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Proteolytic
Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Protein degradation is a major regulatory mechanism of gene expression and contributes substantially to shaping mammalian proteomes. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteases, but may also occur by intra-molecular digestion. Proteolysis in organisms serves many purposes; for example, digestive enzymes break down proteins in food to provide amino acids for the organism, while proteolytic processing of a polypeptide chain after its synthesis may be necessary for the production of an active protein. It is also important in the regulation of some physiological and cellular processes including apoptosis, as well as preventing the accumulation of unwanted or misfolded proteins in cells. Consequently, abnormality in the regulation of proteolysis can cause diseases. Proteolysis can al ...
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Protease
A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalysis, catalyzes proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products. They do this by cleaving the peptide bonds within proteins by hydrolysis, a reaction where water breaks Covalent bond, bonds. Proteases are involved in numerous biological pathways, including Digestion#Protein digestion, digestion of ingested proteins, protein catabolism (breakdown of old proteins), and cell signaling. In the absence of functional accelerants, proteolysis would be very slow, taking hundreds of years. Proteases can be found in all forms of life and viruses. They have independently convergent evolution, evolved multiple times, and different classes of protease can perform the same reaction by completely different catalytic mechanisms. Classification Based on catalytic residue Proteases can be classified into seven broad ...
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Apoptosis
Apoptosis (from ) is a form of programmed cell death that occurs in multicellular organisms and in some eukaryotic, single-celled microorganisms such as yeast. Biochemistry, Biochemical events lead to characteristic cell changes (Morphology (biology), morphology) and death. These changes include Bleb (cell biology), blebbing, Plasmolysis, cell shrinkage, Karyorrhexis, nuclear fragmentation, Pyknosis, chromatin condensation, Apoptotic DNA fragmentation, DNA fragmentation, and mRNA decay. The average adult human loses 50 to 70 1,000,000,000, billion cells each day due to apoptosis. For the average human child between 8 and 14 years old, each day the approximate loss is 20 to 30 billion cells. In contrast to necrosis, which is a form of traumatic cell death that results from acute cellular injury, apoptosis is a highly regulated and controlled process that confers advantages during an organism's life cycle. For example, the separation of fingers and toes in a developing human embryo ...
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Nidovirales
''Nidovirales'' is an order of Viral envelope, enveloped, positive-strand RNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, Mollusca, molluscs, and helminths. The order includes the families ''Coronaviridae'', ''Arteriviridae, Roniviridae,'' ''Tobaniviridae'', and ''Mesoniviridae''. Member viruses have a viral envelope and a Sense (molecular biology), positive-sense, single-stranded RNA, RNA genome which is Five-prime cap, capped and Polyadenylation, polyadenylated. Nidoviruses are named for the Latin ''nidus'', meaning nest, as all viruses in this order produce a 3' co-terminal nested set of subgenomic mRNAs during infection. Virology Structure Nidoviruses have a viral envelope and a positive-sense, single-stranded RNA genome which is capped and polyadenylated. The group expresses structural proteins separately from the nonstructural ones. The structural proteins are encoded at the 3' reg ...
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ORF1ab
ORF1ab (also ORF1a/b) refers collectively to two open reading frames (ORFs), ORF1a and ORF1b, that are conserved in the genomes of nidoviruses, a group of viruses that includes coronaviruses. The genes express large polyproteins that undergo proteolysis to form several nonstructural proteins with various functions in the viral life cycle, including proteases and the components of the replicase-transcriptase complex (RTC). Together the two ORFs are sometimes referred to as the replicase gene. They are related by a programmed ribosomal frameshift that allows the ribosome to continue translating past the stop codon at the end of ORF1a, in a -1 reading frame. The resulting polyproteins are known as pp1a and pp1ab. Expression ORF1a is the first open reading frame at the 5' end of the genome. Together ORF1ab occupies about two thirds of the genome, with the remaining third at the 3' end encoding the structural proteins and accessory proteins. It is translated from a 5' capped ...
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Retrovirus
A retrovirus is a type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. After invading a host cell's cytoplasm, the virus uses its own reverse transcriptase enzyme to produce DNA from its RNA genome, the reverse of the usual pattern, thus ''retro'' (backward). The new DNA is then retroviral integration, incorporated into the host cell genome by an integrase enzyme, at which point the retroviral DNA is referred to as a provirus. The host cell then treats the viral DNA as part of its own genome, transcribing and translating the viral genes along with the cell's own genes, producing the proteins required to assemble new copies of the virus. Many retroviruses cause serious diseases in humans, other mammals, and birds. Retroviruses have many subfamilies in three basic groups. * Oncovirus, Oncoretroviruses (cancer-causing retroviruses) include human T-lymphotropic virus (HTLV) causing a type of leuk ...
