RNA polymerase II
RNA polymerase II is a multiprotein complex. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells, it catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription. Early studies suggested a minimum of two RNAPs: one which synthesized rRNA in the nucleolus, one which synthesized other RNA in the nucleoplasm, part of the nucleus but outside the nucleolus. In 1969, science experimentalists Robert Roeder and William Rutter definitively discovered an additional RNAP, responsible for transcription of some kind of RNA in the nucleoplasm; the finding was obtained by the use of DEAE-Sephadex ion-exchange chromatography. The technique separated the enzymes by the order of the corresponding elutions, Ι,ΙΙ,ΙΙΙ, by increasing the concentration of ammonium sulfate.
The enzymes were named according to the order of the elutions, RNAP I, RNAP II, RNAP IΙI. This discovery demonstrated that there was an additional enzyme present in the nucleoplasm, which allowed for the differentiation between RNAP II and RNAP III; the eukaryotic core RNA polymerase II was first purified using transcription assays. The purified enzyme has 10-12 subunits and is incapable of specific promoter recognition. Many subunit-subunit interactions are known. DNA-directed RNA polymerase II subunit RPB1 – an enzyme that in humans is encoded by the POLR2A gene and in yeast is encoded by RPO21. RPB1 is the largest subunit of RNA polymerase II, it contains a carboxy terminal domain composed of up to 52 heptapeptide repeats that are essential for polymerase activity. The CTD was first discovered in the laboratory of C. J. Ingles by JL Corden at Johns Hopkins University. In combination with several other polymerase subunits, the RPB1 subunit forms the DNA binding domain of the polymerase, a groove in which the DNA template is transcribed into RNA.
It interacts with RPB8. RPB2 – the second-largest subunit that in combination with at least two other polymerase subunits forms a structure within the polymerase that maintains contact in the active site of the enzyme between the DNA template and the newly synthesized RNA. RPB3 – the third-largest subunit. Exists as a heterodimer with another polymerase subunit, POLR2J forming a core subassembly. RPB3 interacts with RPB1-5, 7, 10-12. RNA polymerase II subunit B4 – encoded by the POLR2D gene is the fourth-largest subunit and may have a stress protective role. RPB5 – In humans is encoded by the POLR2E gene. Two molecules of this subunit are present in each RNA polymerase II. RPB5 interacts with RPB1, RPB3, RPB6. RPB6 – forms a structure with at least two other subunits that stabilizes the transcribing polymerase on the DNA template. RPB7 -- may play a role in regulating polymerase function. RPB7 interacts with RPB1 and RPB5. RPB8 – interacts with subunits RPB1-3, 5, 7. RPB9 – The groove in which the DNA template is transcribed into RNA is composed of RPB9 and RPB1.
RPB10 – the product of gene POLR2L. It interacts with RPB1-3 and 5, with RPB3. RPB11 – the RPB11 subunit is itself composed of three subunits in humans: POLR2J, POLR2J2, POLR2J3. RPB12 – Also interacts with RPB3 is RPB12. RPB3 is involved in RNA polymerase II assembly. A subcomplex of RPB2 and RPB3 appears soon after subunit synthesis; this complex subsequently interacts with RPB1. RPB3, RPB5, RPB7 interact with themselves to form homodimers, RPB3 and RPB5 together are able to contact all of the other RPB subunits, except RPB9. Only RPB1 binds to RPB5; the RPB1 subunit contacts RPB7, RPB10, more weakly but most efficiently with RPB8. Once RPB1 enters the complex, other subunits such as RPB5 and RPB7 can enter, where RPB5 binds to RPB6 and RPB8 and RPB3 brings in RPB10, RPB 11, RPB12. RPB4 and RPB9 may enter. RPB4 forms a complex with RPB7. Enzymes can catalyze up to several million reactions per second. Enzyme rates depend on substrate concentration. Like other enzymes POLR2 has a maximum velocity, it has a kcat.
The specificity constant is given by kcat/Km. The theoretical maximum for the specificity constant is the diffusion limit of about 108 to 109, where every collision of the enzyme with its substrate results in catalysis. In yeast, mutation in the Trigger-Loop domain of the largest subunit can change the kinetics of the enzyme. Bacterial RNA polymerase, a relative of RNA Polymerase II, switches between inactivated and activated states by translocating back and forth along the DNA. Concentrations of eq = 10 μM GTP, 10 μM UTP, 5 μM ATP and 2.5 μM CTP, produce a mean elongation rate, turnover number, of ~1 bp −1 for bacterial RNAP, a relative of RNA polymerase II. RNA polymerase II is inhibited by other amatoxins. Α-Amanitin is a poisonous substance found in many mushrooms. The mushroom poison has different effects on the each of the RNA Polyermases: I, II, III. RNAP I is unresponsive to the substance and will function while RNAP III has a moderate sensitivity. RNAP II, however, is inhibited by the toxin.
