Publication
Automated reconstruction of E-coli metabolic network from labeled metabolites
Related concepts (32)
Isotopic labeling
Isotopic labeling (or isotopic labelling) is a technique used to track the passage of an isotope (an atom with a detectable variation in neutron count) through a reaction, metabolic pathway, or cell. The reactant is 'labeled' by replacing specific atoms by their isotope. The reactant is then allowed to undergo the reaction. The position of the isotopes in the products is measured to determine the sequence the isotopic atom followed in the reaction or the cell's metabolic pathway.
Metabolic network modelling
Metabolic network modelling, also known as metabolic network reconstruction or metabolic pathway analysis, allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology. A reconstruction breaks down metabolic pathways (such as glycolysis and the citric acid cycle) into their respective reactions and enzymes, and analyzes them within the perspective of the entire network.
Metabolic pathway
In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes. In most cases of a metabolic pathway, the product of one enzyme acts as the substrate for the next. However, side products are considered waste and removed from the cell. These enzymes often require dietary minerals, vitamins, and other cofactors to function.
Hydrogen atom
A hydrogen atom is an atom of the chemical element hydrogen. The electrically neutral atom contains a single positively charged proton and a single negatively charged electron bound to the nucleus by the Coulomb force. Atomic hydrogen constitutes about 75% of the baryonic mass of the universe. In everyday life on Earth, isolated hydrogen atoms (called "atomic hydrogen") are extremely rare. Instead, a hydrogen atom tends to combine with other atoms in compounds, or with another hydrogen atom to form ordinary (diatomic) hydrogen gas, H2.
Metabolic engineering
Metabolic engineering is the practice of optimizing genetic and regulatory processes within cells to increase the cell's production of a certain substance. These processes are chemical networks that use a series of biochemical reactions and enzymes that allow cells to convert raw materials into molecules necessary for the cell's survival. Metabolic engineering specifically seeks to mathematically model these networks, calculate a yield of useful products, and pin point parts of the network that constrain the production of these products.
Atom
An atom is a particle that consists of a nucleus of protons and neutrons surrounded by a cloud of electrons. The atom is the basic particle of the chemical elements, and the chemical elements are distinguished from each other by the number of protons that are in their atoms. For example, any atom that contains 11 protons is sodium, and any atom that contains 29 protons is copper. The number of neutrons defines the isotope of the element. Atoms are extremely small, typically around 100 picometers across.
Atomic electron transition
In atomic physics and chemistry, an atomic electron transition (also called an electronic (de-)excitation, atomic transition, or quantum jump) is a change (or jump) of an electron from one energy level to another within an atom or artificial atom. It appears discontinuous as the electron "jumps" from one quantized energy level to another, typically in a few nanoseconds or less. Electron transitions cause the emission or absorption of electromagnetic radiation in the form of quantized units called photons.
Metabolism
Metabolism (məˈtæbəlɪzəm, from μεταβολή metabolē, "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the conversion of food to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments.
Degenerate energy levels
In quantum mechanics, an energy level is degenerate if it corresponds to two or more different measurable states of a quantum system. Conversely, two or more different states of a quantum mechanical system are said to be degenerate if they give the same value of energy upon measurement. The number of different states corresponding to a particular energy level is known as the degree of degeneracy (or simply the degeneracy) of the level.
Metabolic network
A metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell. As such, these networks comprise the chemical reactions of metabolism, the metabolic pathways, as well as the regulatory interactions that guide these reactions. With the sequencing of complete genomes, it is now possible to reconstruct the network of biochemical reactions in many organisms, from bacteria to human.