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Edman Degradation
Edman degradation, developed by Pehr Edman, is a method of sequencing amino acids in a peptide. In this method, the amino-terminal residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues. Mechanism Phenyl isothiocyanate is reacted with an uncharged N-terminal amino group, under mildly alkaline conditions, to form a cyclical ''phenylthiocarbamoyl'' derivative. Then, under acidic conditions, this derivative of the terminal amino acid is cleaved as a thiazolinone derivative. The thiazolinone amino acid is then selectively extracted into an organic solvent and treated with acid to form the more stable phenylthiohydantoin (PTH)- amino acid derivative that can be identified by using chromatography or electrophoresis. This procedure can then be repeated again to identify the next amino acid. A major drawback to this technique is that the peptides being sequenced in this manner cannot have more than 50 to 60 residues (and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pehr Edman
Pehr Victor Edman (14 April 1916 — 19 March 1977) was a Swedish biochemist. He developed a method for sequencing proteins; the Edman degradation. Early life Edman was born in Stockholm, Sweden. In 1935 he started studying medicine at Karolinska Institutet, where he became interested in basic research and received a bachelor in medicine in 1938. His research was interrupted by the outbreak of World War II, where he was drafted to serve in the Swedish army. He returned to the Karolinska Institutet where he earned his doctoral degree under advice from Professor Erik Jorpes in 1946. Developing the Edman Degradation At the time Edman started working on Angiotensin, it was just being recognized that proteins are distinct entities with a defined molecular mass, electric charge and structure. This inspired Edman to develop a method, that could be used to determine the sequence of amino acids in the protein. In 1947, he was awarded a travel stipend to go to Rockefeller Institute ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
N-terminus
The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the amine group is bonded to the carboxylic group of another amino acid, making it a chain. That leaves a free carboxylic group at one end of the peptide, called the C-terminus, and a free amine group on the other end called the N-terminus. By convention, peptide sequences are written N-terminus to C-terminus, left to right (in LTR writing systems). This correlates the translation direction to the text direction, because when a protein is translated from messenger RNA, it is created from the N-terminus to the C-terminus, as amino acids are added to the carboxyl end of the protein. Chemistry Each amino acid has an amine group and a carboxylic group. Amino acids link to one another by peptide bonds which form through a dehydration reaction that ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Name Reactions
A name reaction is a chemical reaction named after its discoverers or developers. Among the tens of thousands of organic reactions that are known, hundreds of such reactions are well-known enough to be named after people. Well-known examples include the Grignard reaction, the Sabatier reaction, the Wittig reaction, the Claisen condensation, the Friedel-Crafts acylation, and the Diels-Alder reaction. Books have been published devoted exclusively to name reactions;Alfred Hassner, C. Stumer. ''Organic syntheses based on name reactions''. Elsevier, 2002. Li, Jie Jack. ''Name Reactions: A Collection of Detailed Reaction Mechanisms''. Springer, 2003. the Merck Index, a chemical encyclopedia, also includes an appendix on name reactions. As organic chemistry developed during the 20th century, chemists started associating synthetically useful reactions with the names of the discoverers or developers; in many cases, the name is merely a mnemonic. Some cases of reactions that were not reall ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteomics
Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body. The proteome is the entire set of proteins produced or modified by an organism or system. Proteomics enables the identification of ever-increasing numbers of proteins. This varies with time and distinct requirements, or stresses, that a cell or organism undergoes. Proteomics is an interdisciplinary domain that has benefited greatly from the genetic information of various genome projects, including the Human Genome Project. It covers the exploration of proteomes from the overall level of protein composition, structure, and activity, and is an important component of functional genomics. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a ''residue'' indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of non-covalent interactions such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. This is t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Organic Reactions
Organic reactions are chemical reactions involving organic compounds. The basic organic chemistry reaction types are addition reactions, elimination reactions, substitution reactions, pericyclic reactions, rearrangement reactions, photochemical reactions and redox reactions. In organic synthesis, organic reactions are used in the construction of new organic molecules. The production of many man-made chemicals such as drugs, plastics, food additives, fabrics depend on organic reactions. The oldest organic reactions are combustion of organic fuels and saponification of fats to make soap. Modern organic chemistry starts with the Wöhler synthesis in 1828. In the history of the Nobel Prize in Chemistry awards have been given for the invention of specific organic reactions such as the Grignard reaction in 1912, the Diels-Alder reaction in 1950, the Wittig reaction in 1979 and olefin metathesis in 2005. Classifications Organic chemistry has a strong tradition of naming a specific reac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Biology
Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physical structure of biological macromolecules is known as molecular biology. Molecular biology was first described as an approach focused on the underpinnings of biological phenomena - uncovering the structures of biological molecules as well as their interactions, and how these interactions explain observations of classical biology. In 1945 the term molecular biology was used by physicist William Astbury. In 1953 Francis Crick, James Watson, Rosalind Franklin, and colleagues, working at Medical Research Council unit, Cavendish laboratory, Cambridge (now the MRC Laboratory of Molecular Biology), made a double helix model of DNA which changed the entire research scenario. They proposed the DNA structure based on previous research done by Ro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dansyl Chloride
Dansyl chloride or 5-(DimethylAmino)Naphthalene-1-SulfonYL chloride is a reagent that reacts with primary amino groups in both aliphatic and aromatic amines to produce stable blue- or blue-green–fluorescent sulfonamide adducts. It can also be made to react with secondary amines. Dansyl chloride is widely used to modify amino acids; specifically, protein sequencing and amino acid analysis. Dansyl chloride may also be denoted DNSC. Likewise, a similar derivative, dansyl amide is known as DNSA. In addition, these protein-DNSC conjugates are sensitive to their immediate environment. This, in combination with their ability to accept energy (as in fluorescence resonance energy transfer) from the amino acid tryptophan, allows this labeling technique to be used in investigating protein folding and dynamics. The fluorescence of these sulfonamide adducts can be enhanced by adding alpha-cyclodextrin. Dansyl chloride is unstable in dimethyl sulfoxide, which should never be used to prep ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bergmann Degradation
The Bergmann degradation is a series of chemical reactions designed to remove a single amino acid from the carboxylic acid (C-terminal) end of a peptide. First demonstrated by Max Bergmann in 1934, it is a rarely used method for sequencing peptides. The later developed Edman degradation is an improvement upon the Bergmann degradation, instead cleaving the N-terminal amino acid of peptides to produce a hydantoin containing the desired amino acid. The Bergmann degradation follows the earlier work of Bergmann and his close colleague Leonidas Zervas, combining the organic azide degradation of the Curtius rearrangement with the Bergmann-Zervas carbobenzoxy method, which they designed to occur under relatively mild conditions so as to allow peptide sequencing. A single round of the Bergmann degradation yields an aldehyde containing the sought after amino acid residue and the remaining fragment of the original peptide in amide form. The acyl azide of a peptide (1) undergoes a Curtius r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Isoaspartate
Isoaspartic acid (isoaspartate, isoaspartyl, β-aspartate) is an aspartic acid residue isomeric to the typical α peptide linkage. It is a β-amino acid, with the side chain carboxyl moved to the backbone. Such a change is caused by a chemical reaction in which the nitrogen atom on the N+1 following peptide bond (in black at top right of Figure 1) nucleophilically attacks the γ-carbon of the side chain of an asparagine or aspartic acid residue, forming a succinimide intermediate (in red). Hydrolysis of the intermediate results in two products, either aspartic acid (in black at left) or isoaspartic acid, which is a β-amino acid (in green at bottom right). The reaction also results in the deamidation of the asparagine residue. Racemization may occur leading to the formation of D-aminoacids. Kinetics of isoaspartyl formation Isoaspartyl formation reactions have been conjectured to be one of the factors that limit the useful lifetime of proteins. Isoaspartyl formation proceeds muc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pyroglutamic Acid
Pyroglutamic acid (also known as PCA, 5-oxoproline, pidolic acid) is a ubiquitous but little studied natural amino acid derivative in which the free amino group of glutamic acid or glutamine cyclizes to form a lactam. The names of pyroglutamic acid conjugate base, anion, salts, and esters are pyroglutamate, 5-oxoprolinate, or pidolate. It is a metabolite in the glutathione cycle that is converted to glutamate by 5-oxoprolinase. Pyroglutamate is found in many proteins including bacteriorhodopsin. ''N''-terminal glutamic acid and glutamine residues can spontaneously cyclize to become pyroglutamate, or enzymatically converted by glutaminyl cyclases. This is one of several forms of blocked ''N''-termini which present a problem for ''N''-terminal sequencing using Edman chemistry, which requires a free primary amino group not present in pyroglutamic acid. The enzyme pyroglutamate aminopeptidase can restore a free ''N''-terminus by cleaving off the pyroglutamate residue. Pyroglutam ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Acetylation
: In organic chemistry, acetylation is an organic esterification reaction with acetic acid. It introduces an acetyl group into a chemical compound. Such compounds are termed ''acetate esters'' or simply '' acetates''. Deacetylation is the opposite reaction, the removal of an acetyl group from a chemical compound. Organic synthesis Acetate esters and acetamides are generally prepared by acetylations. Acetylations are often used in making C-acetyl bonds in Friedel-Crafts reactions. Carbanions and their equivalents are susceptible to acetylations. Acetylation reagents Many acetylations are achieved using these three reagents: * Acetic anhydride. This reagent is common in the laboratory; its use cogenerates acetic acid. *Acetyl chloride. This reagent is also common in the laboratory, but its use cogenerates hydrogen chloride, which can be undesirable. *Ketene. At one time acetic anhydride was prepared by the reaction of ketene with acetic acid: :H2C=C=O + CH3COOH -> (CH3CO)2 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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