1.
Cell nucleus
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In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. Eukaryotes usually have a nucleus, but a few cell types, such as mammalian red blood cells, have no nuclei. Cell nuclei contain most of the genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones. The genes within these chromosomes are the nuclear genome and are structured in such a way to promote cell function. The nucleus maintains the integrity of genes and controls the activities of the cell by regulating gene expression—the nucleus is, therefore, because the nuclear membrane is impermeable to large molecules, nuclear pores are required to regulate nuclear transport of molecules across the envelope. The pores cross both nuclear membranes, providing a channel through which larger molecules must be transported by carrier proteins while allowing free movement of small molecules. Movement of large molecules such as proteins and RNA through the pores is required for gene expression and the maintenance of chromosomes. The best-known of these is the nucleolus, which is involved in the assembly of ribosomes. After being produced in the nucleolus, ribosomes are exported to the cytoplasm where they translate mRNA, the nucleus was the first organelle to be discovered. What is most likely the oldest preserved drawing dates back to the early microscopist Antonie van Leeuwenhoek and he observed a lumen, the nucleus, in the red blood cells of salmon. Unlike mammalian red blood cells, those of other vertebrates still contain nuclei, the nucleus was also described by Franz Bauer in 1804 and in more detail in 1831 by Scottish botanist Robert Brown in a talk at the Linnean Society of London. Brown was studying orchids under microscope when he observed an opaque area and he did not suggest a potential function. In 1838, Matthias Schleiden proposed that the plays a role in generating cells. He believed that he had observed new cells assembling around cytoblasts, Franz Meyen was a strong opponent of this view, having already described cells multiplying by division and believing that many cells would have no nuclei. The function of the nucleus remained unclear, between 1877 and 1878, Oscar Hertwig published several studies on the fertilization of sea urchin eggs, showing that the nucleus of the sperm enters the oocyte and fuses with its nucleus. This was the first time it was suggested that an individual develops from a nucleated cell, therefore, the necessity of the sperm nucleus for fertilization was discussed for quite some time. However, Hertwig confirmed his observation in other groups, including amphibians. Eduard Strasburger produced the results for plants in 1884
2.
Amniote
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Amniotes are a clade of tetrapod vertebrates comprising the reptiles, birds, and mammals that lay their eggs on land or retain the fertilized egg within the mother. They are distinguished from the anamniotes, which lay their eggs in water. Older sources, particularly prior to the 20th century, may refer to amniotes as higher vertebrates and anamniotes as lower vertebrates, based on the discredited idea of the Great Chain of Being. Amniotes are tetrapods that are characterised by having an egg equipped with an amnion, amniotes include synapsids and sauropsids, as well as their ancestors, back to amphibians. Amniote embryos, whether laid as eggs or carried by the female, are protected and aided by several extensive membranes, in eutherian mammals, these membranes include the amniotic sac that surrounds the fetus. These embryonic membranes and the lack of a larval stage distinguish amniotes from tetrapod amphibians, the first amniotes, referred to as basal amniotes, resembled small lizards and evolved from the amphibian reptiliomorphs about 312 million years ago, in the Carboniferous geologic period. Their eggs could survive out of the water, allowing amniotes to branch out into drier environments, the eggs could also breathe and cope with wastes, allowing the eggs and the amniotes themselves to evolve into larger forms. From this point the amniotes spread around the globe, eventually to become the dominant land vertebrates, very early in the evolutionary history of amniotes, basal amniotes diverged into two main lines, the synapsids and the sauropsids, both of which persist into the modern era. Amniotes can be characterized in part by embryonic development that includes the formation of several extensive membranes, the amnion, chorion, and allantois. Amniotes develop directly into a form with limbs and a thick stratified epithelium. In amniotes, the transition from a two-layered periderm to cornified epithelium is triggered by thyroid hormone during embryonic development and their kidneys and large intestines are also well-suited to water retention. Most mammals do not lay eggs, but corresponding structures may be found inside the placenta, the ancestors of true amniotes, such as Casineria kiddi, which lived about 340 million years ago, evolved from amphibian reptiliomorphs and resembled small lizards. At the late Devonian mass extinction 360 million years ago, all known tetrapods were essentially aquatic, indeed, many modern day amniotes are dependent on moisture to keep their eggs from desiccating. Although some modern amphibians lay eggs on land, they all lack advanced traits like an amnion, the amniotic egg was formed through a series of evolutionary steps. This allowed the egg to both its size and the rate of gas exchange, permitting a larger, metabolically more active embryo to reach full development before hatching. Further development of the design, like extraembryonic membranes and a shell, were not essential. The only way for the eggs to increase in size would be to develop new internal structures specialized for respiration, as this happened, it would also affect how much the juveniles could grow before they reached adulthood. In fish and amphibians there is one inner membrane, the embryonic membrane
3.
