query: enzymes are usually composed of which type of molecule

pos: Enzyme their amino acid sequences and unusual 'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules. The latter are called ribozymes. Enzymes' specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the reaction rate 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 otherwise take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst

pos: Human nutrition food through the intestines. Additionally, fiber, perhaps especially that from whole grains, may help lessen insulin spikes and reduce the risk of type 2 diabetes. Proteins are the basis of many animal body structures (e.g. muscles, skin, and hair) and form the enzymes which catalyse chemical reactions throughout the body. Each protein molecule is composed of amino acids which contain nitrogen and sometimes sulphur (these components are responsible for the distinctive smell of burning protein, such as the keratin in hair). The body requires amino acids to produce new proteins (protein retention) and to replace damaged proteins (maintenance). Amino acids

pos: Chlorophyll a each type of chlorophyll molecule, and alters the absorption spectrum of light. Chlorophyll "a" has a long hydrophobic tail, which anchors the molecule to other hydrophobic proteins in the thylakoid membrane of the chloroplast. Once detached from the porphyrin ring, this long hydrocarbon tail becomes the precursor of two biomarkers, pristane and phytane, which are important in the study of geochemistry and the determination of petroleum sources. Chlorophyll "a" biosynthetic pathway utilizes a variety of enzymes. Genes code for the enzymes on the Mg-tetrapyrroles of both bacteriochlorophyll "a" and chlorophyll "a". It begins with glutamic acid, which is transformed into

pos: Regulatory enzyme molecule and its form changes. When this happens, the aconitase is converted to IRPF1, a translation repressor or mRNA stabilizer that represses the formation of iron-binding proteins and favours formation of proteins that can get iron from the cell's reservations Here, the active and inactive form of the enzymes are altered due to covalent modification of their structures which is catalysed by other enzymes. This type of regulation consists of the addition or elimination of some molecules which can be attached to the enzyme protein. The most important groups that work as modifiers are phosphate, methyl, uridine, adenine and adenosine

pos: Enzyme catalysis; instead, the enzyme contains sites to bind and orient catalytic cofactors. Enzyme structures may also contain allosteric sites where the binding of a small molecule causes a conformational change that increases or decreases activity. A small number of RNA-based biological catalysts called ribozymes exist, which again can act alone or in complex with proteins. The most common of these is the ribosome which is a complex of protein and catalytic RNA components. Enzymes must bind their substrates before they can catalyse any chemical reaction. Enzymes are usually very specific as to what substrates they bind and then the chemical

pos: Transfer RNA a covalent attachment to the amino acid that corresponds to the anticodon sequence. Each type of tRNA molecule can be attached to only one type of amino acid, so each organism has many types of tRNA. Because the genetic code contains multiple codons that specify the same amino acid, there are several tRNA molecules bearing different anticodons which carry the same amino acid. The covalent attachment to the tRNA 3’ end is catalyzed by enzymes called aminoacyl tRNA synthetases. During protein synthesis, tRNAs with attached amino acids are delivered to the ribosome by proteins called elongation factors, which aid in

pos: Animal nutrition incompletely absorbed in some animals. Proteins are the basis of many animal body structures (e.g. muscles, skin, and hair). They also form the enzymes which control chemical reactions throughout the body. Each molecule is composed of amino acids which are characterized by the inclusion of nitrogen and sometimes sulfur. The body requires amino acids to produce new proteins (protein retention) and to replace damaged proteins (maintenance). As there is no protein or amino acid storage provision, amino acids must be present in the diet. Excess amino acids are discarded, typically in the urine. For all animals, some amino acids are

pos: Environmental effects of laundry wastewater compounds are usually sodium perborate and sodium percarbonate. Enzymes and fluorescent whitening agents are added into detergents as auxiliary agents. Surfactants own both hydrophilic and lipophilic properties in one molecule, so they are called surface active agents, and are widely used in various washing process. With the lipophilic tails, surfactants are biologically active. Anionic surfactants have the ability of binding to bioactive macromolecules like enzymes, DNA, peptides, causing changes of surface charge and the folding of polypeptide chain(structure of protein). The function of proteins will be different. Cationic surfactant can bind to the inner membrane of bacteria, and by this

pos: Nutrition much of the animal body (e.g. muscles, skin, and hair). They also form the enzymes that control chemical reactions throughout the body. Each protein molecule is composed of amino acids, which are characterized by inclusion of nitrogen and sometimes sulphur (these components are responsible for the distinctive smell of burning protein, such as the keratin in hair). The body requires amino acids to produce new proteins (protein retention) and to replace damaged proteins (maintenance). As there is no protein or amino acid storage provision, amino acids must be present in the diet. Excess amino acids are discarded, typically in the

pos: Transaminase Transaminase Transaminases or aminotransferases are enzymes that catalyze a transamination reaction between an amino acid and an α-keto acid. They are important in the synthesis of amino acids, which form proteins. An amino acid contains an amine (NH) group. A keto acid contains a keto (=O) group. In transamination, the NH group on one molecule is exchanged with the =O group on the other molecule. The amino acid becomes a keto acid, and the keto acid becomes an amino acid. Most transaminases are protein enzymes. However, some transamination activities of the ribosome have been found to be catalyzed by ribozymes

pos: Oxidoreductase O is the acceptor. Oxidoreductases are classified as EC 1 in the EC number classification of enzymes. Oxidoreductases can be further classified into 22 subclasses: Oxidoreductase In biochemistry, an oxidoreductase is an enzyme that catalyzes the transfer of electrons from one molecule, the reductant, also called the electron donor, to another, the oxidant, also called the electron acceptor. This group of enzymes usually utilizes NADP or NAD+ as cofactors. Transmembrane oxidoreductases create electron transport chains in bacteria, chloroplasts and mitochondria, including respiratory complexes I, II and III. Some others can associate with biological membranes as peripheral membrane proteins or be

pos: Malate dehydrogenase 2 functionally distinct domains. The first is the NAD-binding domain, which exists in the amino-terminal half of each molecule, and contains a parallel-sheet structure, otherwise known as a Rosman fold motif. The core dinucleotide binding structure is composed of four beta-sheets and one alpha-helix. The other domain is a carboxy-terminal domain that contains the substrate binding site and amino acids that are necessary for catalysis. The active site of these enzymes is in a cleft between two domains. Crystallography reveals the dimer interface, which consists mainly of interacting alpha-helices that form a compact interaction. The active sites in these dimeric proteins

pos: Enzyme mimic Enzyme mimic Enzyme mimic (or Artificial enzyme) is a branch of biomimetic chemistry, which aims at imitating the function of natural enzymes. An enzyme mimic is a small molecule complex that models the molecular structure, spectroscopic properties, or reactivity of an enzyme, sometimes called bioinspired complexes. Enzymes are biological catalysts: biopolymers that catalyze a reaction. Although a small number of natural enzymes are built from RNA–termed Ribozymes–most enzymes are proteins. Like any other protein an enzyme is an amino acid polymer with added cofactors and other post-translational modifications. Often most of the amino acid polymer is indirectly involved with the

