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{{MitoPedia O2k and high-resolution respirometry | |||
|mitopedia O2k and high-resolution respirometry=O2k hardware, O2k-Open Support, O2k-FluoRespirometry | |||
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'''Table 8. Terms, symbols, and units.''' SI base units are used, except for the liter [L = dm<sup>3</sup>]. SI refers to ref. [[Bureau International des Poids et Mesures 2019 The International System of Units (SI) |[11]]]. | '''Table 8. Terms, symbols, and units.''' SI base units are used, except for the liter [L = dm<sup>3</sup>]. SI refers to ref. [[Bureau International des Poids et Mesures 2019 The International System of Units (SI) |[11]]]. | ||
Revision as of 15:09, 16 September 2020
Description
Descr
Abbreviation: Abbr
Reference: Ref
MitoPedia O2k and high-resolution respirometry:
O2k hardware,
O2k-Open Support,
O2k-FluoRespirometry
Table 8. Terms, symbols, and units. SI base units are used, except for the liter [L = dm3]. SI refers to ref. [11].
Term | Link to MitoPedia term | Symbol | Unit | Links and comments |
---|---|---|---|---|
alternative quinol oxidase] | Alternative oxidase | AOX | - | Fig. 1B |
adenosine monophosphate | AMP | AMP | - | 2 ADP ↔ ATP+AMP |
adenosine diphosphate | ADP | ADP | - | Tab. 1; Fig. 1, 2, 5 |
adenosine triphosphate | ATP | ATP | - | Fig. 2, 5 |
adenylates | Adenylates | AMP, ADP, ATP | - | Section 2.5.1 |
amount of substance X | Amount | nX or n(X) | [mol] | SI |
ATP yield per O2 | ATP yield | YP»/O2 | 1 | P»/O2 ratio measured in any respiratory state |
catabolic reaction | Respiration | k | - | Fig. 1, 3 |
catabolic rate of respiration | Respiration | JkO2; IkO2 | varies | Fig. 1, 3; see flux J and flow I |
cell count | Count | Nce | [x] | Tab. 4; Fig. 5; see number of cells |
cell mass | Mass | mce | [kg] | Tab. 5; Fig. 5 |
cell mass, mass per cell | Mass | MNce | [kg∙x-1] | Tab. 5; Fig. 5 |
cell-mass concentration | Concentration | Cmce | [kg∙L-1] | see Cms: Tab. 4; Cmce = mce∙V-1 |
cell-count concentration | Concentration | Cce | [x∙L-1] | Tab. 4; Cce = Nce∙V-1 |
cell viability index | Cell viability | VI | - | VI = Nvce∙Nce-1 = 1 - Ndce∙Nce-1 |
charge number of entity B | Charge number | zB | 1 | Tab. 6; zO2 = 4 [[[Cohen 2008 IUPAC Green Book |24]]] |
Complexes I to IV | Complex I | CI to CIV | - | respiratory ET Complexes are redox proton pumps; Fig. 1B; F1FO-ATPase is not a redox proton pump of the ETS, hence the term CV is not recommended |
concentration of X, count | Concentration | CX = NX∙V-1 | [x∙L-1] | Tab. 4 (number concentration [[[Cohen 2008 IUPAC Green Book |24]]]) |
concentration of B, amount | Concentration | cB = NB∙V-1 | [mol∙L-1] | SI: amount of substance concentration [[[Cohen 2008 IUPAC Green Book |24]]] |
concentration of O2, amount | Concentration | cO2 = nO2∙V-1 | [mol∙L-1] | Box 2; [O2] |
count format | Format | N | [x] | Tab. 4, 5; Fig. 5 |
count of X | Count | NX | [x] | SI; see number of entities X |
coupling control state | Coupling control state | CCS | - | Section 2.4.1 |
dead cells | Cell viability | dce | - | Tab. 5 |
electrical format | Format | e | [C] | Tab. 6 |
electron transfer, state | Electron transfer pathway | ET | - | Tab. 1; Fig. 2B, 4 (State 3u) |
electron transfer system | Electron transfer pathway | ETS | - | Fig. 2B, 4 (electron transport chain) |
entity | Entity | X | [x] | single countable object; Tab. 4 |
ET capacity | ET capacity | E | varies | rate; Tab. 1; Fig. 2 |
ET-excess capacity | ET capacity | E-P | varies | Fig. 2 |
flow, for O2 | Flow | IO2 | [mol∙s-1] | system-related extensive quantity; Fig. 5 |
flux, for O2 | Flux | JO2 | varies | size-specific quantity; Fig. 5 |
inorganic phosphate | Phosphate | Pi | - | Fig. 1C |
inorganic phosphate carrier | Phosphate carrier | PiC | - | Fig. 1C |
isolated mitochondria | Isolated mitochondria | imt | - | Tab. 5 |
living cells | Living cells | ce | - | Tab. 5 (intact cells) |
LEAK-state | LEAK-state | LEAK | - | Tab. 1; Fig. 2 (compare State 4) |
LEAK respiration | LEAK respiration | L | varies | rate; Tab. 1; Fig. 2 |
mass concentration of sample s | Concentration | Cms | [kg∙L-1] | Tab. 4 |
mass format | Format | m | [kg] | Tab. 4 |
mass of diluted sample | Mass | ms | [kg] | SI: mass of pure sample mS |
mass per single object | Mass | MNX | [kg∙x1] | Fig. 5; Tab. 4; SI: m(X); compare molar mass M(X) |
mass, dry mass | Mass | md | [kg] | Fig. 5 (dry weight) |
mass, wet mass | Mass | mw | [kg] | Fig. 5 (wet weight) |
MITOCARTA | MITOCARTA | |||
