1.
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
2.
Base excision repair
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In biochemistry and genetics, base excision repair is a cellular mechanism that repairs damaged DNA throughout the cell cycle. It is responsible primarily for removing small, non-helix-distorting base lesions from the genome, the related nucleotide excision repair pathway repairs bulky helix-distorting lesions. BER is important for removing damaged bases that could cause mutations by mispairing or lead to breaks in DNA during replication. BER is initiated by DNA glycosylases, which recognize and remove damaged or inappropriate bases. These are then cleaved by an AP endonuclease, the resulting single-strand break can then be processed by either short-patch or long-patch BER. Single bases in DNA can be damaged by a variety of mechanisms, the most common ones being deamination, oxidation. These modifications can affect the ability of the base to hydrogen-bond, resulting in incorrect base-pairing, for example, incorporation of adenine across from 8-oxoguanine during DNA replication causes a G, C base pair to be mutated to T, A. Xanthine formed from deamination of guanine, uracil inappropriately incorporated in DNA or formed by deamination of cytosine In addition to base lesions, the downstream steps of BER are also utilized to repair single-strand breaks. The choice between short- and long-patch repair is currently under investigation, various factors are thought to influence this decision, including the type of lesion, the cell cycle stage, and whether the cell is terminally differentiated or actively dividing. Some lesions, such as oxidized or reduced AP sites, are resistant to pol β lyase activity and, therefore, pathway preference may differ between organisms, as well. The recent discovery that the poly-A polymerase Trf4 possesses 5 dRP lyase activity has challenged this view, DNA glycosylases are responsible for initial recognition of the lesion. They flip the damaged base out of the helix, as pictured. There are two categories of glycosylases, monofunctional and bifunctional, monofunctional glycosylases have only glycosylase activity, whereas bifunctional glycosylases also possess AP lyase activity. Therefore, bifunctional glycosylases can convert a base lesion into a break without the need for an AP endonuclease. β-Elimination of an AP site by a yields a 3 α, β-unsaturated aldehyde adjacent to a 5 phosphate. Some glycosylase-lyases can further perform δ-elimination, which converts the 3 aldehyde to a 3 phosphate, a wide variety of glycosylases have evolved to recognize different damaged bases. Examples of DNA glycosylases include Ogg1, which recognizes 8-oxoguanine, Mag1, which recognizes 3-methyladenine, and UNG, the AP endonucleases cleave an AP site to yield a 3 hydroxyl adjacent to a 5 deoxyribosephosphate. AP endonucleases are divided into two based on their homology to the ancestral bacterial AP endonucleaes endonuclease IV and exonuclease III
3.
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
4.
DNA base flipping
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DNA base flipping, or nucleotide flipping, is a mechanism in which a single nucleotide base, or nucleobase, is rotated outside the nucleic acid double helix. This occurs when a nucleic acid-processing enzyme needs access to the base to work on it. It was first observed in 1994 using X-ray crystallography in an enzyme catalyzing methylation of a cytosine base in DNA. Since then, it has shown to be used by different enzymes in many biological processes such as DNA methylation, various DNA repair mechanisms. It can also occur in RNA double helices or in the DNA, RNA intermediates formed during RNA transcription, DNA base flipping occurs by breaking the hydrogen bonds between the bases and unstacking the base from its neighbors. It can be detected using X-ray crystallography, NMR spectroscopy, fluorescence spectroscopy, the methyltransferase they used was the C5-cytosine methyltransferase from Haemophilus haemolyticus. This enzyme recognizes a specific sequence of the DNA and methylates the first cytosine base of the sequence at its C5 location. Upon crystallization of the M. HhaI-DNA complex, they saw the target cytosine base was rotated out of the double helix and was positioned in the active site of the M. HhaI. It was held in place by numerous interactions between the M. HhaI and DNA, the authors theorized that base flipping was a mechanism used by many other enzymes, such as helicases, recombination enzymes, RNA polymerases, DNA polymerases, and Type II topoisomerases. Much research has been done in the years subsequent to this discovery, DNA nucleotides are held together with hydrogen bonds, which are relatively weak and can be easily broken. Base flipping occurs on a millisecond timescale by breaking the bonds between bases and unstacking the base from its neighbors. The base is rotated out of the double helix by 180 degrees, typically via the major groove, and into the active site of an enzyme. This opening leads to conformational changes in the DNA backbone which are quickly stabilized by the increased enzyme-DNA interactions. Studies looking at the free-energy profiles of base flipping have shown that the barrier to flipping can be lowered by 17 kcal/mol for M. HhaI in the closed conformation. There are two mechanisms of DNA base flipping, active and passive, research has demonstrated both mechanisms, uracil-DNA glycosylase follows the passive mechanism and Tn10 transposase follows the active mechanism. DNA can have mutations that cause a base in the DNA strand to be damaged, to ensure genetic integrity of the DNA, enzymes need to repair any damage. There are many types of DNA repair, DNA glycosylases interact with DNA, flipping bases to determine a mismatch. An example of base excision repair occurs when a base is deaminated
5.
Glycosidic bond
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In chemistry, a glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate molecule to another group, which may or may not be another carbohydrate. A glycosidic bond is formed between the hemiacetal or hemiketal group of a saccharide and the group of some compound such as an alcohol. A substance containing a glycosidic bond is a glycoside, glycosidic bonds of the form discussed above are known as O-glycosidic bonds, in reference to the glycosidic oxygen that links the glycoside to the aglycone or reducing end sugar. In analogy, one also considers S-glycosidic bonds, where the oxygen of the bond is replaced with a sulfur atom. In the same way, N-glycosidic bonds, have the glycosidic oxygen replaced with nitrogen. Substances containing N-glycosidic bonds are known as glycosylamines. C-glycosyl bonds have the oxygen replaced by a carbon, the term C-glycoside is considered a misnomer by IUPAC and is discouraged. All of these modified glycosidic bonds have different susceptibility to hydrolysis, one distinguishes between α- and β-glycosidic bonds based on the relative stereochemistry of the anomeric position and the stereocenter furthest from C1 in the saccharide. An α-glycosidic bond is formed when both carbons have the same stereochemistry, whereas a β-glycosidic bond occurs when the two carbons have different stereochemistry. One complicating issue is that the alpha and beta conformations were originally defined based on the orientation of the major constituents in a Haworth projection. In this case, for D-sugars, a beta conformation would see the major constituent at each carbon drawn above the plane of the ring, for L-sugars, the definitions would then, necessarily, reverse. This is worth noting as these older definitions still permeate the literature, pharmacologists often join substances to glucuronic acid via glycosidic bonds in order to increase their water solubility, this is known as glucuronidation. Many other glycosides have important physiological functions, Nüchter et al. have shown a new approach to Fischer Glycosylation. Employing a microwave oven equipped with refluxing apparatus in a reactor with pressure bombs, Nüchter et al. were able to achieve 100% yield of α-. This method can be performed on a multi-kilogram scale, ondruschka, and W. Lautenschläger, Synthetic Communications 31,1277. Vishal Y Joshis method Joshi et al, d-glucose is first protected by forming the peracetate by addition of acetic anhydride in acetic acid, and then addition of hydrogen bromide which brominates at the 5-position. On addition of the alcohol ROH and lithium carbonate, the OR replaces the bromine and it was suggested by Joshi et al. that lithium acts as the nucleophile that attacks the carbon at the 5-position and through a transition state the alcohol is substituted for the bromine group. Glycoside hydrolases, are enzymes that break glycosidic bonds, glycoside hydrolases typically can act either on α- or on β-glycosidic bonds, but not on both
6.
