MitoPedia | Abbr. | Definition Last update 2010-08-17 | Web
Link |
A | | | |
Additive effect of convergent CI+II electron flow | Aα+β | ►Convergent electron flow simultaneously through ►CI+II into the ►Q-junction supports higher ►OXPHOS and ETS capacities than separate electron flow through either CI or CII. Physiological substrate combinations supporting convergent CI+II e-input are required for reconstitution of intracellular ►TCA cycle function. The convergent CI+II effect may be completely or partially additive, suggesting that conventional bioenergetic protocols with mt-preparations have underestimated cellular OXPHOS capacities. | MiPNet12.12 |
Adenine nucleotide translocator | ANT | The adenine nucleotide translocator exchanges ADP for ATP in an electrogenic antiport across the inner mt-membrane. | |
ADP | D | Adenosine 5’diphosphate, C10H15N5O10P2K, potassium salt; substrate of ►ANT and ►ATP synthase. | MiPNet03.02 |
Amytal | | Inhibitor of ►CI; barbiturate drug. | |
Anaplerotic reaction | | Anaplerotic reactions replenish the pool of TCA cycle intermediates. | |
ANT | | ►Adenine nucleotide translocator | |
Antimycin A | Ama | Inhibitor of CIII. | |
Ascorbate | As | Ascorbate sodium salt, C6H7O6Na | MiPNet03.02 |
ATP | T | Adenosine 5’-triphosphate, C10H14N5O13P3Na2 | MiPNet03.02 |
ATP synthase | CV | ATP synthase (Complex V) catalyzes the phosphorylation of ADP to ATP in an exergonic process that is driven by proton translocation along the electrochemical proton gradient. | |
Atractyloside | Atr | Inhibitor of ►adenine nucleotide translocator. | MiPNet03.02 |
Azide | Azd | Inhbitor of cytochrome c oxidase. | MiPNet03.02 |
B | | | |
Biochemical threshold effect | | Due to threshold effects, even a large defect diminishing the velocity of an individual enzyme results in only minor changes of pathway flux. | |
BIOPS | | Biopsy preservation solution, for preparation of muscle fibres and permeabilization with ►saponin. | MiPNet03.02 |
Bovine serum albumine | BSA | Bovine serum albumine is a membane stabilizer, oxygen radical scavenger, and binds Ca2+ and free fatty acids, hence the rather expensive essentially free fatty acid free BSA is required in mitochondrial isolation and respiration media. Sigma A 6003 fraction V. | Wikipedia |
C | | | |
Calibration, dynamic, of POS | | Calibration of the sensor response time. | |
Calibration, static, of POS | | Two-point calibration of the polarographic oxygen sensor. | |
Calibration, systemic, of respirometry chamber | | Evaluation of instrumental background oxygen flux. | |
Carboxyatractyloside | Cat | Inhibitor of ►ANT (10 µM). | MiPNet03.02 |
Cataplerosis | | Cataplerosis is the exit of TCA cycle intermediates from the mt-matrix space. | |
Cell respiration | | Cell respiration channels metabolic fuels into the bioenergetic machinery of oxidative phosphorylation, regulating oxygen consumption and being regulated by molecular redox states, ion gradients, mitochondrial membrane potential, the phosphorylation state of the ATP system, and heat dissipation in response to intrinsic and extrinsic energy demands. | |
Chemical background correction of oxygen flux | | Correction of oxygen flux for the side reaction of autooxidation, as a function of oxygen concentration. | MiPNet06.06 |
Chemical blank experiment for ISE | | Determination of the influence of different chemicals on the ISE signal. | MiPNet14.05 |
Choline dehydrogenase | | Choline dehydrogenase (EC 1.1.99.1) is bound to the inner mt-membrane, oxidizes choline in kidney and liver mitochondria, with FAD-linked electron transfer into the ►Q-junction, and is thus part of the ►ETS. | |
Citrate synthase | CS | Condensation of oxaloacate with acetyl-CoA yields citrate as an entry into the TCA cycle, with CS located in the mt-matrix. | MiPNet08.14 |
Closed system | | A system with boundaries that allow external exchange of energy (heat and work), but do not allow exchange of matter. A limiting case is light and electrons which cross the system boundary when work is exchanged in the form of light or electric energy. If the surroundings are maintained at constant temperature, and heat exchange is rapid to prevent the generation of thermal gradients, then the closed system is isothermal. Changes of closed systems can be partitioned according to internal and external sources. | Gnaiger 1993 PAC |
Coenzyme Q | Q, CoQ | Coenzyme Q, redox system (ubiquinol/ubiquinone) of the ETS. | MiPNet12.12 |
CI+II e-input | | Electron input though Complexes CI plus CII simultaneously into the Q-junction corresponds to TCA-cycle function in vivo. In mt-preparations, CI+II e-input requires addition not only of CI substrate (pyruvate+malate or glutamate+malate), but of succinate simultaneously, since metabolite depletion in the absence of succinate prevents a significant activity of CII. | |
