Prokaryote



The prokaryotes ( or ) are a group of organisms that lack a cell nucleus (= karyon), or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles. The word prokaryote comes from the Greek πρό- (pro-) "before" + καρυόν (karyon) "nut or kernel". Prokaryotes do not have a nucleus, mitochondria, or any other membrane-bound organelles. In other words, neither their DNA nor any of their other sites of metabolic activity are collected together in a discrete membrane-enclosed area. Instead, everything is openly accessible within the cell, some of which is free-floating.

Prokaryotes belong to two taxonomic domains: the bacteria and the archaea. Archaea were recognized as a domain of life in 1990. These organisms were originally thought to live only in inhospitable conditions such as extremes of temperature, pH, and radiation but have since been found in all types of habitats.

Relationship to eukaryotes
A distinction between prokaryotes and eukaryotes (meaning true kernel, also spelled "eucaryotes") is that eukaryotes do have "true" nuclei containing their DNA. Unlike prokaryotes, eukaryotic organisms may be unicellular, as in amoebae, or multicellular, as in plants and animals. The difference between the structure of prokaryotes and eukaryotes is so great that it is sometimes considered to be the most important distinction among groups of organisms.

The cell structure of prokaryotes differs greatly from that of eukaryotes. The defining characteristic is the absence of a nucleus. Also the size of Ribosomes in prokaryotes is smaller than that in eukaryotes, but two organelles found in eukaryotic cells, the mitochondria and the chloroplast, contain ribosomes similar in size and makeup to those found in prokaryotes. This is due to the fact that both mitochondria and chloroplasts are themselves descended from free-living bacteria, and therefore share the same transcriptional machinery. The genomes of prokaryotes are held within an irregular DNA/protein complex in the cytosol called the nucleoid, which lacks a nuclear envelope. In general, prokaryotes lack the following membrane-bound cell compartments: mitochondria and chloroplasts. Instead, processes such as oxidative phosphorylation and photosynthesis take place across the prokaryotic plasma membrane. However, prokaryotes do possess some internal structures, such as cytoskeletons, and the bacterial order Planctomycetes have a membrane around their nucleoid and contain other membrane-bound cellular structures. Both eukaryotes and prokaryotes contain large RNA/protein structures called ribosomes, which produce protein. Prokaryotes are usually much smaller than eukaryotic cells.

Prokaryotes also differ from eukaryotes in that they contain only a single loop of stable chromosomal DNA stored in an area named the nucleoid, whereas eukaryote DNA is found on tightly bound and organized chromosomes. Although some eukaryotes have satellite DNA structures called plasmids, in general these are regarded as a prokaryote feature, and many important genes in prokaryotes are stored on plasmids.

Prokaryotes have a larger surface-area-to-volume ratio giving them a higher metabolic rate, a higher growth rate, and, as a consequence, a shorter generation time compared to Eukaryotes.

One criticism of this classification points out that the word "prokaryote" is based on what these organisms are not (they are not eukaryotic), rather than what they are (either archaea or bacteria).

In 1977, Carl Woese proposed dividing prokaryotes into the Bacteria and Archaea (originally Eubacteria and Archaebacteria) because of the major differences in the structure and genetics between the two groups of organisms. This arrangement of Eukaryota (also called "Eukarya"), Bacteria, and Archaea is called the three-domain system, replacing the traditional two-empire system.

Sociality
While prokaryotes are still commonly imagined to be strictly unicellular, most are capable of forming stable aggregate communities. When such communities are encased in a stabilizing polymer matrix  (“slime”), they may be called “biofilms”. Cells in biofilms often show distinct patterns of gene expression (phenotypic differentiation) in time and space. Also, as with multicellular eukaryotes, these changes in expression appear to often result from cell-to-cell signaling, a phenomenon known as quorum sensing.

Biofilms may be highly heterogeneous and structurally complex and may attach to solid surfaces, or exist at liquid-air interfaces, or potentially even liquid-liquid interfaces. Bacterial biofilms are often made up of microcolonies (approximately dome-shaped masses of bacteria and matrix) separated by “voids” through which the medium (e.g., water) may flow relatively uninhibited. The microcolonies may join together above the substratum to form a continuous layer, closing the network of channels separating microcolonies. This structural complexity — combined with observations that oxygen limitation (a ubiquitous challenge for anything growing in size beyond the scale of diffusion) is at least partially eased by movement of medium throughout the biofilm — has led some to speculate that this may constitute a circulatory system and many researchers have started calling prokaryotic communities multicellular (for example ). Differential cell expression, collective behavior, signaling, programmed cell death, and (in some cases) discrete biological dispersal events all seem to point in this direction. However, these colonies are seldom if ever founded by a single founder (in the way that animals and plants are founded by single cells), which presents a number of theoretical issues. Most explanations of co-operation and the evolution of multicellularity have focused on high relatedness between members of a group (or colony, or whole organism). If a copy of a gene is present in all members of a group, behaviors that promote cooperation between members may permit those members to have (on average) greater fitness than a similar group of selfish individuals (see inclusive fitness and Hamilton's rule).