Phosphodiester bond
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A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds. Phosphodiester bonds are central to all life on Earth, as make up the backbone of the strands of nucleic acid. In DNA and RNA, the bond is the linkage between the 3 carbon atom of one sugar molecule and the 5 carbon atom of another, deoxyribose in DNA. Strong covalent bonds form between the group and two 5-carbon ring carbohydrates over two ester bonds. The phosphate groups in the bond are negatively charged. Because the phosphate groups have a pKa near 0, they are charged at pH7. This repulsion forces the phosphates to take opposite sides of the DNA strands and is neutralized by proteins, metal ions such as magnesium, when a single phosphate or two phosphates known as pyrophosphates break away and catalyze the reaction, the phosphodiester bond is formed. Hydrolysis of phosphodiester bonds can be catalyzed by the action of phosphodiesterases which play an important role in repairing DNA sequences, the phosphodiester linkage between two ribonucleotides can be broken by alkaline hydrolysis, whereas the linkage between two deoxyribonucleotides is more stable under these conditions. The relative ease of RNA hydrolysis is an effect of the presence of the 2 hydroxyl group, a phosphodiesterase is an enzyme that catalyzes the hydrolysis of phosphodiester bonds, for instance a bond in a molecule of cyclic AMP or cyclic GMP. An enzyme that plays an important role in the repair of oxidative DNA damage is the 3-phosphodiesterase, during the replication of DNA, there is a hole between the phosphates in the backbone left by DNA polymerase I. DNA ligase is able to form a bond between the nucleotides. Phosphodiesterase Phosphodiesterase inhibitor DNA replication, DNA, ATP Teichoic acid, DNase I PDE5 Nick
7.
AP endonuclease
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Apurinic/apyrimidinic endonuclease is an enzyme that is involved in the DNA base excision repair pathway. Its main role in the repair of damaged or mismatched nucleotides in DNA is to create a nick in the backbone of the AP site created when DNA glycosylase removes the damaged base. There are four types of AP endonucleases that have been classified according to their mechanism, class I AP endonucleases cleave 3 to AP sites by a β-lyase mechanism, leaving an unsaturated aldehyde, termed a 3- residue, and a 5-phosphate. Class II AP endonucleases incise DNA5 to AP sites by a mechanism, leaving a 3-hydroxyl. Class III and class IV AP endonucleases also cleave DNA at the phosphate groups 3´ and 5´to the baseless site, but they generate a 3´-phosphate, humans have two AP endonucleases, APE1 and APE2. APE1 exhibits robust AP-endonuclease activity, which accounts for >95% of the total cellular activity, human AP Endonuclease, like most AP endonucleases, is of class II and requires an Mg2+ in its active site in order to carry out its role in base excision repair. The yeast homolog of this enzyme is APN1, human AP Endonuclease 2, like most AP endonucleases, is also of class II. The exonuclease activity of APE2 is strongly dependent upon metal ions, however, APE2 was more than 5-fold more active in the presence of manganese than of magnesium ions. The conserved domains involved in activity are located at the N-terminal part of both APE1 and APE2. In addition, the APE2 protein has a C-terminal extension, which is not present in APE1, APE1 contains several amino acid residues that enable it to react selectively with AP sites. This extreme kinking forces the baseless portion of DNA into APE1’s active site and this active site is bordered by Phe266, Trp280, and Leu282, which pack tightly with the hydrophobic side of the AP site, discriminating against sites that do have bases. The phosphate group 3 to the AP site is stabilized through hydrogen bonding to Arg177.5, the APE1 enzyme creates a nick in the phosphodiester backbone at an abasic site through a simple acyl substitution mechanism. First, the Asp210 residue in the active site deprotonates a water molecule, known inhibitors of APE1 include 7-nitroindole-2-carboxylic acid and lucanthone. Both of these structures possess rings attached to chains, which appear similar to the deoxyribose sugar ring without a base attached. Because APE1 performs a function in DNA base-excision repair pathway. As such, knocking down APE1 could lead to tumor cell sensitivity, APE2 has much weaker AP endonuclease activity than APE1, but its 3-5 exonuclease activity is strong compared with APE1 and it has a fairly strong 3-phosphodiesterase activity. The APE23 –5 exonuclease activity has the ability to hydrolyze blunt-ended duplex DNA, the APE2 3-phosphodiesterase activity can remove modified 3-termini, such as 3-phosphoglycolate as well as mismatched nucleotides from the 3 primer end of DNA
8.
Crystallography
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Crystallography is the experimental science of determining the arrangement of atoms in the crystalline solids. The word crystallography derives from the Greek words crystallon cold drop, frozen drop, with its meaning extending to all solids with some degree of transparency, and graphein to write. In July 2012, the United Nations recognised the importance of the science of crystallography by proclaiming that 2014 would be the International Year of Crystallography, X-ray crystallography is used to determine the structure of large biomolecules such as proteins. Before the development of X-ray diffraction crystallography, the study of crystals was based on measurements of their geometry. This involved measuring the angles of crystal faces relative to other and to theoretical reference axes. This physical measurement is carried out using a goniometer, the position in 3D space of each crystal face is plotted on a stereographic net such as a Wulff net or Lambert net. The pole to face is plotted on the net. Each point is labelled with its Miller index, the final plot allows the symmetry of the crystal to be established. Crystallographic methods now depend on analysis of the patterns of a sample targeted by a beam of some type. X-rays are most commonly used, other beams used include electrons or neutrons and this is facilitated by the wave properties of the particles. Crystallographers often explicitly state the type of beam used, as in the terms X-ray crystallography and these three types of radiation interact with the specimen in different ways. X-rays interact with the distribution of electrons in the sample. Electrons are charged particles and therefore interact with the charge distribution of both the atomic nuclei and the electrons of the sample. Neutrons are scattered by the atomic nuclei through the nuclear forces, but in addition. They are therefore also scattered by magnetic fields, when neutrons are scattered from hydrogen-containing materials, they produce diffraction patterns with high noise levels. However, the material can sometimes be treated to substitute deuterium for hydrogen, because of these different forms of interaction, the three types of radiation are suitable for different crystallographic studies. An image of an object is made using a lens to focus the beam. However, the wavelength of light is three orders of magnitude longer than the length of typical atomic bonds and atoms themselves
9.
Schiff base
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A Schiff base is a compound with the general structure R2C=NR. They can be considered a sub-class of imines, being either secondary ketimines or secondary depending on their structure. The term is synonymous with azomethine which refers specifically to secondary aldimines. A number of naming systems exist for these compounds. For instance a Schiff base derived from an aniline, where R3 is a phenyl or a substituted phenyl, can be called an anil, the term Schiff base is normally applied to these compounds when they are being used as ligands to form coordination complexes with metal ions. Such complexes do occur naturally, for instance in Corrin, but the majority of Schiff bases are artificial and are used to form many important catalysts, such as Jacobsens catalyst. Schiff bases can be synthesized from an aliphatic or aromatic amine, the common enzyme cofactor PLP forms a Schiff base with a lysine residue and is transaldiminated to the substrate. Similarly, the cofactor retinal forms a Schiff base in rhodopsins, including human rhodopsin, an example where the substrate forms a Schiff base to the enzyme is in the fructose 1, 6-bisphosphate aldolase catalyzed reaction during glycolysis and in the metabolism of amino acids. Schiff bases are common ligands in coordination chemistry, the imine nitrogen is basic and exhibits pi-acceptor properties. The ligands are derived from alkyl diamines and aromatic aldehydes. Chiral Schiff bases were one of the first ligands used for asymmetric catalysis, in 1968 Ryōji Noyori developed a copper-Schiff base complex for the metal-carbenoid cyclopropanation of styrene. For this work he was awarded a share of the 2001 Nobel Prize in Chemistry. Their simple and clean chemistry make them a candidate as a low cost alternative to currently used conjugated materials. Schiff base chemistry is used to prepare covalent organic framework
10.
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
11.