Complex I | CI | NADH:ubiquinone oxidoreductase, EC 1.6.5.3. CI is the segment of the electron transfer system (integral enzyme of the inner mt-membrane) responsible for electron transfer from NADH to ubiquinone. CI is a proton pump. News: www.nature.com/nature/journal/v465/n7297/full/465428a.html | MiPNet08.15 |
Complex II | CII | Complex II is the only membrane-bound enzyme in the tricarboxylic acid cycle and is part of the ►ETS. The flavoprotein succinate dehydrogenase is the largest polypeptide of CII, located on the matrix face of the inner mt-membrane. Following succinate oxidation, the enzyme transfers electrons directly to the quinone pool. | MiPNet11.09 |
Complex III | CIII | | |
Complex IV | CIV | ►Cytochrome c oxidase. | |
Convergent electron flow | | Electron flow converges at the ►Q-junction from respiratory Complexes I and II (CI+II e-input), glycerophosphate dehydrogenase and electron-transferring flavoprotein. Convergent electron flow corresponds to the operation of the TCA cycle and mitochondrial substrate supply in vivo. Due to the ►additive effect of convergent CI+II electron flow on respiratory flux, respiration is increased up to 2-fold relative to flux supported only by Complex I substrates. | MiPNet12.12 |
Coupled respiration | | The coupled part of respiratory oxygen flux that pumps the fraction of protons across the inner mt-membrane that are utilized by the phosphorylation system to produce ATP from ADP and Pi. | MiPNet12.15 |
Coupled respiration in intact cells | | | |
Coupled respiration in mt-preparations | | | |
Coupling control ratio | CCR | | MiPNet12.15 |
Cyanide, calium | Kcn | KCN; inhibitor of cytochrome c oxidase (CIV). | |
Cyanohydroxycinnamate | | α-Cyanohydroxycinnamate is an inhibitor of pyruvate transport (0.65 mM). | |
Cytochrome c | c | | MiPNet09.12 |
Cytochrome c oxidase | CIV | Cytochrome c oxidase or Complex IV (CIV) is the terminal oxidase of the mitochondrial ETS, reducing oxygen to water. CIV is frequently abbreviated as COX or CcO. It is the 'ferment' (Atmungsferment) of Otto Warburg, shown to be related to the cytochromes by David Keilin. | |
D | | | |
Dicarboxylate carrier | | The dicarboxylate carrier catalyses the electroneutral exchange of malate2- (or succinate2-) for HPO42-. | MiPNet11.04 |
Digitonin | Dig | Digitonin is a mild detergent that ►permeabilizes plasma membranes completely and selectively due to their high cholesterol content, whereas mt-membranes with lower cholesterol content are affected only at higher concentrations. Optimum digitonin concentrations for complete plasma membrane permeabilization of cultured cells can be determined directly in a respirometric protocol. | MiPNet09.12 |
Dilution effect | | Dilution of the concentration of a compound or sample in the experimental chamber by a titration of another solution into the chamber. | MiPNet14.05 |
Dinitrophenol | DNP | 2,4-dinitrophenol; ►uncoupler. | |
Dithionite | Na2S2O4. | Zero solution powder, Na2S2O4. | |
Dyscoupled respiration | | In addition to intrinsic ►uncoupling, dyscoupling occurs under pathological and toxicological conditions. Thus a distinction is made between physiological uncoupling and pathologically defective dyscoupling in mitochondrial respiration. | |
E | | | |
Electron flow | | Electron flow through the mitochondrial electron transfer system (ETS) is the scalar component of chemical reactions in oxidative phosphorylation (OXPHOS). Electron flow is most conveniently measured as oxygen consumption, with four electrons being taken up when oxygen (O2) is reduced to water. | |
Electron transfer system | ETS | The mitochondrial ETS transfers electrons at steady state from externally supplied reduced substrates to oxygen. It consists of the membrane-bound ETS (►mETS) with enzyme complexes located in the inner mt-membrane, mt-matrix dehydrogenases generating NADH, and the transport systems involved in metabolite exchange across the mt-membranes. | MiPNet12.12 |
Electron-transferring flavoprotein | ETF | ETF is located on the matrix face of the inner mitochondrial membrane, supplies electrons from fatty acid β-oxidation to CoQ, and is thus an enzyme complex of the mitochondrial ►electron transfer system, ETS. | MiPNet11.09 |
Ethylene glycol tetraacetic acid | EGTA | EGTA is general chelator for heavy metals, with high affinity for Ca2+ but low affinity for Mg2+. Sigma E 4378. | Wikipedia |
ETS capacity | | Respiratory electron transfer system capacity of mitochondria in the experimentally controlled non-coupled (fully uncoupled) state E, obtained in intact cells or mitochondrial preparations with defined substrates, by titration of an established uncoupler up to optimum concentration at maximum flux. Non-coupled respiration yields an estimate of ETS capacity. In this state E, the mt-membrane potential is collapsed, which provides a reference state for flux control ratios and for measurement of the mt-membrane potential. | MiPNet12.15 |
