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Template:Keywords-MitoPedia BEC 2020.1

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Keywords—MitoPedia, including 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
adenosine diphosphate ADP ADP - Tab. 1; Fig. 1, 2, 5
adenosine monophosphate AMP AMP - 2 ADP ↔ ATP+AMP
adenosine triphosphate ATP ATP - Fig. 2, 5
adenylates Adenine nucleotides AMP, ADP, ATP - Section 2.5.1
alternative quinol oxidase Alternative oxidase AOX - Fig. 1B
amount of substance B Amount nB or n(B) [mol] SI; amount nB of B versus count NB of B
ATP yield per O2 ATP yield YP»/O2 1 P»/O2 ratio measured in any respiratory state
catabolic rate of respiration Cell respiration JkO2; IkO2 varies Fig. 1, 3; flux J versus flow I
catabolic reaction Cell respiration k - Fig. 1, 3
cell count Count Nce [x] Tab. 4; Fig. 5; see number of cells; countable object s=ce
cell-count concentration Concentration Cce [x∙L­-1] Tab. 4; Cce = NceV-1; count concentration C versus amount concentration c; subscript ce indicates the entity type: concentration of ce. But it does not signal 'per entity', which would be written as 'per cell' Xce.
cell mass Body mass mce [kg] Tab. 5; Fig. 5; mass of cells m versus mass per cell (per single entity cell) MXce
cell mass, mass per cell Body mass MXce [kg∙x­-1] Tab. 5; Fig. 5; mass per single cell MXce; upper case M and subscript X signal 'per count', subscript ce signals the entity s=ce; in a context restricted to cells or molecules or a particular organism such as humans, the abbreviated symbol M [kg∙x­-1] provides a sufficiently informative signal, particularly in combination with the explicit unit.
cell-mass concentration in chamber Concentration Cmce [kg∙L­-1] see Cms: Tab. 4; Cmce = mceV-1; upper case C alone would signal 'count concentration' (CN is more explicit), whereas the signal for 'mass concentration' is in the combination Cm.
cell viability index Cell viability VI - VI = NvceNce­-1 = 1 - NdceNce­-1
charge number per entity XB Charge number zB 1 zB = QB·e-1 (IUPAC); Tab. 6; zO2 = = QO2·e-1 = 4; IUPAC uses the term 'charge number of an ion' which should be changed to 'charge number per ion', or more clearly to 'charge number per ion number'. The symbol z carries the message 'number of elementary charges per number', and the subscript carries the message on the type of entity X.
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 B, amount Concentration cB = NB-1 [mol∙L­-1] SI: amount of substance concentration [[[Cohen 2008 IUPAC Green Book |24]]]; the molar and count formats are distinguished as nB and NB, respectively.
concentration of O2, amount Concentration cO2 = nO2-1 [mol∙L­-1] Box 2; [O2]
concentration of s, count Concentration Cs = Ns-1 [x∙L-1] Tab. 4 (number concentration [[[Cohen 2008 IUPAC Green Book |24]]]); the signal for count concentration is given by the upper case C in contrast to c for amount concentration. In both cases, the subscript X indicates the entity type, not to be confused with a number of entities.