Electron microscope
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An electron microscope is a microscope that uses a beam of accelerated electrons as a source of illumination. Transmission electron microscopes use electrostatic and electromagnetic lenses to control the electron beam and these electron optical lenses are analogous to the glass lenses of an optical light microscope. Industrially, electron microscopes are used for quality control and failure analysis. Modern electron microscopes produce electron micrographs using specialized digital cameras and frame grabbers to capture the image, the first electromagnetic lens was developed in 1926 by Hans Busch. According to Dennis Gabor, the physicist Leó Szilárd tried in 1928 to convince Busch to build an electron microscope, two years later, in 1933, Ruska built an electron microscope that exceeded the resolution attainable with an optical microscope. Moreover, Reinhold Rudenberg, the director of Siemens-Schuckertwerke, obtained the patent for the electron microscope in May 1931. In 1932, Ernst Lubcke of Siemens & Halske built and obtained images from an electron microscope. Five years later, the firm financed the work of Ernst Ruska and Bodo von Borries, also in 1937, Manfred von Ardenne pioneered the scanning electron microscope. The first commercial electron microscope was produced in 1938 by Siemens, although contemporary transmission electron microscopes are capable of two million-power magnification, as scientific instruments, they remain based upon Ruska’s prototype. The original form of electron microscope, the electron microscope uses a high voltage electron beam to illuminate the specimen. The electron beam is produced by a gun, commonly fitted with a tungsten filament cathode as the electron source. When it emerges from the specimen, the electron beam carries information about the structure of the specimen that is magnified by the lens system of the microscope. The image detected by the camera may be displayed on a monitor or computer. The resolution of TEMs is limited primarily by spherical aberration, but a new generation of aberration correctors have been able to partially overcome spherical aberration to increase resolution. The ability to determine the positions of atoms within materials has made the HRTEM an important tool for nano-technologies research, transmission electron microscopes are often used in electron diffraction mode. The major disadvantage of the electron microscope is the need for extremely thin sections of the specimens. Biological specimens are required to be chemically fixed, dehydrated and embedded in a polymer resin to stabilize them sufficiently to allow ultrathin sectioning. Sections of biological specimens, organic polymers and similar materials may require treatment with heavy atom labels in order to achieve the required image contrast
4.
Yeast
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Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The yeast lineage originated hundreds of millions of years ago, and 1,500 species are currently identified and they are estimated to constitute 1% of all described fungal species. Yeast sizes vary greatly, depending on species and environment, typically measuring 3–4 µm in diameter, most yeasts reproduce asexually by mitosis, and many do so by the asymmetric division process known as budding. Yeasts, with their growth habit, can be contrasted with molds. Fungal species that can take both forms are called dimorphic fungi and it is also a centrally important model organism in modern cell biology research, and is one of the most thoroughly researched eukaryotic microorganisms. Researchers have used it to information about the biology of the eukaryotic cell. Other species of yeasts, such as Candida albicans, are opportunistic pathogens, yeasts have recently been used to generate electricity in microbial fuel cells, and produce ethanol for the biofuel industry. Yeasts do not form a taxonomic or phylogenetic grouping. The budding yeasts are classified in the order Saccharomycetales, within the phylum Ascomycota, the word yeast comes from Old English gist, gyst, and from the Indo-European root yes-, meaning boil, foam, or bubble. Yeast microbes are probably one of the earliest domesticated organisms, archaeologists digging in Egyptian ruins found early grinding stones and baking chambers for yeast-raised bread, as well as drawings of 4, 000-year-old bakeries and breweries. In 1680, Dutch naturalist Anton van Leeuwenhoek first microscopically observed yeast, but at the time did not consider them to be living organisms, researchers were doubtful whether yeasts were algae or fungi, but in 1837 Theodor Schwann recognized them as fungi. In 1857, French microbiologist Louis Pasteur proved in the paper Mémoire sur la fermentation alcoolique that alcoholic fermentation was conducted by living yeasts and not by a chemical catalyst. Pasteur showed that by bubbling oxygen into the yeast broth, cell growth could be increased, by the late 18th century, two yeast strains used in brewing had been identified, Saccharomyces cerevisiae and S. carlsbergensis. S. cerevisiae has been sold commercially by the Dutch for bread-making since 1780, while, around 1800, in 1825, a method was developed to remove the liquid so the yeast could be prepared as solid blocks. The industrial production of yeast blocks was enhanced by the introduction of the press in 1867. In 1872, Baron Max de Springer developed a process to create granulated yeast. Yeasts are chemoorganotrophs, as they use organic compounds as a source of energy, carbon is obtained mostly from hexose sugars, such as glucose and fructose, or disaccharides such as sucrose and maltose. Some species can metabolize pentose sugars such as ribose, alcohols, Yeast species either require oxygen for aerobic cellular respiration or are anaerobic, but also have aerobic methods of energy production
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.
