Archaea and Bacteria

• Bacteria and archaea
• Taxonomy


  The scientific definition of taxonomy is that it involves the classification of organisms both alive and extinct. It includes the naming and arranging of organisms in higher groups. Taxonomy involves studying living organisms such as animals, plants, microorganisms, and humans to classify them in different categories to study further and identify.
• Taxonomy (biology definition)


  The science of finding, describing, classifying, and naming organisms, including the studying of the relationships between taxa and the principles underlying such a classification. Etymology: from Greek taxis, meaning "arrangement", "order".
• For instance, humans and whales are two unrelated organisms from different perspectives; however, both are considered mammals and taxonomically related.
• Biological classification


  Grouping organisms into various taxa—species, genera, families, orders, classes, phyla, kingdoms, and domains. A lot of information about an organism may be retrieved based on its classification.
• Phylogeny


  Deducing evolutionary relationships between organisms. The widely used method is cladistic analysis which involves examining shared derived traits within a clade. A clade is a group of organisms with features that were inherited from a common ancestor. The reconstruction of evolutionary history of a given lineage does not rely only on similarities of body parts, habitat, and behavior but also on similarities in biochemistry and molecular biology.
• Domain


  The three domains—Bacteria, Archaea, and Eukarya—reflect the major branchings in the evolution of life.
• Kingdom


  The modern classification scheme that is largely based on fairly recent molecular data uses six kingdoms to organize organisms: Bacteria, Archaea, Protista, Fungi, Plantae, and Animalia.
• Prokarya


  Any organism that lacks a distinct nucleus and other organelles due to the absence of internal membranes.
• Eukarya


  Coming from the Greek words "eu," which means "true," and "karyon" which means "nut," the domain Eukarya is composed of organisms having "true nucleus". Eukaryotic cells, as their cells are called, are perhaps the most complex in terms of both external and internal structures and physiological and reproductive processes. Eukarya members have the most significant body size and body mass among all domains in the biological world.
• Cell size


  The average diameter of prokaryotes ranges from 1 to 10 μm. The smallest prokaryotes that have been observed measure 0.3 to 0.5 μm. These are the phytoplasmas and mycoplasmas which lack cell walls and cause disease in other organisms. The largest prokaryote is Thiomargarita namibiensis, also known as "the sulfur pearl of Namibia," which is 0.75 μm in size. The discoverers at first thought that they were seeing a protist because of its unusually large size. T. namibiensis is 100 times larger than the average prokaryote.
• Cocci


  Spherical prokaryotes. They appear singly, in pairs, in long chains, or as irregular clumps.
• Bacilli


  Rod-shaped prokaryotes. They appear as single rods or as a string of rods.
• Spirilla


  Spiral or corkscrew-shaped prokaryotes.
• Cellular Structure


  The genetic material of prokaryotes is not enclosed by a membrane. Instead, their DNA is found in a region of the cytosol referred to as the nucleoid. The DNA and its genes are meshed with proteins in a long, single, circular chromosome. Extra DNA may also be contained in small, self-replicating rings called plasmids.
• Prokaryotic cell vs eukaryotic cell

  Both prokaryotic cell and eukaryotic cell contain DNA, ribosomes, cell membrane, cytoplasm. While prokaryotes lack membranous organelles, including mitochondria, endoplasmic reticulum, Golgi apparatus, and lysosomes. No compartments for specialized functions are found inside their cells.
• Prokaryote: Cell Membrane


  While all membranes are made up of phospholipids, (some) prokaryotes differ in some other chemical components. Bacterial membranes, like those of eukaryotes, contain unbranched fatty acids attached to glycerol. Archaeal membranes have branched isoprene chains made up of 20 carbon atoms. The chains may be either linear or ring-like in structure. This unique structure gives stability to archaeal cells in environments with extreme conditions.
• Cell wall


  A bacterial cell wall contains a carbohydrate called peptidoglycan. Most archaea lack peptidoglycan, which is replaced by a similar carbohydrate layer.
• Christian Gram (1853–1938)


  Bacteria can be classified into two groups based on their reaction to a staining procedure developed in 1884 by the Danish physician Christian Gram (1853–1938)
• Gram positive bacteria


  Bacteria whose cell walls are thick and contain many layers of peptidoglycan keep hold of the violet color of one of the stains used in the procedure. The growth of Gram- positive bacteria can be inhibited by using the antibiotic penicillin. This drug obstructs the formation of peptidoglycan layers.
• Gram negative bacteria


  Have only a thin layer of peptidoglycan. Gram-negative bacteria also have a thick second outer layer of lipids and other carbohydrate molecules. They show a pink color after Gram staining. The antibiotics tetracycline and streptomycin can kill Gram-negative bacteria.
• Gram Staining test