pos: Glycogen debranching enzyme as Glycogen storage disease type III can result. Glucosyltransferase and glucosidase are performed by a single enzyme in mammals, yeast, and some bacteria, but by two distinct enzymes in "E. coli" and other bacteria, complicating nomenclature. Proteins that catalyze both functions are referred to as glycogen debranching enzymes (GDEs). When glucosyltransferase and glucosidase are catalyzed by distinct enzymes, "glycogen debranching enzyme" usually refers to the glucosidase enzyme. In some literature, an enzyme capable only of glucosidase is referred to as a "debranching enzyme". Together with phosphorylase, glycogen debranching enzymes function in glycogen breakdown and glucose mobilization. When phosphorylase has digested

pos: Spermatozoon and the exposure of enzymes attached to the inner acrosomal membrane of the sperm. This occurs after the sperm first meets the egg. This lock-and-key type mechanism is species-specific and prevents the sperm and egg of different species from fusing. There is some evidence that this binding is what triggers the acrosome to release the enzymes that allow the sperm to fuse with the egg. ZP3, one of the proteins that make up the zona pellucida, then binds to a partner molecule on the sperm. Enzymes on the inner acrosomal membrane digest the zona pellucida. After the sperm penetrates the

pos: Haem peroxidase a substrate radical and Compound II, which can then oxidize a second substrate molecule. Haem peroxidases include two superfamilies: one found in bacteria, fungi, and plants, and the second found in animals. The first one can be viewed as consisting of 3 major classes: The crystal structures of a number of these proteins show that they share the same architecture - two all-alpha domains between which the haem group is embedded. Another family of haem peroxidases is the DyP-type peroxidase family. Haem peroxidase Haem peroxidases (or heme peroxidases) are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to

pos: Restriction enzyme of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction digestion , although it has no enzymatic activity on its own. Type III enzymes recognise short 5–6 bp-long asymmetric DNA sequences and cleave 25–27 bp downstream to leave short, single-stranded 5' protrusions. They require the

pos: Biochemistry that they specifically bind to a certain molecule or class of molecules—they may be "extremely" selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. Antibodies are composed of heavy and light chains. Two heavy chains would be linked to two light chains through disulfide linkages between their amino acids. Antibodies are specific through variation based on differences in the N-terminal domain. In fact, the enzyme-linked immunosorbent assay (ELISA), which uses antibodies, is one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins,

neg: HindIII Lys-92, Asp-90, and Asp-74 in EcoRV, respectively. Lys-125 positions the attacking water molecule while Asp-108 improves its nucleophilicity. Asp-123 coordinates to Mg2+ which in turn stabilizes the leaving hydroxide ion. HindIII as well as other type II restriction endonucleases are very useful in modern science, particularly in DNA sequencing and mapping. Unlike type I restriction enzymes, type II restriction endonucleases perform very specific cleaving of DNA. Type I restriction enzymes recognize specific sequences, but cleave DNA randomly at sites other than their recognition site whereas type II restriction enzymes cleave only at their specific recognition site. Since their discovery in

neg: Guanylyltransferase Guanylyltransferase Guanylyl transferases are enzymes that transfer a guanosine mono phosphate group, usually from GTP to another molecule, releasing pyrophosphate. Many eukaryotic guanylyl transferases are capping enzymes that catalyze the formation of the 5' cap in the co-transcriptional modification of messenger RNA. Because the 5' end of the RNA molecule ends in a phosphate group, the bond formed between the RNA and the GTP molecule is an unusual 5'-5' triphosphate linkage, instead of the 3'-5' linkages between the other nucleotides that form an RNA strand. In capping enzymes, a highly conserved lysine residue serves as the catalytic residue that forms

neg: 6-Deoxyerythronolide B synthase be used in different combinations to create segments of polyketide that are saturated, unsaturated, or have a hydroxyl or carbonyl functional group. There are also enzymes used in both fatty acid synthesis and polyketide synthesis that can make modifications to the molecule after it has been synthesized. As far as regulating the length of the molecule being synthesized, the specific mechanism by which fatty acid chain length remains unknown but it is expected that ACP-bound fatty acid chains of the correct length act as allosteric inhibitors of the fatty acid synthesis enzymes. In polyketide synthesis, the synthases are composed of

neg: Glycogen storage disease type III enzymes to further convert these branched glycogen polymers to glucose, limit dextrinosis abnormally accumulates in the cytoplasm. Glycogen is a molecule the body uses to store carbohydrate energy. Symptoms of GSD-III are caused by a deficiency of the enzyme amylo-1,6 glucosidase, or debrancher enzyme. This causes excess amounts of an abnormal glycogen to be deposited in the liver, muscles and, in some cases, the heart. Glycogen storage disease type III presents during infancy with hypoglycemia and failure to thrive. Clinical examination usually reveals hepatomegaly. Muscular disease, including hypotonia and cardiomyopathy, usually occurs later. The liver pathology typically regresses as the

neg: Asymmetric ester hydrolysis with pig-liver esterase Asymmetric ester hydrolysis with pig-liver esterase Asymmetric ester hydrolysis with pig liver esterase is the enantioselective conversion of an ester to a carboxylic acid through the action of the enzyme pig liver esterase (EC 3.1.1.1). Asymmetric ester hydrolysis involves the selective reaction of one of a pair of either enantiotopic (within the same molecule and related by a symmetry plane of the molecule) or enantiomorphic (in enantiomeric molecules and related as mirror images) ester groups. Enzymes, which are composed of chiral amino acids, catalyze chemical reactions with high stereoselectivity. Specifically, esterase enzymes catalyze the hydrolysis of esters to carboxylic acids.

neg: Collagen, type II, alpha 1 the C-propeptide of this collagen molecule, are also associated with chondrodysplasia. There are two transcripts identified for this gene. Type II collagen, which adds structure and strength to connective tissues, is found primarily in cartilage, the jelly-like substance that fills the eyeball (the vitreous), the inner ear, and the center portion of the discs between the vertebrae in the spine (nucleus pulposus). Three pro-alpha1(II) chains twist together to form a triple-stranded, ropelike procollagen molecule. These procollagen molecules must be processed by enzymes in the cell. Once these molecules are processed, they leave the cell and arrange themselves into long, thin

neg: Regulatory enzyme function through reversible, non-covalent binding of a regulatory metabolite in the allosteric site (which is not the active site). When bound, these metabolites do not participate in catalysis directly, but they are still essential: they lead to conformational changes in a concrete part of the enzyme. These changes affect the overall conformation of the active site, causing modifications on the activity of the reaction. Properties Allosteric enzymes are generally larger in mass than other enzymes. Different from having a single subunit enzyme, in this case they are composed of multiple subunits, which contain active sites and regulatory molecule binding sites.