count format Format N [x] Tab. 4, 5; Fig. 5
count of Xs Count Ns [x] SI; see number of entities Xs
coupling control Coupling-control ratio CCR - Section 2.4.1
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 pathway Electron transfer pathway ET pathway - Overview; Fig. 1
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)
elementary entity Entity Xs [x] single countable object of sample type s; 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
flux control ratio Flux control ratio FCR 1 background/reference flux; Fig. 5
hyphenation Hyphenation - - Updates in comparison to Gnaiger 2019 MitoFit Preprints
inorganic phosphate Phosphate Pi - Fig. 1C
inorganic phosphate carrier Phosphate carrier PiC - Fig. 1C
International Union of Pure and Applied Chemistry, IUPAC IUPAC IUPAC - [[[Cohen 2008 IUPAC Green Book |24]]]
International System of Units International System of Units SI - [[[Cohen 2008 IUPAC Green Book |24]]]
isolated mitochondria Isolated mitochondria imt - [11]
LEAK state LEAK respiration LEAK - Tab. 1; Fig. 2 (compare State 4)
LEAK respiration LEAK respiration L varies rate; Tab. 1; Fig. 2
living cells Living cells ce - Tab. 5 (intact cells)
mass, dry mass Body mass md [kg] Fig. 5 (dry weight)
mass, wet mass Body mass mw [kg] Fig. 5 (wet weight)
mass concentration of sample s in chamber Concentration Cms [kg∙L-1] Tab. 4
mass format Format m [kg] Tab. 4
mass of sample s in a mixture Mass ms [kg] SI: mass of pure sample mS
mass per single object Body mass MNX [kg∙x­1] Fig. 5; Tab. 4; SI: m(X); compare molar mass M(X)
MITOCARTA MITOCARTA
mitochondria or mitochondrial Mitochondria mt - Box 1
mitochondrial concentration Mitochondrial marker, Concentration CmtE = mtEV-1 [mtEU∙L-1] Tab. 4
mitochondrial content per X Mitochondrial marker mtENX [mtEU∙x­-1] mtENX = mtENX-1; Tab. 4
mitochondrial density per ms Mitochondrial marker, Density DmtE/ms [mtEU∙kg­-1] DmtE/ms=mtEms-1; Tab. 4
mitochondrial density per Vs Mitochondrial marker, Density DmtE/Vs [mtEU∙kg­-1] DmtE/Vs=mtEVs-1; Tab. 4
mitochondrial DNA Mitochondria mtDNA - Box 1
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 preparations Mitochondrial preparations mt-prep - Tab. 5
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=YmtEDmtE
MitoPedia MitoPedia, MitoPedia: Respiratory states
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
normalization of rate Normalization of rate - - Tab. 4; Fig. 5
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-capacity OXPHOS-capacity P varies rate; Tab. 1; Fig. 2
OXPHOS state OXPHOS-capacity OXPHOS - Tab. 1; Fig. 2; OXPHOS-state distinguished from the process OXPHOS (State 3 at kinetically-saturating [ADP] and [Pi])
oxygen concentration Oxygen concentration cO2 = nO2-1 [mol∙L­-1] [O2]; Section 3.2
oxygen solubility Oxygen solubility SO2 [µmol·kPa-1] Section 2.6.3
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 - Tab. 1, 2; Fig. 1, 4
phosphorylation efficiency Ergodynamic efficiency ε 1 Section 2.4.1
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
publication efficiency publication efficiency Harmonization of nomenclature; Executive summary
quantities, symbols, and units Quantities, symbols, and units - - An explanation of symbols and unit [x]
rate in ET state Electron transfer pathway E varies ET capacity; Tab. 1; Fig. 2, 4
rate in LEAK state LEAK respiration L varies Tab. 1: L(n), L(T), L(Omy); Fig. 2, 4
rate in OXPHOS-state OXPHOS-capacity 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 Respirometry JrO2 varies rate of reaction r; Overview
respiratory state MitoPedia: Respiratory states - - Tab. 1, 3; Fig. 2, 4
respiratory supercomplex Supercomplex SCInIIInIVn - supramolecular assemblies with variable copy numbers (n) of CI, CIII and CIV; Box 1
sample in a mixture Sample s - diluted sample; Tab. 4, 5
steay state Steady state - - Section 2.5.6
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
system System - - Fig. 5
tissue homogenate Tissue homogenate thom - Tab. 5
unit elementary entity Entity UX [x] single countable object; Tab. 4, 5
uncoupling Uncoupler titrations - - Tab 2; Fig. 3
viable cells Viable cells vce - Tab. 5
volume format Format V [L] Tab. 6
volume of experimental chamber Volume V [L] liquid volume V including the sample s; Tab. 4, 7; Fig. 5
volume of sample s in a mixture Volume Vs [L] Tab. 5; Fig. 5