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Ligase
In biochemistry, a ligase is an enzyme that can catalyze the joining ( ligation) of two large molecules by forming a new chemical bond. This is typically via hydrolysis of a small pendant chemical group on one of the larger molecules or the enzyme catalyzing the linking together of two compounds, e.g., enzymes that catalyze joining of C-O, C-S, C-N, etc. In general, a ligase catalyzes the following reaction: :Ab + C → A–C + b or sometimes :Ab + cD → A–D + b + c + d + e + f where the lowercase letters can signify the small, dependent groups. Ligase can join two complementary fragments of nucleic acid and repair single stranded breaks that arise in double stranded DNA during replication. Nomenclature The common names of ligases often include the word "ligase", such as DNA ligase, an enzyme commonly used in molecular biology laboratories to join together DNA fragments. Other common names for ligases include the word "synthetase", because they are used to synt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Ligase
DNA ligase is a specific type of enzyme, a ligase, () that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such as DNA ligase IV) may specifically repair double-strand breaks (i.e. a break in both complementary strands of DNA). Single-strand breaks are repaired by DNA ligase using the complementary strand of the double helix as a template, with DNA ligase creating the final phosphodiester bond to fully repair the DNA. DNA ligase is used in both DNA repair and DNA replication (see '' Mammalian ligases''). In addition, DNA ligase has extensive use in molecular biology laboratories for recombinant DNA experiments (see '' Research applications''). Purified DNA ligase is used in gene cloning to join DNA molecules together to form recombinant DNA. Enzymatic mechanism The mechanism of DNA ligase is to form two cova ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ubiquitin Ligase
A ubiquitin ligase (also called an E3 ubiquitin ligase) is a protein that recruits an E2 ubiquitin-conjugating enzyme that has been loaded with ubiquitin, recognizes a protein substrate, and assists or directly catalyzes the transfer of ubiquitin from the E2 to the protein substrate. In simple and more general terms, the ligase enables movement of ubiquitin from a ubiquitin carrier to another thing (the substrate) by some mechanism. The ubiquitin, once it reaches its destination, ends up being attached by an isopeptide bond to a lysine residue, which is part of the target protein. E3 ligases interact with both the target protein and the E2 enzyme, and so impart substrate specificity to the E2. Commonly, E3s polyubiquitinate their substrate with Lys48-linked chains of ubiquitin, targeting the substrate for destruction by the proteasome. However, many other types of linkages are possible and alter a protein's activity, interactions, or localization. Ubiquitination by E3 ligases r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ligation (molecular Biology)
In molecular biology, ligation is the joining of two nucleic acid fragments through the action of an enzyme. It is an essential laboratory procedure in the molecular cloning of DNA, whereby DNA fragments are joined to create recombinant DNA molecules (such as when a foreign DNA fragment is inserted into a plasmid). The ends of DNA fragments are joined by the formation of phosphodiester bonds between the 3'-hydroxyl of one DNA terminus with the 5'-phosphoryl of another. RNA may also be ligated similarly. A co-factor is generally involved in the reaction, and this is usually ATP or NAD+. Ligation in the laboratory is normally performed using T4 DNA ligase. However, procedures for ligation without the use of standard DNA ligase are also popular. Ligation reaction The mechanism of the ligation reaction was first elucidated in the laboratory of I. Robert Lehman. Two fragments of DNA may be joined by DNA ligase which catalyzes the formation of a phosphodiester bond between the 3' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nuclease
A nuclease (also archaically known as nucleodepolymerase or polynucleotidase) is an enzyme capable of cleaving the phosphodiester bonds between nucleotides of nucleic acids. Nucleases variously effect single and double stranded breaks in their target molecules. In living organisms, they are essential machinery for many aspects of DNA repair. Defects in certain nucleases can cause genetic instability or immunodeficiency. Nucleases are also extensively used in molecular cloning. There are two primary classifications based on the locus of activity. Exonucleases digest nucleic acids from the ends. Endonucleases act on regions in the ''middle'' of target molecules. They are further subcategorized as deoxyribonucleases and ribonucleases. The former acts on DNA, the latter on RNA. History In the late 1960s, scientists Stuart Linn and Werner Arber isolated examples of the two types of enzymes responsible for phage growth restriction in Escherichia coli ( E. coli) bacteria. One of t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protease
A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalyzes (increases reaction rate or "speeds up") proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products. They do this by cleaving the peptide bonds within proteins by hydrolysis, a reaction where water breaks bonds. Proteases are involved in many biological functions, including digestion of ingested proteins, protein catabolism (breakdown of old proteins), and cell signaling. In the absence of functional accelerants, proteolysis would be very slow, taking hundreds of years. Proteases can be found in all forms of life and viruses. They have independently evolved multiple times, and different classes of protease can perform the same reaction by completely different catalytic mechanisms. Hierarchy of proteases Based on catalytic residue Proteases can be classified into seven broad groups: * Serine prot ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Argininosuccinate Synthetase