neg: Metalloproteinase activated water molecule. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main protease types, with more than 50 families classified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play

neg: Glutamine amidotransferase been identified: class-I (also known as trpG-type) and class-II (also known as purF-type). Class-I GATase domains are defined by a conserved catalytic triad consisting of cysteine, histidine and glutamate. Class-I GATase domains have been found in the following enzymes: the second component of anthranilate synthase and 4-amino-4-deoxychorismate (ADC) synthase; CTP synthase; GMP synthase; glutamine-dependent carbamoyl-phosphate synthase; phosphoribosylformylglycinamidine synthase II; and the histidine amidotransferase hisH. Glutamine amidotransferase In molecular biology, glutamine amidotransferases (GATase) are enzymes which catalyse the removal of the ammonia group from a glutamine molecule and its subsequent transfer to a specific substrate, thus creating a new carbon-nitrogen group

neg: Sticky and blunt ends molecule and a complementary 5' overhang in the other. These ends are called cohesive since they are easily joined back together by a ligase. Also, since different restriction endonucleases usually create different overhangs, it is possible to cut a piece of DNA with two different enzymes and then join it with another DNA molecule with ends created by the same enzymes. Since the overhangs have to be complementary in order for the ligase to work, the two molecules can only join in one orientation. This is often highly desirable in molecular biology. For example, these two "sticky" ends are compatible:

neg: Active site enzymes. An active site can catalyse a reaction repeatedly as residues are not altered at the end of the reaction (they may change during the reaction, but are regenerated by the end). This process is achieved by lowering the activation energy of the reaction, so more substrates have enough energy to undergo reaction. Usually, an enzyme molecule has only two active sites, and the active sites fit with one specific type of substrate. An active site contains a binding site that binds the substrate and orients it for catalysis. The orientation of the substrate and the close proximity between it

neg: Citrate synthase family process (aldol-Claisen condensation followed by the hydrolysis of citryl-CoA). Citrate synthase enzymes are found in two distinct structural types: type I enzymes (found in eukaryotes, Gram-positive bacteria and archaea) form homodimers and have shorter sequences than type II enzymes, which are found in Gram-negative bacteria and are hexameric in structure. In both types, the monomer is composed of two domains: a large alpha-helical domain consisting of two structural repeats, where the second repeat is interrupted by a small alpha-helical domain. The cleft between these domains forms the active site, where both citrate and acetyl-coenzyme A bind. The enzyme undergoes a

neg: Hypermethioninemia altered gene in each cell is sufficient to cause the disorder. In these cases, an affected person usually has one parent with the condition. Inherited hypermethioninemia that is not associated with other metabolic disorders can be caused by shortages in the enzymes that break down methionine. These enzymes are produced from the "MAT1A", "GNMT" and "AHCY" genes. The reactions involved in metabolizing methionine help supply some of the amino acids needed for protein production. These reactions are also involved in transferring methyl groups, consisting of a carbon atom and three hydrogen atoms, from one molecule to another (transmethylation), which is

neg: Glycoside a glucoside; if it is fructose, then the molecule is a fructoside; if it is glucuronic acid, then the molecule is a glucuronide; etc. In the body, toxic substances are often bonded to glucuronic acid to increase their water solubility; the resulting glucuronides are then excreted. Depending on whether the glycosidic bond lies "below" or "above" the plane of the cyclic sugar molecule, glycosides are classified as α-glycosides or β-glycosides. Some enzymes such as α-amylase can only hydrolyze α-linkages; others, such as emulsin, can only affect β-linkages. There are four type of linkages present between glycone and aglycone: Glycosides are

neg: Restriction site largest noncommercial database is REBASE. Restriction site Restriction sites, or restriction recognition sites, are locations on a DNA molecule containing specific (4-8 base pairs in length) sequences of nucleotides, which are recognized by restriction enzymes. These are generally palindromic sequences (because restriction enzymes usually bind as homodimers), and a particular restriction enzyme may cut the sequence between two nucleotides within its recognition site, or somewhere nearby. For example, the common restriction enzyme EcoRI recognizes the palindromic sequence GAATTC and cuts between the G and the A on both the top and bottom strands, leaving an overhang (an end-portion of a

neg: Restriction site Restriction site Restriction sites, or restriction recognition sites, are locations on a DNA molecule containing specific (4-8 base pairs in length) sequences of nucleotides, which are recognized by restriction enzymes. These are generally palindromic sequences (because restriction enzymes usually bind as homodimers), and a particular restriction enzyme may cut the sequence between two nucleotides within its recognition site, or somewhere nearby. For example, the common restriction enzyme EcoRI recognizes the palindromic sequence GAATTC and cuts between the G and the A on both the top and bottom strands, leaving an overhang (an end-portion of a DNA strand with no attached

neg: Ubiquitin-conjugating enzyme molecule, a greater diversity of E2s, and a very large variety of E3s. The E3 molecules responsible for substrate identification and binding are thus the mechanisms of substrate specificity in proteasomal degradation. Each type of E2 can associate with many E3s. The following human genes encode ubiquitin-conjugating enzymes: Ubiquitin-conjugating enzyme Ubiquitin-conjugating enzymes, also known as E2 enzymes and more rarely as ubiquitin-carrier enzymes, perform the second step in the ubiquitination reaction that targets a protein for degradation via the proteasome. The ubiquitination process covalently attaches ubiquitin, a short protein of 76 amino acids, to a lysine residue on the target

neg: Collagen, type XXIII, alpha 1 the brain where the shed form is predominant, whereas in the lungs the molecule is generally found as the full-length form. It has been reported that the cell is able to regulate the amounts of collagen XXIII in the membrane-bound form and in the secreted shed form, influencing the production of one form or the other when it is needed. For that reason, the shedding process of collagen XXIII has been described as a selective proteolysis, carried out principally by furin, although there are other enzymes, like serine and cysteine proteases, which are able to shed the molecule too. When

neg: Nicotinamide adenine dinucleotide In addition to these metabolic functions, NAD emerges as an adenine nucleotide that can be released from cells spontaneously and by regulated mechanisms, and can therefore have important extracellular roles. The main role of NAD in metabolism is the transfer of electrons from one molecule to another. Reactions of this type are catalyzed by a large group of enzymes called oxidoreductases. The correct names for these enzymes contain the names of both their substrates: for example NADH-ubiquinone oxidoreductase catalyzes the oxidation of NADH by coenzyme Q. However, these enzymes are also referred to as "dehydrogenases" or "reductases", with NADH-ubiquinone oxidoreductase

neg: Enzyme inhibitor targets that are not enzymes, such as ion channels or membrane receptors. An example of a medicinal enzyme inhibitor is sildenafil (Viagra), a common treatment for male erectile dysfunction. This compound is a potent inhibitor of cGMP specific phosphodiesterase type 5, the enzyme that degrades the signalling molecule cyclic guanosine monophosphate. This signalling molecule triggers smooth muscle relaxation and allows blood flow into the corpus cavernosum, which causes an erection. Since the drug decreases the activity of the enzyme that halts the signal, it makes this signal last for a longer period of time. Another example of the structural similarity

neg: ATPase transport a variety of different compounds, like ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transports a specific type of ion. P-ATPases may be composed of one or two polypeptides, and can usually take two main conformations, E1 and E2. ATPase ATPases (, "adenylpyrophosphatase", "ATP monophosphatase", "triphosphatase", "SV40 T-antigen", "adenosine 5'-triphosphatase", "ATP hydrolase", "complex V (mitochondrial electron transport)", "(Ca + Mg)-ATPase", "HCO-ATPase", "adenosine triphosphatase") are a class of enzymes that catalyze the decomposition of ATP into ADP and a free phosphate ion. This dephosphorylation reaction releases energy, which the

neg: ADME the body. The majority of small-molecule drug metabolism is carried out in the liver by redox enzymes, termed cytochrome P450 enzymes. As metabolism occurs, the initial (parent) compound is converted to new compounds called metabolites. When metabolites are pharmacologically inert, metabolism deactivates the administered dose of parent drug and this usually reduces the effects on the body. Metabolites may also be pharmacologically active, sometimes more so than the parent drug (see prodrug). Compounds and their metabolites need to be removed from the body via excretion, usually through the kidneys (urine) or in the feces. Unless excretion is complete, accumulation of

