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Bacteroid-trp RNA Motif
The Bacteroid-''trp'' RNA motif is a conserved RNA element detected by bioinformatics. It is found in the phylum Bacteroidota in the apparent 5' untranslated regions of genes that encode enzymes used in the synthesis of the amino acid tryptophan. A short open reading frame is found within the motif that encodes at least two tryptophan codons. Similar motifs have been identified regulating tryptophan genes in Pseudomonadota (see ''trp'' operon), but not in Bacteroidota. However, the Bacteroid-''trp'' RNA motif likely operates via the same mechanism of attenuation In physics, attenuation (in some contexts, extinction) is the gradual loss of flux intensity through a Transmission medium, medium. For instance, dark glasses attenuate sunlight, lead attenuates X-rays, and water and air attenuate both light and .... References External links * Cis-regulatory RNA elements {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Secondary Structure
Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein protein folding, folds into its three dimensional protein tertiary structure, tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the Amine, amino hydrogen and carboxyl oxygen atoms in the peptide backbone chain, backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone Dihedral angle#Dihedral angles of proteins, dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. The concept of secondary structure was first introduced by Kaj Ulrik ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacteroidota
The phylum (biology), phylum Bacteroidota (synonym Bacteroidetes) is composed of three large classes of Gram-negative bacteria, Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and sea water, as well as in the guts and on the skin of animals. Although some ''Bacteroides'' spp. can be Opportunistic Pathogens, opportunistic pathogens, many ''Bacteroidota'' are Symbiotic bacteria, symbiotic species highly adjusted to the gastrointestinal tract. ''Bacteroides'' are highly abundant in intestines, reaching up to 1011 cells g−1 of intestinal material. They perform metabolic conversions that are essential for the host, such as degradation of proteins or complex sugar polymers. ''Bacteroidota'' colonize the gastrointestinal tract already in infants, as non-digestible Human milk oligosaccharide, oligosaccharides in mother milk support the growth of both ''Bacteroides'' and ''Bifidoba ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylum
In biology, a phylum (; : phyla) is a level of classification, or taxonomic rank, that is below Kingdom (biology), kingdom and above Class (biology), class. Traditionally, in botany the term division (taxonomy), division has been used instead of phylum, although the International Code of Nomenclature for algae, fungi, and plants accepts the terms as equivalent. Depending on definitions, the animal kingdom Animalia contains about 31 phyla, the plant kingdom Plantae contains about 14 phyla, and the fungus kingdom Fungi contains about eight phyla. Current research in phylogenetics is uncovering the relationships among phyla within larger clades like Ecdysozoa and Embryophyta. General description The term phylum was coined in 1866 by Ernst Haeckel from the Greek (, "race, stock"), related to (, "tribe, clan"). Haeckel noted that species constantly evolved into new species that seemed to retain few consistent features among themselves and therefore few features that distinguishe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
5' Untranslated Region
The 5′ untranslated region (also known as 5′ UTR, leader sequence, transcript leader, or leader RNA) is the region of a messenger RNA (mRNA) that is directly upstream from the initiation codon. This region is important for the regulation of translation of a transcript by differing mechanisms in viruses, prokaryotes and eukaryotes. Despite its name, the 5′ UTR, or a portion of it is sometimes translated into a protein product. This product may involve in regulation of transcription, and translation of the main coding sequence of the mRNA, such as the sex-lethal gene in ''Drosophila''. Regulatory elements within 5′ UTRs have also been linked to mRNA export. In many organisms, however, the 5′ UTR is completely untranslated, instead forming a complex secondary structure to regulate translation. General structure Length The 5′ UTR begins at the transcription start site and ends one nucleotide (nt) before the initiation sequence (usually AUG) of the coding region. In pr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and non-coding genes. During gene expression (the synthesis of Gene product, RNA or protein from a gene), DNA is first transcription (biology), copied into RNA. RNA can be non-coding RNA, directly functional or be the intermediate protein biosynthesis, template for the synthesis of a protein. The transmission of genes to an organism's offspring, is the basis of the inheritance of phenotypic traits from one generation to the next. These genes make up different DNA sequences, together called a genotype, that is specific to every given individual, within the gene pool of the population (biology), population of a given species. The genotype, along with environmental and developmental factors, ultimately determines the phenotype ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amino Acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 appear in the genetic code of life. Amino acids can be classified according to the locations of the core structural functional groups ( alpha- , beta- , gamma- amino acids, etc.); other categories relate to polarity, ionization, and side-chain group type ( aliphatic, acyclic, aromatic, polar, etc.). In the form of proteins, amino-acid '' residues'' form the second-largest component (water being 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. It is thought that they played a key role in enabling life on Earth and its emergence. Amino acids are formally named by the IUPAC- IUBMB Joint Commi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tryptophan
