1.
Archaea
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The Archaea constitute a domain and kingdom of single-celled microorganisms. These microbes are prokaryotes, meaning that they have no cell nucleus or any other membrane-bound organelles in their cells, Archaea were initially classified as bacteria, receiving the name archaebacteria, but this classification is outdated. Archaeal cells have unique properties separating them from the two domains of life, Bacteria and Eukaryota. The Archaea are further divided into multiple recognized phyla, classification is difficult because the majority have not been isolated in the laboratory and have only been detected by analysis of their nucleic acids in samples from their environment. Archaea and bacteria are generally similar in size and shape, although a few archaea have very strange shapes, such as the flat, other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols. Archaea use more energy sources than eukaryotes, these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea use sunlight as a source, and other species of archaea fix carbon, however, unlike plants and cyanobacteria. Archaea reproduce asexually by fission, fragmentation, or budding, unlike bacteria and eukaryotes. They are also found in the colon, oral cavity. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet, Archaea are a major part of Earths life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, one example is the methanogens that inhabit human and ruminant guts, where their vast numbers aid digestion. Methanogens are also used in production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures. For much of the 20th century, prokaryotes were regarded as a group of organisms and classified based on their biochemistry, morphology. For example, microbiologists tried to classify based on the structures of their cell walls, their shapes. In 1965, Emile Zuckerkandl and Linus Pauling proposed instead using the sequences of the genes in different prokaryotes to work out how they are related to each other and this approach, known as phylogenetics, is the main method used today. Archaea were first classified as a group of prokaryotes in 1977 by Carl Woese. These two groups were named the Archaebacteria and Eubacteria and treated as kingdoms or subkingdoms, which Woese. Woese argued that group of prokaryotes is a fundamentally different sort of life
2.
Bacteria
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Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea
3.
Plant
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Plants are mainly multicellular, predominantly photosynthetic eukaryotes of the kingdom Plantae. The term is generally limited to the green plants, which form an unranked clade Viridiplantae. This includes the plants, conifers and other gymnosperms, ferns, clubmosses, hornworts, liverworts, mosses and the green algae. Green plants have cell walls containing cellulose and obtain most of their energy from sunlight via photosynthesis by primary chloroplasts and their chloroplasts contain chlorophylls a and b, which gives them their green color. Some plants are parasitic and have lost the ability to produce amounts of chlorophyll or to photosynthesize. Plants are characterized by sexual reproduction and alternation of generations, although reproduction is also common. There are about 300–315 thousand species of plants, of which the great majority, green plants provide most of the worlds molecular oxygen and are the basis of most of Earths ecologies, especially on land. Plants that produce grains, fruits and vegetables form humankinds basic foodstuffs, Plants play many roles in culture. They are used as ornaments and, until recently and in variety, they have served as the source of most medicines. The scientific study of plants is known as botany, a branch of biology, Plants are one of the two groups into which all living things were traditionally divided, the other is animals. The division goes back at least as far as Aristotle, who distinguished between plants, which generally do not move, and animals, which often are mobile to catch their food. Much later, when Linnaeus created the basis of the system of scientific classification. Since then, it has become clear that the plant kingdom as originally defined included several unrelated groups, however, these organisms are still often considered plants, particularly in popular contexts. When the name Plantae or plant is applied to a group of organisms or taxon. The evolutionary history of plants is not yet settled. Those which have been called plants are in bold, the way in which the groups of green algae are combined and named varies considerably between authors. Algae comprise several different groups of organisms which produce energy through photosynthesis, most conspicuous among the algae are the seaweeds, multicellular algae that may roughly resemble land plants, but are classified among the brown, red and green algae. Each of these groups also includes various microscopic and single-celled organisms
4.
