Difference between revisions of "Template:Keywords-MitoPedia BEC 2020.1"
From Bioblast
(2 intermediate revisions by the same user not shown) | |||
Line 45: | Line 45: | ||
| Complexes I to IV || [[Complex I]] || CI to CIV || - || respiratory ET Complexes are redox proton pumps; Fig. 1B; F<sub>1</sub>F<sub>O</sub>-ATPase is not a redox proton pump of the ETS, hence the term CV is not recommended | | Complexes I to IV || [[Complex I]] || CI to CIV || - || respiratory ET Complexes are redox proton pumps; Fig. 1B; F<sub>1</sub>F<sub>O</sub>-ATPase is not a redox proton pump of the ETS, hence the term CV is not recommended | ||
|- | |- | ||
| concentration of B, amount || [[Concentration]] || ''c''<sub>B</sub> = ''N''<sub>B</sub>∙''V''<sup>-1</sup> || [mol∙L<sup>-1</sup>] || SI: amount of substance concentration | | concentration of B, amount || [[Concentration]] || ''c''<sub>B</sub> = ''N''<sub>B</sub>∙''V''<sup>-1</sup> || [mol∙L<sup>-1</sup>] || SI: amount of substance concentration [[Cohen 2008 IUPAC Green Book]]; the molar and count formats are distinguished as ''n''<sub>B</sub> and ''N''<sub>B</sub>, respectively. | ||
|- | |- | ||
| concentration of O<sub>2</sub>, amount || [[Concentration]] || ''c''<sub>O<sub>2</sub></sub> = ''n''<sub>O<sub>2</sub></sub>∙''V''<sup>-1</sup> || [mol∙L<sup>-1</sup>] || Box 2; [O<sub>2</sub>] | | concentration of O<sub>2</sub>, amount || [[Concentration]] || ''c''<sub>O<sub>2</sub></sub> = ''n''<sub>O<sub>2</sub></sub>∙''V''<sup>-1</sup> || [mol∙L<sup>-1</sup>] || Box 2; [O<sub>2</sub>] | ||
|- | |- | ||
| concentration of s, count || [[Concentration]] || ''C''<sub>s</sub> = ''N''<sub>s</sub>∙''V''<sup>-1</sup> || [x∙L<sup>-1</sup>] Tab. 4 (number concentration | | concentration of s, count || [[Concentration]] || ''C''<sub>s</sub> = ''N''<sub>s</sub>∙''V''<sup>-1</sup> || [x∙L<sup>-1</sup>] Tab. 4 (number concentration [[Cohen 2008 IUPAC Green Book]]); 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]] || <u>''N''</u> || [x] || Tab. 4, 5; Fig. 5 | | count format || [[Format]] || <u>''N''</u> || [x] || Tab. 4, 5; Fig. 5 | ||
Line 81: | Line 81: | ||
| flux control ratio || [[Flux control ratio]] || ''FCR'' || 1 || [[Background state |background]]/[[Reference state |reference]] flux; Fig. 5 | | flux control ratio || [[Flux control ratio]] || ''FCR'' || 1 || [[Background state |background]]/[[Reference state |reference]] flux; Fig. 5 | ||
|- | |- | ||
| hyphenation || [[Hyphenation]] || - || - || Updates in comparison to [[Gnaiger 2019 MitoFit | | hyphenation || [[Hyphenation]] || - || - || Updates in comparison to [[Gnaiger 2019 MitoFit Preprints]] | ||
|- | |- | ||
| inorganic phosphate || [[Phosphate]] || P<sub>i</sub> || - || Fig. 1C | | inorganic phosphate || [[Phosphate]] || P<sub>i</sub> || - || Fig. 1C | ||
Line 87: | Line 87: | ||
| inorganic phosphate carrier || [[Phosphate carrier]] || PiC || - || Fig. 1C | | inorganic phosphate carrier || [[Phosphate carrier]] || PiC || - || Fig. 1C | ||
|- | |- | ||
| International Union of Pure and Applied Chemistry, IUPAC || [[International Union of Pure and Applied Chemistry, IUPAC |IUPAC]] || IUPAC || - || | | International Union of Pure and Applied Chemistry, IUPAC || [[International Union of Pure and Applied Chemistry, IUPAC |IUPAC]] || IUPAC || - || [[Cohen 2008 IUPAC Green Book]] | ||
|- | |- | ||
