Instruct: Given a question, retrieve relevant documents that answer the question.
Query: Why is RNA needed?
At first, regulatory RNA was thought to be a eukaryotic phenomenon, a part of the explanation for why so much more transcription in higher organisms was seen than had been predicted. But as soon as researchers began to look for possible RNA regulators in bacteria, they turned up there as well. Currently, the ubiquitous nature of systems of RNA regulation of genes has been discussed as support for the RNA World theory. Bacterial small RNAs generally act via antisense pairing with mRNA to down-regulate its translation, either by affecting stability or affecting cis-binding ability. Riboswitches have also been discovered. They are cis-acting regulatory RNA sequences acting allosterically. They change shape when they bind metabolites so that they gain or lose the ability to bind chromatin to regulate expression of genes.
The steps contributing to the production of primary transcripts involve a series of molecular interactions that initiate transcription of DNA within a cell's nucleus. Based on the needs of a given cell, certain DNA sequences are transcribed to produce a variety of RNA products to be translated into functional proteins for cellular use. To initiate the transcription process in a cell's nucleus, DNA double helices are unwound and hydrogen bonds connecting compatible nucleic acids of DNA are broken to produce two unconnected single DNA strands. One strand of the DNA template is used for transcription of the single-stranded primary transcript mRNA. This DNA strand is bound by an RNA polymerase at the promoter region of the DNA.
In genetics, a transcription terminator is a section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription. This sequence mediates transcriptional termination by providing signals in the newly synthesized transcript RNA that trigger processes which release the transcript RNA from the transcriptional complex. These processes include the direct interaction of the mRNA secondary structure with the complex and/or the indirect activities of recruited termination factors. Release of the transcriptional complex frees RNA polymerase and related transcriptional machinery to begin transcription of new mRNAs.
The first step of SELEX involves the synthesis of fully or partially randomized oligonucleotide sequences of some length flanked by defined regions which allow PCR amplification of those randomized regions and, in the case of RNA SELEX, in vitro transcription of the randomized sequence. While Ellington and Szostak demonstrated that chemical synthesis is capable of generating ~10 unique sequences for oligonucleotide libraries in their 1990 paper on in vitro selection, they found that amplification of these synthesized oligonucleotides led to significant loss of pool diversity due to PCR bias and defects in synthesized fragments. The oligonucleotide pool is amplified and a sufficient amount of the initial library is added to the reaction so that there are numerous copies of each individual sequence to minimize the loss of potential binding sequences due to stochastic events. Before the library is introduced to target for incubation and selective retention, the sequence library must be converted to single stranded oligonucleotides to achieve structural conformations with target binding properties.
cDNA cloning is a major technology for analysis of the expression of genomes. The full-length first-strand can be synthesized through the commercially available reverse transcriptases. Synthesis of the second-strand was once a major limitation to cDNA cloning. Two groups of methods differing by the mechanism of initiation were developed to synthesize the second-strand. In a first group of methods, initiation of second-strand synthesis takes place within the sequence of the first strand. However, the digestion of the 3' end of the first strand is required and therefore results in the loss of the sequences corresponding to the 5'end of the mRNA. In a second group of methods, initiation of second-strand synthesis takes place outside the sequence of the first strand. This group of methods does not require digestion of the 3' end of the first strand. However, the limitation of this group of method lies upon the elongation. Cloning with T7 DNA polymerase helps overcome this limitation by allowing digestion of the poly(dT) tract during the second-strand synthesis reaction. Therefore, the size of the tract synthesized with terminal transferase is not required to be within a given size range and the resulting clones contain a tract of a limited size. Moreover, due to high 3’ exonuclease activity of T7 DNA polymerase, high yield of the full-length second-strand can be obtained.
