 atmospheres.
The size of archaebacteria varies from 1/10th of a micrometer to more than 15 micrometers. Some of archaebacteria have flagella. Like all prokaryotes, archaebacteria don't have the membrane-bound organelles. They don't contain nuclei, endoplasmic reticula, Golgi complexes, mitochondria, chloroplasts or lysosomes. The cells consist of a thick cytoplasm that includes all the compounds and molecules needed for metabolism and nutrition. Their cell wall doesn't contain peptidoglycan. The rigid cell wall backings the cell and allows archaebacterium to hold its shape. It also defends the cell from overflowing when present in a hypotonic environment. Archaebacteria have lipids in their cell membranes. They are self-possessed of branched hydrocarbon chains, linked to glycerol by ether linkages.
Since these organisms don't have a nucleus, the genetic material drifts freely in the cytoplasm. They contain rRNA. DNA contains a single, circular molecule, which is compact and tightly twisted. None of the protein is associated with DNA. The archaebacterial cell may contain plasmids, which are small, circular pieces of DNA. They can replace independent of larger, genomic DNA circle. Plasmids often code for antibiotic resistance or particular enzymes.
Archaebacteria duplicates by an asexual procedure known as binary fission. During this process, the bacterial DNA replicates. The cell wall pinches off in the center, due to which the organism is divided into two new cells. Each cell consists of a copy of circular DNA. It is quite fast method. Some species separate every 20 minutes. Although genetic material can be exchanged between the cells by three various processes, sexual reproduction is not seen in archaebacteria.
During transformation, DNA fragments unrestricted by one bacterium are taken up by another bacterium. In the process of transduction, a bacterial phage transfers genetic material from one organism to another. In the process of conjugation, genetic material is interchanged between two bacteria. These mechanisms lead to genetic recombination, causing the continual evolution of archaebacteria.
Slonczewski, Joan, and John Watkins. Foster. Microbiology: An Evolving Science. New York: W.W. Norton, 2011. 717-21. Print.