| International System of Units || [[International System of Units]] || SI || - || | | International System of Units || [[International System of Units]] || SI || - || [[Cohen 2008 IUPAC Green Book]] | ||
|- | |- | ||
| isolated mitochondria || [[Isolated mitochondria]] || imt || - || [[Bureau International des Poids et Mesures 2019 The International System of Units (SI) |[11]]] | | isolated mitochondria || [[Isolated mitochondria]] || imt || - || [[Bureau International des Poids et Mesures 2019 The International System of Units (SI) |[11]]] | ||
Line 153: | Line 153: | ||
| number of dead cells || [[Cell viability]] || ''N''<sub>dce</sub> || [x] || non-viable cell count, loss of plasma membrane barrier function; Tab. 5 | | number of dead cells || [[Cell viability]] || ''N''<sub>dce</sub> || [x] || non-viable cell count, loss of plasma membrane barrier function; Tab. 5 | ||
|- | |- | ||
| number of entities B || [[Count]] || ''N''<sub>B</sub> || [x] || Tab. 4 | | number of entities B || [[Count]] || ''N''<sub>B</sub> || [x] || Tab. 4 [[Cohen 2008 IUPAC Green Book]] | ||
|- | |- | ||
| number of entities ''X''; count || [[Count]] || ''N<sub>X</sub>'' || [x] || ‘count’ is an SI quantity [11], but the counting unit [x] is not in the SI [95]; Tab. 4; Fig. 5 | | number of entities ''X''; count || [[Count]] || ''N<sub>X</sub>'' || [x] || ‘count’ is an SI quantity [11], but the counting unit [x] is not in the SI [95]; Tab. 4; Fig. 5 | ||
Line 203: | Line 203: | ||
| rate in ET state || [[Electron transfer pathway]] || ''E'' || ''varies'' || ET capacity; Tab. 1; Fig. 2, 4 | | 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 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 OXPHOS-state || [[OXPHOS-capacity]] || ''P'' || ''varies'' || OXPHOS-capacity; Tab.1; Fig. 2, 4 |
Latest revision as of 21:53, 29 September 2021
Keywords—MitoPedia - >>>>>>> - Click on [Expand] or [Collapse] - >>>>>>>
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 = Nce∙V-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 = mce∙V-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 = Nvce∙Nce-1 = 1 - Ndce∙Nce-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∙V-1 | [mol∙L-1] | SI: amount of substance concentration Cohen 2008 IUPAC Green Book; the molar and count formats are distinguished as nB and NB, respectively. |
concentration of O2, amount | Concentration | cO2 = nO2∙V-1 | [mol∙L-1] | Box 2; [O2] |
concentration of s, count | Concentration | Cs = Ns∙V-1 | [x∙L-1] Tab. 4 (number concentration Cohen 2008 IUPAC Green Book); 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 |
International System of Units | International System of Units | SI | - | Cohen 2008 IUPAC Green Book |
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 = mtE∙V-1 | [mtEU∙L-1] | Tab. 4 |
mitochondrial content per X | Mitochondrial marker | mtENX | [mtEU∙x-1] | mtENX = mtE∙NX-1; Tab. 4 |
mitochondrial density per ms | Mitochondrial marker, Density | DmtE/ms | [mtEU∙kg-1] | DmtE/ms=mtE∙ms-1; Tab. 4 |
mitochondrial density per Vs | Mitochondrial marker, Density | DmtE/Vs | [mtEU∙kg-1] | DmtE/Vs=mtE∙Vs-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=YmtE∙DmtE |
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 |
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∙V-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 | P» | - | 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 |