Metabolic pathwayIn 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.
Metabolic network modellingMetabolic 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.
Flux (metabolism)Flux, or metabolic flux is the rate of turnover of molecules through a metabolic pathway. Flux is regulated by the enzymes involved in a pathway. Within cells, regulation of flux is vital for all metabolic pathways to regulate the pathway's activity under different conditions. Flux is therefore of great interest in metabolic network modelling, where it is analysed via flux balance analysis and metabolic control analysis.
MetabolomicsMetabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles. The metabolome represents the complete set of metabolites in a biological cell, tissue, organ, or organism, which are the end products of cellular processes.
Thermodynamic processClassical thermodynamics considers three main kinds of thermodynamic process: (1) changes in a system, (2) cycles in a system, and (3) flow processes. (1)A Thermodynamic process is a process in which the thermodynamic state of a system is changed. A change in a system is defined by a passage from an initial to a final state of thermodynamic equilibrium. In classical thermodynamics, the actual course of the process is not the primary concern, and often is ignored.
Thermodynamic equilibriumThermodynamic equilibrium is an axiomatic concept of thermodynamics. It is an internal state of a single thermodynamic system, or a relation between several thermodynamic systems connected by more or less permeable or impermeable walls. In thermodynamic equilibrium, there are no net macroscopic flows of matter nor of energy within a system or between systems. In a system that is in its own state of internal thermodynamic equilibrium, no macroscopic change occurs.
Thermodynamic systemA thermodynamic system is a body of matter and/or radiation, considered as separate from its surroundings, and studied using the laws of thermodynamics. Thermodynamic systems may be isolated, closed, or open. An isolated system exchanges no matter or energy with its surroundings, whereas a closed system does not exchange matter but may exchange heat and experience and exert forces. An open system can interact with its surroundings by exchanging both matter and energy.
Thermodynamic stateIn thermodynamics, a thermodynamic state of a system is its condition at a specific time; that is, fully identified by values of a suitable set of parameters known as state variables, state parameters or thermodynamic variables. Once such a set of values of thermodynamic variables has been specified for a system, the values of all thermodynamic properties of the system are uniquely determined. Usually, by default, a thermodynamic state is taken to be one of thermodynamic equilibrium.
Metabolic networkA 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.
Thermodynamic cycleA thermodynamic cycle consists of linked sequences of thermodynamic processes that involve transfer of heat and work into and out of the system, while varying pressure, temperature, and other state variables within the system, and that eventually returns the system to its initial state. In the process of passing through a cycle, the working fluid (system) may convert heat from a warm source into useful work, and dispose of the remaining heat to a cold sink, thereby acting as a heat engine.
Thermodynamic equationsThermodynamics is expressed by a mathematical framework of thermodynamic equations which relate various thermodynamic quantities and physical properties measured in a laboratory or production process. Thermodynamics is based on a fundamental set of postulates, that became the laws of thermodynamics. One of the fundamental thermodynamic equations is the description of thermodynamic work in analogy to mechanical work, or weight lifted through an elevation against gravity, as defined in 1824 by French physicist Sadi Carnot.
Thermodynamic potentialA thermodynamic potential (or more accurately, a thermodynamic potential energy) is a scalar quantity used to represent the thermodynamic state of a system. Just as in mechanics, where potential energy is defined as capacity to do work, similarly different potentials have different meanings. The concept of thermodynamic potentials was introduced by Pierre Duhem in 1886. Josiah Willard Gibbs in his papers used the term fundamental functions. One main thermodynamic potential that has a physical interpretation is the internal energy U.
Systems biologySystems biology is the computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach (holism instead of the more traditional reductionism) to biological research. Particularly from the year 2000 onwards, the concept has been used widely in biology in a variety of contexts.
Fundamental thermodynamic relationIn thermodynamics, the fundamental thermodynamic relation are four fundamental equations which demonstrate how four important thermodynamic quantities depend on variables that can be controlled and measured experimentally. Thus, they are essentially equations of state, and using the fundamental equations, experimental data can be used to determine sought-after quantities like G (Gibbs free energy) or H (enthalpy).
Metabolic engineeringMetabolic 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.
MetabolismMetabolism (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.
MetabolomeThe metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism. The small molecule chemicals found in a given metabolome may include both endogenous metabolites that are naturally produced by an organism (such as amino acids, organic acids, nucleic acids, fatty acids, amines, sugars, vitamins, co-factors, pigments, antibiotics, etc.
Metabolic theory of ecologyThe metabolic theory of ecology (MTE) is the ecological component of the more general Metabolic Scaling Theory and Kleiber's law. It posits that the metabolic rate of organisms is the fundamental biological rate that governs most observed patterns in ecology. MTE is part of a larger set of theory known as metabolic scaling theory that attempts to provide a unified theory for the importance of metabolism in driving pattern and process in biology from the level of cells all the way to the biosphere.
Metabolic disorderA metabolic disorder is a disorder that negatively alters the body's processing and distribution of macronutrients, such as proteins, fats, and carbohydrates. Metabolic disorders can happen when abnormal chemical reactions in the body alter the normal metabolic process. It can also be defined as inherited single gene anomaly, most of which are autosomal recessive. Some of the symptoms that can occur with metabolic disorders are lethargy, weight loss, jaundice and seizures.
State functionIn the thermodynamics of equilibrium, a state function, function of state, or point function for a thermodynamic system is a mathematical function relating several state variables or state quantities (that describe equilibrium states of a system) that depend only on the current equilibrium thermodynamic state of the system (e.g. gas, liquid, solid, crystal, or emulsion), not the path which the system has taken to reach that state. A state function describes equilibrium states of a system, thus also describing the type of system.
