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Chymotrypsin (EC 3.4.21.1, chymotrypsins A and B, alpha-chymar ophth, avazyme, chymar, chymotest, enzeon, quimar, quimotrase, alpha-chymar, alpha-chymotrypsin A, alpha-chymotrypsin) is a digestive enzyme component of pancreatic juice acting in the duodenum, where it performs proteolysis, the breakdown of proteins and polypeptides. Chymotrypsin preferentially cleaves peptide amide bonds where the side chain of the amino acid N-terminal to the scissile amide bond (the P1 position) is a large hydrophobic amino acid (tyrosine, tryptophan, and phenylalanine). These amino acids contain an aromatic ring in their side chain that fits into a hydrophobic pocket (the S1 position) of the enzyme. It is activated in the presence of trypsin. The hydrophobic and shape complementarity between the peptide substrate P1 side chain and the enzyme S1 binding cavity accounts for the substrate specificity of this enzyme. Chymotrypsin also hydrolyzes other amide bonds in peptides at slower rates, particularly those containing leucine at the P1 position.
Cysteine is a semiessential proteinogenic amino acid with the formula HOOC−CH(−NH2)−CH2−SH. The thiol side chain in cysteine often participates in enzymatic reactions as a nucleophile. Cysteine is chiral, but interestingly, both D and L-cysteine are found in nature with D-cysteine having been found in developing brain. Cysteine is named after its discovery in urine, which comes from the urinary bladder or cyst, from kystis "bladder".
In chemistry, a disulfide is a compound containing a R−S−S−R′ functional group or the S2−
2 anion. The linkage is also called an SS-bond or sometimes a disulfide bridge and usually derived from two thiol groups.
Glutathione is an organic compound with the chemical formula HOCOCH(NH2)CH2CH2CONHCH(CH2SH)CONHCH2COOH. It is an antioxidant in plants, animals, fungi, and some bacteria and archaea. Glutathione is capable of preventing damage to important cellular components caused by sources such as reactive oxygen species, free radicals, peroxides, lipid peroxides, and heavy metals. It is a tripeptide with a gamma peptide linkage between the carboxyl group of the glutamate side chain and cysteine. The carboxyl group of the cysteine residue is attached by normal peptide linkage to glycine.
In molecular biology, post-translational modification (PTM) is the covalent process of changing proteins following protein biosynthesis. PTMs may involve enzymes or occur spontaneously. Proteins are created by ribosomes, which translate mRNA into polypeptide chains, which may then change to form the mature protein product. PTMs are important components in cell signalling, as for example when prohormones are converted to hormones.
In biochemistry, biotinylation is the process of covalently attaching biotin to a protein, nucleic acid or other molecule. Biotinylation is rapid, specific and is unlikely to disturb the natural function of the molecule due to the small size of biotin. Biotin binds to streptavidin and avidin with an extremely high affinity, fast on-rate, and high specificity, and these interactions are exploited in many areas of biotechnology to isolate biotinylated molecules of interest. Biotin-binding to streptavidin and avidin is resistant to extremes of heat, pH and proteolysis, making capture of biotinylated molecules possible in a wide variety of environments. Also, multiple biotin molecules can be conjugated to a protein of interest, which allows binding of multiple streptavidin, avidin or neutravidin protein molecules and increases the sensitivity of detection of the protein of interest. There is a large number of biotinylation reagents available that exploit the wide range of possible labelling methods. Due to the strong affinity between biotin and streptavidin, the purification of biotinylated proteins has been a widely used approach to identify protein-protein interactions and post-translational events such as ubiquitylation in molecular biology.
Protein sequencing is the practical process of determining the amino acid sequence of all or part of a protein or peptide. This may serve to identify the protein or characterize its post-translational modifications. Typically, partial sequencing of a protein provides sufficient information to identify it with reference to databases of protein sequences derived from the conceptual translation of genes.
The Bradford protein assay was developed by Marion M. Bradford in 1976. It is a quick and accurate spectroscopic analytical procedure used to measure the concentration of protein in a solution. The reaction is dependent on the amino acid composition of the measured proteins.
In organic chemistry, peptide synthesis is the production of peptides, compounds where multiple amino acids are linked via amide bonds, also known as peptide bonds. Peptides are chemically synthesized by the condensation reaction of the carboxyl group of one amino acid to the amino group of another. Protecting group strategies are usually necessary to prevent undesirable side reactions with the various amino acid side chains. Chemical peptide synthesis most commonly starts at the carboxyl end of the peptide (C-terminus), and proceeds toward the amino-terminus (N-terminus). Protein biosynthesis in living organisms occurs in the opposite direction.
In chemistry, a chemical test is a qualitative or quantitative procedure designed to identify, quantify, or characterise a chemical compound or chemical group.