Extensive quantity | | Extensive quantities pertain to a total system, e.g. oxygen ►flow. | Gnaiger 1993 PAC |
External flow | | External flows across the system boundaries are formally reversible. Their irreversible facet is accounted for internally as part of a heterogenous system. | |
External unspecific binding of TPP+ | | Unspecific binding of the probe molecule TPP+ outside of the inner mitochondrial membrane or on the outer side of the inner mt-membrane. | MiPNet14.05 |
F | | | |
FCCP | Fx | Carbonyl cyanide p-(trifluoro-methoxy) phenyl-hydrazone,
C10H5F3N4O; ►uncoupler, added at concentration x | MiPNet10.04 |
Flux control ratio | FCR | Flux control ratios, FCR, are ratios of oxygen flux in different respiratory control states, normalized for maximum flux in a common reference state, to obtain theoretical lower and upper limits of 0.0 and 1.0 (0% and 100%). FCR obtained from a single respirometric incubation (sequential protocol) provide an internal normalization, expressing respiratory control independent of mitochondrial content and thus independent of a marker for mitochondrial amount. FCR obtained from separate (parallel) protocols depend on determination of a common mitochondrial marker. | MiPNet12.15 |
Force | Ftr | A generalized force (intensive quantity) in thermodynamics or ergodynamics is the partial Gibbs (Helmholtz) energy change per advancement. | |
Fumarase | | | |
Fumarate | F | | MiPNet11.09 |
G | | | |
Gentle Science | GS | Gentle Science recognizes the special responsibility of the scientific community, for the quality of science, the quality of life in science, and its mission. While the individual scientist contributes her/his share, the scientific community requires concerted actions to encourage Gentle Science on institutional, national and world-wide levels. | http://www.oroboros.at/index.php?gentle-science |
Glutamate | G | Glutamate as the sole substrate is transported by the electroneutral glutamate-/OH- exchanger (Fig. 4), and is oxidized via glutamate dehydrogenase in the mitochondrial matrix. Ammonia can pass freely through the mitochondrial membrane. | MiPNet11.04 |
Glutamate-aspartate carrier | | | MiPNet11.04 |
Glycerophosphate dehydrogenase | GpDH | Mitochondrial glycerophosphate dehydrogenase is on the outer face of the inner mt-membrane and oxidizes glycerophosphate to dihydroxyacetone phosphate. A flavin prosthesic group of GpDH donates its reducing equivalents to Q. | MiPNet11.09 |
Glycerophosphate shuttle | Gp shuttle | Makes cytoplasmic NADH available for mitochondrial oxidative phosphorylation. Cytoplasmic NADH reacts with dihydroxyacetone phosphate catalyzed by cytoplasmic glycerophosphate dehydrogenase. On the outer face of the inner mitochondrial membrane, mitochondrial glycerophosphate dehydrogenase oxidizes glycerophosphate back to dihydroxyacetone phosphate, a reaction not generating NADH but reducing a flavin prosthesic group. The reduced flavoprotein donates its reducing equivalents to the electron transfer system at the level of CoQ. | MiPNet11.09 |
H | | | |
High-resolution respirometry | HRR | High-resolution respirometry is based on the OROBOROS Oxygraph-2k, combining chamber design, application of oxygen-tight materials, electrochemical sensors and electronics, Peltier-temperature control and software features (►DatLab) to obtain a unique level of quantitative resolution of oxygen concentration and oxygen flux, with a closed-chamber or open-chamber mode of operation (►TIP2k). Standardized two-point ►calibration of the polarographic oxygen sensor (static sensor calibration), calibration of the sensor response time (dynamic sensor calibration), and evaluation of ►instrumental background oxygen flux (systemic flux compensation) provide the experimental basis for high accuracy of quantitative results and quality control in HRR. | HRR |
HRR | | ►High-resolution respirometry. | HRR |
Hydroxycinnamate | Hci | Inhibitor of the pyruvate carrier. Above 10 mM pyruvate, hydroxycinnamate cannot inhibit respiration from pyruvate. | MiPNet11.04 |
I | | | |
Inorganic phosphate | Pi | Pi concentration in mitochondrial respiration media should be saturating for measurement of OXPHOS capacity (10 mM in►MiR06). | MiPNet14.13 |
Instrumental background oxygen flux | J°O2 | Instrumental background oxygen flux in a respirometer is due to oxygen consumption by the POS, and oxygen diffusion into or out of the aqueous medium in the O2k-chamber. It is measured in the range of experimental oxygen levels by a standardized instrumental background test, and is a property of the instrumental system. Instrumental background correction eliminates errors by systemic flux compensation, automatically performed by DatLab. | MiPNet14.06 |