Protozoa
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In 21st-century systems of biological classification, the Protozoa are defined as a diverse group of unicellular eukaryotic organisms. Historically, protozoa were defined as single-celled animals or organisms with animal-like behaviors, such as motility, the group was regarded as the zoological counterpart to the protophyta, which were considered to be plant-like, as they are capable of photosynthesis. The terms protozoa and protozoans are now mostly used informally to designate single-celled, non-photosynthetic protists, such as the ciliates, amoebae and flagellates. The term Protozoa was introduced in 1818 for a taxonomic class, in several classification systems proposed by Thomas Cavalier-Smith and his collaborators since 1981, Protozoa is ranked as a kingdom. The seven-kingdom scheme proposed by Ruggiero et al. in 2015, places eight phyla under Protozoa, Euglenozoa, Amoebozoa, Metamonada, Choanozoa, Loukozoa, Percolozoa, Microsporidia and Sulcozoa. This kingdom does not form a clade, but an evolutionary grade or paraphyletic group, from which the fungi, for this reason, the terms protists, Protista or Protoctista are sometimes preferred for the high-level classification of eukaryotic microbes. In 2005, members of the Society of Protozoologists voted to change the name of organization to the International Society of Protistologists. The word protozoa was coined in 1818 by zoologist Georg August Goldfuss, as the Greek equivalent of the German Urthiere, meaning primitive, Goldfuss erected Protozoa as a class containing what he believed to be the simplest animals. Originally, the group included not only microbes, but also some lower animals, such as rotifers, corals, sponges, jellyfish, bryozoa. In 1848, in light of advancements in cell theory pioneered by Theodore Schwann and Matthias Schleiden, von Siebold redefined Protozoa to include only such unicellular forms, to the exclusion of all metazoa. At the same time, he raised the group to the level of a phylum containing two broad classes of microbes, Infusoria, and Rhizopoda. As a phylum under Animalia, the Protozoa were firmly rooted in the old two-kingdom classification of life, criticism of this system began in the latter half of the 19th century, with the realization that many organisms met the criteria for inclusion among both plants and animals. For example, the algae Euglena and Dinobryon have chloroplasts for photosynthesis, as an alternative, he proposed a new kingdom called Primigenum, consisting of both the protozoa and unicellular algae, which he combined together under the name Protoctista. In Hoggss conception, the animal and plant kingdoms were likened to two great pyramids blending at their bases in the Kingdom Primigenum, six years later, Ernst Haeckel also proposed a third kingdom of life, which he named Protista. Despite these proposals, Protozoa emerged as the taxonomic placement for heterotrophic microbes such as amoebae and ciliates. A variety of systems were proposed, and Kingdoms Protista and Protoctista became well established in biology texts. While many taxonomists have abandoned Protozoa as a group, Thomas Cavalier-Smith has retained it as a kingdom in the various classifications he has proposed. As of 2015, Cavalier-Smiths Protozoa excludes several major groups of organisms traditionally placed among the protozoa, including the ciliates, dinoflagellates, Protozoa, as traditionally defined, are mainly microscopic organisms, ranging in size from 10 to 52 micrometers
5.
Eukaryote
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A eukaryote is any organism whose cells contain a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eukarya or Eukaryota, the presence of a nucleus gives eukaryotes their name, which comes from the Greek εὖ and κάρυον. Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, in addition, plants and algae contain chloroplasts. Eukaryotic organisms may be unicellular or multicellular, only eukaryotes form multicellular organisms consisting of many kinds of tissue made up of different cell types. Eukaryotes can reproduce asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two identical cells. In meiosis, DNA replication is followed by two rounds of division to produce four daughter cells each with half the number of chromosomes as the original parent cell. These act as sex cells resulting from genetic recombination during meiosis, the domain Eukaryota appears to be monophyletic, and so makes up one of the three domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and have none of the above features, eukaryotes represent a tiny minority of all living things. However, due to their larger size, eukaryotes collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1. 6–2.1 billion years ago, in 1905 and 1910, the Russian biologist Konstantin Mereschkowsky argued three things about the origin of nucleated cells. Firstly, plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic host, secondly, the host had earlier in evolution formed by symbiosis between an amoeba-like host and a bacteria-like cell that formed the nucleus. Thirdly, plants inherited photosynthesis from cyanobacteria, the split between the prokaryotes and eukaryotes was introduced in the 1960s. The concept of the eukaryote has been attributed to the French biologist Edouard Chatton, the terms prokaryote and eukaryote were more definitively reintroduced by the Canadian microbiologist Roger Stanier and the Dutch-American microbiologist C. B. van Niel in 1962. In his 1938 work Titres et Travaux Scientifiques, Chatton had proposed the two terms, calling the bacteria prokaryotes and organisms with nuclei in their cells eukaryotes. However he mentioned this in one paragraph, and the idea was effectively ignored until Chattons statement was rediscovered by Stanier. In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in cells in her paper. In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA and this helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles, mitochondria and chloroplasts
6.