MitoPedia | MitoPedia | |||
mitochondria or mitochondrial | Mitochondria | mt | - | Box 1 |
mitochondrial DNA | Mitochondria | mtDNA | - | Box 1 |
mitochondrial concentration | Concentration | CmtE = mtE∙V-1 | [mtEU∙L-1] | Tab. 4 |
mitochondrial content | Mitochondria | mtENX | [mtEU∙x-1] | mtENX = mtE∙NX-1; Tab. 4 |
mitochondrial density | Density | DmtE=mtE∙ms-1 | [mtEU∙kg-1] | tissue-mass specific mt-density; Tab. 4 |
mitochondrial elementary marker | Mitochondria | mtE | [mtEU] | quantity of mt-marker; Tab. 4 |
mitochondrial elementary unit | Mitochondria | mtEU | varies | specific units for mt-marker; Tab. 4 |
mitochondrial inner membrane | Mitochondrial inner membrane | mtIM | - | Fig. 1; Box 1 (MIM) |
mitochondrial outer membrane | Mitochondrial outer membrane | mtOM | - | Fig. 1; Box 1 (MIM) |
mitochondrial recovery | Mitochondrial recovery | YmtE | 1 | fraction of mtE recovered from the tissue sample in imt-stock |
mitochondrial yield | Mitochondrial yield | YmtE/ms | [mtEU∙kg-1] | mt-yield in imt-stock per mass of tissue sample; YmtE/ms=YmtE∙DmtE |
molar format | Format | n | [mol] | Tab. 6 |
molar mass | Molar mass | MB | [kg∙mol-1] | compare MNB [kg∙x-1]; SI M(X) |
negative | Protonmotive force | neg | - | Fig. 4 |
number of cells | Count | Nce | [x] | total cell count of living cells, Nce = Nvce + Ndce; Tab. 4, 5 |
number of dead cells | Cell viability | Ndce | [x] | non-viable cell count, loss of plasma membrane barrier function; Tab. 5 |
number of entities B | Count | NB | [x] | Tab. 4 [[[Cohen 2008 IUPAC Green Book |24]]] |
number of entities X; count | Count | NX | [x] | ‘count’ is an SI quantity [11], but the counting unit [x] is not in the SI [95]; Tab. 4; Fig. 5 |
number of viable cells | Cell viability | Nvce | [x] | viable cell count, intact plasma membrane barrier function; Tab. 5 |
organisms | Organism | org | - | Tab. 5 |
oxidative phosphorylation | Oxidative phosphorylation | OXPHOS | - | Tab. 1 |
OXPHOS-state | OXPHOS-state | OXPHOS | - | Tab. 1; Fig. 2; OXPHOS-state distinguished from the process OXPHOS (State 3 at kinetically-saturating [ADP] and [Pi]) |
OXPHOS capacity | OXPHOS capacity | P | varies | rate; Tab. 1; Fig. 2 |
oxygen concentration | Oxygen concentration | cO2 = nO2∙V-1 | [mol∙L-1] | [O2]; Section 3.2 |
oxygen flux, in reaction r | Oxygen flux | JrO2 | varies | Overview |
pathway control state | Pathway control state | PCS | - | Section 2.2 |
permeability transition | Permeability transition | mtPT | - | Fig. 3; Section 2.4.3 (MPT) |
permeabilized cells | Permeabilized cells | pce | - | experimental permeabilization of plasma membrane; Tab. 5 |
permeabilized muscle fibers | Permeabilized muscle fibers | pfi | - | Tab. 5 |
permeabilized tissue | Permeabilized tissue | pti | - | Tab. 5 |
phosphorylation of ADP to ATP | Oxidative phosphorylation | P» | - | Tab. 1, 2; Fig. 1, 4 |
P»/O2 ratio | Oxidative phosphorylation | P»/O2 | 1 | mechanistic YP»/O2, calculated from pump stoichiometries; Fig. 1c |
positive | positive | Protonmotive force | - | Fig. 4 |
proton in the neg compartment | Protonmotive force | H+neg | [x] | Fig. 4 |
proton in the pos compartment | proton in the positive compartment | H+pos | [x] | Fig. 4 |
protonmotive force | protonmotive force | pmF | [V] | Overview; Tab. 1; Fig 1a, 2, 4 |
rate in ET-state | Electron transfer pathway | E | varies | ET capacity; Tab. 1; Fig. 2, 4 |
rate in LEAK-state | LEAK | L | varies | Tab. 1: L(n), L(T), L(Omy); Fig. 2, 4 |
rate in OXPHOS-state | OXPHOS | P | varies | OXPHOS capacity; Tab.1; Fig. 2, 4 |
rate in ROX state | Residual oxygen consumption | Rox | varies | Overview; Tab. 1 |
residual oxygen consumption | Residual oxygen consumption | ROX; Rox | - | state ROX; rate Rox; Tab. 1 |
respiration | Respiration | JrO2 | varies | rate of reaction r; Overview |
respiratory supercomplex | Supercomplex | SCInIIInIVn | - | supramolecular assemblies with variable copy numbers (n) of CI, CIII and CIV; Box 1 |
sample | Sample | s | - | diluted sample; Tab. 4, 5 |
substrate concentration at half-maximal rate | Concentration | c50 | [mol∙L-1] | Section 2.1.2 |
substrate-uncoupler-inhibitor-titration | Substrate-uncoupler-inhibitor-titration | SUIT | - | Section 2.2 |
tissue homogenate | Tissue homogenate | thom | - | Tab. 5 |
viable cells | Viable cells | vce | - | Tab. 5 |
volume of chamber | Volume | V | [L] | Tab. 4, 7; Fig. 5 |
volume format | Format | V | [L] | Tab. 6 |
volume of sample s | Volume | Vs | [L] | Tab. 5; Fig. 5 |
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