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Oxidative phosphorylation + ([[File:P.jpg |link=OXPHOS capacity]] '''Ox … [[File:P.jpg |link=OXPHOS capacity]] '''Oxidative phosphorylation''' (OXPHOS) is the oxidation of reduced fuel substrates by electron transfer to oxygen, chemiosmotically coupled to the phosphorylation of [[ADP]] to [[ATP]] (P») and accompanied by an intrinsically uncoupled component of respiration. The OXPHOS state of respiration provides a measure of [[OXPHOS capacity]] (''P''), which is frequently corrected for [[residual oxygen consumption]] (ROX).[residual oxygen consumption]] (ROX).)
State 3 + ([[File:P.jpg |link=OXPHOS capacity]] '''St … [[File:P.jpg |link=OXPHOS capacity]] '''State 3''' respiration is the ADP stimulated respiration of isolated coupled mitochondria in the presence of high ADP and Pi concentrations, supported by a defined substrate or substrate combination at saturating oxygen levels [[Chance_1955_JBC-III|(Chance and Williams, 1955]]). State 3 respiration can also be induced in [[Permeabilized tissue or cells|permeabilized cells]], including permeabilized tissue preparations and tissue homogenates. ADP concentrations applied in State 3 are not necessarily saturating, whereas [[OXPHOS capacity]] is measured at saturating concentrations of ADP and Pi (OXPHOS state). 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 2000 Proc Natl Acad Sci U S A|Gnaiger et al 2000]]; [[Puchowicz_2004_Mitochondrion|Puchowicz et al 2004]]). Respiration in the OXPHOS state or in State 3 is well [[coupled respiration|coupled]], and partially [[uncoupled respiration|uncoupled]] (physiological) or partially [[dyscoupled respiration|dyscoupled]] (pathological). A high [[mt-membrane potential]] provides the driving force for oxidative phosphorylation, to phosphorylate ADP to ATP and to transport ADP and ATP across the mitochondrial inner membrane (mtIM) through the [[adenine nucleotide translocase]] (ANT). The mt-membrane potential is reduced, however, in comparison to the [[LEAK state]] of respiration, whereas the cytochromes are in a more oxidized redox state.ation, whereas the cytochromes are in a more oxidized redox state.)
OXPHOS capacity + ([[File:P.jpg]] '''OXPHOS capacity''' ''P'' … [[File:P.jpg]] '''OXPHOS capacity''' ''P'' is the respiratory capacity of mitochondria in the ADP-activated state of [[oxidative phosphorylation]], at saturating concentrations of [[ADP]] and inorganic phosphate (which may not be the case in [[State 3]]), oxygen, and defined reduced CHNO-fuel substrates. and defined reduced CHNO-fuel substrates.)
PGM-pathway control state + ([[File:PGM.jpg|left|200px|PGM]] '''PGM''': … [[File:PGM.jpg|left|200px|PGM]] '''PGM''': [[Pyruvate]] & [[Glutamate]] & [[Malate]].'''MitoPathway control state:''' [[NADH electron transfer-pathway state]][[Pyruvate]] (P) is oxidatively decarboxylated to acetyl-CoA and CO2, yielding [[NADH]] catalyzed by pyruvate dehydrogenase. [[Malate]] (M) is oxidized to oxaloacetate by mt-malate dehydrogenase located in the mitochondrial matrix. Condensation of oxaloacate with acetyl-CoA yields citrate (citrate synthase). Glutamate&malate is a substrate combination supporting an N-linked pathway control state, when glutamate is transported into the mt-matrix via the [[glutamate-aspartate carrier]] and reacts with [[oxaloacetate]] in the [[transaminase]] reaction to form [[aspartate]] and [[oxoglutarate]]. Glutamate as the sole substrate is transported by the electroneutral glutamate-/OH- exchanger, and is oxidized in the mitochondrial matrix by [[glutamate dehydrogenase]] to α-ketoglutarate ([[oxoglutarate | 2-oxoglutarate]]), representing the [[glutamate-anaplerotic pathway control state]]. 2-oxoglutarate (α-ketoglutarate) is formed from isocitrate (isocitrate dehydrogenase, from oxaloacetate and glutamate by the transaminase, and from glutamate by the glutamate dehydrogenase.tate and glutamate by the transaminase, and from glutamate by the glutamate dehydrogenase.)
PGMS-pathway control state + ([[File:PGMS.png|left|200px|PGMS]] '''PGMS' … [[File:PGMS.png|left|200px|PGMS]] '''PGMS''': [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]].'''MitoPathway control state:''' [[NS|NS-pathway control state]]2-oxoglutarate is produced through the citric acid cycle from citrate by isocitrate dehydrogenase, from oxaloacetate and glutamate by the transaminase, and from glutamate by the glutamate dehydrogenase. If the 2-oxoglutarate carrier does not outcompete these sources of 2-oxoglutarate, then the TCA cycle operates in full circle with external pyruvate&malate&glutamate&succinatercle with external pyruvate&malate&glutamate&succinate)
O2k-pH ISE-Module + ([[File:PH new.jpg|right|180px]]'''O2k-pH ISE-Module''': two pH electrodes and reference electrodes and accessories)
PMS-pathway control state + ([[File:PMS.jpg|left|200px|PMS]]'''PMS''': … [[File:PMS.jpg|left|200px|PMS]]'''PMS''': [[Pyruvate]] & [[Malate]] & [[Succinate]].'''MitoPathway control:''' CI&II[[Pyruvate]] (P) is oxidatively decarboxylated to acetyl-CoA and CO2, yielding [[NADH]] catalyzed by pyruvate dehydrogenase. [[Malate]] (M) is oxidized to oxaloacetate by mt-malate dehydrogenase located in the mitochondrial matrix. Condensation of oxaloacate with acetyl-CoA yields citrate (citrate synthase). This documents an additive effect of convergent CI&II electron flow to the Q-junction, with consistent results obtained with permeabilized muscle fibres and isolated mitochondria (Gnaiger 2009). permeabilized muscle fibres and isolated mitochondria (Gnaiger 2009).)