When taken up into the human body from the diet, the 20 standard amino acids either are used to synthesize proteins and other biomolecules or are oxidized to urea and carbon dioxide as a source of energy. The oxidation pathway starts with the removal of the amino group by a transaminase; the amino group is then fed into the urea cycle. The other product of transamidation is a keto acid that enters the citric acid cycle. Glucogenic amino acids can also be converted into glucose, through gluconeogenesis. Of the 20 standard amino acids, nine (His, Ile, Leu, Lys, Met, Phe, Thr, Trp and Val) are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food. In addition, cysteine, taurine, tyrosine, and arginine are considered semiessential amino-acids in children (though taurine is not technically an amino acid), because the metabolic pathways that synthesize these amino acids are not fully developed. The amounts required also depend on the age and health of the individual, so it is hard to make general statements about the dietary requirement for some amino acids. Dietary exposure to the non-standard amino acid BMAA has been linked to human neurodegenerative diseases, including ALS.
Glutamine (symbol Gln or Q) is an α-amino acid that is used in the biosynthesis of proteins. Its side chain is similar to that of glutamic acid, except the carboxylic acid group is replaced by an amide. It is classified as a charge-neutral, polar amino acid. It is non-essential and conditionally essential in humans, meaning the body can usually synthesize sufficient amounts of it, but in some instances of stress, the body's demand for glutamine increases, and glutamine must be obtained from the diet. It is encoded by the codons CAA and CAG.
To obtain the desired oligonucleotide, the building blocks are sequentially coupled to the growing oligonucleotide chain in the order required by the sequence of the product (see Synthetic cycle below). The process has been fully automated since the late 1970s. Upon the completion of the chain assembly, the product is released from the solid phase to solution, deprotected, and collected. The occurrence of side reactions sets practical limits for the length of synthetic oligonucleotides (up to about 200 nucleotide residues) because the number of errors accumulates with the length of the oligonucleotide being synthesized. Products are often isolated by high-performance liquid chromatography (HPLC) to obtain the desired oligonucleotides in high purity. Typically, synthetic oligonucleotides are single-stranded DNA or RNA molecules around 15–25 bases in length.
Artificial gene synthesis, sometimes known as DNA printing is a method in synthetic biology that is used to create artificial genes in the laboratory. Based on solid-phase DNA synthesis, it differs from molecular cloning and polymerase chain reaction (PCR) in that it does not have to begin with preexisting DNA sequences. Therefore, it is possible to make a completely synthetic double-stranded DNA molecule with no apparent limits on either nucleotide sequence or size
Cell nuclei contain most of the cell's genetic material, organized as multiple long linear DNA molecules in a complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these chromosomes are the cell's 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, the control center of the cell. The main structures making up the nucleus are the nuclear envelope, a double membrane that encloses the entire organelle and isolates its contents from the cellular cytoplasm, and the nuclear matrix (which includes the nuclear lamina), a network within the nucleus that adds mechanical support, much like the cytoskeleton, which supports the cell as a whole.
In eukaryotes, DNA is organized with the help of histones into compact particles called nucleosomes, where sequences of about 147 DNA base pairs make ~1.65 turns around histone protein octamers. DNA within nucleosomes is inaccessible to many transcription factors. Some transcription factors, so-called pioneering factors are still able to bind their DNA binding sites on the nucleosomal DNA. For most other transcription factors, the nucleosome should be actively unwound by molecular motors such as chromatin remodelers. Alternatively, the nucleosome can be partially unwrapped by thermal fluctuations, allowing temporary access to the transcription factor binding site. In many cases, a transcription factor needs to compete for binding to its DNA binding site with other transcription factors and histones or non-histone chromatin proteins. Pairs of transcription factors and other proteins can play antagonistic roles (activator versus repressor) in the regulation of the same gene.
DNA synthesis is the natural or artificial creation of deoxyribonucleic acid (DNA) molecules. The term DNA synthesis can refer to DNA replication - DNA biosynthesis ("in vivo" DNA amplification), polymerase chain reaction - enzymatic DNA synthesis ("in vitro" DNA amplification) or gene synthesis - physically creating artificial gene sequences.
