Prokaryotes are the simplest of all organisms and include all bacteria. Prokaryotes do not contain any membrane-bound organelles, and their genetic material is organized into a single circular molecule of DNA concentrated in an area of the cell called the nucleoid region. There are three overarching domains into which all life is classified: Archaea, Bacteria, and Eukarya. Two of these, Archaea and Bacteria, contain prokaryotes. Initially, Archaea and Bacteria were classified together into the kingdom of Monera. However, techniques in molecular biology have since revealed that the evolutionary pathways between Archaea and Bacteria are significantly different and it is comparable as the differences between either of these domains and Eukarya. The single celled Archaea visually appears similar to bacteria, but contain genes along with several metabolic pathways that resemble eukaryotes more than bacteria. Archaea are generally viewed as extremophiles, as they are able to survive in harsh environments that most other organisms would die from. This includes habitats with extremely high temperatures, high salinity, poor light conditions and even high radiation. According to current research, the human body is also a habitat for Archaea. Archaea are capable of utilising alternative sources of energy. There are a few photosynthetic types but many are chemosynthetic. This means they are able to produce energy from inorganic compounds such as ammonia. It is a theory that eukaryotes and the domain Archaea share a common origin due to the similarities of this domain to eukaryotes. Translation begins with methionine for both eukaryotes and Archaea, they both contain RNA polymerases that are similar, and histones accompany their DNA. However, Archaea contain a one circular chromosome, reproduce through binary fission or, less commonly, budding, and the overall structure looks closer to bacteria. Archaea are resistant to several types of antibiotics. All bacteria contain a cell membrane and cytoplasm, and some have flagella or fimbriae. Analogous structures are often found in bacteria and eukaryotes and this makes it difficult to develop medicines that affect bacteria only. However, there are occasions where there is enough biochemical difference between seemingly similar structures to allow one organism to be targeted over another. Bacterial flagella and eukaryotic flagella have enough biochemical differences that antibacterial vaccines are effective against only bacterial cells when they specifically target the bacterial flagellum. Many antibiotics also preferentially target the bacterial ribosome, which is significantly smaller in size to the ribosomes of a eukaryote. We can classify bacteria by their shape and this allows scientists a way to identify different species of bacteria. Most bacteria exist in one of three shapes. Spherical bacteria, known as cocci, include common pathogens such as Streptococcus pyogenes. Rod-shaped bacteria, like Escherichia coli, are known as bacilli. Finally, spiral-shaped bacteria, known as spirilli, include such species as Treponema pallidum, which causes syphilis.
Prokaryotes lack a nucleus and membrane-bound organelles and this is a major difference with them from eukaryotes. Due to the fact that prokaryotes are also single-celled organisms, each cell must be able to perform all of the necessary functions for life and no specialisation unlike with many eukaryotic cells cannot occur. Prokaryotes can, however, live in colonies with other types of cells and may signal cells in the colony to share information about the environment. The cell wall forms the outer barrier of the cell. The next layer is the cell membrane (plasma membrane), which is composed of phospholipids, similar to that of a eukaryote. Together, the cell wall and the cell membrane are known as the envelope. The cell wall both provides structure and controls the movement of solutes into and out of the bacterium. This allows the cell to maintain concentration gradients relative to the environment. In bacteria, there are two main types of cell wall: gram positive and gram negative. The type of cell wall is determined by the Gram staining process with a crystal violet stain, followed by a counterstain with a substance called safranin. The cell is said to be gram positive when it appears purple as the envelope of gram positive bacteria will absorb the crystal violet stain. The cell is said to be gram negative when it appears pink as the envelope of gram negative bacteria will absorb the safranin counterstain instead of the violet stain.
Flagella are whip-like structures that are usually used for microbial propulsion. Bacteria may have a range of flagella, depending on the species being looked at. Flagella can move the organism towards food or away from toxins. This ability of a cell to detect chemical stimuli and move toward or away from them is called chemotaxis. The flagella are composed of a filament, a basal body, and a hook. The filament is a hollow, helical structure composed of flagellin. The basal body is a complex structure that holds the flagellum firmly to the cytoplasmic membrane as well as function as the organic motor of the flagellum, with rotation rates up to 300 Hz. The hook allows the basal body to exert a torque on the filament through the rotation of the basal body. This in turn can spin the bacterium and propel it forward. The flagella in gram-positive and gram-negative bacteria contain slight differences attributed to a difference in physical structure and chemical composition of their envelopes.
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