O-ring\Viton\8x1 mm + ([[File:POS O-ring for sensor head or POS mounting tool.jpg|right|180px]]'''O-ring\Viton\8x1 mm''': for [[OroboPOS]] sensor head. Replaces the O-ring\Viton\9x1 mm)
O-ring\Viton\6x1 mm + ([[File:POS O-ring for sensor head or POS mounting tool.jpg|right|180px]]'''O-ring\Viton\6x1 mm''' for [[POS-Mounting Tool]].)
POS-Membrane Ring + ([[File:POS membrane holder ring.jpg|right|180px|link=]]'''POS-Membrane Ring''', [[PEEK]], holds the membrane against the inner O-ring on the POS housing.)
SUIT-002 O2 pfi D006 + ([[File:Pfi;1D;2M.1;3Oct;3c;4M2;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd.png|400px|SUIT-RP2]])
SUIT-001 O2 pfi D002 + ([[File:Pfi;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd.png|400px|SUIT-RP1]])
Phosphorylation pathway + ([[File:Phosphorylation system.jpg|thumb|le … [[File:Phosphorylation system.jpg|thumb|left|250px|From Gnaiger 2014 MitoPathways]]The '''phosphorylation pathway''' (phosphorylation system) is the functional unit utilizing the protonmotive force to phosphorylate ADP (D) to ATP (T), and may be defined more specifically as the '''P»-system'''. The P»-system consists of [[adenine nucleotide translocase]], [[phosphate carrier]], and [[ATP synthase]]. Mitochondrial [[adenylate kinase]], mt-[[creatine kinase]] and mt-[[hexokinase]] constitute extended components of the P»-system, controlling local AMP and ADP concentrations and forming [[metabolic channel]]s. Since substrate-level phosphorylation is involved in the TCA-cycle, the P»-system includes [[succinyl-CoA ligase]] (GDP to GTP or ADP to ATP).ccinyl-CoA ligase]] (GDP to GTP or ADP to ATP).)
Pipette\Plastic\1 ml ungraded + ([[File:Pipette Plastic 1 ml-ungraded.JPG|180px|right]]'''Pipette\Plastic\1 mL ungraded''', for filling electrolyte into the reservoir of the [[OroboPOS]].)
Power O2k Numbers + ([[File:Power O2k Numbers.JPG|right|180px]]'''Power O2k Numbers''': Single number to label the O2k in a Power O2k-Lab.)
Proline + ([[File:Proline.png|left|100px|Proline]] '' … [[File:Proline.png|left|100px|Proline]]'''Proline''' (Pro), C5H9NO2, is an amino acid which occurs under physiological conditions mainly in the nonpolar form, with ''p''Ka1 = 1.99 ''p''Ka2 = 10.96.Proline is an [[anaplerotic]] substrate that supports both the proline pathway control state and the [[glutamate-anaplerotic pathway control state]]. Proline is used as a single substrate or in combination with carbohydrate-derived metabolites in mitochondria particularly of flight muscle of many (but not all) insects. Proline is oxidized to delta-1-pyrroline-5-carboxylate by the [[mtIM]] L-proline:quinone oxidoreductase ([[proline dehydrogenase]], ProDH), with reduction of FAD to FADH2 and direct entry into the [[Q-junction]]. delta-1-pyrroline-5-carboxylate is converted to [[glutamate]] by 1-pyrroline-5-carboxylate dehydrogenase.[[glutamate]] by 1-pyrroline-5-carboxylate dehydrogenase.)
Pyruvate + ([[File:Pyruvic_acid.jpg|left|80px|Pyruvic … [[File:Pyruvic_acid.jpg|left|80px|Pyruvic acid]]'''Pyruvic acid''', C3H4O3, is an alpha-keto monocarboxylic acid which occurs under physiological conditions mainly as the anion '''pyruvate-, P''', with ''p''Ka = 2.5. Pyruvate is formed in glycolysis from phosphoenolpyruvate. In the cytosol, pyruvate is a substrate of [[lactate dehydrogenase]]. Pyruvate enters the mitochondrial matrix via a specific low ''K''m' H+/monocarboxylate cotransporter known as the [[pyruvate carrier]]. Similarly, the plasma membrane of many cell types has H+/monocarboxylate cotransporter activity and pyruvate can thus be added as a substrate to living cells. In the mt-matrix the oxidative decarboxylation of pyruvate is catalyzed by [[pyruvate dehydrogenase]] and yields [[acetyl-CoA]]. Pyruvate competitively reverses the inhibition of [[Complex IV | cytochrome ''c'' oxidase]] by [[cyanide]]. Pyruvate is an antioxidant reacting with [[hydrogen peroxide]].[[hydrogen peroxide]].)