DNA
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Deoxyribonucleic acid is a molecule that carries the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and RNA are nucleic acids, alongside proteins, lipids and complex carbohydrates, most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are termed polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases—cytosine, guanine, adenine, or thymine —a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison the total mass of the biosphere has been estimated to be as much as 4 trillion tons of carbon. The DNA backbone is resistant to cleavage, and both strands of the double-stranded structure store the same biological information and this information is replicated as and when the two strands separate. A large part of DNA is non-coding, meaning that these sections do not serve as patterns for protein sequences, the two strands of DNA run in opposite directions to each other and are thus antiparallel. Attached to each sugar is one of four types of nucleobases and it is the sequence of these four nucleobases along the backbone that encodes biological information. RNA strands are created using DNA strands as a template in a process called transcription, under the genetic code, these RNA strands are translated to specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells DNA is organized into structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, eukaryotic organisms store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast prokaryotes store their DNA only in the cytoplasm, within the eukaryotic chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed, DNA was first isolated by Friedrich Miescher in 1869. DNA is used by researchers as a tool to explore physical laws and theories, such as the ergodic theorem. The unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro-, among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a polymer made from repeating units called nucleotides
7.
Cell (biology)
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The cell is the basic structural, functional, and biological unit of all known living organisms. A cell is the smallest unit of life that can replicate independently, the study of cells is called cell biology. Cells consist of cytoplasm enclosed within a membrane, which contains many such as proteins. Organisms can be classified as unicellular or multicellular, while the number of cells in plants and animals varies from species to species, humans contain more than 10 trillion cells. Most plant and animal cells are only under a microscope. The cell was discovered by Robert Hooke in 1665, who named the unit for its resemblance to cells inhabited by Christian monks in a monastery. Cells emerged on Earth at least 3.5 billion years ago, Cells are of two types, eukaryotic, which contain a nucleus, and prokaryotic, which do not. Prokaryotes are single-celled organisms, while eukaryotes can be either single-celled or multicellular, prokaryotic cells were the first form of life on Earth, characterised by having vital biological processes including cell signaling and being self-sustaining. They are simpler and smaller than eukaryotic cells, and lack membrane-bound organelles such as the nucleus, prokaryotes include two of the domains of life, bacteria and archaea. The DNA of a prokaryotic cell consists of a chromosome that is in direct contact with the cytoplasm. The nuclear region in the cytoplasm is called the nucleoid, most prokaryotes are the smallest of all organisms ranging from 0.5 to 2.0 µm in diameter. Though most prokaryotes have both a cell membrane and a wall, there are exceptions such as Mycoplasma and Thermoplasma which only possess the cell membrane layer. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, the cell wall consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and bursting from osmotic pressure due to a hypotonic environment, some eukaryotic cells also have a cell wall. Inside the cell is the region that contains the genome, ribosomes. The genetic material is found in the cytoplasm. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular, linear bacterial plasmids have been identified in several species of spirochete bacteria, including members of the genus Borrelia notably Borrelia burgdorferi, which causes Lyme disease. Though not forming a nucleus, the DNA is condensed in a nucleoid, plasmids encode additional genes, such as antibiotic resistance genes
8.