Cholesterol
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Cholesterol, from the Ancient Greek chole- and stereos followed by the chemical suffix -ol for an alcohol, is an organic molecule. Cholesterol enables animal cells to dispense with a wall, thereby allowing animal cells to change shape rapidly. In addition to its importance for cell structure, cholesterol also serves as a precursor for the biosynthesis of steroid hormones, bile acid. Cholesterol is the principal sterol synthesized by all animals, in vertebrates, hepatic cells typically produce the greatest amounts. It is absent among prokaryotes, although there are exceptions, such as Mycoplasma. François Poulletier de la Salle first identified cholesterol in solid form in gallstones in 1769, however, it was not until 1815 that chemist Michel Eugène Chevreul named the compound cholesterine. Furthermore, it can be absorbed directly from animal-based foods, a human male weighing 68 kg normally synthesizes about 1 gram per day, and his body contains about 35 g, mostly contained within the cell membranes. Typical daily cholesterol dietary intake for a man in the United States is 307 mg, most ingested cholesterol is esterified, and esterified cholesterol is poorly absorbed. The body also compensates for any absorption of cholesterol by reducing cholesterol synthesis. For these reasons, cholesterol in food, seven to ten hours after ingestion, has little and it is also important to recognize, however, that the concentrations measured in the samples of blood plasma vary with the measurement methods used. Cholesterol is recycled in the body, the liver excretes it in a non-esterified form into the digestive tract. Typically, about 50% of the excreted cholesterol is reabsorbed by the small intestine back into the bloodstream, plants make cholesterol in very small amounts. Plants manufacture phytosterols, which can compete with cholesterol for reabsorption in the intestinal tract, when intestinal lining cells absorb phytosterols, in place of cholesterol, they usually excrete the phytosterol molecules back into the GI tract, an important protective mechanism. Cholesterol, given that it composes about 30% of all cell membranes, is required to build. The membrane remains stable and durable without being rigid, allowing cells to change shape. In this structural role, cholesterol also reduces the permeability of the membrane to neutral solutes, hydrogen ions. Within the cell membrane, cholesterol also functions in intracellular transport, cell signaling, cholesterol is essential for the structure and function of invaginated caveolae and clathrin-coated pits, including caveola-dependent and clathrin-dependent endocytosis. The role of cholesterol in endocytosis of these types can be investigated by using methyl beta cyclodextrin to remove cholesterol from the plasma membrane, in multiple layers, cholesterol and phospholipids, both electrical insulators, can facilitate speed of transmission of electrical impulses along nerve tissue
7.