ROUTINE respiration + ([[File:R.jpg]] In the living cell, '''ROUT … [[File:R.jpg]] In the living cell, '''ROUTINE respiration''' (''R'') or ROUTINE activity in the physiological coupling state is controlled by cellular energy demand, energy turnover and the degree of coupling to phosphorylation (intrinsic [[uncoupling]] and pathological [[dyscoupling]]). The conditions for measurement and expression of respiration vary ([[oxygen flux]] in state ''R'', ''J''O2''R'' or [[oxygen flow]] in state ''R'', ''I''O2''R''). If these conditions are defined and remain consistent within a given context, then the simple symbol ''R'' for respiratory state can be used to substitute the more explicit expression for respiratory activity. ''R'' and growth of cells is supported by exogenous substrates in culture media. In media without energy substrates, ''R'' depends on endogenous substrates. ''R'' cannot be measured in [[permeabilized cells]] or [[isolated mitochondria]]. ''R'' is corrected for [[residual oxygen consumption]] (ROX), whereas ''R''´ is the uncorrected apparent ROUTINE respiration or total cellular oxygen consumption of cells including ROX. apparent ROUTINE respiration or total cellular oxygen consumption of cells including ROX.)
State 2 + ([[File:ROX.jpg |link=Residual oxygen consu … [[File:ROX.jpg |link=Residual oxygen consumption]] Substrate limited state of [[residual oxygen consumption]], after addition of [[ADP]] to isolated mitochondria suspended in mitochondrial respiration medium in the absence of reduced substrates (ROXD). Residual endogenous substrates are oxidized during a transient stimulation of oxygen flux by ADP. The peak – supported by endogenous substrates – is, therefore, a pre-steady state phenomenon preceding State 2. Subsequently oxygen flux declines to a low level (or zero) at the steady '''State 2''' ([[Chance_1955_JBC-III|Chance and Williams 1955]]). ADP concentration (D) remains high during ROXD.concentration (D) remains high during ROXD.)
Residual oxygen consumption + ([[File:ROX.jpg|100px|link=https://wiki.oro … [[File:ROX.jpg|100px|link=https://wiki.oroboros.at/images/3/30/ROX.jpg]] '''Residual oxygen consumption''' ''Rox'' — respiration in the ROX state — is due to oxidative side reactions remaining after inhibition of the [[electron transfer pathway]] (ET pathway) in [[mitochondrial preparation]]s or living cells. Different conditions designated as ROX states (different combinations of inhibitors of CI, CII, CIII and CIV) may result in consistent or significantly different levels of oxygen consumption. Hence the best quantitative estimate of ''Rox'' has to be carefully evaluated. Mitochondrial respiration is frequently corrected for ''Rox'' as the [[baseline state]]. Then, total [[ROUTINE]], [[LEAK respiration]], [[OXPHOS]] or [[Electron transfer pathway |ET]] (''R'', ''L'', ''P'' and ''E'') respiration are distinguished from the corresponding ''Rox''-corrected, mitochondrial (ET-pathway linked) fluxes: ''R''(mt), ''L''(mt), ''P''(mt) and ''E''(mt). Alternatively, ''R'', ''L'', ''P'' and ''E'' are defined as ''Rox''-corrected rates, in contrast to total rates ''R''´, ''L''´, ''P''´ and ''E''´. When expressing ''Rox'' as a fraction of ET capacity ([[flux control ratio]]), total flux ''E''´ (not corrected for ''Rox''), should be taken as the reference. ''Rox'' may be related to, but is of course different from [[ROS]] production.In previous editions, (including [[Gnaiger 2020 BEC MitoPathways]]), the [[REN]] state was not distinguished from the ROX state. However, in novel applications (Q-Module and NADH-Module), a distinction of these states is necessary. Care must be taken when assuming ''Ren'' as a substitute of ''Rox'' correction of mitochondrial respiration.' correction of mitochondrial respiration.)
Ambiguity crisis + ([[File:Rabbit or duck.jpg|right|300px|thum … [[File:Rabbit or duck.jpg|right|300px|thumb|'''Graphical ambiguity:''' ''Fliegende Blätter'' (1892-10-23): Perception versus interpretation (Ludwig Wittgenstein) or paradigm shift (Thomas Kuhn)]]The '''ambiguity crisis''' is a contemporary crisis comparable to the credibility or [[reproducibility crisis]] in the biomedical sciences. The term 'crisis' is rooted etymologically in the Greek word ''krinein'': meaning to 'separate, decide, judge'. In this sense, science and communication in general are a continuous crisis at the edge of separating clarity or certainty from confusing double meaning, or obscure 'alchemical' gibberish, or even fake-news. Reproducibility relates to the condition of repeating and confirming calculations or experiments presented in a published resource. While ambiguity is linked to relevant issues of reproducibility, it extends to the communications space of terminological and graphical representations of concepts. Type 1 ambiguities are the inevitable consequence of conceptual evolution, in the process of which ambiguities are replaced by experimentally and theoretically supported paradigm shifts to clear-cut theorems. In contrast, type 2 ambiguities are traced in publications that reflect merely a disregard and ignorance of established concepts without an attempt to justify the inherent deviations from high-quality science. There are many shades of grey between these types of ambiguity. of grey between these types of ambiguity.)