Intensive quantity | | Intensive quantities are partial derivatives of an extensive quantity by the advancement, dtrξ, of an energy transformation. | |
Internal flow | | Within the system boundaries, irreversible internal flows of heat and matter along gradients contribute to the internal entropy production, diS. | |
Internal unspecific binding of TPP+ | | Unspecific binding of the probe molecule TPP+ in the matrix phase of mitochondria. | MiPNet14.05 |
IO2 | | ►Oxygen flow. | |
IOC | | International Oxygraph Course, O2k-workshop | IOC |
Isocitrate dehydrogenase | IDH | 2-oxoglutarate is formed from isocitrate in the TCA cycle. | MiPNet11.04 |
Isolated system | | The boundaries of isolated systems are impermeable for all forms of energy and matter. Changes of isolated systems have exclusively internal origins. | |
J | | | |
JO2 | | Oxygen flux, respiration expressed per unit system size, e.g. per volume or per mg wet weight. | |
K | | | |
KCN | Kcn | KCN | MiPNet09.12 |
Ketoglutarate | Og | ►2-oxoglutarate; α-ketoglutarate. | |
L | | | |
L/E | | The LEAK control ratio is an index of ►uncoupling or ►dyscoupling at constant ETS capacity. L/E increases with uncoupling from a theoretical minimum of 0.0 for a fully coupled system, to 1.0 for a fully uncoupled system. | MiPNet12.15 |
L/P | | L/P control ratio = (L/E) / (P/E); 1/RCR. | MiPNet12.15 |
Lactate dehydrogenase | LDH | Glycolytic marker enzyme in the cytosol, regenerating NAD+ from NADH and pyruvate, forming lactate. | MiPNet08.18 |
LEAK control ratio | L/E | ►L/E. | MiPNet12.15 |
LEAK respiration | L | LEAK oxygen flux, compensating for proton leak, slip and cation cycling, is measured as mitochondrial respiration in state L, in the presence of reducing substrate(s), but absence of inorganic phosphate or ADP, or after inhibition of the phosphorylation system. In this non-phosphorylating resting state, the electrochemical proton gradient is increased to a maximum, exerting feedback control by depressing oxygen flux to a level determined by the proton leak and the H+/O ratio. In this state of maximum protonmotive force, LEAK respiration is higher than the LEAK component in state P. | MiPNet12.15 |
LEAK state | L | Non-phosphorylating resting state of intrinsic ►uncoupled or ►dyscoupled respiration when oxygen flux is maintained mainly to compensate for the proton leak when ATP synthase is not active. | MiPNet12.15 |
LEAK state with ATP | LT | State 4 where - in mt-preparations without ATPase activity - LT is obtained after ADP is fully phosphorylated to ATP (Chance and Williams 1955) or after addition of high ATP in the absence of ADP (Gnaiger et al. 2000). | MiPNet12.15 |
LEAK state with Omy | LOmy | LEAK state induced by inhibition of ATP synthase by oligomycin (LOmy; State 4o). | MiPNet12.15 |
LEAK state without adenylates | LN | Respiration after addition of substrates, which decreases slowly to the LEAK state after oxidation of endogenous substrates with no adenylates (LN); State 2'. State 2 was re-defined as functionally the same as State 4 (Nicholls and Ferguson 2002), with reference to Chance and Williams (1956). State 2 (Chance and Williams 1955, 1956), however, is substrate-limited residual oxygen consumption at high ADP (ROXD), whereas State 2’ (LN) and State 4 (LT) are LEAK states in the absence of adenylates (LN: no ADP, no ATP) or presence of ATP (LT). | MiPNet12.15 |
M | | | |
Malate | M | Malate alone cannot support respiration of mt-preparations. | MiPNet11.04 |
Malate dehydrogenase | MDH | Malate dehydrogenase located in the mitochondrial matrix oxidizes malate to oxaloacetate. | MiPNet11.04 |
Malate transport | | The dicarboxylate carrier catalyses the electroneutral exchange of malate2- (or succinate2-) for HPO42-. The tricarboxylate carrier exchanges malate2- for citrate3- or isocitrate3- (with co-transport of H+). The 2-oxoglutarate carrier exchanges malate2- for 2-oxoglutarate2-. | MiPNet11.04 |
Malonic acid | Mna | Inhibitor of SDH (CII). | MiPNet09.12 |
Membrane bound ETS | mETS | The membrane-bound electron transfer system (►ETS) consists in mitochondria mainly of respiratory complexes CI, CII, electron transferring flavoprotein, glycerophosphate dehydrogenase and choline dehydrogenase, with convergent electron supply at the Q-junction (Coenzyme Q), and the two downstream respiratory complexes connected by cytochrome c, CIII and CIV, with oxygen as the final electron acceptor. | MiPNet12.12 |
Mersalyl | | Mersalyl is an inhibitor of the Pi symporter. | |
MiP society | | Mitochondiral Physiology Society - www.mitophysiology.org | MiP |
MiPArt Gallery | | The OROBOROS MiPArt Gallery forms a triangle connecting science, the scientific company OROBOROS INSTRUMENTS, and scientific art on the topic of mitochondrial physiology and links of science and art in general. | MiPArt |
MiPNet | | Mitochondrial physiology network, OROBOROS reference laboratories.