Escherichia coli
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Escherichia coli is a gram-negative, facultatively anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms. Most E. coli strains are harmless, but some serotypes can cause food poisoning in their hosts. The harmless strains are part of the flora of the gut, and can benefit their hosts by producing vitamin K2. E. coli is expelled into the environment within fecal matter, the bacterium grows massively in fresh fecal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards. E. coli and other facultative anaerobes constitute about 0. 1% of gut flora, cells are able to survive outside the body for a limited amount of time, which makes them potential indicator organisms to test environmental samples for fecal contamination. A growing body of research, though, has examined environmentally persistent E. coli which can survive for extended periods outside of a host, the bacterium can be grown and cultured easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. E. coli is a chemoheterotroph whose chemically defined medium must include a source of carbon, under favorable conditions, it takes only 20 minutes to reproduce. E. coli is a Gram-negative, facultative anaerobic and nonsporulating bacterium, cells are typically rod-shaped, and are about 2.0 μm long and 0. 25–1.0 μm in diameter, with a cell volume of 0. 6–0.7 μm3. E. coli stains Gram-negative because its cell wall is composed of a peptidoglycan layer. During the staining process, E. coli picks up the color of the counterstain safranin, the outer membrane surrounding the cell wall provides a barrier to certain antibiotics such that E. coli is not damaged by penicillin. Strains that possess flagella are motile, the flagella have a peritrichous arrangement. E. coli can live on a variety of substrates and uses mixed-acid fermentation in anaerobic conditions, producing lactate, succinate, ethanol, acetate. Optimum growth of E. coli occurs at 37 °C, and it uses oxygen when it is present and available. It can, however, continue to grow in the absence of oxygen using fermentation or anaerobic respiration, the ability to continue growing in the absence of oxygen is an advantage to bacteria because their survival is increased in environments where water predominates. The bacterial cell cycle is divided into three stages, the B period occurs between the completion of cell division and the beginning of DNA replication. The C period encompasses the time it takes to replicate the chromosomal DNA, the D period refers to the stage between the conclusion of DNA replication and the end of cell division. The doubling rate of E. coli is higher when more nutrients are available, However, the length of the C and D periods do not change, even when the doubling time becomes less than the sum of the C and D periods. At the fastest growth rates, replication begins before the round of replication has completed, resulting in multiple replication forks along the DNA
8.
Mycobacterium tuberculosis
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Mycobacterium tuberculosis is an obligate pathogenic bacterial species in the family Mycobacteriaceae and the causative agent of tuberculosis. First discovered in 1882 by Robert Koch, M. tuberculosis has an unusual and this coating makes the cells impervious to Gram staining, and as a result, M. tuberculosis can appear either Gram-negative or Gram-positive. Acid-fast stains such as Ziehl-Neelsen, or fluorescent stains such as auramine are used instead to identify M. tuberculosis with a microscope, the physiology of M. tuberculosis is highly aerobic and requires high levels of oxygen. Primarily a pathogen of the respiratory system, it infects the lungs. The most frequently used methods for tuberculosis are the tuberculin skin test, acid-fast stain, culture. The M. tuberculosis genome was sequenced in 1998. M. tuberculosis is part of a complex that has at least 9 species, M. tuberculosis sensu strictu, M. africanum, M. canetti, M. bovis, M. caprae, M. microti, M. pinnipedii, M. mungi, and M. orygis. It requires oxygen to grow, does not produce spores, and is nonmotile, M. tuberculosis divides every 15–20 hours. This is extremely slow compared with other bacteria, which tend to have division times measured in minutes and it is a small bacillus that can withstand weak disinfectants and can survive in a dry state for weeks. Its unusual cell wall is rich in such as mycolic acid and is likely responsible for its resistance to desiccation and is a key virulence factor. Other bacteria are identified with a microscope by staining them with Gram stain. However, the acid in the cell wall of M. tuberculosis does not absorb the stain. Instead, acid-fast stains such as Ziehl-Neelsen stain, or fluorescent stains such as auramine are used, cells are curved rod-shaped and are often seen wrapped together, due to the presence of fatty acids in the cell wall that stick together. This appearance is referred to as cording, like strands of cord that make up a rope, M. tuberculosis is characterized in tissue by caseating granulomas containing Langhans giant cells, which have a horseshoe pattern of nuclei. M. tuberculosis can be grown in the laboratory, compared to other commonly studied bacteria, M. tuberculosis has a remarkably slow growth rate, doubling roughly once per day. Commonly used media include liquids such as Middlebrook 7H9 or 7H12, egg-based solid media such as Lowenstein-Jensen, visible colonies require several weeks to grow on agar plates. It is distinguished from other mycobacteria by its production of catalase, other tests to confirm its identity include gene probes and MALDI-TOF. Humans are the only known reservoirs of M. tuberculosis, a misconception is that M. tuberculosis can be spread by shaking hands, making contact with toilet seats, sharing food or drink, sharing toothbrushes, or kissing
9.