Should these instances of prokaryotic sociality prove to be the rule rather than the exception, it would have serious implications for the way we view prokaryotes in general and the way we deal with them in medicine. Bacterial biofilms may be 100 times more resistant to antibiotics than free-living unicells and may be nearly impossible to remove from surfaces once they have colonized them. Other aspects of bacterial cooperation — such as bacterial conjugation and quorum-sensing-mediated pathogenicity — present additional challenges to researchers and medical professionals seeking to treat the associated diseases.

Reproduction
Bacteria and archaea reproduce through asexual reproduction, usually by binary fission or budding. Genetic exchange and recombination still occur, but this is a form of horizontal gene transfer and is not a replicative process, simply involving the transference of DNA between two cells, as in bacterial conjugation.

Structure


Recent research indicates that all prokaryotes actually do have cytoskeletons, albeit more primitive than those of eukaryotes. Besides homologues of actin and tubulin (MreB and FtsZ), the helically arranged building-block of the flagellum, flagellin, is one of the most significant cytoskeletal proteins of bacteria, as it provides structural backgrounds of chemotaxis, the basic cell physiological response of bacteria. At least some prokaryotes also contain intracellular structures that can be seen as primitive organelles. Membranous organelles (a.k.a. intracellular membranes) are known in some groups of prokaryotes, such as vacuoles or membrane systems devoted to special metabolic properties, e.g., photosynthesis or chemolithotrophy. In addition, some species also contain protein-enclosed microcompartments, which have distinct physiological roles (e.g., carboxysomes or gas vacuoles).

Most prokaryotes are between 1 µm and 10 µm, but they can vary in size from 0.2 µm to 750 µm (Thiomargarita namibiensis).

Morphology of prokaryotic cells
Prokaryotic cells have various shapes; the four basic shapes are:
 * Cocci - spherical
 * Bacilli - rod-shaped
 * Spirochaete - spiral-shaped
 * Vibrio - comma-shaped

Environment
Prokaryotes live in nearly all environments on earth where there is liquid water. Some archaea and bacteria thrive in harsh conditions, such as high temperatures (thermophiles) or high salinity (halophiles). Organisms such as these are referred to as extremophiles. Many archaea grow as plankton in the oceans. Symbiotic prokaryotes live in or on the bodies of other organisms, including humans.

Evolution of prokaryotes
The current model of the evolution of the first living organisms is that these were some form of prokaryotes, which may have evolved out of protobionts. In general, the eukaryotes are thought to have evolved later in the history of life. However, some authors have questioned this conclusion, arguing that the current set of prokaryotic species may have evolved from more complex eukaryotic ancestors through a process of simplification. Others have argued that the three domains of life arose simultaneously, from a set of varied cells that formed a single a gene pool. This controversy was summarized in 2005:

There is no consensus among biologists concerning the position of the eukaryotes in the overall scheme of cell evolution. Current opinions on the origin and position of eukaryotes span a broad spectrum including the views that eukaryotes arose first in evolution and that prokaryotes descend from them, that eukaryotes arose contemporaneously with eubacteria and archeabacteria and hence represent a primary line of descent of equal age and rank as the prokaryotes, that eukaryotes arose through a symbiotic event entailing an endosymbiotic origin of the nucleus, that eukaryotes arose without endosymbiosis, and that eukaryotes arose through a symbiotic event entailing a simultaneous endosymbiotic origin of the flagellum and the nucleus, in addition to many other models, which have been reviewed and summarized elsewhere.

The oldest known fossilized prokaryotes were laid down approximately 3.5 billion years ago, only about 1 billion years after the formation of the Earth's crust. Even today, prokaryotes are perhaps the most successful and abundant life-forms. Eukaryotes only appear in the fossil record later, and may have formed from endosymbiosis of multiple prokaryote ancestors. The oldest known fossil eukaryotes are about 1.7 billion years old. However, some genetic evidence suggests eukaryotes appeared as early as 3 billion years ago.

While Earth is the only place in the universe where life is known to exist, some have suggested that there is evidence on Mars of fossil or living prokaryotes; but this possibility remains the subject of considerable debate and skepticism.

Prokaryotes have diversified greatly throughout their long existence. The metabolism of prokaryotes is far more varied than that of eukaryotes, leading to many highly distinct prokaryotic types. For example, in addition to using photosynthesis or organic compounds for energy, as eukaryotes do, prokaryotes may obtain energy from inorganic compounds such as hydrogen sulfide. This enables prokaryotes to thrive in harsh environments as cold as the snow surface of Antarctica, and as hot as undersea hydrothermal vents and land-based hot springs.