See also ►MiPNet-Publications. | Net |
MiPNet-Publications | | MiPNet is the abbreviation for the 'OROBOROS Journal 'Mitochondrial Physiol. Network', including chapters of the O2k-Manual, protocols, application notes, O2k-workshops, and other announcements, starting with MiPNet 1 in 1996. | ref-mipnet |
MiR06 | | Mitochondrial respiration medium 06, developed for oxygraph incubations of mitochondrial preparations; MiR05 plus catalase | MiPNet14.13 |
Mitochondria | | Greek mitos: thread; chondros: granule | |
Mitochondria, isolated | Imt | Isolated mitochondria, separated from the cell by centrifugation steps after breaking the plasma membrane. | MiPNet11.05 |
mitochondrial | mt | | |
Mitochondrial preparations | | mt-preparations are isolated mitochondria, mechanically or chemically permeabilized tissues and cells, or tissue homogenates with mechanically broken cell membranes. | |
Mitochondrial respiration | | Integrative measure of the dynamics of complex coupled metabolic pathways, including metabolite transport across the mt-membranes, TCA cycle function with electron transfer through dehydrogenases in the mt-matrix, membrane-bound electron transfer, the transmembrane proton circuit, and the phosphorylation system. | |
Multiwell respirometer | | Multiwell systems are developed as a tool for qualitative high-throughput screening, for pharmacologic testing of a large number of substances. Designed for high-throughput qualitative measurements, they should not be advertised for quantitative measurements. Reliable quantitative results cannot be obtained with the present technology offered and advertised. | HRR-FAQ |
Myxothiazol | Myx | Inhibitor of CIII (inhibits also CI; G. Lenaz). | |
N | | | |
NADH | | Nicotinadeninedinucleotide (NADH) is not permeable through the inner mt-membrane. The NADH pool integrates the activity of the TCA cycle and various matrix dehydrogenases upstream of CI, and thus forms a junction or funnel of electron transfer to CI. Cytosolic NADH is effectively made available for mitochondrial respiration through the glutamate-aspartate shuttle or glycerophosphate dehydrogenase. | |
natoms O | | 0.5 nmol O2; in bioenergetics a variety of expressions is used for units of amount of half a nmol molecular oxygen (natoms oxygen; natoms O; ng.atom O; nmol O), with the identical meaning: 0.5 nmol O2. | MiPNet12.15 |
N-ethylmaleimide | | N-ethylmaleimide blocks endogenous Pi transport. | |
netROUTINE control ratio | (R-L)/E | The netROUTINE control ratio, (R-L)/E, expresses phosphorylation-related respiration (corrected for LEAK respiration) as a fraction of ETS capacity. (R-L)/E remains constant, if dyscoupling is fully compensated by an increase of ROUTINE respiration and a constant rate of oxidative phosphorylation is maintained | MiPNet12.15 |
Nigericin | | Nigericin catalyzes K+/H+ antiport | |
Non-coupled respiration | | ►Electron flow in an open-transmembrane proton circuit mode of operation; ►ETS capacity. | MiPNet12.15 |
O | | | |
O2k | | ►Oxygraph-2k | O2k |
O2k-Publications | | Publication list of applications of the OROBOROS Oxygraph-2k and OROBOROS Oxygraph Paar. | O2k-publications |
Octanic acid | Oca | | |
Octanoyl carnitine | Oct | | |
Oligomycin | Omy | Inhibitor of ATP synthase. | MiPNet09.12 |
Open system | | A system with boundaries that allow external exchange of energy and matter; the surroundings are merely considered as a source or sink for quantities transferred across the system boundary. | Gnaiger 1993 PAC |
OroboroPedia | | Scientific terms, items and links for the O2k and instrumental aspects of OROBOROS INSTRUMENTS. | OroboroPedia |
OROBOROS INSTRUMENTS | | OROBOROS INSTRUMENTS - a new Quality in Science
Oxygraph-2k and O2k-MultiSensor MiPNetAnalyzer
unique for high-resolution respirometry - HRR
quantitative, non-plastic, scientific | Oroboros |
Oxaloacetate | | Oxaloacetate is formed from malate by MDH, and cannot permeate the inner mitochondrial membrane. | MiPNet11.04 |
Oxoglutarate | Og | 2-Oxoglutarate is a product of isocitrate dehydrogenase in the TCA cycle, and is converted by oxoglutarate dehydrogenase (OgDH). The 2-oxoglutarate carrier exchanges malate2- for 2-oxoglutarate2- as part of the malate-aspartate shuttle. | MiPNet11.04 |
OXPHOS | | Oxidative phosphorylation is the reaction of oxidation of reduced substrates partially coupled to the phosphorylation of ADP to ATP. | |
OXPHOS capacity | P | Respiration in state P: Respiratory capacity of mitochondria in the ADP-activated state of oxidative phosphorylation, at saturating concentrations of ADP, inorganic phosphate, oxygen, and defined reduced substrates; ►State 3. Since OXPHOS is partially coupled, intrinsic uncoupling and dyscoupling contribute to the control of flux in state P. | MiPNet12.15 |
OXPHOS control ratio | | ►P/E. | MiPNet12.15 |
Oxygen flow | IO2 | Oxygen consumption per total system, ►extensive quantity. Flow is advancement of a transformation in a system per time. Oxygen flow of a cell, or respiration per million cells, is distinguished from ►oxygen flux (e.g. per mg protein or wet weight). | MiPNet10.05 |