Steroid hormone
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A steroid hormone is a steroid that acts as a hormone. Steroid hormones can be grouped into two classes, corticosteroids and sex steroids, within those two classes are five types according to the receptors to which they bind, glucocorticoids, mineralocorticoids, androgens, estrogens, and progestogens. Vitamin D derivatives are a closely related hormone system with homologous receptors. They have some of the characteristics of true steroids as receptor ligands, Steroid hormones help control metabolism, inflammation, immune functions, salt and water balance, development of sexual characteristics, and the ability to withstand illness and injury. The term steroid describes both hormones produced by the body and artificially produced medications that duplicate the action for the naturally occurring steroids, the natural steroid hormones are generally synthesized from cholesterol in the gonads and adrenal glands. These forms of hormones are lipids and they can pass through the cell membrane as they are fat-soluble, and then bind to steroid hormone receptors to bring about changes within the cell. Steroid hormones are generally carried in the blood, bound to specific carrier proteins such as sex hormone-binding globulin or corticosteroid-binding globulin, further conversions and catabolism occurs in the liver, in other peripheral tissues, and in the target tissues. A variety of synthetic steroids and sterols have also been contrived, most are steroids, but some non-steroidal molecules can interact with the steroid receptors because of a similarity of shape. Some synthetic steroids are weaker or stronger than the natural steroids whose receptors they activate, some examples are sex hormone-binding globulin, corticosteroid-binding globulin, and albumin. Most studies say that hormones can affect cells when they are not bound by serum proteins. This idea is known as the free hormone hypothesis and this idea is shown in Figure 1 to the right. One study has found that these complexes are bound by megalin, a membrane receptor. The hormone then follows a pathway of action. This process is shown in Figure 2 to the right, the role of endocytosis in steroid hormone transport is not well understood and is under further investigation. In order for steroid hormones to cross the lipid bilayer of cells they must overcome barriers that would prevent their entering or exiting the membrane. Gibbs free energy is an important concept here and these hormones, which are all derived from cholesterol, have hydrophilic functional groups at either end and hydrophobic carbon backbones. These energy barriers and wells are reversed for hormones exiting membranes, Steroid hormones easily enter and exit the membrane at physiologic conditions. They have been shown experimentally to cross membranes near a rate of 20 μm/s, though it is energetically more favorable for hormones to be in the membrane than in the ECF or ICF, they do in fact leave the membrane once they have entered it
10.
