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.
Pyrophosphate
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In chemistry, a pyrophosphate is a phosphorus oxyanion. Compounds such as salts and esters are called pyrophosphates. The group is also called diphosphate or dipolyphosphate, although this should not be confused with phosphates, as a food additive, diphosphates are known as E450. A number of hydrogen pyrophosphates also exist, such as Na2H2P2O7, pyrophosphates were originally prepared by heating phosphates. They generally exhibit the highest solubilities among the phosphates, moreover, pyrophosphate is the first member of an entire series of polyphosphates. The term pyrophosphate is also the name of esters formed by the condensation of a phosphorylated biological compound with inorganic phosphate and this bond is also referred to as a high-energy phosphate bond. The synthesis of tetraethyl pyrophosphate was first described in 1854 by Philippe de Clermont at a meeting of the French Academy of Sciences, pyrophosphates are very important in biochemistry. The anion P2O74− is abbreviated PPi and is formed by the hydrolysis of ATP into AMP in cells, ATP → AMP + PPi For example, when a nucleotide is incorporated into a growing DNA or RNA strand by a polymerase, pyrophosphate is released. The pyrophosphate anion has the structure P2O74−, and is an anhydride of phosphate. This hydrolysis to inorganic phosphate effectively renders the cleavage of ATP to AMP and PPi irreversible, PPi occurs in synovial fluid, blood plasma, and urine at levels sufficient to block calcification and may be a natural inhibitor of hydroxyapatite formation in extracellular fluid. Cells may channel intracellular PPi into ECF, ANK is a nonenzymatic plasma-membrane PPi channel that supports extracellular PPi levels. Defective function of the membrane PPi channel ANK is associated with low extracellular PPi, ectonucleotide pyrophosphatase/phosphodiesterase may function to raise extracellular PPi. AMP + ATP →2 ADP2 ADP +2 Pi →2 ATP The plasma concentration of inorganic pyrophosphate has a range of 0. 58-3.78 µM. Various diphosphates are used as emulsifiers, stabilisers, acidity regulators, raising agents, sequestrants, schröder HC, Kurz L, Muller WE, Lorenz B. Pyrophosphates at the US National Library of Medicine Medical Subject Headings
3.
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
4.
Capping enzyme
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The addition of the cap occurs co-transcriptionally, after the growing RNA molecule contains as little as 25 nucleotides. The enzymatic reaction is catalyzed specifically by the phosphorylated carboxyl-terminal domain of RNA polymerase II, the 5 cap is therefore specific to RNAs synthesized by this polymerase rather than those synthesized by RNA polymerase I or RNA polymerase III. Three enzymes, RNA triphosphatase, guanylyltransferase, and methyltransferase are involved in the addition of the methylated 5 cap to the mRNA, capping is a three-step process that utilizes the enzymes RNA triphosphatase, guanylyltransferase, and methyltransferase. Through a series of three steps, the cap is added to the first nucleotides 5 hydroxyl group of the growing mRNA strand while transcription is still occurring, first, RNA5 triphosphatase hydrolyzes the 5 triphosphate group to make diphospate-RNA. Then, the addition of GMP by guanylyltransferase produces the guanosine cap, last, RNA methyltransferase transfers a methyl group to the guanosine cap to yield 7-methylguanosine cap that is attached to the 5 end of the transcript. When this complex of RNA polymerase II and the enzymes is achieved. 5 capping is essential for mRNA stability, enhancing mRNA processing, mRNA export, after successful capping, an additional phosphorylation event initiates the recruitment of machinery necessary for RNA splicing, a process by which introns are removed to produce a mature mRNA. The function of the 5 cap is essential to the expression of the RNA. The capping enzyme is part of the covalent nucleotidyl transferases superfamily, the NTase domain, conserved in capping enzymes, DNA and RNA ligases, is made up 5 motifs, I, III, IIIa, IV and V. Motif I or KxDG is the site where the covalent -N-GMP intermediate is formed. Both the NTase and OB domains undergo conformational changes that assist in the capping reaction, capping enzymes are found in the nucleus of eukaryotic cells. Depending on the organism, the enzyme is either a monofunctional or bifunctional polypeptide. The guanylyltransferases of Saccharomyces cerevisiae is encoded by the CEG1 gene and is composed of 459 amino acids, the RNA triphosphatase is a separate 549 amino acid polypeptide, encoded by the CET1 gene. The human capping enzyme is an example of a bifunctional polypeptide, the enzyme structure has three sub-domains referred to hinge, base and lid. The GTP binding site is located between the hinge and base domain, the lid domain determines the conformation of the active site cleft, which consists of the GTP binding site, phosphoamide linking lysine and surrounding residues. The guanylyltransferase domain is linked to the triphosphatase domain via a 25 amino acid flexible loop structure, splicing is dependent on the presence of the 7-methylguanosine cap. A defect in splicing can occur as a result of mutation in the guanylytransferase, however the severity of the effect is dependent on the guanlyltransferase mutation. Furthermore, the guanylyltransferase relieves transcriptional repression mediated by NELF, NELF together with DSIF prevents transcription elongation
5.