Tryptophan (symbol Trp or W) is an α-amino acid that is used in the biosynthesis of proteins. Tryptophan contains an α-amino group, an α-carboxylic acid group, and a side chain indole, making it a polar molecule with a non-polar aromatic beta carbon substituent. Tryptophan is also a precursor to the neurotransmitter serotonin, the hormone melatonin, and vitamin B3 (niacin). It is encoded by the codon UGG. Like other amino acids, tryptophan is a zwitterion at physiological pH where the amino group is protonated (–; pKa = 9.39) and the carboxylic acid is deprotonated ( –COO−; pKa = 2.38). Humans and many animals cannot synthesize tryptophan: they need to obtain it through their diet, making it an essential amino acid. Tryptophan is named after the digestive enzymes trypsin, which were used in its first isolation from casein proteins. It was assigned the one-letter symbol W based on the double ring being visually suggestive to the bulky letter. Function ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Reading Frame
In molecular biology, reading frames are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible reading frames will be "open" (the "reading", however, refers to the RNA produced by transcription of the DNA and its subsequent interaction with the ribosome in translation). Such an open reading frame (ORF) may contain a start codon (usually AUG in terms of RNA) and by definition cannot extend beyond a stop codon (usually UAA, UAG or UGA in RNA). That start codon (not necessarily the first) indicates where translation may start. The transcription termination site is located after the ORF, beyond the translation stop codon. If transcription were to cease before the stop codon, an incomplete protein would be made during translation. In eukaryotic genes with multiple exons, introns are removed and exons are then joined together after transcription to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Codon
Genetic code is a set of rules used by living cells to translate information encoded within genetic material (DNA or RNA sequences of nucleotide triplets or codons) into proteins. Translation is accomplished by the ribosome, which links proteinogenic amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries. The codons specify which amino acid will be added next during protein biosynthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme (see the RNA codon table). That scheme is often called the canonical or standard genetic code, or simply ''the'' genetic code, though variant codes (such as in mitochondria) exist. History Efforts to understan ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pseudomonadota
Pseudomonadota (synonym "Proteobacteria") is a major phylum of gram-negative bacteria. Currently, they are considered the predominant phylum within the domain of bacteria. They are naturally found as pathogenic and free-living (non- parasitic) genera. The phylum comprises six classes ''Acidithiobacillia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia'', and '' Zetaproteobacteria.'' The Pseudomonadota are widely diverse, with differences in morphology, metabolic processes, relevance to humans, and ecological influence. Classification American microbiologist Carl Woese established this grouping in 1987, calling it informally the "purple bacteria and their relatives". The group was later formally named the 'Proteobacteria' after the Greek god Proteus, who was known to assume many forms. In 2021 the International Committee on Systematics of Prokaryotes designated the synonym Pseudomonadota, and renamed many other prokaryotic phyla as well. Th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Trp Operon
The ''trp'' operon is a group of genes that are transcribed together, encoding the enzymes that produce the amino acid tryptophan in bacteria. The ''trp'' operon was first characterized in ''Escherichia coli,'' and it has since been discovered in many other bacteria. The operon is regulated so that, when tryptophan is present in the environment, the genes for tryptophan synthesis are repressed. The ''trp'' operon contains five structural genes: ''trpE'', ''trpD'', ''trpC'', ''trpB'', and ''trpA'', which encode the enzymes needed to synthesize tryptophan. It also contains a repressive regulator gene called ''trpR''. When tryptophan is present, the trpR protein binds to the Operator (biology), operator, blocking transcription of the ''trp'' operon by RNA polymerase. This operon is an example of Operon#Regulation, repressible negative regulation of gene expression. The repressor protein binds to the operator (biology), operator in the presence of tryptophan (repressing Transcript ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