Oxygen flux | JO2 | Oxygen consumption per system size, ►specific quantity. Oxygen flux is oxygen flow divided by system size. Flux may be volume-specific (flow per volume), mass-specific (flow per mass), or marker-specific (e.g. flow per mtDNA). Oxygen flux (e.g. per body mass) is distinguished from ►oxygen flow (per subject). | MiPNet10.05 |
Oxygen kinetics | | The dependence of respiration of isolated mitochondria or cells on oxygen partial pressure. Frequently, a strictly hyperbolic kinetics is observed, with two parameters, the oxygen pressure at half-maximum flux, p50, and maximum flux, Jmax. The p50 is in the range of 0.2 to 0.8 kPa for cytochrome c oxidase, isolated mitochondria and small cells, strongly dependent on Jmax and coupling state. | Oxygen Kinetics |
Oxygen pressure | pO2 | Partial pressure of oxygen [kPa], related to oxygen concentration in solution by the oxygen solubility, SO2 [µmol/kPa]. | MiPNet06.03 |
Oxygen pressure, intracellular | pO2,i | Physiological, intracellular oxygen levels are significantly lower than air saturation under normoxia, hence respiratory measurements carried out at air saturation are effectively hyperoxic for cultured cells and isolated mitochondria. | MiPNet06.03 |
Oxygen solubility | SO2 | The oxygen solubility [µM/kPa] expresses the oxygen concentration in solution in equilibrium with the oxygen pressure in a gas phase, as a function of temperature and composition of the solution. SO2 is 10.56 µM/kPa in pure water at 37 °C. At standard barometric pressure (100 kPa), the oxygen concentration at air saturation is 207.3 µM at 37 °C (19.6 kPa partial oxygen pressure). In MiR06 and serum, the corresponding saturation concentrations are 191 and 184 µM. | MiPNet06.03 |
Oxygen solubility factor | FM | The oxygen solubility factor of the incubation medium, FM, expresses the effect of the salt concentration on oxygen solubility relative to pure water. In mitochondrial respiration medium MiR06, FM is 0.92 determined at 30 and 37 °C, and FM is 0.89 in serum at 37 °C. | MiPNet06.03 |
Oxygraph-2k | O2k | Two-chamber high-resolution respirometer for monitoring oxygen consumption with small amounts of biological material, developed by OROBOROS INSTRUMENTS in cooperation with WGT, produced in Austria by WGT, and distributed world-wide by OROBOROS INSTRUMENTS. | O2k |
P | | | |
P/E | | The OXPHOS control ratio or OXPHOS/ETS capacity decreases with limitation by the phosphorylation system. P/E increases from the lower boundary set by L/E (zero capacity of the phosphorylation system), to the upper limit of 1.0, when there is no limitation of P by the phosphorylation system or the proton backpressure (capacity of the phosphorylation system fully matches the ETS capacity; or if the system is fully uncoupled). It is important to separate the effect of ADP limitation from limitation by enzymatic capacity at saturating ADP concentration. | MiPNet12.15 |
Palmitic acid | Paa | | |
Palmitoyl carnitine | Pal | | |
Permeabilization of plasma membrane | | Plasma membrane permeabilization with ►digitonin or ►saponin yields effective wash-out of free cytosolic molecules including adenylates, substrates, and cytosolic enzymes, making externally added compounds accessible to the mitochondria. | |
Permeabilized tissue or cells | Ptic | Permeabilized tissue or cells are mitochondrial preparations obtained by selectively permeabilizing the plasma membrane mechanically or chemically, for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the mitochondrial membranes. | MiPNet11.05 |
Phenylsuccinate | | Phenylsuccinate is a competitive inhibitor of succinate transport (20 mM). | |
Phosphorylation control protocol | PCP | | |
Phosphorylation system | PS | The phosphorylation system is a functional unit consisting of adenylate nucleotide translocase, phosphate carrier, and ATP synthase. | |
Piericidine | | Piericidine is a competitive inhibitor of ►CI, ubiquinone structure; antibiotic. | |
Polarographic oxygen sensor | POS | Electrochemical oxygen sensor, introduced by L Clark, with application of a polarization voltage (0.6 to 0.8 V) and measurement of a current (amperometric), which is converted to a voltage. | POS |
POS | | ►Polarographic oxygen sensor; OROBoPOS. | POS |
Power | P | Power is external work per unit time, the product of internal flows and forces. | |
Proton leak | | Flux of protons along the electrochemical proton gradient across the inner mt-membrane, contributing to ►LEAK respiration. | MiPNet12.15 |
Proton pump | | Mitochondrial proton pumps are large enzyme complexes (CI, CII, CIV, CV) spanning the inner mt-membrane, partially encoded by mtDNA. CI, CII and CIV are proton pumps that drive protons against the electrochemical proton motive force, driven by electron transfer from reduced substrates to oxygen. In contrast, CV is a proton pump that utilizes the energy of proton flow along the proton motive force to drive the phosphorylation of ADP to ATP. | |
Pyruvate | P | | MiPNet11.04 |
Pyruvate carboxylase | | Pyruvate carboxylase synthesizes oxaloacetate from pyruvate as an ►anaplerotic reaction in the mitochondrial matrix. | |
