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  PROKARYOTES By Freda Auyeung and Jackie Sukhontarug
The formatting isn't like it was originally because it was too complicated to convert it all to HTML and I'm lazy... so... yeah. This is really long but incredibly informative as well. It's a really long read. NOTE: Sorry, but we request that you do not use any of this information without permission from either of us... especially the pictures.


Objectives | General | Prokaryotic Classification | Prokaryotic Structure | Prokaryotic Reproduction | Metabolic Activity | Key Words and Concepts | Bibliography

OBJECTIVES
* To identify and recognize the different parts in a prokaryotic cell.
* To be able to state the functions of the different parts of a prokaryotic cell.
* To learn about metabolic activity in prokaryotic cells.
* To gain general knowledge about prokaryotes, including how they are classified.
* To understand the how prokaryotes have a large impact on and are essential for evolution and life.

Various Prokaryotes

GENERAL
    
Prokaryotes (sometimes spelt as procaryotes) are simple, primitive organisms. About 3.5 billion years ago, the first prokaryotic organisms, unicellular bacteria, dominated the Earth. They lived alone for 2 billion years until eukaryotic cells developed from evolution. Nevertheless, prokaryotes today still dominate the Earth, and outnumber eukaryotes significantly because of their amazing ability to adapt to and thrive in extreme environments. There are up to 4000 modern species of prokaryotes known today and possibly 400,000 to four million species that exist, very little of which are multicellular.     Prokaryotes are, on average, 10 times smaller than eukaryotes, or generally 1-5μm in diameter. However, there are exceptions, and some prokaryotes may be larger than eukaryotes. The small size helps prokaryotes to be more adaptable to their environments, since they have a small surface area to volume ratio, and thus ensures their survival. Although they are individually microscopic, collectively, prokaryotes have a gigantic impact on life on Earth. There are three main shapes in which prokaryotes can be found: spheres (cocci), rods (bacilli, as in B on the left), and helices (spirilla or spirochetes, as in A on the left). These shapes are commonly used to identify different types of bacteria.     Prokaryotes also have the ability to live with other organisms or together, in symbiotic relationships. These relationships can be categorized into mutualism, commensalism, or parasitism (such as with infectious bacteria that cause diseases).     In essence, prokaryotes are essential for life on Earth because of their ability to decompose and recycle both inorganic and organic chemical elements to continue nature's chemical cycle. Although eukaryotes could never survive without prokaryotes, prokaryotes could easily survive without eukaryotes, much like they did before the evolution of eukaryotic life forms.

PROKARYOTIC CLASSIFICATION

Cell classifications

    There are two ways which cells can be classified. The first system involves the five kingdoms:
monera, protista, plantae, fungi, and animalia. Prokaryotes only fall into one of these kingdoms, monera, while the other four kingdoms are for eukaryotic organisms. Technically, this system is inaccurate, since the differences between prokaryotes are not accurately defined, while those of eukaryotes are. However, monera are divided two sub categories, archaebacteria and eubacteria, according to their DNA and RNA structure as well as their structural, biochemical, and physiological characteristic differences. These differences can be considered more significant than those between eukaryotes, since evolution has resulted in many more species of prokaryotes. Therefore, another more systematic organization used to classify cells involving three categories, domain bacteria/eubacteria, domain archaera/archaebacteria, and domain eukarya/eukaryotes, is often used. As shown in Figure 1 above, eukarya and archaebacteria share a common ancestor, which evolved from the same ancestor as that of the eubacteria.     Archaebacteria are the primitive and ancient prokaryotes that are known for being able to survive in extreme environmental conditions. There are three sub categories of archaebacteria. Methanogens are decomposers that use H2 to reduce CO2 to form CH4 (methane), which makes what is known as marsh gas. They are easily poisoned by O2, so they tend to live in swampy or marsh-like areas where other organisms use up O2 in the atmosphere. Extreme halophiles live and thrive in areas with a high salt concentration. They can only tolerate salinity, and require an environment with at least 10 times more salt than present in seawater. Lastly, extreme thermophiles are prokaryotes that live in extremely hot environments (on average, 60-80°C). They oxidize sulfur to produce energy.     Most prokaryotes are included in one of the five sub categories of eubacteria. There are usually many differences between the various eubacterial prokaryotes, mostly due to RNA sequences. Proteobacteria are very diverse, but in general perform a variety of metabolic activities that may help or harm other organisms that it may feed on or live among. Gram positive eubacteria are chemoheterotrophs that perform photosynthesis, such as primitive chloroplasts. They often form endospores, which allow the plant to be more resistant to harsh environments. Many of the smallest cells are classified into this category and they are often a source of antibiotics. Cyanobacteria also perform photosynthesis and are closely related to modern chloroplasts. Spirochetes are long, thin, chemoheterotrophs which include many cells that are responsible for causing diseases such as syphilis or Lyme disease. Chalmydias are usually in the form of parasites that are found in animals and may cause disorders related to STDs or blindness.