Residual endogenous substrates + ([[File:Ren.png|100px|link=https://wiki.oro … [[File:Ren.png|100px|link=https://wiki.oroboros.at/index.php/File:Ren.png]] Oxygen consumption due to '''residual endogenous substrates'''. ''Ren'' is the respiration in the REN state. It is due to oxidative reactions in [[mt-preparation]]s incubated without addition of fuel substrates in the absence or presence of ADP (in the presence of ADP to stimulate the consumption of endogenous fuel substrates: [[State 2]]). ''Ren'' values may be used as technical replicates when obtained from the same mt-preparation in different protocols. ''Ren'' may be higher than ''Rox''. Correspondingly, Q and NAD are not fully oxidized in the REN state compared to the ROX state. In previous editions (including [[Gnaiger 2020 BEC MitoPathways]]), the REN state was not distinguished from the [[ROX]] state. However, in novel applications (Q-Module and NADH-Module), a distinction of these states is necessary. Care must be taken when assuming ''Ren'' as a substitute of ''Rox'' correction of mitochondrial respiration.' correction of mitochondrial respiration.)
Society for Heart and Vascular Metabolism + ([[File:SHVM.png|100px|left]]The '''Society … [[File:SHVM.png|100px|left]]The '''Society for Heart and Vascular Metabolism''' (SHVM) The Society for Heart and Vascular Metabolism was founded in 2001, with the intent of providing a forum for the free exchange of ideas by a group of investigators that had a special interest in the multiple roles of intermediary metabolism in the cardiovascular system. An important aim of the Society is to foster interactions between young investigators and senior scientists and our meetings are deliberately designed to maximize these interactions. There is growing recognition across many areas of scientific investigation and in the cardiovascular arena of the importance of metabolic homeostasis. The Society for Heart and Vascular Metabolism intends to remain at the vanguard of this rapidly expanding area.e vanguard of this rapidly expanding area.)
Society for Mitochondrial Research and Medicine - India + ([[File:SMRM.JPG|150px|left]]The Society fo … [[File:SMRM.JPG|150px|left]]The Society for '''Mitochondria Research and Medicine - India''' (SMRM-India) is a nonprofit organization of scientists, clinicians and academicians. The purpose of SMRM is to foster research on basic science of mitochondria, mitochondrial pathogenesis, prevention, diagnosis and treatment through out India and abroad.nd treatment through out India and abroad.)
Serbian Society for Mitochondrial and Free Radical Physiology + ([[File:SSMFRP.jpg|left|200px]] The '''Serb … [[File:SSMFRP.jpg|left|200px]] The '''Serbian Society for Mitochondrial and Free Radical Physiology (SSMFRP)''' was established in 2008 as a national Society and has 150 members who gather research in the fields of molecular biology, biochemistry, medicine, chemistry, agriculture, physics and other related disciplines. The SSMFRP was founded as a '''voluntary non-governmental and non-profit association''' for researchers whose goal is to support the creative improvement of scientific knowledge about the '''physiology of mitochondria and free radicals''', support for the development of modern research approaches and integration of fundamental research in order to better understand the role of free radicals in pathophysiological states, as well as promoting scientific knowledge in the country and abroad.tific knowledge in the country and abroad.)
SUIT-003 pH ce D067 + ([[File:SUIT-003 O2 ce D067 diagram.png|350px]])

SUIT-026 AmR mt D064 + ([[File:SUIT-026 AmR mt D064.png|400px]])
SUIT-026 AmR mt D077 + ([[File:SUIT-026 AmR mt D064.png|400px]])

F-junction + ([[File:SUIT-catg F.jpg|right|300px|F-junct … [[File:SUIT-catg F.jpg|right|300px|F-junction]]The '''F-junction''' is a junction for [[convergent electron flow]] in the [[electron transfer pathway]] (ET-pathway) from fatty acids through [[fatty acyl CoA dehydrogenase]] (reduced form [[FADH2]]) to [[electron transferring flavoprotein]] (CETF), and further transfer through the [[Q-junction]] to [[Complex III]] (CIII). The concept of the F-junction and [[N-junction]] provides a basis for defining [[categories of SUIT protocols]]. Fatty acid oxidation, in the [[F-pathway control state]], not only depends on electron transfer through the F-junction (which is typically rate-limiting) but simultaneously generates NADH and thus depends on N-junction throughput. Hence FAO can be inhibited completely by inhibition of Complex I (CI). In addition and independent of this source of NADH, the N-junction substrate malate is required as a co-substrate for FAO in mt-preparations, since accumulation of AcetylCoA inhibits FAO in the absence of malate. Malate is oxidized in a reaction catalyzed by malate dehydrogenase to oxaloacetate (yielding NADH), which then stimulates the entry of AcetylCoA into the TCA cycle catalyzed by citrate synthase.e TCA cycle catalyzed by citrate synthase.)