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Virus (biology)
A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, more than 16,000 of the millions of List of virus species, virus species have been described in detail. The study of viruses is known as virology, a subspeciality of microbiology. When infected, a host cell is often forced to rapidly produce thousands of copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent viral particles, or ''virions'', consisting of (i) genetic material, i.e., long ...
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Digestive Enzymes
Digestive enzymes take part in the chemical process of digestion, which follows the mechanical process of digestion. Food consists of macromolecules of proteins, carbohydrates, and fats that need to be broken down chemically by digestive enzymes in the mouth, stomach, pancreas, and duodenum, before being able to be absorbed into the bloodstream. Initial breakdown is achieved by chewing (mastication) and the use of digestive enzymes of saliva. Once in the stomach further mechanical churning takes place mixing the food with secreted gastric acid. Digestive gastric enzymes take part in some of the chemical process needed for absorption. Most of the enzymatic activity, and hence absorption takes place in the duodenum. Digestive enzymes are found in the digestive tracts of animals (including humans) and in the tracts of carnivorous plants, where they aid in the digestion of food, as well as inside cells, especially in their lysosomes, where they function to maintain cellular surv ...
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Pro-opiomelanocortin
Pro-opiomelanocortin (POMC) is a precursor polypeptide with 241 amino acid residues. POMC is Protein biosynthesis, synthesized in Corticotropic cell, corticotrophs of the anterior pituitary from the 267-amino-acid-long Precursor polypeptide, polypeptide precursor pre-pro-opiomelanocortin (pre-POMC), by the removal of a 26-amino-acid-long signal peptide sequence during translation (biology), translation. POMC is part of the central melanocortin system. Function POMC is cut (cleaved) to give rise to multiple peptide hormones. Each of these peptides is packaged in large dense-core vesicle (biology), vesicles that are released from the cells by exocytosis in response to appropriate stimulation: * Melanocyte-stimulating hormone, α-MSH produced by neurons in the ventromedial nucleus has important roles in the regulation of appetite (POMC neuron stimulation results in Hunger (motivational state), satiety.) and Human sexual activity, sexual behavior, while α-MSH secreted from the pa ...
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Signal Peptide
A signal peptide (sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short peptide (usually 16–30 amino acids long) present at the N-terminus (or occasionally nonclassically at the C-terminus or internally) of most newly synthesized proteins that are destined toward the secretory pathway. These proteins include those that reside either inside certain organelles (the endoplasmic reticulum, Golgi or endosomes), secreted from the cell, or inserted into most cellular membranes. Although most type I membrane-bound proteins have signal peptides, most type II and multi-spanning membrane-bound proteins are targeted to the secretory pathway by their first transmembrane domain, which biochemically resembles a signal sequence except that it is not cleaved. They are a kind of target peptide. Function (translocation) Signal peptides function to prompt a cell to transloc ...
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Group-specific Antigen
Group-specific antigen, or gag, is the polyprotein that contains the core structural proteins of an Ortervirus (except ''Caulimoviridae''). It was named as such because scientists used to believe it was antigenic. Now it is known that it makes up the inner shell, not the envelope exposed outside. It makes up all the structural units of viral conformation and provides supportive framework for mature virion. All orthoretroviral ''gag'' proteins are processed by the protease (PR or ''pro'') into MA (matrix), CA (capsid), NC (nucleocapsid) parts, and sometimes more. If Gag fails to cleave into its subunits, virion fails to mature and remains uninfective. It comprises part of the ''gag-onc'' fusion protein. Gag in HIV Numbering system By convention, the HIV genome is numbered according to HIV-1 group M subtype B reference strain HXB2. Transcription and mRNA processing After a virus enters a target cell, the viral genome is integrated into the host cell chromatin. RNA polym ...
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Polycistronic
A cistron is a region of DNA that is conceptually equivalent to some definitions of a gene, such that the terms are synonymous from certain viewpoints, especially with regard to the molecular gene as contrasted with the Mendelian gene. The question of which scope of a subset of DNA (that is, how large a segment of DNA) constitutes a unit of selection is the question that governs whether cistrons are the same thing as genes. The word ''cistron'' is used to emphasize that molecular genes exhibit a specific behavior in a complementation test (cis-trans test); distinct positions (or loci) within a genome are cistronic. History The words ''cistron'' and ''gene'' were coined before the advancing state of biology made it clear to many people that the concepts they refer to, at least in some senses of the word ''gene'', are either equivalent or nearly so. The same historical naming practices are responsible for many of the synonyms in the life sciences. The term ''cistron'' was coi ...
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