Pyruvate carrier | | The monocarboxylic acid pyruvate- is exchanged electroneutrally for OH- by the pyruvate carrier. H+/anion symport is equivalent to OH-/anion antiport. | MiPNet11.04 |
Pyruvate dehydrogenase | PDH | Oxidative decarboxylation of pyruvate is catalyzed by pyruvate dehydrogenase in the mt-matrix, and yields acetyl-CoA. | MiPNet11.04 |
Q | | | |
Q-junction | | Junction for convergent electron entry from CI, CII, glycerophosphate DH and ETF into the Q-cycle (ubiquinol/ubiquinone) and further to CIII. | MiPNet12.12 |
R | | | |
R/E | | The ROUTINE control ratio is the ratio of (coupled) ROUTINE respiration and (non-coupled) ETS capacity. The R/E control ratio is an expression of how close ROUTINE respiration operates to ETS capacity. | |
RCR | | The respiratory control ratio, RCR, is defined as State 3/State 4 (Chance and Williams 1955). Considering an index of uncoupling, RCR should be replaced by the ►L/E ratio, if P/E<1.0 (Gnaiger, 2009). In intact cells, RCR has been used for the ratio State 3u/State 4o, i.e. for the inverse L/E ratio (Hütter et al., 2004).. | MiPNet12.15 |
Reactive oxygen species | ROS | | |
Residual oxygen consumption | ROX | Respiration remaining after application of ETS inhibitors to mitochondrial preparations or cells, or incubation of mt-preparations without substrates (State 2). | MiPNet12.15 |
Respiratory control ratio | RCR | ►RCR. | MiPNet12.15 |
Reverse electron flow from CII to CI | | Reverse electron flow from CII to CI stimulates production of ROS when mitochondria are incubated with succinate without rotenone. | MiPNet11.09 |
Rotenone | Rot | Inhibitor of CI. | MiPNet11.09 |
ROUTINE control ratio | R/E | ►R/E. | |
ROUTINE respiration | R | In the intact cell, ROUTINE respiration in the physiological coupling state, R, is controlled by physiological energy demands, energy turnover and the degree of coupling to phosphorylation (intrinsic uncoupling and pathological dyscoupling). R and growth of cells is supported by exogenous substrates in culture media, or endogenous substrates in media without energy substrates. | MiPNet12.15 |
ROX | | ►Residual oxygen consumption | MiPNet12.15 |
S | | | |
Saponin | | Saponin is a mild detergent that ►permeabilizes plasma membranes completely and selectively due to their high cholesterol content, whereas mt-membranes with lower cholesterol content are affected only at higher concentrations. Applied for permeabilization of muscle fibres. | |
Specific quantity | | Specific quantities are obtained when the ►extensive quantity is divided by system size, in contrast to ►intensive quantities. | Gnaiger 1993 PAC |
State 2 | ROXD | Substrate limited state of residual oxygen consumption, after addition of ADP (ROXD). Residual endogenous substrates are oxidized during a transient stimulation of oxygen flux by ADP; ADP concentration (D) remains high during ROXD. | MiPNet12.15 |
State 3 | P | Whereas ►OXPHOS capacity is measured at saturating concentrations of ADP and Pi, State 3 is defined as ADP stimulated respiration in the presence of high ADP and Pi concentrations (Chance and Williams, 1955) which are not necessarily saturating. For instance, non-saturating ADP concentrations are applied in State 3 in pulse titrations to determine the P/O ratio in State 3→4 (D→T) transitions, when saturating ADP concentrations would deplete the oxygen concentration in the closed oxygraph chamber before State 4 is obtained (Gnaiger et al 2000; Puchowicz et al 2004). | MiPNet12.15 |
State 3u | E | Non-coupled state of ►ETS capacity. State 3u (u for uncoupled) has been used frequently in bioenergetics, without sufficient emphasis (e.g. Villani et al 1998) on the fundamental difference between partially coupled ►OXPHOS capacity (State 3) and non-coupled ETS capacity (State 3u; Gnaiger et al 1998; Gnaiger 2009; Rasmussen and Rasmussen 2000). | MiPNet12.15 |
State 4 | LT | Respiratory state of isolated mitochondria obtained after complete phosphorylation of added ADP to ATP, which is LEAK respiration, LT, or an overestimation of LEAK respiration if ATPase activity prevents final accumulation of ATP and maintains a continuous stimulation of respiration by recycled ADP. | MiPNet12.15 |
State E | | ►ETS | capacity, E. | MiPNet12.15 |
State L | | ►LEAK | respiration, L. | MiPNet12.15 |
State P | | ►OXPHOS | capacity, P. | MiPNet12.15 |
State R | | ►ROUTINE | respiration, R. | MiPNet12.15 |
Substrate control | | Substrate control with electron entry separately through Complex I (pyruvate+malate or glutamate+malate) or Complex II (succinate+rotenone) restricts ETS capacity and artificially enhances flux control upstream of the Q-cycle, providing diagnostic information on specific branches of the ETS. Physiological combinations of Complex I+II substrates support maximum ETS and OXPHOS capacities, due to the additive effect of multiple electron supply pathways converging at the Q-junction. | MiPNet12.12 |
Substrates as electron donors | | Mitochondrial respiration depends on a continuous flow of electron-supplying substrates across the mitochondrial membranes into the matrix space. Many substrates are strong anions that cannot permeate lipid membranes and hence require carriers. | |
