Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, transporting molecules from one location to another. Proteins differ from one another in their sequence of amino acids, dictated by the nucleotide sequence of their genes, which results in protein folding into a specific three-dimensional structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are considered to be proteins and are called peptides, or sometimes oligopeptides; the individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, encoded in the genetic code.
In general, the genetic code specifies 20 standard amino acids. Shortly after or during synthesis, the residues in a protein are chemically modified by post-translational modification, which alters the physical and chemical properties, stability and the function of the proteins. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can work together to achieve a particular function, they associate to form stable protein complexes. Once formed, proteins only exist for a certain period and are degraded and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan covers a wide range, they can exist for years with an average lifespan of 1 -- 2 days in mammalian cells. Abnormal or misfolded proteins are degraded more either due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in every process within cells.
Many proteins are enzymes that are vital to metabolism. Proteins have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized. Digestion breaks the proteins down for use in the metabolism. Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation and chromatography. Methods used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance and mass spectrometry. Most proteins consist of linear polymers built from series of up to 20 different L-α- amino acids. All proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, a variable side chain are bonded.
Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO–NH amide moiety into a fixed conformation. The side chains of the standard amino acids, detailed in the list of standard amino acids, have a great variety of chemical structures and properties; the amino acids in a polypeptide chain are linked by peptide bonds. Once linked in the protein chain, an individual amino acid is called a residue, the linked series of carbon and oxygen atoms are known as the main chain or protein backbone; the peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are coplanar. The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone; the end with a free amino group is known as the N-terminus or amino terminus, whereas the end of the protein with a free carboxyl group is known as the C-terminus or carboxy terminus.
The words protein and peptide are a little ambiguous and can overlap in meaning. Protein is used to refer to the complete biological molecule in a stable conformation, whereas peptide is reserved for a short amino acid oligomers lacking a stable three-dimensional structure. However, the boundary between the two is not well defined and lies near 20–30 residues. Polypeptide can refer to any single linear chain of amino acids regardless of length, but implies an absence of a defined conformation. Proteins can interact with many types of molecules, including with other proteins, with lipids, with carboyhydrates, with DNA, it has been estimated. Smaller bacteria, such as Mycoplasma or spirochetes contain fewer molecules, on the order of 50,000 to 1 million. By contrast, eukaryotic cells are larger and thus contain much more pro
In chemistry, a trivial name is a nonsystematic name for a chemical substance. That is, the name is not recognized according to the rules of any formal system of chemical nomenclature such as IUPAC inorganic or IUPAC organic nomenclature. A trivial name is not a formal name and is a common name. Trivial names are not useful in describing the essential properties of the thing being named. Properties such as the molecular structure of a chemical compound are not indicated. And, in some cases, trivial names can be ambiguous or will carry different meanings in different industries or in different geographic regions. On the other hand, systematic names can be so convoluted and difficult to parse that their trivial names are preferred; as a result, a limited number of trivial chemical names are retained names, an accepted part of the nomenclature. Trivial names arise in the common language. Many trivial names pre-date the institution of formal naming conventions. Names can be based on a property of the chemical, including appearance and crystal structure.
All elements that have been isolated have trivial names. In scientific documents, international treaties and legal definitions, names for chemicals are needed that identify them unambiguously; this need is satisfied by systematic names. One such system, established by the International Union of Pure and Applied Chemistry, was established in 1950. Other systems have been developed by the American Chemical Society, the International Organization for Standardization, the World Health Organization. However, chemists still use many names that are not systematic because they are traditional or because they are more convenient than the systematic names; these are called trivial names. The word "trivial" used in a pejorative sense, was intended to mean "commonplace". In addition to trivial names, chemists have constructed semi-trivial names by appending a standard symbol to a trivial stem; some trivial and semi-trivial names are so used that they have been adopted by IUPAC. Traditional names of elements are trivial, some originating in alchemy.
IUPAC has accepted these names, but has defined systematic names of elements that have not yet been prepared. It has adopted a procedure by which the scientists who are credited with preparing an element can propose a new name. Once the IUPAC has accepted such a name, it replaces the systematic name. Nine elements were known by the Middle Ages – gold, tin, copper, iron and carbon. Mercury was named after the planet, but its symbol was derived from the Latin hydrargyrum, which itself comes from the greek υδράργυρος, meaning liquid silver; the symbols for the other eight are derived from descriptions of their properties in Latin. Systematic nomenclature began after Louis-Bernard Guyton de Morveau stated the need for “a constant method of denomination, which helps the intelligence and relieves the memory”; the resulting system was popularized by Antoine Lavoisier's publication of Méthode de nomenclature chimique in 1787. Lavoisier proposed. For the next 125 years, most chemists followed this suggestion, using Greek and Latin roots to compose the names.