neg: Lantibiotics the transport of the molecule out of the synthesising cell. They are synthesized by ribosomes, which distinguishes them from most natural antibiotics. There are four known enzymes (lanthipeptide synthetases) responsible for producing lanthionine rings. Lantibiotics show substantial specificity for some components (e.g., lipid II) of bacterial cell membranes especially of Gram-positive bacteria. Type A lantibiotics kill rapidly by pore formation, type B lantibiotics inhibit peptidoglycan biosynthesis. They are active in very low concentrations. Lantibiotics are produced by Gram-positive bacteria and show strong antimicrobial action toward a wide range of other Gram-positive bacteria. As such, they have become attractive candidates for

neg: Autolysis (biology) Autolysis (biology) In biology, autolysis, more commonly known as self-digestion, refers to the destruction of a cell through the action of its own enzymes. It may also refer to the digestion of an enzyme by another molecule of the same enzyme. The term derives from the Greek words αὐτο- ("self") and λύσις ("splitting"). Autolytic cell destruction is uncommon in living adult organisms and usually occurs in injured cells and dying tissue. Autolysis is initiated by the cells' lysosomes releasing digestive enzymes into the cytoplasm. These enzymes are released due to the cessation of active processes in the cell, not as

neg: Restriction enzyme sites; this characteristic is widely used to perform in-vitro cloning techniques such as Golden Gate cloning. These enzymes may function as dimers. Similarly, Type IIT restriction enzymes (e.g., Bpu10I and BslI) are composed of two different subunits. Some recognize palindromic sequences while others have asymmetric recognition sites. Type III restriction enzymes (e.g., EcoP15) recognize two separate non-palindromic sequences that are inversely oriented. They cut DNA about 20–30 base pairs after the recognition site. These enzymes contain more than one subunit and require AdoMet and ATP cofactors for their roles in DNA methylation and restriction digestion , respectively. They are components

neg: Collagenase putative signal sequence. Within this stretch is found PLGP, an amino acid sequence typical of collagenase substrates. This sequence may thus be implicated in self-processing of the collagenase. Metalloproteases are the most diverse of the seven main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp, or Lys and at least one other residue is required for catalysis, which may play an electrophillic

neg: Vitreoscilla are obligate aerobic bacteria, which are morphologically colourless filaments that contain cells with diameters of 1-3 μm and 1-12 μm long. Each filament may contain from 1 to 40 cells. Locomotion is by gliding, and no special locomotor organelles are present. The cell walls are composed of the amino acids alanine, glutamate, and diaminopimelic acid, with approximate molar ratios of 2:1:1. "Vitreoscilla" bacteria have a unique property in that they produces a type of haemoglobin, VHb. This molecule unlike classic haemoglobin is composed only of a single globin molecule. VHb is known to have a wide variety of functions including

neg: Borrelidin by type I polyketide synthase (PKS), followed by post-PKS modifications. Six genes ("bor"A1 to "bor"A6) encode the type I PKS, composed of a loading domain and six extending modules, rather than the expected eight. Each extension module consists of the ketosynthase (KS) condensing an extender unit, either malonyl-CoA or methylmalonyl-CoA, that is loaded by the acyl transferase (AT) onto the growing polyketide, which can then be modified by further enzymes. Tailoring enzymes of type I PKS that can be involved in each module are ketoreductase (KR), dehydratase (DH), and enoyl reductase (ER). Once polyketide has gone through all of the

neg: Cytochrome c peroxidase fast growing yeast strains are exhausted, the cells turn to respiration which raises the concentration of mitochondrial HO In addition to its peroxidase activity, it acts as a sensor and a signaling molecule to exogenous HO, which activates mitochondrial catalase activity. In eukaryotes, CCP contain a mono-"b"-type haem cofactor and is targeted to the intermembrane space of the mitochondria. In prokaryotes, CCP contains a "c-"type dihaem cofactor and is localized to the periplasm of the cell. Both enzymes work to resist peroxide-induced cellular stress. CCP plays an integral role in enabling inter-protein biological electron transfer. The negative charge transfer process

neg: Cytochrome P450 omega hydroxylase (i.e. furthest from the fatty acids' carboxy residue) carbons; in the reaction, the two atoms of molecular oxygen(O[ are reduced to one hydroxyl group and one water (HO molecule) by the concomitant oxidation of NAD(P)H (see monooxygenase). RH + O + NADPH + H → ROH + HO + NADP CYP450 enzymes belong to a superfamily which in humans is composed of at least 57 CYPs; within this superfamily, members of six CYP4A subfamilies, (which are CYP4A, CYP4B, CYP4F, CYP4V, CYP4X, and CYP4z) possess ω-hydroxylase activity viz., CYP4A, CYP4B, and CYP4F CYP2U1 also possesses ω hydroxylase activity. These CYP ω-hydroxylases

neg: Burgess Shale type preservation film plus phyllosilicate. For this preservation to occur, the organisms must be protected from decay. There are a few ways that this can happen; for instance they can be chemically protected within the sediment by phyllosilicates or biopolymers, which inhibit the action of decay related enzymes. Alternatively the sediment could be "sealed" soon after the organisms were buried within it, with a reduction in porosity preventing oxygen from reaching the organic material. The fossils usually comprise a reflective film; when the part bears an opaque, silvery film composed of organic carbon (kerogen), the counterpart's film is blue, less reflective, and

neg: DNA polymerase DNA polymerase DNA polymerase is an enzyme that synthesizes DNA molecules from deoxyribonucleotides, the building blocks of DNA. These enzymes are essential for DNA replication and usually work in pairs to create two identical DNA strands from a single original DNA molecule. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing ones. These enzymes catalyze the following chemical reaction DNA polymerase adds nucleotides to the three prime (3')-end of a DNA strand, one nucleotide at a time. Every time a cell divides, DNA polymerases are required to help duplicate the

neg: Guanylyltransferase a covalent enzyme-GMP complex. The transfer RNA (tRNA) for histidine is unique among eukaryotic tRNAs in requiring the addition of a guanine nucleotide before being aminoacylated by the histidine tRNA synthetase. The yeast guanylyl transferase specific to tRNA is unique in being the only known non-tRNA synthetase enzyme that specifically recognizes the tRNA anticodon. Guanylyl transferases also exist for transferring guanosine nucleotides to sugar molecules, such as mannose and fucose. Guanylyltransferase Guanylyl transferases are enzymes that transfer a guanosine mono phosphate group, usually from GTP to another molecule, releasing pyrophosphate. Many eukaryotic guanylyl transferases are capping enzymes that catalyze the

neg: Lysosome rough endoplasmic reticulum. The enzymes are imported from the Golgi apparatus in small vesicles, which fuse with larger acidic vesicles. Enzymes destined for a lysosome are specifically tagged with the molecule mannose 6-phosphate, so that they are properly sorted into acidified vesicles. Synthesis of lysosomal enzymes is controlled by nuclear genes. Mutations in the genes for these enzymes are responsible for more than 30 different human genetic disorders, which are collectively known as lysosomal storage diseases. These diseases result from an accumulation of specific substrates, due to the inability to break them down. These genetic defects are related to several