Substrates, cellular | Ce | Cellular substrates in vivo, endogenous | MiPNet12.15 |
Substrates, cellular | Cm | Cellular substrates in vivo, with exogenous substrate supply from culture medium or serum | MiPNet12.15 |
Substrate-uncoupler-inhibitor titration | SUIT | Titration protocol used with mt-preparations to study respiratory control in a sequence of coupling and substrates states. | MiPNet12.12 |
Succinate | S | Succinate2- is formed in the TCA cycle, and is a substrate of CII, reacting to fumarate and feeding electrons into the Q-junction through flavin adenine dinucleotide (FADH2). Succinate supports electron flux exclusively through Complex II via FADH2. | MiPNet11.09 |
Succinate dehydrogenase | SDH | TCA cycle enzyme converting succinate to fumarate, largest component of the inner mt-membrane ►CII and thus part of the ETS. | MiPNet11.09 |
Succinate transport | | The dicarboxylate carrier catalyses the electroneutral exchange of succinate2- for HPO42-. | MiPNet11.09 |
Succinate+rotenone | S(Rot) | Inhibition of Complex I by rotenone (Rot; or amytal, piericidine) prevents accumulation of oxaloacetate which is a potent inhibitor of SDH. | MiPNet11.09 |
SUIT protocol | | ►Substrate-uncoupler-inhibitor titration. | MiPNet12.12 |
T | | | |
TMPD | Tm | N,N,N’,N’-Tetramethyl-p-phenylenediamine dihydrochloride, C10H16N2.2HCl; applied as an artificial substrate for reducing cytochrome c in the respirometric assay for cytochrome c oxidase activity; is maintained in a reduced state by ascorbate; undergoes autooxidation as a function of oxygen pressure, ascrobate and cytochrome c concentration. | MiPNet06.06 |
TPP+ calibration | | | |
TPP+ electrode | | | |
TPP+ inhibitory effect | | | |
Tricarboxylate carrier | | The tricarboxylate carrier in the inner mt-membrane exchanges malate2- for citrate3- or isocitrate3-, with co-transport of H+. | MiPNet11.04 |
Tricarboxylic acid cycle | TCA cycle | A system of enzymes in the mitochondrial matrix (and SDH in the inner mt-membrane) arranged in cyclic metabolic structure, including dehydrogenases that converge in the NADH pool and succinate for entry into the ETS. Citrate synthase is a marker enzyme of the TCA cycle, at the gateway into the cycle from pyruvate via acteyl-CoA. Sections of TCA cycle are required for β-oxidation. Anaplerotic reactions fuel the TCA cycle with other intermediary metabolites. In the cell, the TCA cycle serves biosynthetic functions by metabolite export from the matrix into the cytosol. | MiPNet12.12 |
U | | | |
Uncoupled respiration | | The uncoupled part of respiration in state P pumps protons to compensate for intrinsic uncoupling, which is a property of (a) the inner mt-membrane (proton leak), (b) the proton pumps (proton slip; decoupling), and (c) is regulated by molecular uncouplers (uncoupling protein, UCP1). Uncoupled and ►dyscoupled respiration are summarized as ►LEAK respiration. In contrast, ►non-coupled respiration is induced experimentally for evaluation of ETS capacity. | MiPNet12.15 |
Uncoupler | u | Protonophore (FCCP, CCCP, DNP) which cycles across the inner mt-membrane with transport of protons and dissipation of the electrochemical proton gradient. | |
Uncoupler titration | | ►Uncouplers are applied to uncouple mitochondrial electron transfer through Colmplexes CI and CII to CIV from phosphorylation (ATP synthase, ANT and phosphate transport), particularly with the aim to obtain the ►non-coupled state E at maximum oxygen flux. | UncouplerTitrations |
Uncoupling control ratio | UCR | The uncoupling control ratio, UCR, is the ratio of ETS/ROUTINE respiration in intact cells (Steinlechner et al., 1996). ►R/E control ratio (Gnaiger, 2008). | |
Unspecific binding | | Unspecific binding of a probe molecule by which the free concentration is reduced; for instance ►internal and ►external unspecific binding of TPP+. | MiPNet14.05 |
V | | | |
V, volume | | Volume of oxygraph chamber. | MiPNet09.01 |
Valinomycin | | Valinomycin catalyzes electrogenic K+ transport down the electrochemical transmembrane gradient (150 ng∙mg-1 protein). | |
W | | | |
Wet weight | Ww | Wet weight of a tissue or biological sample, obtained after blotting the sample to remove an arbitrary amount of water adhering externally to the sample. | MiPNet14.14 |
Wiki.Oroboros | | OroboroPedia and MitoPedia were started by OROBOROS INSTRUMENTS on 2010-07-12 as a glossary and index to our website, in an attempt to help the users finding particular topics more quickly, and to provide short definitions of terms, abbreviations and symbols frequently used in the context of high-resolution respirometry and mitochondrial physiology. OROBOROS INSTRUMENTS aims at open access and high scientific quality of information. This can be achieved only with feedback and input by contributions to OroboroPedia and MitoPedia, by the experienced users of the OROBOROS-O2k. If you find this page useful, we appreciate if you refer to OroboroPedia in the spirit of ►Gentle Science. | http://wiki.oroboros.at |
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