Bacillus cereus
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Bacillus cereus is a Gram-positive, rod-shaped, aerobic, motile, beta hemolytic bacterium commonly found in soil and food. Some strains are harmful to humans and cause illness, while other strains can be beneficial as probiotics for animals. It is the cause of fried rice syndrome, as the bacteria are classically contracted from fried rice dishes that have been sitting at room temperature for hours, B. cereus bacteria are facultative anaerobes, and like other members of the genus Bacillus, can produce protective endospores. Its virulence factors include cereolysin and phospholipase C and it was from this species that two new enzymes, named AlkC and AlkD, which are involved in DNA repair, were discovered in 2006. Colonies of Bacillus cereus were originally isolated from an agar plate left exposed to the air in a cow shed, B. cereus competes with other microorganisms such as Salmonella and Campylobacter in the gut, so its presence reduces the numbers of those microorganisms. In food animals such as chickens, rabbits and pigs, some strains of B. cereus are used as a probiotic feed additive to reduce Salmonella in the intestines. This improves the growth as well as food safety for humans who eat their meat. Some strains of B. cereus produce cereins, bacteriocins active against different B. cereus strains or other Gram-positive bacteria. At 30 °C, a population of B. cereus can double in as little as 20 minutes or as long as 3 hours, B. cereus is responsible for a minority of foodborne illnesses, causing severe nausea, vomiting, and diarrhea. Bacillus foodborne illnesses occur due to survival of the bacterial endospores when food is improperly cooked, cooking temperatures less than or equal to 100 °C allow some B. cereus spores to survive. This problem is compounded when food is then refrigerated, allowing the endospores to germinate. Cooked foods not meant for immediate consumption or rapid cooling. Germination and growth generally occur between 10 °C and 50 °C, though some strains are psychrotrophic, Bacterial growth results in production of enterotoxins, one of which is highly resistant to heat and acids, ingestion leads to two types of illness, diarrheal and emetic syndrome. The diarrheal type is associated with a range of foods, has an 8. 0- to 16-hour incubation time. Also known as the form of B. cereus food poisoning. Cereus spores within the intestine may be the cause of illness. The emetic form is caused by rice cooked for a time and temperature insufficient to kill any spores present. It can produce a toxin, cereulide, which is not inactivated by later reheating and this form leads to nausea and vomiting one to five hours after consumption
12.
Saccharomyces cerevisiae
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Saccharomyces cerevisiae is a species of yeast. It has been instrumental to winemaking, baking, and brewing since ancient times and it is believed to have been originally isolated from the skin of grapes. It is one of the most intensively studied model organisms in molecular and cell biology. It is the microorganism behind the most common type of fermentation, S. cerevisiae cells are round to ovoid, 5–10 μm in diameter. It reproduces by a process known as budding. Many proteins important in biology were first discovered by studying their homologs in yeast, these proteins include cell cycle proteins, signaling proteins. S. cerevisiae is currently the only yeast cell known to have Berkeley bodies present, antibodies against S. cerevisiae are found in 60–70% of patients with Crohns disease and 10–15% of patients with ulcerative colitis. Saccharomyces derives from Latinized Greek and means sugar-mold or sugar-fungus, saccharo being the combining form sugar, cerevisiae comes from Latin and means of beer. Refinements in microbiology following the work of Louis Pasteur led to more advanced methods of culturing pure strains, in 1879, Great Britain introduced specialized growing vats for the production of S. The company created yeast that would rise twice as fast, cutting down on baking time, lesaffre would later create instant yeast in the 1970s, which has gained considerable use and market share at the expense of both fresh and dry yeast in their various applications. In nature, yeast cells are primarily on ripe fruits such as grapes. Since S. cerevisiae is not airborne, it requires a vector to move, queens of social wasps overwintering as adults can harbor yeast cells from autumn to spring and transmit them to their progeny. The intestine of Polistes dominula, a wasp, hosts S. cerevisiae strains as well as S. cerevisiae × S. paradoxus hybrids. The optimum temperature for growth of S. cerevisiae is 30–35 °C, two forms of yeast cells can survive and grow, haploid and diploid. The haploid cells undergo a simple lifecycle of mitosis and growth and this is the asexual form of the fungus. The diploid cells undergo a simple lifecycle of mitosis and growth. The rate at which the cell cycle progresses often differs substantially between haploid and diploid cells. Under conditions of stress, diploid cells can undergo sporulation, entering meiosis and producing four haploid spores and this is the sexual form of the fungus
13.
DNA-3-methyladenine glycosylase
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DNA-3-methyladenine glycosylase also known as 3-alkyladenine DNA glycosylase or N-methylpurine DNA glycosylase is an enzyme that in humans is encoded by the MPG gene. Alkyladenine DNA glycosylase is a type of DNA glycosylase. To date, the human AAG is the only glycosylase identified that excises alkylation-damaged purine bases, DNA bases are subject to a large number of anomalies, spontaneous alkylation or oxidative deamination. It is estimated that 104 mutations appear in a human cell per day. Specifically, hAAG is able to identify and excise 3-methyladenine, 7-methyladenine, 7-methylguanine, 1N-ethenoadenine and hypoxanthine. Oxanine DNA Glycolase activity is the capability of some DNA Glycosylases of repairing Oxanines, among the known human DNA glycosylases tested, the human alkyladenine DNA glycosylase also shows ODG activity. In addition hAAG is capable of removing Oxa from single-stranded Oxa- containing DNA and this occurs because the ODG activity of the hAAG does not require a complementary strand. Alkyladenine DNA glycosylase is a monomeric protein compounded by 298 amino acids and its canonical primary structure consists of the following sequence. However, also other functional isoforms have been found and it folds into a single domain of mixed α/β structure with seven α helices and eight β strands. The core of the consists of a curved, antiparallel β sheet with a protruding β hairpin that inserts into the minor groove of the bound DNA. A series of α helices and connecting loops form the remainder of the DNA binding interface and it lacks the helix-hairpin-helix motif associated with other base excision-repair proteins and, in fact, it does not resemble any other model in the Protein Data Bank. Alkyladenine DNA glycosylase is part of the family of enzymes that follow the BER, the process of recognition of damaged bases involves initial non-specific binding followed by diffusion along the DNA. Formed the AAG-DNA complex, a redundant process of search occurs because of the lifetime of this complex. This provides ample opportunity to recognize and excise lesions that minimally perturb the structure of the DNA, due to its broad specificity, the hAAG performs the substrate selection through a combination of selectivity filters. The first selectivity filter occurs at the nucleotide flipping step of base pairs that present lesions. The second selectivity filter is constituted by the mechanism which ensures that only purine bases are excised. The active site pocket it’s designed to accommodate a diverse set of modified purines so it would be difficult to sterically exclude the smaller pyrimidine bases from binding. The third selectivity filter consist of unfavorable steric clashes that allow a preferential recognition of purine lesions lacking exocyclic amino groups of guanine and adenine and its structure contains an antiparallel β sheet with protruding β hairpin that inserts into the minor groove of the bound DNA
14.
Oxoguanine glycosylase
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8-Oxoguanine glycosylase also known as OGG1 is a DNA glycosylase enzyme that, in humans, is encoded by the OGG1 gene. It is involved in excision repair. It is found in bacterial, archaeal and eukaryotic species, OGG1 is the primary enzyme responsible for the excision of 8-oxoguanine, a mutagenic base byproduct that occurs as a result of exposure to reactive oxygen species. OGG1 is a bifunctional glycosylase, as it is able to cleave the glycosidic bond of the mutagenic lesion and cause a strand break in the DNA backbone. Alternative splicing of the C-terminal region of this gene classifies splice variants into two groups, type 1 and type 2, depending on the last exon of the sequence. Type 1 alternative splice variants end with exon 7 and type 2 end with exon 8, one set of spliced forms are designated 1a, 1b, 2a to 2e. All variants have the N-terminal region in common, many alternative splice variants for this gene have been described, but the full-length nature for every variant has not been determined. In eukaryotes, the N-terminus of this contains a mitochondrial targeting signal, essential for mitochondrial localization. However, OGG1-1a also has a location signal at its C-terminal end that suppresses mitochondrial targeting. The main form of OGG1 that localizes to the mitochondria is OGG1-2a, a conserved N-terminal domain contributes residues to the 8-oxoguanine binding pocket. This domain is organised into a copy of a TBP-like fold. Interestingly, mice lacking Ogg1 have been shown to be prone to increased weight and obesity. Mice without a functional OGG1 gene have about a 5-fold increased level of 8-oxo-dG in their livers compared to mice with wild-type OGG1, mice defective in OGG1 also have an increased risk for cancer. Kunisada et al. irradiated mice without a functional OGG1 gene, both types of mice had high levels of 8-oxo-dG in their epidermal cells three hours after irradiation. However,24 hours later, the majority of 8-oxo-dG was absent from the cells of the wild-type mice. As reviewed by Valavanidis et al. increased levels of 8-oxo-dG in a tissue can serve as a biomarker of oxidative stress and they also noted that increased levels of 8-oxo-dG are frequently found during carcinogenesis. In the figure showing examples of mouse colonic epithelium, the epithelium from a mouse on a normal diet was found to have a low level of 8-oxo-dG in its colonic crypts. However, a mouse likely undergoing colonic tumorigenesis was found to have a level of 8-oxo-dG in its colonic epithelium
15.