Fatty acid oxidation pathway control state + ([[File:SUIT-catg F.jpg|right|300px|F-junct … [[File:SUIT-catg F.jpg|right|300px|F-junction]]In the '''fatty acid oxidation pathway control state''' (F- or FAO-pathway), one or several fatty acids are supplied to feed electrons into the [[F-junction]] through fatty acyl CoA dehydrogenase (reduced form [[FADH2]]), to [[electron transferring flavoprotein]] (CETF), and further through the [[Q-junction]] to [[Complex III]] (CIII). FAO not only depends on electron transfer through the F-junction (which is typically rate-limiting relative to the N-pathway branch), but simultaneously generates FADH2 and NADH and thus depends on [[N-junction]] throughput. Hence FAO can be inhibited completely by inhibition of [[Complex I]] (CI). In addition and independent of this source of NADH, the type N substrate malate is required at low concentration (0.1 mM) as a co-substrate for FAO in mt-preparations, since accumulation of Acetyl-CoA inhibits FAO in the absence of malate. Malate is oxidized in a reaction catalyzed by malate dehydrogenase to oxaloacetate (yielding NADH), which then stimulates the entry of Acetyl-CoA into the TCA cycle catalyzed by citrate synthase. Peroxysomal ''β''-oxidation carries out few ''β''-oxidation cycles, thus shortening very-long-chain fatty acids (>C20) for entry into mitochondrial ''β''-oxidation. Oxygen consumption by peroxisomal [[acyl-CoA oxidase]] is considered as [[residual oxygen consumption]] rather than cell respiration.esidual oxygen consumption]] rather than cell respiration.)
FN + ([[File:SUIT-catg FN.jpg|right|300px|F-junc … [[File:SUIT-catg FN.jpg|right|300px|F-junction]]FN is induced in mt-preparations by addition of [[NADH]]-generating substrates ([[N-pathway control state]], or CI-linked pathway control) in combination with one or several fatty acids, which are supplied to feed electrons into the [[F-junction]] through [[fatty acyl CoA dehydrogenase]] (reduced form [[FADH2]]), to [[electron transferring flavoprotein]] (CETF), and further through the [[Q-junction]] to [[Complex III]] (CIII). FAO not only depends on electron transfer through the F-junction (which is typically rate-limiting), but simultaneously generates FADH2 and NADH and thus depends on [[N-junction]] throughput. Hence FAO can be inhibited completely by inhibition of [[Complex I]] (CI). This physiological substrate combination is required for partial reconstitution of [[TCA cycle]] function and convergent electron-input into the [[Q-junction]], to compensate for metabolite depletion into the incubation medium. FS in combination exerts an [[additive effect of convergent electron flow]] in most types of mitochondria.[[additive effect of convergent electron flow]] in most types of mitochondria.)
FNS + ([[File:SUIT-catg FNS.jpg|right|300px|F-jun … [[File:SUIT-catg FNS.jpg|right|300px|F-junction]]FNS is induced in mt-preparations by addition of [[NADH]]-generating substrates ([[N-pathway control state]], or CI-linked pathway control) in combination with [[succinate]] ([[S-pathway control state]]; S- or CII-linked) and one or several fatty acids, which are supplied to feed electrons into the [[F-junction]] through [[fatty acyl CoA dehydrogenase]] (reduced form [[FADH2]]), to [[electron transferring flavoprotein]] (CETF), and further through the [[Q-junction]] to [[Complex III]] (CIII). FAO not only depends on electron transfer through the F-junction (which is typically rate-limiting), but simultaneously generates FADH2 and NADH and thus depends on [[N-junction]] throughput. Hence FAO can be inhibited completely by inhibition of [[Complex I]] (CI). This physiological substrate combination is required for partial reconstitution of [[TCA cycle]] function and convergent electron-input into the [[Q-junction]], to compensate for metabolite depletion into the incubation medium. FNS in combination exerts an [[additive effect of convergent electron flow]] in most types of mitochondria.[[additive effect of convergent electron flow]] in most types of mitochondria.)
Q-junction + ([[File:SUIT-catg FNSGp.jpg|right|300px|Q-j … [[File:SUIT-catg FNSGp.jpg|right|300px|Q-junction]]The '''Q-junction''' is a junction for [[convergent electron flow]] in the [[Electron transfer pathway]] (ET-pathway) from type N substrates and mt-matrix dehydrogenases through [[Complex I]] (CI), from type F substrates and FA oxidation through [[electron-transferring flavoprotein Complex]] (CETF), from succinate (S) through [[Complex II]] (CII), from glycerophosphate (Gp) through [[glycerophosphate dehydrogenase Complex]] (CGpDH), from choline through [[choline dehydrogenase]], from dihydro-orotate through [[dihydro-orotate dehydrogenase]], and other enzyme Complexes into the Q-cycle (ubiquinol/ubiquinone), and further downstream to [[Complex III]] (CIII) and [[Complex IV]] (CIV). The concept of the Q-junction, with the [[N-junction]] and [[F-junction]] upstream, provides the rationale for defining [[Electron-transfer-pathway state]]s and [[categories of SUIT protocols]].[[categories of SUIT protocols]].)
