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In biochemistry and molecular genetics, an AP site (apurinic/apyrimidinic site), also known as an abasic site, is a location in DNA (also in RNA but much less likely) that has neither a purine nor a pyrimidine base, either spontaneously or due to DNA damage. It has been estimated that under physiological conditions 10,000 apurinic sites and 500 ...
Chorismate mutase is an intramolecular transferase and it catalyzes the conversion of chorismate to prephenate, used as a precursor for L-tyrosine and L-phenylalanine in some plants and bacteria. This reaction is a Claisen rearrangement that can proceed with or without the isomerase, though the rate increases 10 6 fold in the presence of ...
Ligation is complicated by the fact that the reaction can involve both inter- and intra-molecular reactions, but the desired ligation products in many ligation reactions (e.g. ligating a DNA fragment into a vector) needed first to be inter-molecular, i.e. between two different DNA molecules, followed by an intra-molecular reaction to seal and ...
This glossary of biology terms is a list of definitions of fundamental terms and concepts used in biology, the study of life and of living organisms.It is intended as introductory material for novices; for more specific and technical definitions from sub-disciplines and related fields, see Glossary of cell biology, Glossary of genetics, Glossary of evolutionary biology, Glossary of ecology ...
Intramolecular reactions, especially ones leading to the formation of 5- and 6-membered rings, are rapid compared to an analogous intermolecular process. This is largely a consequence of the reduced entropic cost for reaching the transition state of ring formation and the absence of significant strain associated with formation of rings of these ...
Crystalline solids and molecular solids are two opposite extreme cases of materials that exhibit substantially different transport mechanisms. While in atomic solids transport is intra-molecular, also known as band transport, in molecular solids the transport is inter-molecular, also known as hopping transport.
There are two main classes of glycosylases: monofunctional and bifunctional. Monofunctional glycosylases have only glycosylase activity, whereas bifunctional glycosylases also possess AP lyase activity that permits them to cut the phosphodiester bond of DNA, creating a single-strand break without the need for an AP endonuclease.
The process for class 1 inteins begins with an N-O or N-S shift when the side chain of the first residue (a serine, threonine, or cysteine) of the intein portion of the precursor protein nucleophilically attacks the peptide bond of the residue immediately upstream (that is, the final residue of the N-extein) to form a linear ester (or thioester) intermediate.