neg: Restriction enzyme the target DNA. The cofactors S-Adenosyl methionine (AdoMet), hydrolyzed adenosine triphosphate (ATP), and magnesium (Mg) ions, are required for their full activity. Type I restriction enzymes possess three subunits called HsdR, HsdM, and HsdS; HsdR is required for restriction digestion; HsdM is necessary for adding methyl groups to host DNA (methyltransferase activity), and HsdS is important for specificity of the recognition (DNA-binding) site in addition to both restriction digestion (DNA cleavage) and modification (DNA methyltransferase) activity. Typical type II restriction enzymes differ from type I restriction enzymes in several ways. They form homodimers, with recognition sites that are usually undivided

neg: Evolution of cells better enzyme has no definitive advantage over its close neighbors. If the molecule is enclosed in a cell membrane, then the enzymes coded will be available only to the replicator molecule itself. That molecule will uniquely benefit from the enzymes it codes for, giving it a better chance to multiply. Partitioning may have begun from cell-like spheroids formed by proteinoids, which are observed by heating amino acids with phosphoric acid as a catalyst. They bear much of the basic features provided by cell membranes. Proteinoid-based protocells enclosing RNA molecules could have been the first cellular life forms on Earth. Another

neg: Carboxypeptidase A pathway. This mechanism involves attack of a water molecule at the scissile peptide linkage of the substrate. This process is promoted by the zinc ion and assisted by residue Glu-270 Carboxypeptidase A Carboxypeptidase A usually refers to the pancreatic exopeptidase that hydrolyzes peptide bonds of C-terminal residues with aromatic or aliphatic side-chains. Most scientists in the field now refer to this enzyme as CPA1, and to a related pancreatic carboxypeptidase as CPA2. In addition, there are 4 other mammalian enzymes named CPA-3 through CPA-6, and none of these are expressed in the pancreas. Instead, these other CPA-like enzymes have diverse

neg: Sulfite reductase siroheme - which deliver electrons to the substrate via this coupling. The systematic name of this enzyme class is hydrogen-sulfide:acceptor oxidoreductase. Other names in common use include assimilatory sulfite reductase, assimilatory-type sulfite reductase, and hydrogen-sulfide:(acceptor) oxidoreductase. Sulfite reductase Sulfite reductases () are enzymes that participate in sulfur metabolism. They catalyze the reduction of sulfite to hydrogen sulfide and water. Electrons for the reaction are provided by a dissociable molecule of either NADPH, bound flavins, or ferredoxins. Sulfite reductases, which belong to the oxidoreductase family, are found in archaea, bacteria, fungi, and plants. They are grouped as either assimilatory or dissimilatory

neg: Exoribonuclease Exoribonuclease An exoribonuclease is an exonuclease ribonuclease, which are enzymes that degrade RNA by removing terminal nucleotides from either the 5' end or the 3' end of the RNA molecule. Enzymes that remove nucleotides from the 5' end are called "5'-3' exoribonucleases", and enzymes that remove nucleotides from the 3' end are called "3'-5' exoribonucleases". Exoribonucleases can use either water to cleave the nucleotide-nucleotide bond (which is called hydrolytic activity) or inorganic phosphate (which is called phosphorolytic activity). Hydrolytic exoribonucleases are classified under EC number 3.1 and phosphorolytic exoribonucleases under EC number 2.7.7. As the phosphorolytic enzymes use inorganic phosphate

neg: Molecule as parentheses, dashes, brackets, and "plus" (+) and "minus" (−) signs. These are limited to one typographic line of symbols, which may include subscripts and superscripts. A compound's empirical formula is a very simple type of chemical formula. It is the simplest integer ratio of the chemical elements that constitute it. For example, water is always composed of a 2:1 ratio of hydrogen to oxygen atoms, and ethyl alcohol or ethanol is always composed of carbon, hydrogen, and oxygen in a 2:6:1 ratio. However, this does not determine the kind of molecule uniquely – dimethyl ether has the same ratios

neg: Amination Amination Amination is the process by which an amine group is introduced into an organic molecule. This type of reaction is important because organonitrogen compounds are pervasive. Enzymes that catalyse this reaction are termed aminases. Amination can occur in a number of ways including reaction with ammonia or another amine such as an alkylation, reductive amination and the Mannich reaction. For example, -COOH --> -CONH. Many alkyl amines are produced industrially by the amination of alcohols using ammonia in the presence of acid catalysts. In electrophilic amination, the amine as the nucleophile react with another the organic compound as the

neg: Hh blood group final step in the synthesis of the molecule. Depending upon a person's ABO blood type, the H antigen is converted into either the A antigen, B antigen, or both. If a person has group O blood, the H antigen remains unmodified. Therefore, the H antigen is present more in blood type O and less in blood type AB. Two regions of the genome encode two enzymes with very similar substrate specificities: the H locus (FUT1) which encodes the Fucosyl transferase and the Se locus (FUT2) that instead indirectly encodes a soluble form of the H antigen, which is found in

neg: Aspartic protease BACE1; BACE2; CTSD; CTSE; NAPSA; PGA5; PGC; REN; Aspartic protease Aspartic proteases are a catalytic type of protease enzymes that use an activated water molecule bound to one or more aspartate residues for catalysis of their peptide substrates. In general, they have two highly conserved aspartates in the active site and are optimally active at acidic pH. Nearly all known aspartyl proteases are inhibited by pepstatin. Aspartic endopeptidases of vertebrate, fungal and retroviral origin have been characterised. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin and archaean preflagellin have been described. Eukaryotic aspartic proteases include

neg: Aspartic protease Aspartic protease Aspartic proteases are a catalytic type of protease enzymes that use an activated water molecule bound to one or more aspartate residues for catalysis of their peptide substrates. In general, they have two highly conserved aspartates in the active site and are optimally active at acidic pH. Nearly all known aspartyl proteases are inhibited by pepstatin. Aspartic endopeptidases of vertebrate, fungal and retroviral origin have been characterised. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin and archaean preflagellin have been described. Eukaryotic aspartic proteases include pepsins, cathepsins, and renins. They have a two-domain

neg: Catalysis intermediate between homogeneous and heterogeneous catalysts, although strictly speaking soluble enzymes are homogeneous catalysts and membrane-bound enzymes are heterogeneous. Several factors affect the activity of enzymes (and other catalysts) including temperature, pH, concentration of enzyme, substrate, and products. A particularly important reagent in enzymatic reactions is water, which is the product of many bond-forming reactions and a reactant in many bond-breaking processes. In biocatalysis, enzymes are employed to prepare many commodity chemicals including high-fructose corn syrup and acrylamide. Some monoclonal antibodies whose binding target is a stable molecule which resembles the transition state of a chemical reaction can function as

neg: Enzyme the penicillin molecule. Another example comes from enzymes in the liver called cytochrome P450 oxidases, which are important in drug metabolism. Induction or inhibition of these enzymes can cause drug interactions. Enzyme levels can also be regulated by changing the rate of enzyme degradation. The opposite of enzyme induction is enzyme repression. Enzymes can be compartmentalized, with different metabolic pathways occurring in different cellular compartments. For example, fatty acids are synthesized by one set of enzymes in the cytosol, endoplasmic reticulum and Golgi and used by a different set of enzymes as a source of energy in the mitochondrion, through