Alpha-Amanitin inhibits RNAP II by strong interactions in the enzyme's "funnel", "cleft", the key "bridge α-helix" regions of the RPB-1 subunit. RNA polymerase II
Maize known as corn, is a cereal grain first domesticated by indigenous peoples in southern Mexico about 10,000 years ago. The leafy stalk of the plant produces pollen inflorescences and separate ovuliferous inflorescences called ears that yield kernels or seeds, which are fruits. Maize has become a staple food in many parts of the world, with the total production of maize surpassing that of wheat or rice. However, little of this maize is consumed directly by humans: most is used for corn ethanol, animal feed and other maize products, such as corn starch and corn syrup; the six major types of maize are dent corn, flint corn, pod corn, flour corn, sweet corn. Maize is the most grown grain crop throughout the Americas, with 361 million metric tons grown in the United States in 2014. 40% of the crop—130 million tons—is used for corn ethanol. Genetically modified maize made up 85% of the maize planted in the United States in 2009. Sugar-rich varieties called sweet corn are grown for human consumption as kernels, while field corn varieties are used for animal feed, various corn-based human food uses, as chemical feedstocks.
Maize is used in making ethanol and other biofuels. Most historians believe. Recent research in the early 21st century has modified this view somewhat. An influential 2002 study by Matsuoka et al. has demonstrated that, rather than the multiple independent domestications model, all maize arose from a single domestication in southern Mexico about 9,000 years ago. The study demonstrated that the oldest surviving maize types are those of the Mexican highlands. Maize spread from this region over the Americas along two major paths; this is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. Archaeologist Dolores Piperno has said: A large corpus of data indicates that it was dispersed into lower Central America by 7600 BP and had moved into the inter-Andean valleys of Colombia between 7000 and 6000 BP. Since even earlier dates have been published. According to a genetic study by Embrapa, corn cultivation was introduced in South America from Mexico, in two great waves: the first, more than 6000 years ago, spread through the Andes.
Evidence of cultivation in Peru has been found dating to about 6700 years ago. The second wave, about 2000 years ago, through the lowlands of South America. Before domestication, maize plants grew only small, 25 millimetres long corn cobs, only one per plant. In Spielvogel's view, many centuries of artificial selection by the indigenous people of the Americas resulted in the development of maize plants capable of growing several cobs per plant, which were several centimetres/inches long each; the Olmec and Maya cultivated maize in numerous varieties throughout Mesoamerica. It was believed. Research of the 21st century has established earlier dates; the region developed a trade network based on surplus and varieties of maize crops. Mapuches of south-central Chile cultivated maize along with quinoa and potatoes in Pre-Hispanic times, however potato was the staple food of most Mapuches, "specially in the southern and coastal territories where maize did not reach maturity". Before the expansion of the Inca Empire maize was traded and transported as far south as 40°19' S in Melinquina, Lácar Department.
In that location maize remains were found inside pottery dated to 730 ±80 BP and 920 ±60 BP. This maize was brought across the Andes from Chile; the presence of maize in Guaitecas Archipelago, which constitute southernmost outspost of Pre-Hispanic agriculture, is reported by early Spanish explorers. However the Spanish may have misidentified the plant. After the arrival of Europeans in 1492, Spanish settlers consumed maize and explorers and traders carried it back to Europe and introduced it to other countries. Spanish settlers far preferred wheat bread to cassava, or potatoes. Maize flour could not be substituted for wheat for communion bread, since in Christian belief only wheat could undergo transubstantiation and be transformed into the body of Christ; some Spaniards worried that by eating indigenous foods, which they did not consider nutritious, they would weaken and risk turning into Indians. "In the view of Europeans, it was the food they ate more than the environment in which they lived, that gave Amerindians and Spaniards both their distinctive physical characteristics and their characteristic personalities."