Five-prime cap
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In molecular biology, the five-prime cap is a specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA. This process, known as mRNA capping, is regulated and vital in the creation of stable. Mitochondrial and chloroplast mRNA are not capped, in eukaryotes, the 5′ cap, found on the 5′ end of an mRNA molecule, consists of a guanine nucleotide connected to mRNA via an unusual 5′ to 5′ triphosphate linkage. This guanosine is methylated on the 7 position directly after capping in vivo by a methyltransferase and it is referred to as a 7-methylguanylate cap, abbreviated m7G. In multicellular eukaryotes and some viruses, further modifications exist, including the methylation of the 2′ hydroxy-groups of the first 2 ribose sugars of the 5′ end of the mRNA. Cap-1 has a methylated 2-hydroxy group on the first ribose sugar, the 5′ cap is chemically similar to the 3′ end of an RNA molecule. This provides significant resistance to 5′ exonucleases, small nuclear RNAs contain unique 5-caps. Sm-class snRNAs are found with 5-trimethylguanosine caps, while Lsm-class snRNAs are found with 5-monomethylphosphate caps, in bacteria, and potentially also in higher organisms, some RNAs are capped with NAD+, NADH, or 3-dephospho-coenzyme A. In all organisms, mRNA molecules can be decapped in a known as messenger RNA decapping. The starting point for capping with 7-methylguanylate is the unaltered 5′ end of an RNA molecule and this features a final nucleotide followed by three phosphate groups attached to the 5′ carbon. The capping process is initiated before the completion of transcription, as the nascent pre-mRNA is being synthesized, the mechanism of capping with NAD+, NADH, or 3-dephospho-coenzyme A is different. Both bacterial RNA polymerase and eukaryotic RNA polymerase II are able to carry out this ab initio capping mechanism, for capping with 7-methylguanylate, the capping enzyme complex binds to RNA polymerase II before transcription starts. As soon as the 5′ end of the new transcript emerges from RNA polymerase II, the enzymes for capping can only bind to RNA polymerase II, ensuring specificity to only these transcripts, which are almost entirely mRNA. Capping with NAD+, NADH, or 3-dephospho-coenzyme A is targeted by promoter sequence, the 5′ cap has four main functions, Regulation of nuclear export, Prevention of degradation by exonucleases, Promotion of translation, Promotion of 5′ proximal intron excision. Nuclear export of RNA is regulated by the cap binding complex, the CBC is then recognized by the nuclear pore complex and exported. Once in the cytoplasm after the round of translation, the CBC is replaced by the translation factors eIF4E. This complex is recognized by other translation initiation machinery including the ribosome. Capping with 7-methylguanylate prevents 5′ degradation in two ways, first, degradation of the mRNA by 5′ exonucleases is prevented by functionally looking like a 3′ end
6.
Messenger RNA
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Messenger RNA is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. As in DNA, mRNA genetic information is in the sequence of nucleotides, each codon encodes for a specific amino acid, except the stop codons, which terminate protein synthesis. It should not be confused with mitochondrial DNA, the brief existence of an mRNA molecule begins with transcription, and ultimately ends in degradation. During its life, a molecule may also be processed, edited. Eukaryotic mRNA molecules often require extensive processing and transport, while prokaryotic mRNA molecules do not, a molecule of eukaryotic mRNA and the proteins surrounding it are together called a messenger RNP. Transcription is when RNA is made from DNA, during transcription, RNA polymerase makes a copy of a gene from the DNA to mRNA as needed. This process is similar in eukaryotes and prokaryotes, the short-lived, unprocessed or partially processed product is termed precursor mRNA, or pre-mRNA, once completely processed, it is termed mature mRNA. Processing of mRNA differs greatly among eukaryotes, bacteria, and archea, non-eukaryotic mRNA is, in essence, mature upon transcription and requires no processing, except in rare cases. Eukaryotic pre-mRNA, however, requires extensive processing, a 5 cap is a modified guanine nucleotide that has been added to the front or 5 end of a eukaryotic messenger RNA shortly after the start of transcription. The 5 cap consists of a terminal 7-methylguanosine residue that is linked through a 5-5-triphosphate bond to the first transcribed nucleotide and its presence is critical for recognition by the ribosome and protection from RNases. Cap addition is coupled to transcription, and occurs co-transcriptionally, such that each influences the other, shortly after the start of transcription, the 5 end of the mRNA being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase. This enzymatic complex catalyzes the reactions that are required for mRNA capping. Synthesis proceeds as a biochemical reaction. In some instances, an mRNA will be edited, changing the composition of that mRNA. An example in humans is the apolipoprotein B mRNA, which is edited in some tissues, the editing creates an early stop codon, which, upon translation, produces a shorter protein. Polyadenylation is the covalent linkage of a moiety to a messenger RNA molecule. In eukaryotic organisms most messenger RNA molecules are polyadenylated at the 3 end, the poly tail and the protein bound to it aid in protecting mRNA from degradation by exonucleases. Polyadenylation is also important for transcription termination, export of the mRNA from the nucleus, MRNA can also be polyadenylated in prokaryotic organisms, where poly tails act to facilitate, rather than impede, exonucleolytic degradation
7.