neg: Collagen, type XXIII, alpha 1 collagen XXIII is inside the Golgi apparatus, furin proteases act, cleaving the protein and originating the shed form of the molecule, which will be released to the extracellular matrix by means of exocytosis. There is also the possibility that the full-length form of the molecule reaches the cell surface before furin cleaves it. When this happens, the full molecule of collagen is introduced in the plasmatic membrane and is stabilized by its non-collagenous transmembranous domains, leaving the collagenous domains outside the cell. Full-length molecules of collagen XXIII are usually found in lipid rafts, which are cholesterol-rich and sphingolipid-rich, tightly-packed microdomains

neg: Enzyme kinetics an RNA lyase. However, some enzymes that only have a single substrate do not fall into this category of mechanisms. Catalase is an example of this, as the enzyme reacts with a first molecule of hydrogen peroxide substrate, becomes oxidised and is then reduced by a second molecule of substrate. Although a single substrate is involved, the existence of a modified enzyme intermediate means that the mechanism of catalase is actually a ping–pong mechanism, a type of mechanism that is discussed in the "Multi-substrate reactions" section below. As enzyme-catalysed reactions are saturable, their rate of catalysis does not show a

neg: Phenylacetic acid an active auxin (a type of plant hormone), found predominantly in fruits. However, its effect is much weaker than the effect of the basic auxin molecule indole-3-acetic acid. In addition the molecule is naturally produced by the metapleural gland of most ant species and used as an antimicrobial. It is also the oxidation product of phenethylamine in humans following metabolism by monoamine oxidase and subsequent metabolism of the intermediate product, phenylacetaldehyde, by the aldehyde dehydrogenase enzyme; these enzymes are also found in many other organisms. This compound may be prepared by the hydrolysis of benzyl cyanide: Phenylacetic acid is used

neg: Drug delivery to the brain through the blood–brain barrier. Similar to the idea of pro-drugs, another way of masking the drugs chemical composition is by masking a peptide’s characteristics by combining with other molecular groups that are more likely to pass through the blood–brain barrier. An example of this is using a cholesteryl molecule instead of cholesterol that serves to conceal the water soluble characteristics of the drug. This type of masking as well as aiding in traversing the blood–brain barrier. It also can work to mask the drug peptide from peptide-degrading enzymes in the brain Also a "targetor" molecule could be attached to the

neg: Tacrolimus Protopic. The biosynthesis of tacrolimus is hybrid synthesis of both type 1 polyketide synthases (PKS 1) and nonribosomal peptide synthases (NRPS). The research shows the hybrid synthesis consists of ten modules of type 1 polyketide synthase and one module of nonribosomal peptide synthase. The synthetic enzymes for tacrolimus are found in 19 gene clusters named fkb. The 19 genes are fkbQ, fkbN, fkbM, fkbD, fkbA, fkbP, fkbO, fkbB, fkbC, fkbL, fkbK, fkbJ, fkbI, fkbH, fkbG, allD, allR, allK and allA. There are several possible ways of biosynthesis of tacrolimus. The fundamental units for biosynthesis are following: one molecule of 4,5-dihydroxycyclohex-1-enecarboxylic

neg: Endoenzyme Endoenzyme An endoenzyme, or intracellular enzyme, is an enzyme that functions within the cell in which it was produced. Because the majority of enzymes fall within this category, the term is used primarily to differentiate a specific enzyme from an exoenzyme. It is possible for a single enzyme to have both endoenzymatic and exoenzymatic functions; for example, glycolytic enzymes of Kreb's Cycle. In most cases the term endoenzyme refers to an enzyme that binds to a bond 'within the body' of a large molecule - usually a polymer. For example an endoamylase would break down large amylose molecules into shorter

neg: Non-bonding orbital orbitals in shape but when viewed as molecular orbitals are thought of as non-bonding. The energy of the orbital does not depend on the length of any bond within the molecule. Its occupation neither increases nor decreases the stability of the molecule, relative to the atoms, since its energy is the same in the molecule as in one of the atoms. For example, there are two rigorously non-bonding orbitals that are occupied in the ground state of the hydrogen fluoride diatomic molecule; these molecular orbitals are localized on the fluorine atom and are composed of p-type atomic orbitals whose orientation

neg: Phosphodiesterase Phosphodiesterase A phosphodiesterase (PDE) is an enzyme that breaks a phosphodiester bond. Usually, "phosphodiesterase" refers to cyclic nucleotide phosphodiesterases, which have great clinical significance and are described below. However, there are many other families of phosphodiesterases, including phospholipases C and D, autotaxin, sphingomyelin phosphodiesterase, DNases, RNases, and restriction endonucleases (which all break the phosphodiester backbone of DNA or RNA), as well as numerous less-well-characterized small-molecule phosphodiesterases. The cyclic nucleotide phosphodiesterases comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They regulate the localization, duration, and amplitude of cyclic nucleotide signaling within

neg: Restriction enzyme Restriction enzyme A restriction enzyme or restriction endonuclease is an enzyme that cleaves DNA into fragments at or near specific recognition sites within the molecule known as restriction sites. Restrictions enzymes are one class of the broader endonuclease group of enzymes. Restriction enzymes are commonly classified into five types, which differ in their structure and whether they cut their DNA substrate at their recognition site, or if the recognition and cleavage sites are separate from one another. To cut DNA, all restriction enzymes make two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the DNA double helix. These

neg: Amino acid activation a considerable part of the energy from the activation reaction. This stored energy provides the majority of the energy needed for peptide bond formation during translation. Each of the 20 amino acids are recognized by its specific aminoacyl-tRNA synthetase. The synthetases are usually composed of one to four protein subunits. The enzymes vary considerably in structure although they all perform the same type of reaction by binding ATP, one specific amino acid and its corresponding tRNA. The specificity of the amino acid activation is as critical for the translational accuracy as the correct matching of the codon with the anticodon.

neg: Restriction enzyme = A or T "General Information:" "Databases:" "Software:" Restriction enzyme A restriction enzyme or restriction endonuclease is an enzyme that cleaves DNA into fragments at or near specific recognition sites within the molecule known as restriction sites. Restrictions enzymes are one class of the broader endonuclease group of enzymes. Restriction enzymes are commonly classified into five types, which differ in their structure and whether they cut their DNA substrate at their recognition site, or if the recognition and cleavage sites are separate from one another. To cut DNA, all restriction enzymes make two incisions, once through each sugar-phosphate backbone (i.e.