Despite these worries, Spaniards did consume maize. Archeological evidence from Florida sites indicate. Maize spread to the rest of the world because of its ability to grow in diverse climates, it was cultivated in Spain just a few decades after Columbus's voyages and spread to Italy, West Africa and elsewhere. The word maize derives from the Spanish form of the indigenous Taíno word for mahiz, it is known by other names around the world. The word "corn" outside North America and New Zealand refers to any cereal crop, its meaning understood to vary geographically to refer to the local staple. In the United Stat
Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, unlike prokaryotes, which have no membrane-bound organelles. Eukaryotes belong to Eukarya, their name comes from the Greek εὖ and κάρυον. Eukaryotic cells contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, in addition, some cells of plants and algae contain chloroplasts. Unlike unicellular archaea and bacteria, eukaryotes may be multicellular and include organisms consisting of many cell types forming different kinds of tissue. Animals and plants are the most familiar eukaryotes. Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two genetically identical cells. In meiosis, DNA replication is followed by two rounds of cell division to produce four haploid daughter cells; these act as sex cells. Each gamete has just one set of chromosomes, each a unique mix of the corresponding pair of parental chromosomes resulting from genetic recombination during meiosis.
The domain Eukaryota appears to be monophyletic, makes up one of the domains of life in the three-domain system. The two other domains and Archaea, are prokaryotes and have none of the above features. Eukaryotes represent a tiny minority of all living things. However, due to their much larger size, their collective worldwide biomass is estimated to be about equal to that of prokaryotes. Eukaryotes evolved 1.6–2.1 billion years ago, during the Proterozoic eon. 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 1937 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 only one paragraph, the idea was ignored until Chatton's statement was rediscovered by Stanier and van Niel.
In 1905 and 1910, the Russian biologist Konstantin Mereschkowski argued that plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic host, itself formed by symbiosis between an amoeba-like host and a bacterium-like cell that formed the nucleus. Plants had thus inherited photosynthesis from cyanobacteria. In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in eukaryotic cells in her paper, On the origin of mitosing cells. In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA; this helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles and chloroplasts. In 1977, Woese and George Fox introduced a "third form of life", which they called the Archaebacteria. In 1979, G. W. Gould and G. J. Dring suggested that the eukaryotic cell's nucleus came from the ability of Gram-positive bacteria to form endospores. In 1987 and papers, Thomas Cavalier-Smith proposed instead that the membranes of the nucleus and endoplasmic reticulum first formed by infolding a prokaryote's plasma membrane.
In the 1990s, several other biologists proposed endosymbiotic origins for the nucleus reviving Mereschkowski's theory. Eukaryotic cells are much larger than those of prokaryotes having a volume of around 10,000 times greater than the prokaryotic cell, they have a variety of internal membrane-bound structures, called organelles, a cytoskeleton composed of microtubules and intermediate filaments, which play an important role in defining the cell's organization and shape. Eukaryotic DNA is divided into several linear bundles called chromosomes, which are separated by a microtubular spindle during nuclear division. Eukaryote cells include a variety of membrane-bound structures, collectively referred to as the endomembrane system. Simple compartments, called vesicles and vacuoles, can form by budding off other membranes. Many cells ingest food and other materials through a process of endocytosis, where the outer membrane invaginates and pinches off to form a vesicle, it is probable that most other membrane-bound organelles are derived from such vesicles.
Alternatively some products produced by the cell can leave in a vesicle through exocytosis. The nucleus is surrounded with pores that allow material to move in and out. Various tube- and sheet-like extensions of the nuclear membrane form the endoplasmic reticulum, involved in protein transport and maturation, it includes the rough endoplasmic reticulum where ribosomes are attached to synthesize proteins, which enter the interior space or lumen. Subsequently, they enter vesicles, which bud off from the smooth endoplasmic reticulum. In most eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles, the Golgi apparatus. Vesicles may be specialized for various purposes. For instance, lysosomes contain digestive enzymes that break down most biomolecules in the cytoplasm. Peroxisomes are used to break down peroxide, otherwise toxic. Many protozoans have contractile vacuoles, which collect and expel excess water, extrusomes, which expel material used to deflect predators or capture prey.