Electron-transfer-pathway state + ([[File:SUIT-catg FNSGpCIV.jpg|right|400px] … [[File:SUIT-catg FNSGpCIV.jpg|right|400px]]'''Electron-transfer-pathway states''' are obtained in [[mitochondrial preparations]] (isolated mitochondria, permeabilized cells, permeabilized tissues, tissue homogenate) by depletion of endogenous substrates and addition to the mitochondrial respiration medium of fuel substrates (CHNO) activating specific mitochondrial pathways, and possibly inhibitors of specific pathways. Mitochondrial electron-transfer-pathway states have to be defined complementary to mitochondrial [[coupling-control state]]s. [[Coupling-control state]]s require [[Electron-transfer-pathway state|ET-pathway competent states]], including oxygen supply. [[Categories of SUIT protocols]] are defined according to mitochondrial ET-pathway states.» [[#ET_pathway_states |'''MiPNet article''']][#ET_pathway_states |'''MiPNet article''']])
N-junction + ([[File:SUIT-catg N.jpg|right|300px|N-junct … [[File:SUIT-catg N.jpg|right|300px|N-junction]]The '''N-junction''' is a junction for [[convergent electron flow]] in the [[electron transfer pathway]] (ET-pathway) from type N substrates (''further details'' »[[N-pathway control state]]) through the mt-[[NADH]] pool to [[Complex I]] (CI), and further transfer through the [[Q-junction]] to [[Complex III]] (CIII). Representative type N substrates are pyruvate (P), glutamate (G) and malate (M). The corresponding dehydrogenases ([[Pyruvate dehydrogenase |PDH]], [[Glutamate dehydrogenase |GDH]], [[Malate dehydrogenase |MDH]]) and some additional TCA cycle dehydrogenases ([[isocitrate dehydrogenase]], [[oxoglutarate dehydrogenase]] generate NADH, the substrate of [[Complex I]] (CI). The concept of the N-junction and [[F-junction]] provides a basis for defining [[categories of SUIT protocols]] based on [[Electron-transfer-pathway state]]s.[Electron-transfer-pathway state]]s.)
NADH electron transfer-pathway state + ([[File:SUIT-catg N.jpg|right|300px|N-junct … [[File:SUIT-catg N.jpg|right|300px|N-junction]]The '''NADH electron transfer-pathway state''' (N) is obtained by addition of [[NADH]]-linked substrates (CI-linked), feeding electrons into the [[N-junction]] catalyzed by various mt-dehydrogenases. N-supported flux is induced in mt-preparations by the addition of NADH-generating substrate combinations of [[pyruvate]] (P), [[glutamate]] (G), [[malate]] (M), [[oxaloacetate]] (Oa), [[oxoglutarate]] (Og), [[citrate]], [[hydroxybutyrate]]. These N-junction substrates are (indirectly) linked to [[Complex I]] by the corresponding dehydrogenase-catalyzed reactions reducing NAD+ to NADH+H+ + H+. The most commonly applied N-junction substrate combinations are: [[PM]], [[GM]], [[PGM]]. The [[malate-anaplerotic pathway control state]] (M alone) is a special case related to [[malic enzyme]] (mtME). The [[glutamate-anaplerotic pathway control state]] (G alone) supports respiration through [[glutamate dehydrogenase]] (mtGDH). Oxidation of [[tetrahydrofolate]] is a NAD(P)H linked pathway with formation of formate. In mt-preparations, succinate dehydrogenase (SDH; [[CII]]) is largely substrate-limited in N-linked respiration, due to metabolite depletion into the incubation medium. The residual involvement of S-linked respiration in the N-pathway control state can be further suppressed by the CII-inhibitor [[malonic acid]]). In the N-pathway control state [[Electron-transfer-pathway state|ET pathway level 4]] is active.[[Electron-transfer-pathway state|ET pathway level 4]] is active.)
NS-pathway control state + ([[File:SUIT-catg NS.jpg|right|300px|NS-pat … [[File:SUIT-catg NS.jpg|right|300px|NS-pathway control]]'''NS-pathway control''' is exerted in the NS-linked substrate state (flux in the NS-linked substrate state, NS; or Complex I&II, CI&II-linked substrate state). NS-OXPHOS capacity provides an estimate of physiologically relevant maximum mitochondrial respiratory capacity. NS is induced in mt-preparations by addition of [[NADH]]-generating substrates ([[N-pathway control state]] in combination with [[succinate]] ([[Succinate pathway]]; S). Whereas NS expresses substrate control in terms of substrate types (N and S), CI&II defines the same concept in terms of convergent electron transfer to the [[Q-junction]] (pathway control). '''NS''' is the abbreviation for the combination of [[NADH]]-linked substrates (N) and [[succinate]] (S). This physiological substrate combination is required for partial reconstitution of [[TCA cycle]] function and convergent electron-input into the [[Q-junction]], to compensate for metabolite depletion into the incubation medium. NS in combination exerts an [[additive effect of convergent electron flow]] in most types of mitochondria.[[additive effect of convergent electron flow]] in most types of mitochondria.)
Glycerophosphate pathway control state + ([[File:SUIT-catg_Gp.jpg|right|300px|Gp-pat … [[File:SUIT-catg_Gp.jpg|right|300px|Gp-pathway]]The '''glycerophosphate pathway control state''' (Gp) is an [[Electron-transfer-pathway state |ET-pathway level 3 control state]], supported by the fuel substrate [[glycerophosphate]] and electron transfer through [[glycerophosphate dehydrogenase Complex]] into the [[Q-junction]]. The [[glycerolphosphate shuttle]] represents an important pathway, particularly in liver and blood cells, of making cytoplasmic [[NADH]] available for mitochondrial [[oxidative phosphorylation]]. Cytoplasmic NADH reacts with dihydroxyacetone phosphate catalyzed by cytoplasmic glycerophos-phate dehydrogenase. On the outer face of the inner mitochondrial membrane, mitochondrial glycerophosphate dehydrogenase oxidises 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-pathway at the level of [[CoQ]].[[CoQ]].)
