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.
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 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.
Flux balance analysisFlux balance analysis (FBA) is a mathematical method for simulating metabolism in genome-scale reconstructions of metabolic networks. In comparison to traditional methods of modeling, FBA is less intensive in terms of the input data required for constructing the model. Simulations performed using FBA are computationally inexpensive and can calculate steady-state metabolic fluxes for large models (over 2000 reactions) in a few seconds on modern personal computers.
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.
ThermodynamicsThermodynamics is a branch of physics that deals with heat, work, and temperature, and their relation to energy, entropy, and the physical properties of matter and radiation. The behavior of these quantities is governed by the four laws of thermodynamics which convey a quantitative description using measurable macroscopic physical quantities, but may be explained in terms of microscopic constituents by statistical mechanics.
BiosynthesisIn molecular biology, biosynthesis is a multi-step, enzyme-catalyzed process where substrates are converted into more complex products in living organisms. In biosynthesis, simple compounds are modified, converted into other compounds, or joined to form macromolecules. This process often consists of metabolic pathways. Some of these biosynthetic pathways are located within a single cellular organelle, while others involve enzymes that are located within multiple cellular organelles.
FermentationFermentation is a metabolic process that produces chemical changes in organic substances through the action of enzymes. In biochemistry, it is narrowly defined as the extraction of energy from carbohydrates in the absence of oxygen. In food production, it may more broadly refer to any process in which the activity of microorganisms brings about a desirable change to a foodstuff or beverage. The science of fermentation is known as zymology.
BiofuelBiofuel is a fuel that is produced over a short time span from biomass, rather than by the very slow natural processes involved in the formation of fossil fuels, such as oil. Biofuel can be produced from plants or from agricultural, domestic or industrial biowaste. The climate change mitigation potential of biofuel varies considerably, from emission levels comparable to fossil fuels in some scenarios to negative emissions in others. Biofuels are mostly used for transportation, but can also be used for heating and electricity.
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.
Lactic acid fermentationLactic acid fermentation is a metabolic process by which glucose or other six-carbon sugars (also, disaccharides of six-carbon sugars, e.g. sucrose or lactose) are converted into cellular energy and the metabolite lactate, which is lactic acid in solution. It is an anaerobic fermentation reaction that occurs in some bacteria and animal cells, such as muscle cells. If oxygen is present in the cell, many organisms will bypass fermentation and undergo cellular respiration; however, facultative anaerobic organisms will both ferment and undergo respiration in the presence of oxygen.
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 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.
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.
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.
Reaction mechanismIn chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical reaction occurs. A chemical mechanism is a theoretical conjecture that tries to describe in detail what takes place at each stage of an overall chemical reaction. The detailed steps of a reaction are not observable in most cases. The conjectured mechanism is chosen because it is thermodynamically feasible and has experimental support in isolated intermediates (see next section) or other quantitative and qualitative characteristics of the reaction.
Second-generation biofuelsSecond-generation biofuels, also known as advanced biofuels, are fuels that can be manufactured from various types of non-food biomass. Biomass in this context means plant materials and animal waste used especially as a source of fuel. First-generation biofuels are made from sugar-starch feedstocks (e.g., sugarcane and corn) and edible oil feedstocks (e.g., rapeseed and soybean oil), which are generally converted into bioethanol and biodiesel, respectively.
Chain reactionA chain reaction is a sequence of reactions where a reactive product or by-product causes additional reactions to take place. In a chain reaction, positive feedback leads to a self-amplifying chain of events. Chain reactions are one way that systems which are not in thermodynamic equilibrium can release energy or increase entropy in order to reach a state of higher entropy. For example, a system may not be able to reach a lower energy state by releasing energy into the environment, because it is hindered or prevented in some way from taking the path that will result in the energy release.
Equilibrium thermodynamicsEquilibrium Thermodynamics is the systematic study of transformations of matter and energy in systems in terms of a concept called thermodynamic equilibrium. The word equilibrium implies a state of balance. Equilibrium thermodynamics, in origins, derives from analysis of the Carnot cycle. Here, typically a system, as cylinder of gas, initially in its own state of internal thermodynamic equilibrium, is set out of balance via heat input from a combustion reaction.
Thermodynamic operationA thermodynamic operation is an externally imposed manipulation that affects a thermodynamic system. The change can be either in the connection or wall between a thermodynamic system and its surroundings, or in the value of some variable in the surroundings that is in contact with a wall of the system that allows transfer of the extensive quantity belonging that variable. It is assumed in thermodynamics that the operation is conducted in ignorance of any pertinent microscopic information.