In higher plants, most of a cell's volume is taken up by a central vacuole, whi
Signal recognition particle
The signal recognition particle is an abundant, universally conserved ribonucleoprotein that recognizes and targets specific proteins to the endoplasmic reticulum in eukaryotes and the plasma membrane in prokaryotes. The function of SRP was discovered by the study of processed and unprocessed immunoglobulin light chains. In eukaryotes, SRP binds to the signal sequence of a newly synthesized peptide as it emerges from the ribosome; this binding leads to the slowing of protein synthesis known as "elongation arrest", a conserved function of SRP that facilitates the coupling of the protein translation and the protein translocation processes. SRP targets this entire complex to the protein-conducting channel known as the translocon, in the ER membrane; this occurs via the interaction and docking of SRP with its cognate SRP receptor, located in close proximity to the translocon. In eukaryotes there are three domains between SRP and its receptor that function in guanosine triphosphate binding and hydrolysis.
These are located in two related subunits in the SRP receptor and the SRP protein SRP54. The coordinated binding of GTP by SRP and the SRP receptor has been shown to be a prerequisite for the successful targeting of SRP to the SRP receptor. Upon docking, the nascent peptide chain is inserted into the translocon channel where it enters into the ER. Protein synthesis resumes; the SRP-SRP receptor complex dissociates via GTP hydrolysis and the cycle of SRP-mediated protein translocation continues. Once inside the ER, the signal sequence is cleaved from the core protein by signal peptidase. Signal sequences are therefore not a part of mature proteins. Despite SRP function being analogous in all organisms, its composition varies greatly; the eukaryotic SRP is composed of six distinct polypeptides bound to an RNA molecule, with GTPase activity. The components of the complex are: SRP9 SRP14 SRP19 SRP54 SRP68 SRP72 SRP RNAThe prokaryotic SRP is composed of one polypeptide bound to an RNA molecule, with GTPase activity.
The components of the complex are: Ffh 4.5S RNAFfh is the structural and functional homolog of the SRP54 protein in eukaryotes. The 4.5S RNA shares sequence and structural homology with one domain of the larger 7S RNA. Anti-signal recognition particle antibodies are associated with, but are not specific for, polymyositis. For individuals with polymyositis, the presence of anti-SRP antibodies are associated with more prominent muscle weakness and atrophy. Signal recognition particle RNA Signal+Recognition+Particle at the US National Library of Medicine Medical Subject Headings Signal Recognition Particle Database www.dnaTube.com video showing an SRP in action Another SRP video at www.dnaTube.com The Nobel Prize in Physiology or Medicine 1999, "for the discovery that proteins have intrinsic signals that govern their transport and localization in the cell" to Günter Blobel, USA. Press Release, Illustrated Presentation, Presentation Speech
Long interspersed nuclear element
Long interspersed nuclear elements are a group of non-LTR retrotransposons which are widespread in the genome of many eukaryotes. They make up around 21.1% of the human genome. LINEs make up a family of transposons. LINEs are translated into protein that acts as a reverse transcriptase; the reverse transcriptase makes a DNA copy of the LINE RNA that can be integrated into the genome at a new site. The only abundant LINE in humans is LINE-1. Our genome contains 4,000 full-length LINE-1 elements. Due to the accumulation of random mutations, the sequence of many LINEs has degenerated to the extent that they are no longer transcribed or translated. Comparisons of LINE DNA sequences can be used to date transposon insertion in the genome; the first description of an 6.4 kb long LINE-derived sequence was published by J. Adams et al. in 1980. Based on structural features and the phylogeny of its key enzyme, the reverse transcriptase, LINEs are grouped into five main groups, called L1, RTE, R2, I and Jockey, which can be subdivided into at least 28 clades.
In plant genomes, so far only LINEs of the L1 and RTE clade have been reported. Whereas L1 elements diversify into several subclades, RTE-type LINEs are conserved constituting a single family. In fungi, Tad, L1, CRE, Deceiver and Inkcap-like elements have been identified, with Tad-like elements appearing in fungal genomes. All LINEs encode a least one protein, ORF2, which contains an RT and an endonuclease domain, either an N-terminal APE or a C-terminal RLE or both. A ribonuclease H domain is present. Except for the evolutionary ancient R2 and RTE superfamilies, LINEs encode for another protein named ORF1, which may contain an Gag-knuckle, a L1-like RRM, and/or an esterase. LINE elements are rare compared to LTR-retrotransposons in plants, fungi or insects, but are dominant in vertebrates and in mammals, where they represent around 20% of the genome; the LINE-1/L1-element is the only element, still active in the human genome today. It is found in all mammals. Remnants of L2 and L3 elements are found in the human genome.