Transcription (biology)
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Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme RNA polymerase. Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a complementary language, during transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript. Transcription proceeds in the general steps, RNA polymerase, together with one or more general transcription factors. RNA polymerase creates a bubble, which separates the two strands of the DNA helix. This is done by breaking the bonds between complementary DNA nucleotides. RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand, hydrogen bonds of the RNA–DNA helix break, freeing the newly synthesized RNA strand. If the cell has a nucleus, the RNA may be further processed and this may include polyadenylation, capping, and splicing. The RNA may remain in the nucleus or exit to the cytoplasm through the pore complex. The stretch of DNA transcribed into an RNA molecule is called a transcription unit, if the gene encodes a protein, the transcription produces messenger RNA, the mRNA, in turn, serves as a template for the proteins synthesis through translation. Alternatively, the gene may encode for either non-coding RNA, ribosomal RNA, transfer RNA. Overall, RNA helps synthesize, regulate, and process proteins, in virology, the term may also be used when referring to mRNA synthesis from an RNA molecule. For instance, the genome of a negative-sense single-stranded RNA virus may be template for a positive-sense single-stranded RNA and this is because the positive-sense strand contains the information needed to translate the viral proteins for viral replication afterwards. This process is catalyzed by a viral RNA replicase, the regulatory sequence before the coding sequence is called the five prime untranslated region, the sequence after the coding sequence is called the three prime untranslated region. As opposed to DNA replication, transcription results in an RNA complement that includes the nucleotide uracil in all instances where thymine would have occurred in a DNA complement, only one of the two DNA strands serve as a template for transcription. The antisense strand of DNA is read by RNA polymerase from the 3 end to the 5 end during transcription. The complementary RNA is created in the direction, in the 5 →3 direction. This directionality is because RNA polymerase can only add nucleotides to the 3 end of the growing mRNA chain and this use of only the 3 →5 DNA strand eliminates the need for the Okazaki fragments that are seen in DNA replication. This also removes the need for an RNA primer to initiate RNA synthesis, the non-template strand of DNA is called the coding strand, because its sequence is the same as the newly created RNA transcript
11.
Plastid
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The plastid is a major double-membrane organelle found, among others, in the cells of plants and algae. Plastids are the site of manufacture and storage of important chemical compounds used by the cell and they often contain pigments used in photosynthesis, and the types of pigments present can change or determine the cells color. They have an evolutionary origin and possess a double-stranded DNA molecule that is circular. Those plastids that contain chlorophyll can carry out photosynthesis, Plastids can also store products like starch and can synthesise fatty acids and terpenes, which can be used for producing energy and as raw material for the synthesis of other molecules. For example, the components of the plant cuticle and its epicuticular wax are synthesized by the cells from palmitic acid. All plastids are derived from proplastids, which are present in the regions of the plant. Proplastids and young chloroplasts commonly divide by fission, but more mature chloroplasts also have this capacity. In plants, plastids may differentiate into several forms, depending upon which function they play in the cell, each plastid creates multiple copies of a circular 75–250 kilobase plastome. The plastome contains about 100 genes encoding ribosomal and transfer ribonucleic acids as well as involved in photosynthesis. However, these only represent a small fraction of the total protein set-up necessary to build and maintain the structure. Plastid DNA exists as large protein-DNA complexes associated with the envelope membrane. Each nucleoid particle may contain more than 10 copies of the plastid DNA, the proplastid contains a single nucleoid located in the centre of the plastid. The developing plastid has many nucleoids, localized at the periphery of the plastid, during the development of proplastids to chloroplasts, and when plastids convert from one type to another, nucleoids change in morphology, size and location within the organelle. The remodelling of nucleoids is believed to occur by modifications to the composition, many plastids, particularly those responsible for photosynthesis, possess numerous internal membrane layers. In plant cells, long thin protuberances called stromules sometimes form and extend from the main body into the cytosol. Proteins, and presumably smaller molecules, can move within stromules, most cultured cells that are relatively large compared to other plant cells have very long and abundant stromules that extend to the cell periphery. In 2014, evidence of possible plastid genome loss was found in Rafflesia lagascae, a non-photosynthetic parasitic flowering plant, and in Polytomella, extensive searches for plastid genes in both Rafflesia and Polytomella yielded no results, however the conclusion that their plastomes are entirely missing is still controversial. Some scientists argue that plastid genome loss is unlikely since even non-photosynthetic plastids contain genes necessary to complete various biosynthetic pathways, in algae, the term leucoplast is used for all unpigmented plastids and their function differs from the leucoplasts of plants
12.
Enzyme
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Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and he wrote that alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase
Orange nodes: carbohydrate metabolism. 
Violet nodes: photosynthesis. 
Red nodes: cellular respiration. 
Pink nodes: cell signaling. 
Blue nodes: amino acid metabolism. 
Grey nodes: vitamin and cofactor metabolism. 
Brown nodes: nucleotide and protein metabolism. 
Green nodes: lipid metabolism.