Anamniotes
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The anamniotes are an informal group comprising the fishes and the amphibians, the so-called lower vertebrates, which lay their eggs in water. They are distinguished from the amniotes, the vertebrates, which lay their eggs on land or retain the fertilized egg within the mother. The name refers to the amnion, an embryonic membrane produced during the development of amniotes which serves to transport oxygen into the egg. As the name suggests, anamniotes do not develop an amnion during fetal life and are able to exchange oxygen, carbon dioxide, the water helps in the diffusion of waste products, allowing the embryo to complete embryonic development without being poisoned by their own waste products. During their development, all anamniote classes pass through a stage which resembles fish, the group is characterized by retaining the primitive vertebrate condition in several traits, Permeable skin allowing diffusion of water and gases directly through the skin. Presence at some period of life of gills Absence of an amnion Absence or rudimentary condition of the allantois Nucleated red blood cells, the features unifying the anamniotes was first noted by Thomas Henry Huxley in 1863, who coined the phrase Ichtioid or Ichthyopsida for the group. It is a taxonomic classification just below the level of Vertebrata, though Huxley presented the Ichtyopsida as an informal unit, the term ichthyopsida means fish-face or fish-like as opposed to the sauropsida or lizard-face animals and the mammals. The group representing a grade rather than a clade, the term anamniote is now used as an informal way of denoting the physical property of the group
9.
RNA
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Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids, and, along with proteins and carbohydrates, like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome, some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these processes is protein synthesis, a universal function where RNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA molecules to deliver amino acids to the ribosome, analysis of these RNAs has revealed that they are highly structured. Unlike DNA, their structures do not consist of long double helices, in this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the enzyme that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA. Each nucleotide in RNA contains a sugar, with carbons numbered 1 through 5. A base is attached to the 1 position, in general, adenine, cytosine, guanine, adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3 position of one ribose, the phosphate groups have a negative charge each, making RNA a charged molecule. The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil, however, other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair. An important structural feature of RNA that distinguishes it from DNA is the presence of a group at the 2 position of the ribose sugar. The A-form geometry results in a deep and narrow major groove. RNA is transcribed with only four bases, but these bases, pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine are found in various places. Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine, inosine plays a key role in the wobble hypothesis of the genetic code. The specific roles of many of these modifications in RNA are not fully understood, the functional form of single-stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule and this leads to several recognizable domains of secondary structure like hairpin loops, bulges, and internal loops
10.
RNA polymerase
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RNA polymerase, also known as DNA-dependent RNA polymerase, is an enzyme that produces primary transcript RNA. In cells, RNAP is necessary for constructing RNA chains using DNA genes as templates, RNA polymerase enzymes are essential to life and are found in all organisms and many viruses. In chemical terms, RNAP is a transferase that polymerizes ribonucleotides at the 3 end of an RNA transcript. RNAP was discovered independently by Charles Loe, Audrey Stevens, the 2006 Nobel Prize in Chemistry was awarded to Roger D. Kornberg for creating detailed molecular images of RNA polymerase during various stages of the transcription process. Therefore, it is surprising that the activity of RNAP is long, complex. In Escherichia coli bacteria, more than 100 transcription factors have been identified, RNAP can initiate transcription at specific DNA sequences known as promoters. It then produces an RNA chain, which is complementary to the template DNA strand, the process of adding nucleotides to the RNA strand is known as elongation, in eukaryotes, RNAP can build chains as long as 2.4 million nucleotides. RNAP will preferentially release its RNA transcript at specific DNA sequences encoded at the end of genes, products of RNAP include, Messenger RNA —template for the synthesis of proteins by ribosomes. Non-coding RNA or RNA genes—a broad class of genes that encode RNA that is not translated into protein, the most prominent examples of RNA genes are transfer RNA and ribosomal RNA, both of which are involved in the process of translation. However, since the late 1990s, many new RNA genes have been found and it is able to do this because specific interactions with the initiating nucleotide hold RNAP rigidly in place, facilitating chemical attack on the incoming nucleotide. Such specific interactions explain why RNAP prefers to start transcripts with ATP, in contrast to DNA polymerase, RNAP includes helicase activity, therefore no separate enzyme is needed to unwind DNA. There are multiple interchangeable sigma factors, each of which recognizes a set of promoters. After binding to the DNA, the RNA polymerase switches from a complex to an open complex. This change involves the separation of the DNA strands to form a section of DNA of approximately 13 bp. Ribonucleotides are base-paired to the template DNA strand, according to Watson-Crick base-pairing interactions, supercoiling plays an important part in polymerase activity because of the unwinding and rewinding of DNA. Because regions of DNA in front of RNAP are unwound, there are compensatory positive supercoils, regions behind RNAP are rewound and negative supercoils are present. As noted above, RNA polymerase makes contacts with the promoter region, however these stabilizing contacts inhibit the enzymes ability to access DNA further downstream and thus the synthesis of the full-length product. Once the open complex is stabilized, RNA polymerase synthesizes an RNA strand to establish a DNA-RNA heteroduplex at the active center, which stabilizes the elongation complex