It is estimated, that L3 elements were active ~ 200-300 million years ago. Unlike L1 elements, L2 elements lack flanking target site duplications; the L2 elements are in the same group as Jockey. In the first human genome draft the fraction of LINE elements of the human genome was given as 21% and their copy number as 850,000. Of these, L1, L2 and L3 elements made up 315,000 and 37,000 copies, respectively; the non-autonomous SINE elements which depend on L1 elements for their proliferation make up 13% of the human genome and have a copy number of around 1.5 million. They originated from the RTE family of LINEs. Recent estimates show the typical human genome contains on average 100 L1 elements with potential for mobilization, however there is a fair amount of variation and some individuals may contain a larger number of active L1 elements, making these individuals more prone to L1-induced mutagenesis. Increased L1 copy numbers have been found in the brains of people with schizophrenia, indicating that LINE elements may play a role in some neuronal diseases.
LINE elements propagate by a so-called target primed reverse transcription mechanism, first described for the R2 element from the silkworm Bombyx mori. ORF2 proteins associate in cis with their encoding mRNA, forming a ribonucleoprotein complex composed of two ORF2s and an unknown number of ORF1 trimers; the complex is transported back into the nucleus, where the ORF2 endonuclease domain opens the DNA. Thus, a 3'OH group is freed for the reverse transcriptase to prime reverse transcription of the LINE RNA transcript. Following the reverse transcription the target strand is cleaved and the newly created cDNA is integratedNew insertions create short TSDs, the majority of new inserts are 5’-truncated and inverted; because they lack their 5’UTR, most of new inserts are non functional. It has been shown that host cells regulate L1 retrotransposition activity, for example through epigenetic silencing. For example, the RNA interference mechanism of small interfering RNAs derived from L1 sequences can cause suppression of L1 retrotransposition.
In plant genomes, epigenetic modification of LINEs can lead to expression changes of nearby genes and to phenotypic changes: In the oil palm genome, methylation of a Karma-type LINE underlies the somaclonal,'mantled' variant of this plant, responsible for drastic yield loss. Human APOBEC3C mediated restriction of LINE-1 elements were reported and it is due to the interaction between A3C with the ORF1p that affects the reverse transcriptase activity. A historic example of L1-conferred disease is Haemophilia A, caused by insertional mutagenesis. There are nearly 100 examples of known diseases caused by retroelement insertions, including some types of cancer and neurological disorders. Correlation between L1 mobilization and oncogenesis has been reported for epithelial cell cancer. Hypomethylation of LINES is associated with chromosomal instability and altered gene expression and is found in various cancer cell types in various tissues types. Hypomethylation of a specific L1 located in the MET onco gene is associated with bladder cancer tumorogenesis, Shift work sleep disorder is associated with increased cancer risk because light exp
Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding and expression of genes. RNA and DNA are nucleic acids, along with lipids and carbohydrates, constitute the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey genetic information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome; some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these active processes is protein synthesis, a universal function in which RNA molecules direct the assembly of proteins on ribosomes; this process uses transfer RNA molecules to deliver amino acids to the ribosome, where ribosomal RNA links amino acids together to form proteins.
Like DNA, most biologically active RNAs, including mRNA, tRNA, rRNA, snRNAs, other non-coding RNAs, contain self-complementary sequences that allow parts of the RNA to fold and pair with itself to form double helices. Analysis of these RNAs has revealed that they are structured. Unlike DNA, their structures do not consist of long double helices, but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the ribosome—an RNA-protein complex that catalyzes peptide bond formation—revealed that its active site is composed of RNA; each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, in general, cytosine, guanine, or uracil. Adenine and guanine are purines and uracil are pyrimidines. A phosphate group is attached to the 5' position of the next; the phosphate groups have a negative charge each. The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.
However, other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair. An important structural component of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar; the presence of this functional group causes the helix to take the A-form geometry, although in single strand dinucleotide contexts, RNA can also adopt the B-form most observed in DNA. The A-form geometry results in a deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule, it can chemically attack the adjacent phosphodiester bond to cleave the backbone. RNA is transcribed with only four bases, but these bases and attached sugars can be modified in numerous ways as the RNAs mature. Pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, ribothymidine are found in various places.
Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine. Inosine plays a key role in the wobble hypothesis of the genetic code. There are more than 100 other occurring modified nucleosides; the greatest structural diversity of modifications can be found in tRNA, while pseudouridine and nucleosides with 2'-O-methylribose present in rRNA are the most common. The specific roles of many of these modifications in RNA are not understood. However, it is notable that, in ribosomal RNA, many of the post-transcriptional modifications occur in functional regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal function; the functional form of single-stranded RNA molecules, just like proteins requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule; this leads to several recognizable "domains" of secondary structure like hairpin loops and internal loops.