DNA glycosylase
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DNA glycosylases are a family of enzymes involved in base excision repair, classified under EC number EC3.2.2. Base excision repair is the mechanism by which damaged bases in DNA are removed and replaced, DNA glycosylases catalyze the first step of this process. They remove the damaged nitrogenous base while leaving the sugar-phosphate backbone intact, creating an apurinic/apyrimidinic site and this is accomplished by flipping the damaged base out of the double helix followed by cleavage of the N-glycosidic bond. Glycosylases were first discovered in bacteria, and have since found in all kingdoms of life. In addition to their role in base excision repair DNA glycosylase enzymes have been implicated in the repression of gene silencing in A. thaliana, N. tabacum, there are two main classes of glycosylases, monofunctional and bifunctional. β-Elimination of an AP site by a yields a 3 α, β-unsaturated aldehyde adjacent to a 5 phosphate. Some glycosylase-lyases can further perform δ-elimination, which converts the 3 aldehyde to a 3 phosphate, the first crystal structure of a DNA glycosylase was obtained for E. coli Nth. This structure revealed that the enzyme flips the damaged base out of the helix into an active site pocket in order to excise it. Other glycosylases have since found to follow the same general paradigm. To cleave the N-glycosidic bond, monofunctional glycosylases use a water molecule to attack carbon 1 of the substrate. Bifunctional glycosylases, instead, use an amine residue as a nucleophile to attack the same carbon, crystal structures of many glycosylases have been solved. Based on structural similarity, glycosylases are grouped into four superfamilies, the UDG and AAG families contain small, compact glycosylases, whereas the MutM/Fpg and HhH-GPD families comprise larger enzymes with multiple domains. A wide variety of glycosylases have evolved to recognize different damaged bases, the table below summarizes the properties of known glycosylases in commonly studied model organisms. DNA glycosylases can be grouped into the following based on their substrate, In molecular biology. The most common mutation is the deamination of cytosine to uracil, UDG is crucial in DNA repair, without it these mutations may lead to cancer. Uracil DNA glycosylases remove uracil from DNA, which can either by spontaneous deamination of cytosine or by the misincorporation of dU opposite dA during DNA replication. The prototypical member of family is E. coli UDG. Four different uracil-DNA glycosylase activities have been identified in cells, including UNG, SMUG1, TDG
16.
Protein
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Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, a linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide, short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds, the sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the code specifies 20 standard amino acids, however. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors, proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only exist for a period of time and are then degraded and recycled by the cells machinery through the process of protein turnover. A proteins lifespan is measured in terms of its half-life and covers a wide range and they can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms, many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized, digestion breaks the proteins down for use in the metabolism. Methods commonly used to study structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance. Most proteins consist of linear polymers built from series of up to 20 different L-α-amino acids, all proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this structure as it contains an unusual ring to the N-end amine group. The amino acids in a chain are linked by peptide bonds. Once linked in the chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen. The peptide bond has two forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar
17.
Uracil-DNA glycosylase
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Uracil-DNA glycosylase, also known as UNG or UDG, is a human gene though orthologs exist ubiquitously among prokaryotes and eukaryotes and even in some DNA viruses. The first uracil DNA-glycosylase was isolated from Escherichia coli, the human gene encodes one of several uracil-DNA glycosylases. Alternative promoter usage and splicing of this leads to two different isoforms, the mitochondrial UNG1 and the nuclear UNG2. One important function of uracil-DNA glycosylases is to prevent mutagenesis by eliminating uracil from DNA molecules by cleaving the N-glycosylic bond, uracil bases occur from cytosine deamination or misincorporation of dUMP residues. After a mutation occurs, the threat of uracil propagates through any subsequent DNA replication steps. Half of all progeny DNA derived from the mutated template inherit a shift from GC to AU at the mutation site, UDG excises uracil in both AU and GU pairs to prevent propagation of the base mismatch to downstream transcription and translation processes. With high efficiency and specificity, this glycosylase repairs more than 10,000 bases damaged daily in the human cell, human cells express five to six types of DNA glycosylases, all of which share a common mechanism of base eversion and excision as a means of DNA repair. UDG is made of a four-stranded parallel β-sheet surrounded by eight α-helices, pinch, UDG scans DNA for uracil by nonspecifically binding to the strand and creating a kink in the backbone, thereby positioning the selected base for detection. The Pro-rich and Gly-Ser loops form polar contacts with the 3’ and this compression of the DNA backbone, or “pinch, ” allows for close contact between UDG and base of interest. Push, To fully assess the nucleotide identity, the intercalation loop penetrates, or pushes into, backbone compression favors eversion of the now extrahelical nucleotide, which is positioned for recognition by the uracil-binding motif. The coupling of intercalation and eversion helps compensate for the disruption of favorable base stacking interactions within the DNA helix, leu272 fills the void left by the flipped nucleotide to create dispersion interactions with neighboring bases and restore stacking stability. Pull, Now accessible to the site, the nucleotide interacts with the uracil binding motif. The active site shape complements the everted uracil structure, allowing for high substrate specificity, purines are too large to fit in the active site, while unfavorable interactions with other pyrimidines discourage binding alternative substrates. Once uracil is recognized, cleavage of the bond proceeds according to the mechanism below. Regardless of position, the identities of the acid and histidine residues are consistent across catalytic studies. Uracil N-glycosylase is an enzyme utilized in a method to eliminate carryover PCR products in Real-Time PCR. While polymerase chain reaction synthesizes abundant amplification products, contamination of new PCRs with trace amounts of these products, called carry-over contamination, yields false positive results. Carry-over contamination from some previous PCR can be a significant problem, UDG cleaves the uracil base from the phosphodiester backbone of uracil-containing DNA, but has no effect on natural DNA
18.
Mutation
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In biology, a mutation is the permanent alteration of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA or other genetic elements. Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements, mutations may or may not produce discernible changes in the observable characteristics of an organism. Mutations play a part in normal and abnormal biological processes including, evolution, cancer, and the development of the immune system. The genomes of RNA viruses are based on RNA rather than DNA, the RNA viral genome can be double stranded or single stranded. In some of these viruses replication occurs quickly and there are no mechanisms to check the genome for accuracy and this error-prone process often results in mutations. Mutation can result in different types of change in sequences. Mutations in genes can either have no effect, alter the product of a gene, mutations can also occur in nongenic regions. Mutations can involve the duplication of large sections of DNA, usually through genetic recombination and these duplications are a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years. Most genes belong to larger families of shared ancestry, known as homology. Here, protein domains act as modules, each with a particular and independent function, that can be mixed together to produce genes encoding new proteins with novel properties. For example, the eye uses four genes to make structures that sense light. Another advantage of duplicating a gene is that this increases engineering redundancy, other types of mutation occasionally create new genes from previously noncoding DNA. Changes in chromosome number may involve even larger mutations, where segments of the DNA within chromosomes break and then rearrange. For example, in the Homininae, two fused to produce human chromosome 2, this fusion did not occur in the lineage of the other apes. Sequences of DNA that can move about the genome, such as transposons, make up a fraction of the genetic material of plants and animals. For example, more than a million copies of the Alu sequence are present in the genome. Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes, nonlethal mutations accumulate within the gene pool and increase the amount of genetic variation. The abundance of some changes within the gene pool can be reduced by natural selection, while other more favorable mutations may accumulate
19.