Indium and thallium were named for the colors of particular lines in their emission spectra. Iridium, which forms compounds of many different colors, takes its name from iris, the Latin for "rainbow"; the noble gases have all been named for their origin or properties. Helium comes from the Greek helios, meaning "sun" because it was first detected as a line in the spectrum of the sun; the other noble gases are neon, krypton and radon. Many more elements have been given names. Elements have been named for celestial bodies, they have been named for mythological figures, including Titans in general and Prometheus in particular. Some elements were named for aspects of the history of their discovery. In particular and promethium were so named because the first samples detected were artificially synthesised; the connection to the Titan Prometheus was that he had been fabled to have stolen fire from the gods for mankind. Discoverers of some elements named them after their home city. Marie Curie named polonium after Poland.
Simplified molecular-input line-entry system
The simplified molecular-input line-entry system is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules; the original SMILES specification was initiated in the 1980s. It has since been extended. In 2007, an open standard called. Other linear notations include the Wiswesser line notation, ROSDAL, SYBYL Line Notation; the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. Acknowledged for their parts in the early development were "Gilman Veith and Rose Russo and Albert Leo and Corwin Hansch for supporting the work, Arthur Weininger and Jeremy Scofield for assistance in programming the system." The Environmental Protection Agency funded the initial project to develop SMILES. It has since been modified and extended by others, most notably by Daylight Chemical Information Systems.
In 2007, an open standard called "OpenSMILES" was developed by the Blue Obelisk open-source chemistry community. Other'linear' notations include the Wiswesser Line Notation, ROSDAL and SLN. In July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is considered to have the advantage of being more human-readable than InChI; the term SMILES refers to a line notation for encoding molecular structures and specific instances should be called SMILES strings. However, the term SMILES is commonly used to refer to both a single SMILES string and a number of SMILES strings; the terms "canonical" and "isomeric" can lead to some confusion when applied to SMILES. The terms are not mutually exclusive. A number of valid SMILES strings can be written for a molecule. For example, CCO, OCC and CC all specify the structure of ethanol. Algorithms have been developed to generate the same SMILES string for a given molecule; this SMILES is unique for each structure, although dependent on the canonicalization algorithm used to generate it, is termed the canonical SMILES.
These algorithms first convert the SMILES to an internal representation of the molecular structure. Various algorithms for generating canonical SMILES have been developed and include those by Daylight Chemical Information Systems, OpenEye Scientific Software, MEDIT, Chemical Computing Group, MolSoft LLC, the Chemistry Development Kit. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database; the original paper that described the CANGEN algorithm claimed to generate unique SMILES strings for graphs representing molecules, but the algorithm fails for a number of simple cases and cannot be considered a correct method for representing a graph canonically. There is no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, double bond geometry; these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES.
A notable feature of these rules is. The term isomeric SMILES is applied to SMILES in which isotopes are specified. In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph; the chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses are used to indicate points of branching on the tree; the resultant SMILES form depends on the choices: of the bonds chosen to break cycles, of the starting atom used for the depth-first traversal, of the order in which branches are listed when encountered. Atoms are represented by the standard abbreviation of the chemical elements, in square brackets, such as for gold. Brackets may be omitted in the common case of atoms which: are in the "organic subset" of B, C, N, O, P, S, F, Cl, Br, or I, have no formal charge, have the number of hydrogens attached implied by the SMILES valence model, are the normal isotopes, are not chiral centers.
All other elements must be enclosed in brackets, have charges and hydrogens shown explicitly. For instance, the SMILES for water may be written as either O or. Hydrogen may be written as a separate atom; when brackets are used, the symbol H is added if the atom in brackets is bonded to one or more hydrogen, followed by the number of hydrogen atoms if greater than 1 by the sign + for a positive charge or by - for a negative charge. For example, for ammonium. If there is more than one charge, it is written as digit.