In nature, DNA molecules are created by all living cells through the process of DNA replication, with replication initiator proteins splitting the cell's DNA and copying each split strand, with the copied strands then joining together with their template strand into a new DNA molecule. Various means exist to artificially stimulate the replication of naturally occurring DNA, or to create artificial gene sequences. The process of DNA replication occurs typically as part of cell division, during interphase.
Various genetic discoveries have been essential in the development of genetic engineering. Genetic inheritance was first discovered by Gregor Mendel in 1865 following experiments crossing peas. Although largely ignored for 34 years he provided the first evidence of hereditary segregation and independent assortment. In 1889 Hugo de Vries came up with the name "(pan)gene" after postulating that particles are responsible for inheritance of characteristics and the term "genetics" was coined by William Bateson in 1905. In 1928 Frederick Griffith proved the existence of a "transforming principle" involved in inheritance, which Avery, MacLeod and McCarty later (1944) identified as DNA. Edward Lawrie Tatum and George Wells Beadle developed the central dogma that genes code for proteins in 1941. The double helix structure of DNA was identified by James Watson and Francis Crick in 1953.As well as discovering how DNA works, tools had to be developed that allowed it to be manipulated. In 1970 Hamilton Smith's lab discovered restriction enzymes that allowed DNA to be cut at specific places and separated out on an electrophoresis gel. This enabled scientists to isolate genes from an organism's genome. DNA ligases, that join broken DNA together, had been discovered earlier in 1967 and by combining the two enzymes it was possible to "cut and paste" DNA sequences to create recombinant DNA. Plasmids, discovered in 1952, became important tools for transferring information between cells and replicating DNA sequences. Frederick Sanger developed a method for sequencing DNA in 1977, greatly increasing the genetic information available to researchers. Polymerase chain reaction (PCR), developed by Kary Mullis in 1983, allowed small sections of DNA to be amplified and aided identification and isolation of genetic material.
The innate immune system relies on germline encoded pattern recognition receptors (PRRs) to recognize distinct pathogen-associated molecular patterns (PAMPs). Upon recognition of a PAMP, PRRs generate signal cascades leading to transcription of genes associated with the immune response. Because all pathogens utilize nucleic acid to propagate, DNA and RNA can be recognized by PRRs to trigger immune activation. In normal cells, DNA is confined to the nucleus or mitochondria. The presence of DNA in the cytosol is indicative of cellular damage or infection and leads to activation of genes associated with the immune response. One way cytosolic DNA is sensed is via the cGAS/STING pathway, specifically by the cyclic-GMP-AMP synthase (cGAS). Upon DNA recognition, cGAS dimerizes and stimulates the formation of cyclic-GMP-AMP (cGAMP). cGAMP then binds directly to stimulator of interferon genes (STING) which triggers phosphorylation/activation of the transcription factor IRF3 via TBK1. IRF3 is able to enter the nucleus to promote transcription of inflammatory genes, such as IFN-β.
To qualify as a metabolite, or to be considered to be part of the metabolome, a small molecule must typically have a molecular weight <1500 Da. This means that molecules such as glycolipids, polysaccharides, short peptides (<14 amino acids) and small oligonucleotides (<5 bases) can be regarded as metabolites or constituents of the metabolome. On the other hand, very large macromolecules such as proteins, messenger RNA, ribosomal RNA, microRNA and DNA are definitely not metabolites and are not considered to be part of the metabolome. The study of the metabolome is called metabolomics.