neg: Imino acid Imino acid In chemistry, an imino acid is any molecule that contains both imino (>C=NH) and carboxyl (-C(=O)-OH) functional groups. Imino acids are related to amino acids, which contain both amino (-NH) and carboxyl (-COOH) functional groups, differing in the bonding to the nitrogen. The D-amino acid oxidase enzymes are able to convert amino acids into imino acids. Also the direct biosynthetic precursor to the amino acid proline is the imino acid ("S")-Δ-pyrroline-5-carboxylate (P5C). Amino acids containing a secondary amine group (the only proteinogenic amino acid of this type is proline) are sometimes named imino acids, though this usage is

neg: Fostriecin PKS pathway of the linear molecule. These enzymes include two cytochrome P450 enzymes (FosJ and FosK), one homoserine kinase (FosH), and one NAD-dependent epimerase/dehydratase family protein (FosM). The first step after the thioesterase domain, which forms a six-membered lactone ring, is the oxidation at C8 by FosJ, followed by a phosphorylation at C9 by FosH. This is then followed by an oxidation at the terminal carbon by FosK, and finally, a loss of malonic acid by FosM yields the desired natural product. Fostriecin Fostriecin is a type I polyketide synthase (PKS) derived natural product, originally isolated from the soil bacterium

neg: Molecule represented with a one-dimensional chemical name, but such chemical nomenclature requires many words and terms which are not part of chemical formulas. Molecules have fixed equilibrium geometries—bond lengths and angles— about which they continuously oscillate through vibrational and rotational motions. A pure substance is composed of molecules with the same average geometrical structure. The chemical formula and the structure of a molecule are the two important factors that determine its properties, particularly its reactivity. Isomers share a chemical formula but normally have very different properties because of their different structures. Stereoisomers, a particular type of isomer, may have very similar

neg: Glycogen debranching enzyme and progressive muscle involvement, with variations caused by age of onset, rate of disease progression and severity. Patients with Type IIIb generally symptoms related to liver disease. Type III patients be distinguished by elevated liver enzymes, with normal uric acid and blood lactate levels, differing from other forms of GSD. In patients with muscle involvement, Type IIIa, the muscle weakness becomes predominant into adulthood and can lead to ventricular hypertrophy and distal muscle wasting. Glycogen debranching enzyme A debranching enzyme is a molecule that helps facilitate the breakdown of glycogen, which serves as a store of glucose in the body,

neg: Calicheamicin binding of calicheamicin to the minor groove of DNA was demonstrated by Crothers et al. (1999) to be due to the aryltetrasaccharide group of the molecule. The core metabolic pathway for biosynthesis of this molecule resembles that of other characterized enediyne compounds and occurs via an iterative polyketide synthase (PKS) pathway. This type I PKS loads Acetyl-CoA and then repeatedly adds a total of seven Malonyl-CoAs. The growing polyketide is acted upon by the ketoreductase domain (KR) and dehydratase domain (DH) during each iteration to produce a 15-carbon polyene, which is then processed by accessory enzymes to yield the putative

neg: BglII the DNA molecule, creating sticky ends with 5' end overhangs. Being a type II restriction enzyme, "Bgl"II does not require ATP (adenosine triphosphate) for its enzymatic function, but only requires association with a divalent metal cation, most likely Mg. Unlike other restriction enzymes of its class, "Bgl"II has been shown to possess some unique structural characteristics, such as a β-sandwich subdomain, and appears to undergo a unique conformational change upon dimerization, but its overall structure and mechanism of catalysis remain consistent with other type II restriction enzymes. Restriction endonucleases play a very important role in modern molecular cloning techniques. Because

neg: Collagen, type I, alpha 1 chain (produced by the COL1A2 gene) to make a molecule of type I procollagen. These triple-stranded, rope-like procollagen molecules must be processed by enzymes outside the cell. Once these molecules are processed, they arrange themselves into long, thin fibrils that cross-link to one another in the spaces around cells. The cross-links result in the formation of very strong mature type I collagen fibers. Collagenous function includes rigidity and elasticity. The COL1A1 gene is located on the long (q) arm of chromosome 17 between positions 21.3 and 22.1, from base pair 45,616,455 to base pair 45,633,991. Mutations in the COL1A1 gene

neg: Molybdopterin some cases, the alkyl phosphate group is replaced by an alkyl diphosphate nucleotide. Enzymes that contain the molybdopterin cofactor include xanthine oxidase, DMSO reductase, sulfite oxidase, and nitrate reductase. The only molybdenum-containing enzymes that do not feature molybdopterins are the nitrogenases (enzymes that fix nitrogen). These contain an iron-sulfur center of a very different type, which also usually contains molybdenum. However, if molybdenum is present, it is directly bonded to other metal atoms. Unlike many other cofactors, Molybdenum cofactor (Moco) cannot be taken up as a nutrient. The cofactor thus requires "de novo" biosynthesis. Molybdenum cofactor biosynthesis occurs in four

neg: Hydrogen sulfide to hydrogen sulfide gas. This is due to providing a warm environment sustainable for sulfur bacteria and maintaining the reaction which interacts between sulfate in the water and the water heater anode, which is usually made from magnesium metal. Hydrogen sulfide can be generated in cells via enzymatic or non enzymatic pathway. in the body acts as a gaseous signaling molecule which is known to inhibit Complex IV of the mitochondrial electron transport chain which effectively reduces ATP generation and biochemical activity within cells. Three enzymes are known to synthesize : cystathionine γ-lyase (CSE), cystathionine β-synthetase (CBS) and 3-mercaptopyruvate sulfurtransferase

neg: Transferase the case of aspartate transaminase, which can act on tyrosine, phenylalanine, and tryptophan, it reversibly transfers an amino group from one molecule to the other. The reaction, for example, follows the following order: L-aspartate +2-oxoglutarate formula_2 oxaloacetate + L-glutamate. While EC 2.7 includes enzymes that transfer phosphorus-containing groups, it also includes nuclotidyl transferases as well. Sub-category phosphotransferase is divided up in categories based on the type of group that accepts the transfer. Groups that are classified as phosphate acceptors include: alcohols, carboxy groups, nitrogenous groups, and phosphate groups. Further constituents of this subclass of transferases are various kinases. A prominent

neg: P3 peptide Aβ in p3 peptides. p3 peptide generates from the 17-40 or 17-42 sequence of the amyloid precursor protein (APP), which is a type I integral membrane protein concerned in neurons’ synapses in many human tissues. Under normal physiological conditions, APP is processed with three different proteolytic enzymes: α-, β- and γ-secretases. At first, APP molecule is cut by α-secretase or β-secretase, and it will produce two different molecules for each case. These products are respectively APPsα or α-CTFs, when cut by α-secretase, or APPsβ and β-CTFs, when processed by β secretase. APPs derivates are sent both to the extra-cell, while

neg: Mitochondrial DNA genomes, classified by their structure (e.g. circular versus linear), size, presence of introns or plasmid like structures, and whether the genetic material is a singular molecule or collection of homogeneous or heterogeneous molecules. There is only one mitochondrial genome type found in animal cells. This genome usually contains one circular molecule with between 11–28 kbp of genetic material (type 1). There are three different genome types found in plants and fungi. The first type is a circular genome that has introns (type 2) and may range from 19 to 1000 kbp in length. The second genome type is a circular

neg: Chimeric RNA of two antiparallel strands which are oriented in opposite directions. DNA is composed of base pairs in which adenine pairs with thymine and guanine pairs with cytosine. While DNA serves as template for production of ribonucleic acid (RNA), RNA is usually responsible for making protein. The process of making RNA from DNA is called transcription. RNA uses a similar set of bases except that thymine is replaced with uracil. A group of enzymes called RNA polymerases (isolated by biochemists Jerard Hurwitz and Samuel B. Weiss) function in the presence of DNA. These enzymes produce RNA using segments of chromosomal DNA

neg: Type II cytokine receptor that are composed of tandem Ig-like domains. The intracellular domain of type II cytokine receptors is typically associated with a tyrosine kinase belonging to the Janus kinase (JAK) family. Type II cytokine receptors include those that bind type I and type II interferons, and those that bind members of the interleukin-10 family (interleukin-10, interleukin-20 and interleukin-22). The interferon receptor is a molecule displayed on the surface of cells which allows them to interact with the anti-viral substance interferon. The receptor is genetically coded for by number of different genes, as there are a few distinct types of interferon. Interferon receptor