PROKARYOTIC STRUCTURE

Color diagram of Prokaryotic structureElectron Micrograph of Prokaryote

    Prokaryotes have a very basic and simple structure. Each cell has a capsule, cell wall, cytoplasm, mesosomes, naked nucleic acid/DNA, nucleoid region, plasma membrane, plasmids, ribosomes, and sometimes flagellum/flagella and pili, or fimbrae, which are explained on the pages to follow. See Figure 2 and Figure 3 to gain a better understanding.     The capsule of a prokaryotic cell is the outermost layer of the cell that protects it against extreme environmental factors including temperature, pH, dryness, salinity, chemicals, or pressure. Capsules hold a record for being the strongest and toughest form of protection, and essentially allow a prokaryote to adapt to its environment with such ease.     The cell wall is the second, very rigid layer of the cell that gives support and protection to the cell, which is especially important for unicellular prokaryotes. It also helps the cell to maintain its shape and prevents it from bursting in the case that the cell becomes turgid from osmosis. Prokaryotic cell walls, unlike plant cell walls, are made of peptidoglycan (a mixture of proteins and carbohydrates). The cytoplasm is a liquid-filled region that holds the free-floating cell genome (DNA) as well as other structures.     Mesosomes are structures that help with cell division and the increasing of surface area. A respiratory chain of mesosomes could possibly be located on folded membranes in aerobic bacterium. Otherwise, any individual mesosomes located on folded membranes in aerobic bacterium. Otherwise, any individual mesosomes present in the membrane could act as photosynthetic pigments used to absorb light in photosynthesis.     DNA within prokaryotes is not surrounded or protected by any form of membrane, as prokaryotic cells lack a nuclear membrane, and is therefore dubbed "naked nucleic acid", or "naked DNA". The nucleoid is the region of the cytoplasm where most of the naked DNA are located. Much like DNA in other organisms, naked DNA in prokaryotes carry the genetic code that controls protein synthesis and various cell characteristics that allow for variation within species. There are also free floating DNA within the cytoplasm in the form of a plasmid, a small circular chain of DNA.     The plasma membrane is the semipermeable layer directly below the cell wall that also helps to protect the cell. Because of its semipermeability, it also selectively controls the passage of substances in and out of the cell. In addition, it contains various protein channels and pigments (usually in the form of chromophores) that harvest light energy, which may aid with the process of photosynthesis.     Ribosomes are small, abundant structures within the cytoplasm which are responsible for protein synthesis. Prokaryotic cells may also have a flagellum, or many flagella. Flagella are protein structures that are attached to the cell's surface, usually the cell wall, that help with the wave-like movement of the cell in liquid environments. Unlike eukaryotic flagella, prokaryotic flagella are powered by a proton motive force, known as chemosmotic potential, that is established on the membrane instead of ATP hydrolysis.     Pili are short hair-like structures on the surface of prokaryotic cells made of a variety of proteins. They are generally shorter, stiffer, and smaller in diameter in comparison to flagella. There are two types of pili. The sex pilus functions as the mediator for the transfer of DNA between mating prokaryotes, while the common pili (fimbrae) are smaller, more numerous pili that are involved with the attachment of prokaryotes to other surfaces in nature.