Fatty acid synthesis is an anabolic process that starts from the conversion of acetyl-CoA to malonyl-CoA by acetyl-CoA carboxylase. Malonyl CoA leads to fatty acid synthesis (FAS) and is involved in the elongation of fatty acids through Fatty acid synthase (FASN). Although aerobic glycolysis is the best documented metabolic phenotype of tumor cells, it is not a universal feature of all human cancers. Amino acids and fatty acids have been shown to function as fuels for tumor cells to proliferate. The carnitine palmitoyltransferase enzymes that regulate the β-oxidation of fatty acids may have a key role in determining some of these phenotypes. Enhanced fatty acid synthesis provides lipids for membrane biogenesis to tumor cells and hence, it gives advantage in both growth and survival of the cell.
Amino acids are organic compounds containing amine (-NH) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid. The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the side chains of certain amino acids. About 500 naturally occurring amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid residues form the second-largest component (water is the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis.
Carbohydrates are a common source of energy in living organisms; however, no single carbohydrate is an essential nutrient in humans. Humans are able to obtain all of their energy requirement from protein and fats, though the potential for some negative health effects of extreme carbohydrate restriction remains, as the issue has not been studied extensively yet. However, in the case of dietary fiber – indigestible carbohydrates which are not a source of energy – inadequate intake can lead to significant increases in mortality.
Polycyclic aromatic hydrocarbons are discussed as possible starting materials for abiotic syntheses of materials required by the earliest forms of life.
A human being can survive an average of three to five days without the intake of water. The issues presented by the need for water dictate that unnecessary water loss by perspiration be avoided in survival situations. The need for water increases with exercise.
Mumps is usually preceded by a set of prodromal symptoms including low-grade fever, headache, and malaise. This is followed by progressive swelling of one or both parotid glands. Parotid gland swelling usually lasts about one week. Other symptoms of mumps can include dry mouth, sore face and/or ears and some patients find it difficult to talk. A vaccine has been available since the 1960s.The mumps virus is an enveloped single-stranded, linear negative-sense RNA virus of the genus "Rubulavirus" and family "Paramyxovirus". The genome consists of 15,384 bases encoding nine proteins. Proteins involved in viral replication are the nucleoprotein, phosphoprotein, and polymerase protein while the genomic RNA forms the ribonucleocapsid. Humans are the only natural host for the virus.
Ġ is used in some Arabic transliteration schemes, such as DIN 31635 and ISO 233, to represent the letter (ġain).
The functional form of single-stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure like hairpin loops, bulges, and internal loops. Since RNA is charged, metal ions such as Mg are needed to stabilise many secondary and tertiary structures.
The enzyme belongs to the group of oxidoreductases according to the EC classification and is dependent on FAD as cofactor, thus it was classified as an external flavoprotein monooxygenase (designated as type E). It forms a two-component system with a reductase (StyB, StyA2B). The reductase utilizes solely NADH to reduce the FAD, which is then transferred to the styrene monooxygenase (StyA, StyA1). Two types of that enzyme are described so far: StyA/StyB (designated E1), first described from "Pseudomonas" species, and StyA1/StyA2B (designated E2), first described from Actinobacteria. The E1-type is more abundant in nature and comprises a single monooxygenase (StyA) supported by a single reductase (StyB), whereas the E2-type has a major monooxygenase (StyA1) which is supported by fusion protein of a monooxygenase and reductase (StyA2B). The latter one is the source of reduced FAD for the monooxygenase subunits and has some side activity as a monooxygenase. So far all styrene monooxygenases perform enantioselective epoxidations of styrene and chemically analogous compounds, which makes them interesting for biotechnological applications.
On January 20, Lt. General Katawal, Royal Nepalese Army (RNA) Chief of General Staff, told Ambassador James F. Moriarty that he was worried that the government did not have a unified strategy for tackling the Maoist insurgency. Katawal reiterated that there was no purely military solution to the insurgency; the RNA could only work to create space for a negotiated political solution. He noted that the civilian government should lead the effort to inform its citizens about Nepal's overall plan to tackle the insurgency. Katawal stressed that a civilian government needed to explain to the people what the military was doing and why, especially why the government needed to restrict civil liberties.