Deamination
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Deamination is the removal of an amino group from a molecule. Enzymes that catalyse this reaction are called deaminases, in the human body, deamination takes place primarily in the liver, however glutamate is also deaminated in the kidneys. In situations of excess protein intake, deamination is used to break down amino acids for energy, the amino group is removed from the amino acid and converted to ammonia. The rest of the acid is made up of mostly carbon and hydrogen. Ammonia is toxic to the system, and enzymes convert it to urea or uric acid by addition of carbon dioxide molecules in the urea cycle. Urea and uric acid can safely diffuse into the blood and then be excreted in urine, spontaneous deamination is the hydrolysis reaction of cytosine into uracil, releasing ammonia in the process. This can occur in vitro through the use of bisulfite, which deaminates cytosine and this property has allowed researchers to sequence methylated DNA to distinguish non-methylated cytosine and methylated cytosine. In DNA, this spontaneous deamination is corrected for by the removal of uracil by uracil-DNA glycosylase, the resulting abasic site is then recognised by enzymes that break a phosphodiester bond in the DNA, permitting the repair of the resulting lesion by replacement with another cytosine. A DNA polymerase may perform this replacement via nick translation, a terminal excision reaction by its 5-->3 exonuclease activity, DNA ligase then forms a phosphodiester bond to seal the resulting nicked duplex product, which now includes a new, correct cytosine. Spontaneous deamination of 5-methylcytosine results in thymine and ammonia and this is the most common single nucleotide mutation. In DNA, this reaction, if detected prior to passage of the fork, can be corrected by the enzyme thymine-DNA glycosylase. This leaves an abasic site that is repaired by AP endonucleases and polymerase, deamination of guanine results in the formation of xanthine. Xanthine, in an analogous to the enol tautomer of guanine. This results in a transition mutation, where the original G-C base pair transforms into an A-T base pair. Correction of this involves the use of alkyladenine glycosylase during base excision repair. Deamination of adenine results in the formation of hypoxanthine, hypoxanthine, in a manner analogous to the imine tautomer of adenine, selectively base pairs with cytosine instead of thymine. This results in a transition mutation, where the original A-T base pair transforms into a G-C base pair
20.
Uracil
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Uracil /ˈjʊərəsɪl/ is one of the four nucleobases in the nucleic acid of RNA that are represented by the letters A, G, C and U. The others are adenine, cytosine, and guanine, in RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced by thymine, Uracil is a demethylated form of thymine. Uracil is a common and naturally occurring pyrimidine derivative, the name uracil was coined in 1885 by the German chemist Robert Behrend, who was attempting to synthesize derivatives of uric acid. Originally discovered in 1900 by Alberto Ascoli, it was isolated by hydrolysis of yeast nuclein, it was found in bovine thymus and spleen, herring sperm. It is a planar, unsaturated compound that has the ability to absorb light, based on 12C/13C isotopic ratios of organic compounds found in the Murchison meteorite, it is believed that uracil, xanthine and related molecules can also be formed extraterrestrially. In 2012, an analysis of data from the Cassini mission orbiting in the Saturn system showed that Titans surface composition may include uracil, in RNA, uracil base-pairs with adenine and replaces thymine during DNA transcription. In DNA, the substitution of thymine for uracil may have increased DNA stability. Uracil pairs with adenine through hydrogen bonding, when base pairing with adenine, uracil acts as both a hydrogen bond acceptor and a hydrogen bond donor. In RNA, uracil binds with a sugar to form the ribonucleoside uridine. When a phosphate attaches to uridine, uridine 5-monophosphate is produced, Uracil undergoes amide-imidic acid tautomeric shifts because any nuclear instability the molecule may have from the lack of formal aromaticity is compensated by the cyclic-amidic stability. The amide tautomer is referred to as the structure, while the imidic acid tautomer is referred to as the lactim structure. These tautomeric forms are predominant at pH7, the lactam structure is the most common form of uracil. Uracil also recycles itself to form nucleotides by undergoing a series of phosphoribosyltransferase reactions, degradation of uracil produces the substrates aspartate, carbon dioxide, and ammonia. C4H4N2O2 → H3NCH2CH2COO− + NH4+ + CO2 Oxidative degradation of uracil produces urea and maleic acid in the presence of H2O2 and Fe2+ or in the presence of diatomic oxygen, the first site of ionization of uracil is not known. The negative charge is placed on the anion and produces a pKa of less than or equal to 12. The basic pKa = -3.4, while the acidic pKa =9.389, in the gas phase, uracil has 4 sites that are more acidic than water. Uracil is rarely found in DNA, and this may have been a change to increase genetic stability
21.
DNA repair
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DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA damage, resulting in as many as 1 million individual molecular lesions per cell per day. Many of these lesions cause structural damage to the DNA molecule, other lesions induce potentially harmful mutations in the cells genome, which affect the survival of its daughter cells after it undergoes mitosis. As a consequence, the DNA repair process is active as it responds to damage in the DNA structure. When normal repair processes fail, and when cellular apoptosis does not occur, irreparable DNA damage may occur, including double-strand breaks and this can eventually lead to malignant tumors, or cancer as per the two hit hypothesis. The rate of DNA repair is dependent on many factors, including the type, the age of the cell. Many genes that were shown to influence life span have turned out to be involved in DNA damage repair. The 2015 Nobel Prize in Chemistry was awarded to Tomas Lindahl, Paul Modrich, there are two types, nucleotide excision repair and base excision repair. DNA damage, due to environmental factors and normal metabolic processes inside the cell, the vast majority of DNA damage affects the primary structure of the double helix, that is, the bases themselves are chemically modified. These modifications can in turn disrupt the molecules regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level, DNA is, however, supercoiled and wound around packaging proteins called histones, and both superstructures are vulnerable to the effects of DNA damage. Daughter cells that inherit these wrong bases carry mutations from which the original DNA sequence is unrecoverable, monoadduct damage cause by change in single nitrogenous base of DNA Diadduct damage Damage caused by exogenous agents comes in many forms. Some examples are, UV-B light causes crosslinking between adjacent cytosine and thymine bases creating pyrimidine dimers and this is called direct DNA damage. UV-A light creates mostly free radicals, the damage caused by free radicals is called indirect DNA damage. Ionizing radiation such as that created by decay or in cosmic rays causes breaks in DNA strands. Intermediate-level ionizing radiation may induce irreparable DNA damage leading to pre-mature aging, thermal disruption at elevated temperature increases the rate of depurination and single-strand breaks. For example, hydrolytic depurination is seen in the thermophilic bacteria, the rate of depurination is too high in these species to be repaired by normal repair machinery, hence a possibility of an adaptive response cannot be ruled out. UV damage, alkylation/methylation, X-ray damage and oxidative damage are examples of induced damage, spontaneous damage can include the loss of a base, deamination, sugar ring puckering and tautomeric shift
22.
Thermophilic
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A thermophile is an organism—a type of extremophile—that thrives at relatively high temperatures, between 41 and 122 °C. Thermophilic eubacteria are suggested to have been among the earliest bacteria, unlike other types of bacteria, thermophiles can survive at much hotter temperatures, whereas other bacteria would be damaged and sometimes killed if exposed to the same temperatures. As a prerequisite for their survival, thermophiles contain enzymes that can function at high temperatures, some of these enzymes are used in molecular biology, and in washing agents. Thermophile is derived from the Greek, θερμότητα, meaning heat, thermophiles are classified into 1. obligate and 2. Facultative 3. hyper thermophiles, Obligate thermophiles require such high temperatures for growth, whereas Facultative thermophiles can thrive at high temperatures, hyperthermophiles are particularly extreme thermophiles for which the optimal temperatures are above 80 °C. Bacteria within the Alicyclobacillus genus are acidophilic thermophiles, which can cause contamination in fruit juice drinks. Thermophiles, meaning heat-loving, are organisms with a growth temperature of 50 °C or more, a maximum of up to 70 °C or more, and a minimum of about 40 °C. Some extreme thermophiles require a high temperature for growth. Their membranes and proteins are stable at these extremely high temperatures. Thus, many important biotechnological processes use thermophilic enzymes because of their ability to withstand intense heat, many of the hyperthermophiles Archea require elemental sulfur for growth. Some are anaerobes that use the sulfur instead of oxygen as an electron acceptor during cellular respiration, some are lithotrophs that oxidize sulfur to sulfuric acid as an energy source, thus requiring the microorganism to be adapted to very low pH. These organisms are inhabitants of hot, sulfur-rich environments usually associated with volcanism, such as hot springs, geysers, in these places, especially in Yellowstone National Park, zonation of microorganisms according to their temperature optima occurs. Often, these organisms are colored, due to the presence of photosynthetic pigments, thermophiles can be discriminated from mesophiles from genomic features. Sulfolobus solfataricus and Sulfolobus acidocaldarius are hyperthermophilic archaea, when these organisms are exposed to the DNA damaging agents UV irradiation, bleomycin or mitomycin C, species-specific cellular aggregation is induced. In S. acidocaldarius, UV-induced cellular aggregation mediates chromosomal marker exchange with high frequency, recombination rates exceed those of uninduced cultures by up to three orders of magnitude. Van Wolferen et al. in discussing DNA exchange in the hyperthermophiles under extreme conditions and they suggested that this process is crucial under DNA damaging conditions such as high temperature. Hyperthermophile Mesophile Psychrophile Anaerobic digestion Archaea Sulfolobus Thermoprotei, Extreme Thermophile
23.