The Jmol applet, among other abilities, offers an alternative to the Chime plug-in, no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, the Sculpt mode. Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS 9. Jmol operates on a wide variety of platforms. For example, Jmol is functional in Mozilla Firefox, Internet Explorer, Google Chrome, Safari. Chemistry Development Kit Comparison of software for molecular mechanics modeling Jmol extension for MediaWiki List of molecular graphics systems Molecular graphics Molecule editor Proteopedia PyMOL SAMSON Official website Wiki with listings of websites and moodles Willighagen, Egon. "Fast and Scriptable Molecular Graphics in Web Browsers without Java3D". Doi:10.1038/npre.2007.50.1
A carboxylic acid is an organic compound that contains a carboxyl group. The general formula of a carboxylic acid is R–COOH, with R referring to the rest of the molecule. Carboxylic acids occur widely. Important examples include acetic acid. Deprotonation of a carboxyl group gives a carboxylate anion. Important carboxylate salts are soaps. Carboxylic acids are identified by their trivial names, they have the suffix -ic acid. IUPAC-recommended names exist. For example, butyric acid is butanoic acid by IUPAC guidelines. For nomenclature of complex molecules containing a carboxylic acid, the carboxyl can be considered position one of the parent chain if there are other substituents, for example, 3-chloropropanoic acid. Alternately, it can be named as a "carboxy" or "carboxylic acid" substituent on another parent structure, for example, 2-carboxyfuran; the carboxylate anion of a carboxylic acid is named with the suffix -ate, in keeping with the general pattern of -ic acid and -ate for a conjugate acid and its conjugate base, respectively.
For example, the conjugate base of acetic acid is acetate. Carboxylic acids are polar; because they are both hydrogen-bond acceptors and hydrogen-bond donors, they participate in hydrogen bonding. Together the hydroxyl and carbonyl group forms the functional group carboxyl. Carboxylic acids exist as dimers in nonpolar media due to their tendency to "self-associate". Smaller carboxylic acids are soluble in water, whereas higher carboxylic acids have limited solubility due to the increasing hydrophobic nature of the alkyl chain; these longer chain acids tend to be rather soluble in less-polar solvents such as ethers and alcohols. Hydrophobic carboxylic acids react aqueous sodium hydroxide to give water soluble sodium salts. For example, enathic acid has a small solubility in water, but its sodium salt is soluble in water: Carboxylic acids tend to have higher boiling points than water, not only because of their increased surface area, but because of their tendency to form stabilised dimers through hydrogen bonds.
For boiling to occur, either the dimer bonds must be broken or the entire dimer arrangement must be vaporised, both of which increase the enthalpy of vaporization requirements significantly. Carboxylic acids are Brønsted -- Lowry acids, they are the most common type of organic acid. Carboxylic acids are weak acids, meaning that they only dissociate into H3O+ cations and RCOO− anions in neutral aqueous solution. For example, at room temperature, in a 1-molar solution of acetic acid, only 0.4% of the acid are dissociated. Electron-withdrawing substituents, such as -CF3 group, give stronger acids. Electron-donating substituents give weaker acids Deprotonation of carboxylic acids gives carboxylate anions; each of the carbon–oxygen bonds in the carboxylate anion has a partial double-bond character. The carbonyl carbon's partial positive charge is weakened by the -1/2 negative charges on the 2 oxygen atoms. Carboxylic acids have strong sour odors. Esters of carboxylic acids tend to have pleasant odors, many are used in perfume.
Carboxylic acids are identified as such by infrared spectroscopy. They exhibit a sharp band associated with vibration of the C–O vibration bond between 1680 and 1725 cm−1. A characteristic νO–H band appears as a broad peak in the 2500 to 3000 cm−1 region. By 1H NMR spectrometry, the hydroxyl hydrogen appears in the 10–13 ppm region, although it is either broadened or not observed owing to exchange with traces of water. Many carboxylic acids are produced industrially on a large scale, they are pervasive in nature. Esters of fatty acids are the main components of lipids and polyamides of aminocarboxylic acids are the main components of proteins. Carboxylic acids are used in the production of polymers, pharmaceuticals and food additives. Industrially important carboxylic acids include acetic acid and methacrylic acids, adipic acid, citric acid, ethylenediaminetetraacetic acid, fatty acids, maleic acid, propionic acid, terephthalic acid. In general, industrial routes to carboxylic acids differ from those used on smaller scale because they require specialized equipment.
Carbonylation of alcohols as illustrated by the Cativa process for production of acetic acid. Formic acid is prepared by a different carbonylation pathway starting from methanol. Oxidation of aldehydes with air using cobalt and manganese catalysts; the required aldehydes are obtained from alkenes by hydroformylation. Oxidation of hydrocarbons using air. For simple alkanes, this method is inexpensive but not selective enough to be useful. Allylic and benzylic compounds undergo more selective oxidations. Alkyl groups on a benzene ring are oxidized to the carboxylic acid, regardless of its chain length. Benzoic acid from toluene, terephthalic acid from para-xylene, phthalic acid from ortho-xylene are illustrative large-scale conversions. Acrylic acid is generated from propene. Base-cata