neg: Helicos single molecule fluorescent sequencing shearing the DNA (the recommended approach), or restriction enzymes. Short fragments are removed to improve yield. DNA samples are hybridized to a primer immobilized on a flow cell for sequencing, so it is usually necessary to generate a nucleic acid with an end compatible for hybridization to those surfaces. The target sequence attached to the flow cell surface could, in theory, be any sequence which can be synthesized, but, in practice, the standard commercially available flow cell is oligo(dT)50. To be compatible with the oligo(dT)50 primer on the flow cell surface, it is necessary to generate a poly(dA) tail of

neg: Ribonuclease H manganese also usually supports enzymatic activity, while calcium may inhibit it. Although two-metal-ion catalytic mechanisms are very common in enzymes involved in phosphate biochemistry, it has been a subject of debate in the literature whether one or two ions are used in RNase H catalysis. In either proposed mechanism, at least one water molecule participates in the reaction. Most experimental evidence for the mechanism of RNase H catalysis comes from measurements performed on members of the H1 group, usually the "E. coli" homolog. According to measurements of this protein, one of the aspartate residues has an elevated pKa, while another

neg: Octaazacubane Octaazacubane Octaazacubane is a hypothetical explosive allotrope of nitrogen with formula N, whose molecules have eight atoms arranged into a cube. (By comparison, nitrogen usually occurs as the diatomic molecule N.) It can be regarded as a cubane-type cluster, where all eight corners are nitrogen atoms bonded along the edges. It is predicted to be a metastable molecule, in which despite the thermodynamic instability caused by bond strain, and the high energy of the N–N single bonds, the molecule remains kinetically stable for reasons of orbital symmetry. Octaazacubane is predicted to have an energy density (assuming decomposition into N) of

neg: Enzyme mimic enzymes function, perhaps providing ancillary structure or connectivity, indirect activity regulation, or molecular identification of the enzyme. As a result, most enzymes are large molecules weighing many kilodaltons. This bulk can obscure various investigative techniques such as NMR, EPR, electrochemistry, crystallography, among others. It is standard practice to compare spectroscopic data from enzymes to similar spectroscopic data derived from better characterized small molecules. In this way the understanding of metalloenzymes and other metalloproteins have developed. In many cases the small molecule analogs were created for other reasons; however, it has been increasingly common for groups to intentionally make small molecule

neg: Homonuclear molecule Homonuclear molecule Homonuclear molecules, or homonuclear species, are molecules composed of only one type of element. Homonuclear molecules may consist of various numbers of atoms, depending on the element's properties. Some elements form molecules of more than one size. Noble gases rarely form bonds, so they only have one atom. The most familiar homonuclear molecules are diatomic, meaning they consist of two atoms, though not all diatomic molecules are homonuclear. Homonuclear diatomic molecules include hydrogen (H), oxygen (O), nitrogen (N) and all of the halogens. Ozone (O) is a common triatomic homonuclear molecule. Homonuclear tetratomic molecules include arsenic (As) and

neg: Skeletal formula Skeletal formula The skeletal formula, also called line-angle formula or shorthand formula, of an organic compound is a type of molecular structural formula that serves as a shorthand representation of a molecule's bonding and some details of its molecular geometry. A skeletal formula shows the skeletal structure or skeleton of a molecule, which is composed of the skeletal atoms that make up the molecule. It is represented in two dimensions, as on a piece of paper. It employs certain conventions to represent carbon and hydrogen atoms, which are the most common in organic chemistry. An early form of this representation

neg: Small molecule molecule" biologics is that many small molecules can be taken orally whereas biologics generally require injection or another parenteral administration. A variety of organisms including bacteria, fungi, and plants, produce small molecule secondary metabolites also known as natural products, which play a role in cell signaling, pigmentation and in defense against predation. Secondary metabolites are a rich source of biologically active compounds and hence are often used as research tools and leads for drug discovery. Examples of secondary metabolites include: Enzymes and receptors are often activated or inhibited by endogenous protein, but can be also inhibited by endogenous or exogenous

neg: Enzyme inhibitor molecule of ricin to kill a cell. Enzyme inhibitor An enzyme inhibitor is a molecule that binds to an enzyme and decreases its activity. Since blocking an enzyme's activity can kill a pathogen or correct a metabolic imbalance, many drugs are enzyme inhibitors. They are also used in pesticides. Not all molecules that bind to enzymes are inhibitors; "enzyme activators" bind to enzymes and increase their enzymatic activity, while enzyme substrates bind and are converted to products in the normal catalytic cycle of the enzyme. The binding of an inhibitor can stop a substrate from entering the enzyme's active site

neg: Fragmentation (cell biology) is necessary to obtain discrete, small regions of an organism's DNA that constitute specific genes. Only relatively small DNA molecules can be cloned in any available vector. Therefore, the long DNA molecules that compose an organism's genome must be cleaved into fragments that can be inserted into the vector DNA. Two enzymes facilitate the production of such recombinant DNA molecules: The key to cloning a DNA fragment is to link it to a vector DNA molecule that can replicate within a host cell. After a single recombinant DNA molecule (composed of a vector plus an inserted DNA fragment) is introduced

neg: Glycosyltransferase Glycosyltransferase Glycosyltransferases (GTFs, Gtfs) are enzymes (EC 2.4) that establish natural glycosidic linkages. They catalyze the transfer of saccharide moieties from an activated nucleotide sugar (also known as the "glycosyl donor") to a nucleophilic glycosyl acceptor molecule, the nucleophile of which can be oxygen- carbon-, nitrogen-, or sulfur-based. The result of glycosyl transfer can be a carbohydrate, glycoside, oligosaccharide, or a polysaccharide. Some glycosyltransferases catalyse transfer to inorganic phosphate or water. Glycosyl transfer can also occur to protein residues, usually to tyrosine, serine, or threonine to give O-linked glycoproteins, or to asparagine to give N-linked glycoproteins. Mannosyl groups may be

neg: DNA polymerase an RNA-dependent DNA polymerase (RdDp) that synthesizes DNA from a template of RNA. The reverse transcriptase family contain both DNA polymerase functionality and RNase H functionality, which degrades RNA base-paired to DNA. An example of a retrovirus is HIV. DNA polymerase DNA polymerase is an enzyme that synthesizes DNA molecules from deoxyribonucleotides, the building blocks of DNA. These enzymes are essential for DNA replication and usually work in pairs to create two identical DNA strands from a single original DNA molecule. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing

neg: Latrotoxin inactive precursor molecule of α-LTX (156.9 kDa) is formed. This precursor molecule undergoes post-translational processing where the eventual, active α-LTX protein (131.5 kDa) is formed. The N-terminus of the α-LTX precursor molecule is preceded by short hydrophilic sequences ending with a cluster of basic amino acids. These clusters are recognized by proteolytic enzymes (furin-like proteases), which cleave and activate the α-LTX precursor molecules by means of hydrolysis. The C-terminus too is recognized by these furin-like proteases and is also cleaved. α-LTX precursor molecules are synthesized by free ribosomes in the cytosol and are therefore cytosolic in the secretory epithelial cells