DNA replication
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In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. This process occurs in all living organisms and is the basis for biological inheritance, DNA is made up of a double helix of two complementary strands. During replication, these strands are separated, each strand of the original DNA molecule then serves as a template for the production of its counterpart, a process referred to as semiconservative replication. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication, in a cell, DNA replication begins at specific locations, or origins of replication, in the genome. Unwinding of DNA at the origin and synthesis of new results in replication forks growing bi-directionally from the origin. A number of proteins are associated with the fork to help in the initiation and continuation of DNA synthesis. Most prominently, DNA polymerase synthesizes the new strands by adding nucleotides that complement each strand, DNA replication occurs during the S-stage of interphase. DNA replication can also be performed in vitro, DNA polymerases isolated from cells and artificial DNA primers can be used to initiate DNA synthesis at known sequences in a template DNA molecule. The polymerase chain reaction, a laboratory technique, cyclically applies such artificial synthesis to amplify a specific target DNA fragment from a pool of DNA. DNA usually exists as a structure, with both strands coiled together to form the characteristic double-helix. Each single strand of DNA is a chain of four types of nucleotides, nucleotides in DNA contain a deoxyribose sugar, a phosphate, and a nucleobase. These nucleotides form phosphodiester bonds, creating the phosphate-deoxyribose backbone of the DNA double helix with the bases pointing inward. Nucleotides are matched between strands through hydrogen bonds to form base pairs, adenine pairs with thymine, and guanine pairs with cytosine. DNA strands have a directionality, and the different ends of a single strand are called the 3 end and the 5 end. By convention, if the sequence of a single strand of DNA is given. The strands of the helix are anti-parallel with one being 5 to 3. These terms refer to the atom in deoxyribose to which the next phosphate in the chain attaches. Directionality has consequences in DNA synthesis, because DNA polymerase can synthesize DNA in only one direction by adding nucleotides to the 3 end of a DNA strand, the pairing of complementary bases in DNA means that the information contained within each strand is redundant
24.
SMUG1
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Single-strand selective monofunctional uracil DNA glycosylase is an enzyme that in humans is encoded by the SMUG1 gene. SMUG1 is a glycosylase that removes uracil from single- and double-stranded DNA in nuclear chromatin, SMUG1 is an important uracil-DNA glycosylases that process uracil in DNA. SMUG1 function is to remove U or its derivatives from DNA, SMUG1 is able to excise uracil from both single- and doubledstranded DNA. Other DNA glycosylases linked to U removal are UNG, TDG, uracil-DNA repair is essential to protect against mutations. Current evidence suggests that UNG and SMUG1 are the enzymes responsible for the repair of the U, G mispairs. Uracil is also introduced into DNA as part of antibody gene diversification, UNG is known to be the major player in uracil removal but when depleted SMUG1 can provide a backup for UNG in the antibody diversification process. In addition to uracil, SMUG1 removes several pyrimidine oxidation products, and has a specific function to remove the thymine oxidation product 5-hydroxymethyl uracil from DNA. Low SMUG1 transcripts can impair DNA repair and thus increase mutation rate, enhance chromosomal instability, loss of SMUG1 was shown to increase cancer predisposition in mice study. In addition low SMUG1 transcripts were shown to be correlated with poor survival. Low SMUG1 expression is associated with BRCA1, ATM, XRCC1. Preclinical study where SMUG1 depletion has been shown to results in sensitivity to 5-FU chemotherapy, low SMUG1 in gastric cancer, however, were showing the opposite result, promoting cancer survival and resistance to therapy. One possible explanation is that in gastric cancer inflammation is the driver for carcinogenesis, thus SMUG1 might have complex roles in carcinogenesis and act differently based on the type of cancer and its properties. 5-Fluorouracil is a used in the treatment of a range of common cancers that causes DNA damage via two mechanisms. Also, 5-FU is directly incorporated into DNA, UNG and SMUG1 are most likely to tackle the genomic incorporation of uracil and 5-FU during replication. Current research suggests that of SMUG1 but not UNG corresponds to increase in sensitivity to 5-FU and it was suggested that SMUG1 can be potentially used as a predictive biomarkers of drug response and a mechanism for acquired resistance in certain types of tumors. SMUG1 glycosylase is a key enzyme for repairing lesions generated during oxidative base damage, investigation of SMUG1 expression in gastric cancers showed that overexpressed SMUG1 was correlated with patients’ poor survival. In gastric cancer inflammation is the driver for carcinogenesis, in this case elevation of SMUG1 as apposed to depletion can be potentially used as a biomarker for survival. SMUG1 has been shown to interact with RBPMS and with DKC1, click on genes, proteins and metabolites below to link to respective articles
25.
Thymine-DNA glycosylase
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G/T mismatch-specific thymine DNA glycosylase is an enzyme that in humans is encoded by the TDG gene. Several bacterial proteins have strong sequence homology with this protein, the protein encoded by this gene belongs to the TDG/mug DNA glycosylase family. Thymine-DNA glycosylase removes thymine moieties from G/T mismatches by hydrolyzing the carbon-nitrogen bond between the backbone of DNA and the mispaired thymine. With lower activity, this enzyme also removes thymine from C/T and T/T mispairings, TDG can also remove uracil and 5-bromouracil from mispairings with guanine. This enzyme plays a role in cellular defense against genetic mutation caused by the spontaneous deamination of 5-methylcytosine and cytosine. This gene may have a pseudogene in the p arm of chromosome 12, additionally, in 2011, the human thymine DNA glycosylase was reported to efficiently excises 5-formylcytosine and 5-carboxylcytosine, the key oxidation products of 5-methylcytosine in genomic DNA. Later on, the structure of the hTDG catalytic domain in complex with duplex DNA containing 5caC was published. Thymine-DNA glycosylase has been shown to interact with, CREB-binding protein, Estrogen receptor alpha, Promyelocytic leukemia protein, SUMO3, click on genes, proteins and metabolites below to link to respective articles
26.
MBD4
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Methyl-CpG-binding domain protein 4 is a protein that in humans is encoded by the MBD4 gene. Human MBD4 protein has 580 amino acids with a domain at amino acids 82–147. These domains are separated by a region that interacts with UHRF1, an E3 ubiquitin ligase, and USP7. DNA methylation is the modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of proteins related by the presence in each of a methyl-CpG-binding domain. Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA, MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein similarity to bacterial DNA repair enzymes. Bases in DNA decay spontaneously, and this decay includes hydrolytic deamination of purines and pyrimidines that contain an amino group. Hypoxanthine and xanthine are generated at a slow rate by deamination of adenine and guanine. However, deamination of pyrimidines occurs at a 50-fold higher rate of approximately 200–300 events per cell per day, deamination of cytosine to uracil and 5-methylcytosine to thymine generates G, U and G, T mismatches, respectively. Upon DNA replication, these mismatches cause C to T transition mutations, notably, for 5mC deamination, these mutations arise predominantly in the context of CpG sites. The deamination rate of 5mC is approximately three times that of C, MBD4 protein binds preferentially to fully methylated CpG sites and to their deamination derivatives G, U and G, T base pairs. MBD4, which is employed in a step of base excision repair. G, U and G, T mismatches, upon DNA replication, the mismatched U or T is usually removed by MBD4 before replication, thus avoiding mutation. Alternatively, for G, T mismatches, the T may be removed by thymine-DNA glycosylase, mutations in the MBD4 gene increase the genomic instability phenotype of a subset of MMR-defective tumors in mice, specifically contributing to elevated G, C to A, T transitions. About 1/3 of all intragenic single base mutations in human cancers occur in CpG dinucleotides and are the result of C to T or G to A transitions. These transitions comprise the most frequent mutations in human cancer, for example, nearly 50% of somatic mutations of the tumor suppressor gene p53 in colorectal cancer are G, C to A, T transitions within CpG sites. MBD4 mRNA expression is reduced in colorectal neoplasms due to methylation of the region of MBD4
27.