Dithiothreitol (DTT) is an organosulfur compound with the formula (CH CH2SH)2. A colorless compound, it is classified as a dithiol and a diol. DTT is redox reagent also known as Cleland's reagent, after W. Wallace Cleland. The reagent is commonly used in its racemic form. Its name derives from the four-carbon sugar, threose. DTT has an epimeric ('sister') compound, dithioerythritol (DTE).
Protein methods are the techniques used to study proteins. There are experimental methods for studying proteins. Computational methods typically use computer programs to analyze proteins. However, many experimental methods require computational analysis of the raw data.
The bicinchoninic acid assay, also known as the Smith assay, after its inventor, Paul K. Smith at the Pierce Chemical Company, now part of Thermo Fisher Scientific, is a biochemical assay for determining the total concentration of protein in a solution, similar to Lowry protein assay, Bradford protein assay or biuret reagent. The total protein concentration is exhibited by a color change of the sample solution from blue to purple in proportion to protein concentration, which can then be measured using colorimetric techniques. The BCA assay was patented by Pierce Chemical Company in 1989 & the patent expired in 2006.
Cyanogen bromide is the inorganic compound with the formula (CN)Br or BrCN. It is a colorless solid that is widely used to modify biopolymers, fragment proteins and peptides, and synthesize other compounds. The compound is classified as a pseudohalogen.
In chemistry, the Biuret test, also known as Piotrowski's test, is a chemical test used for detecting the presence of at least two peptide bonds in a molecule. In the presence of peptides, a copper(II) ion forms mauve-colored coordination complexes in an alkaline solution. The reaction was first observed in 1833; In Poland, the biuret test is also known as Piotrowski's test in honor of the Polish physiologist Gustaw Piotrowski who independently rediscovered it in 1857. Several variants on the test have been developed, such as the BCA test and the Modified Lowry test.
The Folin–Ciocâlteu reagent (FCR) or Folin's phenol reagent or Folin–Denis reagent, is a mixture of phosphomolybdate and phosphotungstate used for the colorimetric in vitro assay of phenolic and polyphenolic antioxidants, also called the gallic acid equivalence method (GAE). It is named after Otto Folin, Vintilă Ciocâlteu, and Willey Glover Denis. The Folin-Denis reagent is prepared by mixing sodium tungstate and phosphomolybdic acid in phosphoric acid. The Folin–Ciocalteu reagent is just a modification of the Folin-Denis reagent. The modification consisted of the addition of lithium sulfate and bromine to the phosphotungstic-phosphomolybdic reagent.
Bioconjugation is a chemical strategy to form a stable covalent link between two molecules, at least one of which is a biomolecule.
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 physical and analytical chemistry, colorimetry or colourimetry is a technique used to determine the concentration of colored compounds in solution. A colorimeter is a device used to test the magnitude of a solution by measuring its absorbance of a specific wavelength of light.
Galactose oxidase is an enzyme that catalyzes the oxidation of D-galactose in some species of fungi.
References
- ↑ Van Noorden, R.; Maher, B.; Nuzzo, R. (2014). "The top 100 papers". Nature . 514 (7524): 550–553. Bibcode:2014Natur.514..550V. doi: 10.1038/514550a . PMID 25355343.
- ↑ Kresge, N.; Simoni, R. D.; Hill, R. L. (2005). "The Most Highly Cited Paper in Publishing History: Protein Determination by Oliver H. Lowry". Journal of Biological Chemistry . 280 (28): e25.
- ↑ Garfield, E. (1990). "The Most-Cited Papers of All Time, SCI 1945-1988. Part 1A. The SCI Top 100—Will the Lowry Method Ever Be Obliterated?" (PDF). Current Contents. 7: 3–14.
- ↑ Becker, Jeffrey M.; Caldwell, Guy A.; Zachgo, Eve Ann (1990). Biotechnology: a laboratory course. San Diego: Academic Pr. ISBN 978-0-12-084560-6.
- ↑ Everette, J. D.; Bryant, Q. M.; Green, A. M.; Abbey, Y. A.; Wangila, G. W.; Walker, R. B. (28 July 2010). "Thorough Study of Reactivity of Various Compound Classes toward the Folin−Ciocalteu Reagent". Journal of Agricultural and Food Chemistry . 58 (14): 8139–8144. doi:10.1021/jf1005935. PMC 4075968 . PMID 20583841.
- ↑ Ninfa, Alexander J. (2010). Fundamental Laboratory Approaches for Biochemistry and Biotechnology. United States of America: John Wiley & Sons, INC. p. 112. ISBN 978-0-470-08766-4.
- ↑ Lowry, O. H.; Rosebrough, N. J.; Farr, A. L.; Randall, R. J. (1951). "Protein measurement with the Folin phenol reagent" (PDF). Journal of Biological Chemistry . 193 (1): 265–75. doi: 10.1016/S0021-9258(19)52451-6 . PMID 14907713.
- Walker, J. M. (2002). The protein protocols handbook. Totowa, N.J: Humana Press.