Categories of SUIT protocols + ([[File:SUIT-catg_MitoPathway types.jpg|rig … [[File:SUIT-catg_MitoPathway types.jpg|right|200px]]'''Categories of SUIT protocols''' group [[MitoPedia: SUIT |SUIT protocols]] according to all substrate types involved in a protocol (F, N, S, Gp), independent of the sequence of titrations of substrates and inhibitors which define the [[Electron-transfer-pathway state]]s. The [[N-pathway control |N-type substrates]] are listed in parentheses, independent of the sequence of titrations. ROX states may or may not be included in a SUIT protocol, which does not change its category. Similarly, the [[CIV]] assay may or may not be added at the end of a SUIT protocol, without effect on the category of a SUIT protocol.* '''F''' - ET-pathway-level 5: [[FADH2 |FADH2]]-linked substrates (FAO) with obligatory support by the N-linked pathway.* '''N''' - ET-pathway-level 4: [[NADH]]-linked substrates (CI-linked).* '''S''' - ET-pathway-level 3: [[Succinate]] (CII-linked).* '''Gp''' - ET-pathway-level 3: [[Glycerophosphate]] (CGpDH-linked).* '''Y(X)'''- In the SUIT general protocols Y makes reference to the ET-pathway state and X to the combination os substrates added for the corresponding pathway.» [[#Categorization of SUIT protocols: ETS pathway control states |'''MiPNet article''']][#Categorization of SUIT protocols: ETS pathway control states |'''MiPNet article''']])
Succinate pathway + ([[File:SUIT-catg_S.jpg|right|300px|Succina … [[File:SUIT-catg_S.jpg|right|300px|Succinate]]The '''Succinate pathway''' (S-pathway; S) is the [[electron transfer pathway]] that supports succinate-linked respiration (succinate-induced respiratory state; previously used nomenclature: CII-linked respiration; SRot; see [[Gnaiger 2009 Int J Biochem Cell Biol]]). The S-pathway describes the electron flux through [[Complex II]] (CII; see [[succinate dehydrogenase]], SDH) from succinate and FAD to fumarate and CII-bound flavin adenine dinucleotide (FADH2) to the [[Q-junction]].The S-pathway control state is usually induced in mt-preparations by addition of succinate&rotenone. In this case, only [[Complex III]] and [[Complex IV]] are involved in pumping protons from the matrix (positive phase, P-phase) to the negative phase (N-phase) with a P»/O2 of 3.5 (P»/O ratio = 1.75).phase) with a P»/O2 of 3.5 (P»/O ratio = 1.75).)
SUIT protocol names + ([[File:SUIT-nomenclature.jpg|300px|right|S … [[File:SUIT-nomenclature.jpg|300px|right|SUIT protocols]]The '''SUIT protocol name''' starts with (i) the [[Categories of SUIT protocols |SUIT category]] which shows the [[Electron-transfer-pathway state]]s (ET pathway types; e.g. N, S, NS, FNS, FNSGp), independent of the actual sequence of titrations. (ii) A further distinction is provided in the SUIT name by listing in parentheses the substrates applied in the [[N-pathway control state]]s, again independent of the sequence of titrations, e.g. NS(GM), NS(PM), FNSGp(PGM). (iii) A sequentially selected number is added, e.g. SUIT_FNS(PM)01 (see [[Coupling/pathway control diagram]]). The '''systematic name''' of a SUIT protocol starts with the [[Categories of SUIT protocols |SUIT category]], followed by an underline dash and the sequence of titration steps (mark names, #''X'', separated by a comma). The [[Marks in DatLab |Marks]] define the section of a [[respiratory state]] in the SUIT protocol. The [[Mark names in DatLab |Mark name]] contains the sequential number and the [[metabolic control variable]], ''X''. The metabolic control variable is the name of the preceding SUIT [[event]]. The [[MitoPedia: SUIT |MitoPedia list of SUIT protocols]] can be sorted by the short name or the systematic name (hence by SUIT protocol category. The '''[[SUIT protocol pattern]]''' is best illustrated by a [[coupling/pathway control diagram]].[[coupling/pathway control diagram]].)
Coupling/pathway control diagram + ([[File:SUIT-nomenclature.jpg|300px|right|S … [[File:SUIT-nomenclature.jpg|300px|right|SUIT protocols]]'''Coupling/pathway control diagrams''' illustrate the respiratory '''states''' obtained step-by-step in substrate-uncoupler-inhibitor titrations in a [[SUIT protocol]]. Each step (to the next state) is defined by an initial state and a [[metabolic control variable]], ''X''. The respiratory states are shown by boxes. ''X'' is usually the titrated substance in a SUIT protocol. If ''X'' ([[ADP]], [[uncoupler]]s, or inhibitors of the [[phosphorylation system]], e.g. oligomycin) exerts '''coupling control''', then a transition is induced between two [[coupling-control state]]s. If ''X'' (fuel substrates, e.g. pyruvate and succinate, or [[Electron transfer pathway]] inhibitors, e.g. rotenone) exerts '''pathway control''', then a transition is induced between two [[Electron-transfer-pathway state]]s. The type of metabolic control (''X'') is shown by arrows linking two respiratory states, with vertical arrows indicating coupling control, and horizontal arrows indicating pathway control. [[Marks - DatLab |Marks]] define the section of an experimental trace in a given [[respiratory state]] (steady state). [[Events - DatLab |Events]] define the titration of ''X'' inducing a transition in the SUIT protocol. The specific sequence of coupling control and pathway control steps defines the [[SUIT protocol pattern]]. The coupling/pathway control diagrams define the [[categories of SUIT protocols]] (see Figure).[[categories of SUIT protocols]] (see Figure).)