Pfam
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Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 31.0, was released in March 2017, the general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains. Originally, the rationale behind creating the database was to have a method of curating information on known protein families to improve the efficiency of annotating genomes. The Pfam classification of families has been widely adopted by biologists because of its wide coverage of proteins. Early genome projects, such as human and fly used Pfam extensively for functional annotation of genomic data, the Pfam website allows users to submit protein or DNA sequences to search for matches to families in the database. If DNA is submitted, a translation is performed, then each frame is searched. Family is the class, which simply indicates that members are related. Domains are defined as a structural unit or reusable sequence unit that can be found in multiple protein contexts. Repeats are not usually stable in isolation, but rather are required to form tandem repeats in order to form a domain or extended structure. Motifs are usually shorter sequence units found outside of globular domains, the descriptions of Pfam families are managed by the general public using Wikipedia. As of release 29.0,76. 1% of protein sequences in UniprotKB matched to at least one Pfam domain, new families come from a range of sources, primarily the PDB and analysis of complete proteomes to find genes with no Pfam hit. For each family, a subset of sequences are aligned into a high-quality seed alignment. Sequences for the alignment are taken primarily from pfamseq with some supplementation from UniprotKB. This seed alignment is used to build a profile hidden Markov model using HMMER. This HMM is then searched against sequence databases, and all hits that reach a curated gathering threshold are classified as members of the protein family, the resulting collection of members is then aligned to the profile HMM to generate a full alignment. For each family, a curated gathering threshold is assigned that maximises the number of true matches to the family while excluding any false positive matches. False positives are estimated by observing overlaps between Pfam family hits that are not from the same clan and this threshold is used to assess whether a match to a family HMM should be included in the protein family. Upon each update of Pfam, gathering thresholds are reassessed to prevent overlaps between new and existing families, domains of Unknown Function represent a growing fraction of the Pfam database
28.
InterPro
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The contents of InterPro consist of diagnostic signatures and the proteins that they significantly match. The signatures consist of models which describe protein families, domains or sites, models are built from the amino acid sequences of known families or domains and they are subsequently used to search unknown sequences in order to classify them. Each of the databases of InterPro contribute towards a different niche, from very high-level. InterPros intention is to provide a one-stop-shop for protein classification, where all the signatures produced by the different member databases are placed into entries within the InterPro database. Signatures which represent equivalent domains, sites or families are put into the same entry, additional information such as a description, consistent names and Gene Ontology terms are associated with each entry, where possible. InterPro contains three main entities, proteins, signatures and entries, the proteins in UniProtKB are also the central protein entities in InterPro. Information regarding which signatures significantly match these proteins are calculated as the sequences are released by UniProtKB, only signatures deemed to be of sufficient quality are integrated into InterPro. InterPro also includes data for splice variants and the contained in the UniParc. The signatures from InterPro come from 11 member databases, which are listed below, cATH-Gene3D describes protein families and domain architectures in complete genomes. Protein families are formed using a Markov clustering algorithm, followed by multi-linkage clustering according to sequence identity, mapping of predicted structure and sequence domains is undertaken using hidden Markov models libraries representing CATH and Pfam domains. Functional annotation is provided to proteins from multiple resources, functional prediction and analysis of domain architectures is available from the Gene3D website. HAMAP stands for High-quality Automated and Manual Annotation of microbial Proteomes, HAMAP profiles are manually created by expert curators they identify proteins that are part of well-conserved bacterial, archaeal and plastid-encoded proteins families or subfamilies. PANTHER is a collection of protein families that have been subdivided into functionally related subfamilies. Hidden Markov models are built for each family and subfamily for classifying additional protein sequences, Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. The primary PIRSF classification unit is the family, whose members are both homologous and homeomorphic. PRINTS is a compendium of protein fingerprints, a fingerprint is a group of conserved motifs used to characterise a protein family, its diagnostic power is refined by iterative scanning of UniProt. Usually the motifs do not overlap, but are separated along a sequence, ProDom domain database consists of an automatic compilation of homologous domains. Current versions of ProDom are built using a procedure based on recursive PSI-BLAST searches
29.
PROSITE
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It consists of entries describing the protein families, domains and functional sites as well as amino acid patterns and profiles in them. These are manually curated by a team of the Swiss Institute of Bioinformatics, PROSITE was created in 1988 by Amos Bairoch, who directed the group for more than 20 years. Since July 2009, the director of the PROSITE, Swiss-Prot, pROSITEs uses include identifying possible functions of newly discovered proteins and analysis of known proteins for previously undetermined activity. Properties from well-studied genes can be propagated to biologically related organisms, PROSITE offers tools for protein sequence analysis and motif detection. It is part of the ExPASy proteomics analysis servers, the database ProRule builds on the domain descriptions of PROSITE. It provides additional information about functionally or structurally critical amino acids and these can automatically generate annotation based on PROSITE motifs. As of 29 June 2016, release 20.128 has 1,762 documentation entries,1,309 patterns,1,161 profiles, uniprot — the universal protein database, a central resource on protein information - PROSITE adds data to it. InterPro — a centralized database, grouping data from databases of protein families, domains, protein subcellular localization prediction — another example of use of PROSITE. Official website ProRule — database of rules based on PROSITE predictors
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Protein Data Bank
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The Protein Data Bank is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The PDB is overseen by a called the Worldwide Protein Data Bank. The PDB is a key resource in areas of structural biology, most major scientific journals, and some funding agencies, now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB, for example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. By 1971, one of Meyers programs, SEARCH, enabled researchers to access information from the database to study protein structures offline. SEARCH was instrumental in enabling networking, thus marking the beginning of the PDB. Upon Hamiltons death in 1973, Tom Koeztle took over direction of the PDB for the subsequent 20 years, in January 1994, Joel Sussman of Israels Weizmann Institute of Science was appointed head of the PDB. In October 1998, the PDB was transferred to the Research Collaboratory for Structural Bioinformatics, the new director was Helen M. Berman of Rutgers University. In 2003, with the formation of the wwPDB, the PDB became an international organization, the founding members are PDBe, RCSB, and PDBj. Each of the four members of wwPDB can act as deposition, data processing, the data processing refers to the fact that wwPDB staff review and annotate each submitted entry. The data are automatically checked for plausibility. The PDB database is updated weekly, likewise, the PDB holdings list is also updated weekly. As of 14 March 2017, the breakdown of current holdings is as follows,103,514 structures in the PDB have a structure factor file,9,057 structures have an NMR restraint file. 2,826 structures in the PDB have a chemical shifts file, therefore, the final conformation of the protein is obtained, in the latter case, by solving a distance geometry problem. A few proteins are determined by cryo-electron microscopy, the significance of the structure factor files, mentioned above, is that, for PDB structures determined by X-ray diffraction that have a structure file, the electron density map may be viewed. The data of such structures is stored on the electron density server, however, since 2007, the rate of accumulation of new protein structures appears to have plateaued. The file format used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line, around 1996, the macromolecular Crystallographic Information file format, mmCIF, which is an extension of the CIF format started to be phased in
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Biomolecular structure