Argininosuccinate synthase or synthetase (ASS; ) is an enzyme that catalyzes the synthesis of argininosuccinate from citrulline and aspartate. In humans, argininosuccinate synthase is encoded by the '' ASS gene'' located on chromosome 9. ASS is responsible for the third step of the urea cycle and one of the reactions of the citrulline-NO cycle. Expression The expressed ASS gene is at least 65 kb in length, including at least 12 introns. In humans, ''ASS'' is expressed mostly in the cells of the liver and kidney. Mechanism In the first step of the catalyzed reaction, citrulline attacks the α-phosphate of ATP to form citrulline adenylate, a reactive intermediate. The attachment of AMP to the ureido (urea-like) group on citrulline activates the carbonyl center for subsequent nucleophilic attack. This activation facilitates the second step, in which the α-amino group of aspartate attacks the ureido group. Attack by aspartate is the rate-limiting step of the react ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Enzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different molecules known as product (chemistry), products. Almost all metabolism, metabolic processes in the cell (biology), cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called ''enzymology'' and the field of pseudoenzyme, pseudoenzyme analysis recognizes that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts are Ribozyme, catalytic RNA molecules, called ribozymes. Enzymes' Chemical specificity, specific ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Enzyme Commission Number
The Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze. As a system of enzyme nomenclature, every EC number is associated with a recommended name for the corresponding enzyme-catalyzed reaction. EC numbers do not specify enzymes but enzyme-catalyzed reactions. If different enzymes (for instance from different organisms) catalyze the same reaction, then they receive the same EC number. Furthermore, through convergent evolution, completely different protein folds can catalyze an identical reaction (these are sometimes called non-homologous isofunctional enzymes) and therefore would be assigned the same EC number. By contrast, UniProt identifiers uniquely specify a protein by its amino acid sequence. Format of number Every enzyme code consists of the letters "EC" followed by four numbers separated by periods. Those numbers represent a progressively finer classification of the enzyme. Preliminary ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chelatase
In biochemistry, chelatases are enzymes that catalyze the insertion ("metalation") of naturally occurring tetrapyrroles. Many tetrapyrrole-based cofactors exist in nature including hemes, chlorophylls, and vitamin B12. These metallo cofactors are derived by the reaction of metal cations with tetrapyrroles, which are not ligands ''per se'', but the conjugate acids thereof. In the case of ferrochelatases, the reaction that chelatases catalyze is: :Fe2+ + H2P → FeP + 2 H+ In the above equation H2P represents a sirohydrochlorin or a porphyrin, such as protoporphyrin IX. Chelatases are required because porphyrins and related macrocyclic ligands are extremely slow to metalate, despite favorable thermodynamics. These low rates are attributed to the tight fit of the metal into the rigid 18- or 17-membered tetrapyrrole macrocycle. Several families of chelatase are known including cobalt chelatase, magnesium chelatase, and ferrochelatase. Nickel insertion into a sirohydrochlor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biochemistry
Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology and metabolism. Over the last decades of the 20th century, biochemistry has become successful at explaining living processes through these three disciplines. Almost all areas of the life sciences are being uncovered and developed through biochemical methodology and research.Voet (2005), p. 3. Biochemistry focuses on understanding the chemical basis which allows biological molecules to give rise to the processes that occur within living cells and between cells, Karp (2009), p. 2. in turn relating greatly to the understanding of tissues and organs, as well as organism structure and function. Miller (2012). p. 62. Biochemistry is closely related to molecular biology, which is the study of the molecular mechanisms of biological phenom ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Peripheral Membrane Protein
Peripheral membrane proteins, or extrinsic membrane proteins, are membrane proteins that adhere only temporarily to the biological membrane with which they are associated. These proteins attach to integral membrane proteins, or penetrate the peripheral regions of the lipid bilayer. The regulatory protein subunits of many ion channels and transmembrane receptors, for example, may be defined as peripheral membrane proteins. In contrast to integral membrane proteins, peripheral membrane proteins tend to collect in the water-soluble component, or fraction, of all the proteins extracted during a protein purification procedure. Proteins with GPI anchors are an exception to this rule and can have purification properties similar to those of integral membrane proteins. The reversible attachment of proteins to biological membranes has shown to regulate cell signaling and many other important cellular events, through a variety of mechanisms. For example, the close association between m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Classical Compound
Neoclassical compounds are compound words composed from combining forms (which act as affixes or stems) derived from classical Latin or ancient Greek roots. New Latin comprises many such words and is a substantial component of the technical and scientific lexicon of English and other languages, via international scientific vocabulary (ISV). For example, ''bio-'' combines with '' -graphy'' to form ''biography'' ("life" + "writing/recording"). Source of international technical vocabulary Neoclassical compounds represent a significant source of Neo-Latin vocabulary. Moreover, since these words are composed from classical languages whose prestige is or was respected throughout the Western European culture, these words typically appear in many different languages. Their widespread use makes technical writing generally accessible to readers who may only have a smattering of the language in which it appears. Not all European languages have been equally receptive to neoclassical ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