SUIT-013 + ([[File:SUIT013 AmR ce D023.png|300px]])
SUIT-013 AmR ce D023 + ([[File:SUIT013 AmR ce D023.png|400px]])
Sample Holder + ([[File:Sample Holder - 28410-01.jpg|right|180px]] Sample Holder - to protect susceptible samples from being damaged by stirring of the medium in the 2.0 mL O2k-chamber.)
O2k series + ([[File:Seires number H-Seires.png|right|20 … [[File:Seires number H-Seires.png|right|200 px|The serial number of each O2k is shown on a sticker at the rear of the O2k.]]The '''O2k series''' is specified as the capital letter in the O2k serial number of the [[Oroboros O2k]]. A serial number G-#### or H-#### denotes an Oxygraph from the G or H series, while A-#### denotes an O2k from the A series. With [[DatLab]] running real-time connected to the O2k, the serial number of the currently connected O2k is displayed: (1) in the right corner of the [[O2k status line|status line]], besides the DatLab version number (bottom), and (2) in windows [[O2k control]] [F7] and [[O2k configuration]].[[O2k configuration]].)
Stopper\black PEEK\angular Shaft\side+6.2+2.6 mm Port + ([[File:Stopper black PEEK angular Shaft si … [[File:Stopper black PEEK angular Shaft side+6.2+2.6 mm Port.JPG|180px|right]]'''Stopper\black PEEK\angular Shaft\side+6.2+2.6 mm Port''', for application with [[ISE]]; side titration port and two additional holes (6.2 mm and 2.6 mm); angular bottom; including [[Volume-Calibration Ring]] (A or B); 2 mounted O-rings, with 8 spare O-rings ([[O-ring\Viton\12.5x1 mm]]).[[O-ring\Viton\12.5x1 mm]]).)
Stopper\black PEEK\conical Shaft\central+2.3+2.6 mm Port + ([[File:Stopper black PEEK conical Shaft ce … [[File:Stopper black PEEK conical Shaft central+2.3+2.6 mm Port.JPG|180px|right]]'''Stopper\black PEEK\conical Shaft\central+2.3+2.6 mm Port''': for pH and reference electrode, central titration port and two additional ports (2.3 mm and 2.6 mm); conical bottom; including Volume-Calibration Ring (A or B), 2 mounted O-rings, with 8 spare O-rings ([[O-ring\Viton\12.5x1 mm]]).[[O-ring\Viton\12.5x1 mm]]).)
Succinate + ([[File:Succinic_acid.jpg|left|100px|Succin … [[File:Succinic_acid.jpg|left|100px|Succinic acid]]'''Succinic acid''', C4H6O4, (butanedioic acid) is a dicarboxylic acid which occurs under physiological conditions as the anion '''succinate2-, S''', with ''p''Ka1 = 4.2 and ''p''Ka2 = 5.6. Succinate is formed in the [[TCA cycle]], and is a substrate of [[Complex II |CII]], reacting to [[fumarate]] and feeding electrons into the [[Q-junction]]. Succinate (CII-linked) and NADH (CI-linked) provide convergent electron entries into the Q-junction. Succinate is transported across the inner mt-membrane by the [[dicarboxylate carrier]]. The plasma membrane of many cell types is impermeable for succinate (but see [[Zhunussova 2015 Am J Cancer Res]] for an exception). Incubation of mt-preparations by succinate alone may lead to accumulation of [[oxaloacetate]], which is a potent inhibitor of Complex II (compare [[Succinate and rotenone]]). High activities of mt-[[Malic enzyme]] (mtME) prevent accumulation of oxaloacetate in incubations with succinate without rotenone.[[Malic enzyme]] (mtME) prevent accumulation of oxaloacetate in incubations with succinate without rotenone.)
Syringe\500 mm3 51/0.41 mm + ([[File:Syringe 500 mm3 51 0.41 mm.JPG |rig … [[File:Syringe 500 mm3 51 0.41 mm.JPG |right|180px]]Hamilton '''Syringe\500 mm3 51/0.41 mm''' for manual titrations, 500 mm3 volume; fixed needle with rounded tip: 51 mm length, 0.41 mm inner diameter; for injections of suspensions of isolated mitochondria and filling of the [[Microsyringe\200 mm3\TIP2k]].[[Microsyringe\200 mm3\TIP2k]].)
Syringe Labels + ([[File:Syringe Labels_2017.JPG|right|180px]]'''Syringe Labels''': set of labels with standard abbreviations (see [[MiPNet09.12_O2k-Titrations | O2k-Titrations]]).)
Syringe Racks + ([[File:Syringe Racks.JPG|right|180px]]'''Syringe Racks''': stainless steel; for proper placement of eight Hamilton microsyringes in HRR experiments; package of two (for a total of 16 microsyringes).)