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Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits. This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels, primary, secondary, tertiary, the scaffold for this multiscale organization of the molecule arises at the secondary level, where the fundamental structural elements are the molecules various hydrogen bonds. The terms primary, secondary, tertiary, and quaternary structure were introduced by Kaj Ulrik Linderstrøm-Lang in his 1951 Lane Medical Lectures at Stanford University, the primary structure of a biopolymer is the exact specification of its atomic composition and the chemical bonds connecting those atoms. For a typical unbranched, un-crosslinked biopolymer, the structure is equivalent to specifying the sequence of its monomeric subunits. Primary structure is sometimes mistakenly termed primary sequence, but there is no such term, the primary structure of a nucleic acid molecule refers to the exact sequence of nucleotides that comprise the whole molecule. Often, the primary structure encodes motifs that are of functional importance. The secondary structure is the pattern of hydrogen bonds in a biopolymer, secondary structure is formally defined by the hydrogen bonds of the biopolymer, as observed in an atomic-resolution structure. In proteins, the structure is defined by patterns of hydrogen bonds between backbone amide and carboxyl groups, where the DSSP definition of a hydrogen bond is used. In nucleic acids, the structure is defined by the hydrogen bonding between the nitrogenous bases. For proteins, however, the bonding is correlated with other structural features. Many other less formal definitions have been proposed, often applying concepts from the geometry of curves, such as curvature. Structural biologists solving a new structure will sometimes assign its secondary structure by eye. The secondary structure of an acid molecule refers to the base pairing interactions within one molecule or set of interacting molecules. The secondary structure of biological RNAs can often be uniquely decomposed into stems, often, these elements or combinations of them can be further classified, e. g. tetraloops, pseudoknots and stem-loops. There are many secondary structure elements of importance to biological RNAs. Famous examples include the Rho-independent terminator stem-loops and the transfer RNA cloverleaf, there is a minor industry of researchers attempting to determine the secondary structure of RNA molecules. Approaches include both experimental and computational methods, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates
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Residue (chemistry)
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In chemistry residue is whatever remains or acts as a contaminant after a given class of events. Residue may be the material remaining after a process of preparation, separation, or purification, such as distillation, evaporation and it may also denote the undesired by-products of a chemical reaction. Toxic chemical residues, wastes or contamination from other processes, are a concern in food safety, for example, the U. S. Food and Drug Administration and the Canadian Food Inspection Agency have guidelines for detecting chemical residues that are possibly dangerous to consume. Residue may refer to an atom or a group of atoms that forms part of a molecule, in biochemistry and molecular biology, a residue refers to a specific monomer within the polymeric chain of a polysaccharide, protein or nucleic acid. One might say, This protein consists of 118 amino acid residues or The histidine residue is considered to be basic because it contains an imidazole ring. Note that a residue is different from a moiety, which, a residue might be one amino acid in a polypeptide or one monosaccharide in a starch molecule
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Base pair
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A base pair is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the blocks of the DNA double helix. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs allow the DNA helix to maintain a regular helical structure that is dependent on its nucleotide sequence. The complementary nature of this structure provides a backup copy of all genetic information encoded within double-stranded DNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes, intramolecular base pairs can occur within single-stranded nucleic acids. The size of a gene or an organisms entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of base pairs is equal to the number of nucleotides in one of the strands. The haploid human genome is estimated to be about 3.2 billion bases long and to contain 20, a kilobase is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. 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 TtC. Hydrogen bonding is the interaction that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen donors and acceptors allows only the right pairs to form stably. Purine-pyrimidine base pairing of AT or GC or UA results in proper duplex structure, the only other purine-pyrimidine pairings would be AC and GT and UG, these pairings are mismatches because the patterns of hydrogen donors and acceptors do not correspond. The GU pairing, with two bonds, does occur fairly often in RNA. Higher GC content results in higher melting temperatures, it is, therefore, on the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often-transcribed genes — are comparatively GC-poor. GC content and melting temperature must also be taken into account when designing primers for PCR reactions, the following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5 end to the 3 end, thus and this is due to their isosteric chemistry. One common mutagenic base analog is 5-bromouracil, which resembles thymine, most intercalators are large polyaromatic compounds and are known or suspected carcinogens. Examples include ethidium bromide and acridine, an unnatural base pair is a designed subunit of DNA which is created in a laboratory and does not occur in nature
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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
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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
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Mitochondrion
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The mitochondrion is a double membrane-bound organelle found in all eukaryotic organisms. Some cells in multicellular organisms may however lack them. A number of organisms, such as microsporidia, parabasalids. To date, only one eukaryote, Monocercomonoides, is known to have completely lost its mitochondria, the word mitochondrion comes from the Greek μίτος, mitos, thread, and χονδρίον, chondrion, granule or grain-like. Mitochondria generate most of the supply of adenosine triphosphate, used as a source of chemical energy. Mitochondria are commonly between 0.75 and 3 μm in diameter but vary considerably in size and structure, unless specifically stained, they are not visible. Mitochondrial biogenesis is in turn temporally coordinated with these cellular processes, Mitochondria have been implicated in several human diseases, including mitochondrial disorders, cardiac dysfunction, heart failure and autism. The number of mitochondria in a cell can vary widely by organism, tissue, for instance, red blood cells have no mitochondria, whereas liver cells can have more than 2000, The organelle is composed of compartments that carry out specialized functions. These compartments or regions include the outer membrane, the space, the inner membrane. Although most of a cells DNA is contained in the cell nucleus, mitochondrial proteins vary depending on the tissue and the species. In humans,615 distinct types of protein have been identified from cardiac mitochondria, the mitochondrial proteome is thought to be dynamically regulated. The first observations of structures that probably represented mitochondria were published in the 1840s. Richard Altmann, in 1890, established them as cell organelles, the term mitochondria was coined by Carl Benda in 1898. Leonor Michaelis discovered that Janus green can be used as a stain for mitochondria in 1900. Benjamin F. Kingsbury, in 1912, first related them with cell respiration, in 1913, particles from extracts of guinea-pig liver were linked to respiration by Otto Heinrich Warburg, which he called grana. Warburg and Heinrich Otto Wieland, who had postulated a similar particle mechanism. It was not until 1925, when David Keilin discovered cytochromes, in the following years, the mechanism behind cellular respiration was further elaborated, although its link to the mitochondria was not known. The introduction of tissue fractionation by Albert Claude allowed mitochondria to be isolated from other cell fractions, in 1946, he concluded that cytochrome oxidase and other enzymes responsible for the respiratory chain were isolated to the mitchondria
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Homo sapiens
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Homo sapiens is the binomial nomenclature for the only extant human species. Homo is the genus, which also includes Neanderthals and many other extinct species of hominid. Modern humans are the subspecies Homo sapiens sapiens, which differentiates them from what has been argued to be their direct ancestor, the binomial name Homo sapiens was coined by Carl Linnaeus. The Latin noun homō means man, human being, subspecies of H. sapiens include Homo sapiens idaltu and the only extant subspecies, Homo sapiens sapiens. Some sources show Neanderthals as a subspecies, similarly, the discovered specimens of the Homo rhodesiensis species have been classified by some as a subspecies, but these last two subspecies classifications are not widely accepted by scientists. Traditionally, there are two competing views in paleoanthropology about the origin of H. sapiens, the recent African origin, since 2010, genetic research has led to the emergence of an intermediate position, characterised by mostly recent African origin plus limited admixture with archaic humans. The recent African origin of humans is the mainstream model that describes the origin. The theory is called the Out-of-Africa model in the press, and academically the recent single-origin hypothesis, Replacement Hypothesis. The hypothesis that humans have a single origin was published in Charles Darwins Descent of Man, the concept was speculative until the 1980s, when it was corroborated by a study of present-day mitochondrial DNA, combined with evidence based on physical anthropology of archaic specimens. The recent single origin of humans in East Africa is the near-consensus position held within the scientific community. However, recent sequencing of the full Neanderthal genome suggests Neanderthals, the authors of the study suggest that their findings are consistent with Neanderthal admixture of up to 4% in some populations. But the study suggests that there may be other reasons why humans. That study however does not explain why only a fraction of humans have Neanderthal DNA. The multiregional origin model provides an explanation for the pattern of evolution proposed by Milford H. Wolpoff in 1988. Scientific study of evolution is concerned, primarily, with the development of the genus Homo. Modern humans are defined as the Homo sapiens species, of which the extant subspecies is known as Homo sapiens sapiens. Homo sapiens idaltu, the known subspecies, is now extinct. Similarly, the specimens of the Homo rhodesiensis species have been classified by some as a subspecies
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