  A Gram stain is a laboratory test that checks for bacteria at the site of a suspected infection or in certain bodily fluids. A medical laboratory scientist processes the Gram stain, which gives relatively quick results, so healthcare providers can know if bacteria are present, and, if so, the general type(s). This can help guide further identification tests and treatment options.
• Gram-positive stain


  Since Gram-positive bacteria have cell walls that contain thick layers of peptidoglycan (about 90% of the cell wall), this causes them to appear blue to purple under a Gram stain.
• Gram-negative stain


  Gram-negative bacteria have cell walls with thin layers of peptidoglycan (10% of the cell wall) and high lipid (fatty acid) content, this causes them to appear red to pink under a Gram stain.
• Antibiotics


  The growth of Gram- positive bacteria can be inhibited by using the antibiotic penicillin. This drug obstructs the formation of peptidoglycan layers. Tetracycline and streptomycin can kill Gram-negative bacteria.
• Capsule


  Some species of prokaryotes produce a capsule, a slimy layer on the outermost surface. The capsule offers protection against defense cells of the host that might engulf pathogenic prokaryotes. Free-living prokaryotes also shield themselves with the capsule against attack by other microorganisms. A type of Streptococcus pneumoniae that lacks the capsule does not cause pneumonia. The capsule also allows attachment to surfaces to form mats. Dental plaques actually consist of bacterial mats.
• Pili (sing. Pilus)


  Attachment to surfaces can also be made possible by outer structures called pili found in some prokaryotes. These hairlike accessories are made up of protein fibers. Pathogenic prokaryotes can cause infection by easily attaching to the surface of their target cells using the pili. Some pili are involved in the transmission of genetic material in prokaryotes. They are thus called sex pili. However, the sexual mode of reproduction rarely happens in prokaryotes.
• Movement


  Many prokaryotes are immobile. Those that move do it in several ways. Some glide in water as they secrete some slippery compounds. Other prokaryotes use flagella to move. Either the flagella can cover the whole cell or they can be found clustered at one end like a ponytail. Others use whip-like structures to thrust themselves forward. Others thrash, or move like a snake or twirling ribbons. Movement allows prokaryotes to scatter to and colonize new habitats. They may also need to move to obtain nutrients that surround them. It also helps them escape unfavorable environments where their chances of survival are at risk.
• Autotrophs


  Refers to any organism that manufactures its own organic molecules for food. Sometimes called self-feeders.
• Photoautotrophs


  Like plants, some prokaryotes photosynthesize, obtaining energy directly from sunlight and using carbon dioxide as a carbon source. They are called photoautotrophs or light-driven self-feeders.
• Photoautotrophs


  Obviously, photoautotrophs reside in places that receive ample exposure to sunlight. These habitats could be on the surface of bodies of water in the warm tropics, or in the cold arctic region. Some prokaryotes can even be found in springs with extremely hot water. Prokaryotes could also be found on land that is barren or covered with grass, or even snow.
• Chemoautotrophs


  Other prokaryotes directly obtain energy released by chemical reactions involving inorganic substances, such as ammonia, gaseous hydrogen, nitrogen compounds, sulfur, and iron. Chemoautotrophs also include those prokaryotes that live on the ocean floor and extract energy from hydrogen sulfide spewed from hydrothermal vents. Like photoautotrophs, chemoautotrophs rely on carbon dioxide as source of carbon.
• Heterotrophs


  Many prokaryotes are heterotrophs, meaning they obtain energy by taking in and breaking down organic compounds from other organisms, just like humans.
• Chemoheterotrophs


  Most prokaryotes are chemoheterotrophs that consume organic molecules, such as glucose, as carbon and energy source.
• Photoheterotrophs


  A small but interesting group of prokaryotes are the photoheterotrophs. They capture sunlight energy to make food but rely on organic compounds from other organisms as carbon source instead of using carbon dioxide.
• Chemoautotrophs


  Prokaryotes that obtain energy from chemical reactions involving inorganic substances, such as ammonia, gaseous hydrogen, nitrogen compounds, sulfur, and iron
• Chemoautotrophs


  Prokaryotes that live on the ocean floor and extract energy from hydrogen sulfide spewed from hydrothermal vents
• Chemoautotrophs


  Rely on carbon dioxide as source of carbon, like photoautotrophs
• Heterotrophs


  Prokaryotes that obtain energy by taking in and breaking down organic compounds from other organisms
• Chemoheterotrophs


  Most prokaryotes that consume organic molecules, such as glucose, as carbon and energy source