Since RNA is charged, metal ions such as Mg2+ are needed to stabilise many secondary and tertiary structures. The occurring enantiomer of RNA is D-RNA composed of D-ribonucleotides. All chirality centers are located in the D-ribose. By the use of L-ribose or rather L-ribonucleotides, L-RNA can be synthesized. L-RNA is much more stable against degradation by RNase. Like other structured biopolymers such as proteins, one can define topology of a folded RNA molecule; this is done based on arrangement of intra-chain contacts within a folded RNA, termed as circuit topology. Synthesis of RNA is catalyzed by an enzyme—RNA polymerase—using DNA as a template, a process known as transcription. Initiation of transcription begins with the binding of the enzyme to a promoter sequence in the DNA; the DNA double helix is unwound by the helicase activity of the enzyme. The enzyme progresses along the template strand in the 3’ to 5’ direction, synthesizing a complementary RNA molecule with elongation occ
Deoxyribonucleic acid is a molecule composed of two chains that coil around each other to form a double helix carrying the genetic instructions used in the growth, development and reproduction of all known organisms and many viruses. DNA and ribonucleic acid are nucleic acids; the two DNA strands are known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases, a sugar called deoxyribose, 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 separate polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA; the complementary nitrogenous bases are divided into two groups and purines. In DNA, the pyrimidines are cytosine. Both strands of double-stranded DNA store the same biological information.
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 are thus antiparallel. Attached to each sugar is one of four types of nucleobases, it is the sequence of these four nucleobases along the backbone. RNA strands are created using DNA strands as a template in a process called transcription. Under the genetic code, these RNA strands specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells, DNA is organized into long structures called chromosomes. Before typical cell division, these chromosomes are duplicated in the process of DNA replication, providing a complete set of chromosomes for each daughter cell. Eukaryotic organisms store most of their DNA inside the cell nucleus as nuclear DNA, some in the mitochondria as mitochondrial DNA, or in chloroplasts as chloroplast DNA. In contrast, prokaryotes store their DNA only in circular chromosomes.
Within eukaryotic chromosomes, chromatin proteins, such as histones and organize DNA. These compacting 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, its molecular structure was first identified by Francis Crick and James Watson at the Cavendish Laboratory within the University of Cambridge in 1953, whose model-building efforts were guided by X-ray diffraction data acquired by Raymond Gosling, a post-graduate student of Rosalind Franklin. DNA is used by researchers as a molecular tool to explore physical laws and theories, such as the ergodic theorem and the theory of elasticity; the unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro- and nano-fabrication. Among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a long polymer made from repeating units called nucleotides.
The structure of DNA is dynamic along its length, being capable of coiling into tight loops and other shapes. In all species it is composed of two helical chains, bound to each other by hydrogen bonds. Both chains are coiled around the same axis, have the same pitch of 34 angstroms; the pair of chains has a radius of 10 angstroms. According to another study, when measured in a different solution, the DNA chain measured 22 to 26 angstroms wide, one nucleotide unit measured 3.3 Å long. Although each individual nucleotide is small, a DNA polymer can be large and contain hundreds of millions, such as in chromosome 1. Chromosome 1 is the largest human chromosome with 220 million base pairs, would be 85 mm long if straightened. DNA does not exist as a single strand, but instead as a pair of strands that are held together; these two long strands coil in the shape of a double helix. The nucleotide contains both a segment of the backbone of a nucleobase. A nucleobase linked to a sugar is called a nucleoside, a base linked to a sugar and to one or more phosphate groups is called a nucleotide.
A biopolymer comprising multiple linked nucleotides is called a polynucleotide. The backbone of the DNA strand is made from alternating sugar residues; the sugar in DNA is 2-deoxyribose, a pentose sugar. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings; these are known as the 3′-end, 5′-end carbons, the prime symbol being used to distinguish these carbon atoms from those of the base to which the deoxyribose forms a glycosidic bond. When imagining DNA, each phosphoryl is considered to "belong" to the nucleotide whose 5′ carbon forms a bond therewith. Any DNA strand therefore has one end at which there is a phosphoryl attached to the 5′ carbon of a ribose and another end a