Directionality (molecular biology)
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Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. In a DNA double helix, the run in opposite directions to permit base pairing between them, which is essential for replication or transcription of the encoded information. The relative positions of structures along a strand of nucleic acid, including genes, directionality is related to, but independent from sense. The other strand is not copied directly, but necessarily its sequence will be similar to that of the RNA, transcription initiation sites generally occur on both strands of an organisms DNA, and specify the location, direction, and circumstances under which transcription will occur. For example, in a typical gene a start codon is a DNA sequence within the sense strand, transcription begins at an upstream site, and as it proceeds through the region it copies the 3′-TAC-5′ from the template strand to produce 5′-AUG-3′ within a messenger RNA. The mRNA is scanned by the ribosome from the 5′ end, by convention, single strands of DNA and RNA sequences are written in a 5′-to-3′ direction except as needed to illustrate the pattern of base pairing. The 5′-end designates the end of the DNA or RNA strand that has the carbon in the sugar-ring of the deoxyribose or ribose at its terminus. A phosphate group attached to the 5′-end permits ligation of two nucleotides, i. e. the covalent binding of a 5′-phosphate to the 3′-hydroxyl group of another nucleotide, removal of the 5′-phosphate prevents ligation. To prevent unwanted nucleic acid ligation, molecular biologists commonly remove the 5′-phosphate with a phosphatase, the 5′-end of nascent messenger RNA is the site at which post-transcriptional capping occurs, a process which is vital to producing mature messenger RNA. Capping increases the stability of the messenger RNA while it undergoes translation and it consists of a methylated nucleotide attached to the messenger RNA in a rare 5′- to 5′-triphosphate linkage. The 5′-flanking region of a gene often denotes a region of DNA which is not transcribed into RNA, the 5′-flanking region contains the gene promoter, and may also contain enhancers or other protein binding sites. The 5′-untranslated region is a region of a gene which is transcribed into mRNA and this region of an mRNA may or may not be translated, but is usually involved in the regulation of translation. The 5′-untranslated region is the portion of the DNA starting from the cap site and this region may have sequences, such as the ribosome binding site and Kozak sequence, which determine the translation efficiency of the mRNA, or which may affect the stability of the mRNA. The 3′-end of a strand is so named due to it terminating at the group of the third carbon in the sugar-ring. The 3′-hydroxyl is necessary in the synthesis of new nucleic acid molecules as it is ligated to the 5′-phosphate of a separate nucleotide, molecular biologists can use nucleotides that lack a 3′-hydroxyl to interrupt the replication of DNA. This technique is known as the dideoxy chain-termination termination method or the Sanger method, the 3′-end of nascent messenger RNA is the site of post-transcriptional polyadenylation, which attaches a chain of 50 to 250 adenosine residues to produce mature messenger RNA. This chain helps in determining how long the messenger RNA lasts in the cell, the 3′-flanking region is a region of DNA that is not copied into the mature mRNA, but which is present adjacent to 3′-end of the gene. The 3′-flanking region often contains sequences that affect the formation of the 3′-end of the message and it may also contain enhancers or other sites to which proteins may bind
8.
RNA
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Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids, and, along with proteins and carbohydrates, like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey 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 processes is protein synthesis, a universal function where RNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA molecules to deliver amino acids to the ribosome, analysis of these RNAs has revealed that they are highly structured. Unlike DNA, their structures do not consist of long double helices, in this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the enzyme that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA. Each nucleotide in RNA contains a sugar, with carbons numbered 1 through 5. A base is attached to the 1 position, in general, adenine, cytosine, guanine, adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3 position of one ribose, the phosphate groups have a negative charge each, making RNA a charged molecule. 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 feature of RNA that distinguishes it from DNA is the presence of a group at the 2 position of the ribose sugar. The A-form geometry results in a deep and narrow major groove. RNA is transcribed with only four bases, but these bases, pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and 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. The specific roles of many of these modifications in RNA are not fully understood, 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 and this leads to several recognizable domains of secondary structure like hairpin loops, bulges, and internal loops