PROKARYOTIC REPRODUCTION
    Prokaryotes reproduce asexually by a process known as binary fission. This basically involves the cell dividing itself by mitosis to form an exact replicate. Because of this asexual reproduction, prokaryotes synthesize DNA continuously to use in recombination during reproduction. There are three main forms of recombination used by prokaryotes:
transformation, conjugation, and transduction (all defined on the next page). These processes allow for mutation, which prokaryotes depend on for genetic variety and adaptability. The division of cells, which is considered growth in eukaryotes, is considered the multiplication of cells or the growth of population in prokaryotes. It occurs with as frequent as 20 minutes or in other types of prokaryotes, every 1-3 hours.     This allows a colony of prokaryotes to grow up to a million kilograms within a day. However, some cells die off due to the consumption of resources or accumulation of metabolic waste. All cells within a colony compete to survive, and often release antibiotics to kill off other cells. These antibiotics are used in modern medicine to cure many diseases.     Prokaryotes reproduce best in conditions with appropriate temperature, pH, salinity, and sufficient nutrient sources. The actual requirements vary from specie to specie, but most prokaryotes do not reproduce well under low temperatures. The prokaryotes that are most resistance usually produce endospores, which allow for increased adaptability. In order to kill these bacteria, an autoclave (a pressure cooker that emits extreme heat) is needed. Nevertheless, some species only remain dormant as a result of this heat.

METABOLIC ACTIVITY
    Prokaryotes perform a variety of metabolic activities to get nutrients to synthesize organic compounds. Usually, this involves the use of energy and a carbon source. The type of metabolic activity used depends on whether the prokaryote is a
photoautotraph, chemoautotroph, photoheterotroph, or chemoheterotroph.     Since proteins and nucleic acids are composed of nitrogen, nitrogen needs to be in a useable form to ensure that proteins and nucleic acids can be synthesized efficiently. This process of making nitrogen into a useable form is known as nitrogen fixation, and allows the organism to be self-sufficient. Nitrogen fixation only uses ammonia (NH3) or nitrate (NO3), never N2, and is usually performed by chemoautotrophic bacteria. For example, nitrosomonas convert NH3 to NO2, and psuedomonas "denitrify" NO2- and NO3- to N2. Chemoautotrophic bacteria then convert the N2 into NH3. Sometimes, nitrogen fixation can be done by photoautotrophs that require CO2, N2, H2O, and minerals to grow. Nitrogen fixation is the only biological mechanism that makes nitrogen available to organisms that need it to make organic compounds.     Glycolysis is a metabolic activity in which glucose is used to make two pyruvate molecules and eventually ATP, using NAD+. The speed in which glycolysis is performed depends on the availability of O2. Glycolysis was first done by chemoautotrophs who used up all their ATP in various processes.     Fermentation is a form of glycolysis that is common to all organisms. Fermentation allows for food to be oxidized without the use of oxygen; therefore it is anaerobic. This is possible since oxidation does not occur due of the availability of O2, but because of the loss of electrons to any electron acceptor. Fermentation involves glycolysis and the regeneration of NAD+. First, electrons are extracted from nutrients during glycolysis and transferred to organic recipients. NAD+ is then regenerated by the transfer of electrons from NADH to pyruvate or other derivatives of it. This can be done by alcohol fermentation or lactic acid fermentation. In alcohol fermentation , pyruvate is converted to ethanol, which is released as CO2. This is then converted to acetaldehyde (a 2-carbon molecule), which generates NAD+. In lactic acid fermentation, pyruvate is reduced into NADH to form lactate. There is no release of CO2 in this process. Sometimes, lactic acid fermentation is used to make cheese and yogurt, using bacteria (usually gram positive cocci).     As prokaryotes use up their organic nutrients, nature uses photosynthesis to replace the used up nutrients. Light absorbing pigments within the membrane are used to absorb excess ultraviolet light, which can be harmful to cells. They are often coupled with electron transport systems that help to make ATP. Modern arachaebacteria, usually extreme halophiles, have bacteriorhodopsin in their plasma membranes, which can be used for simple photophosphorylation. Other organisms can drive electrons from hydrogen sulfide to NADP+ in order to fix CO2. This is where the process of photosynthesis essentially begins.     It is mainly due to these metabolic activities that scientists understand the impact of prokaryotes on life on Earth. Since prokaryotes produce their own energy, many scientists believe that mitochondria and chloroplasts once lived as unicellular organisms until the developed into eukaryotes. This theory is known as endosymbiosis. Overall, it is the general self-sufficiency of prokaryotes that allows them to survive and adapt so well.

BIBLIOGRAPHY
Biology, Fourth Edition (Neil A. Campbell)
Higher Level Biology, Revised Edition (Rita Y. Ghalayini)
Biological Identity of Procaryotes
Characteristics of Prokaryotes and Eukaryotes
Introductory Biology Courseware (103) - Viruses and Unicellular Organisms
Major Groups of Procaryotes
Prokaryotes: Archaea and Bacteria

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