Difference between revisions of "Template:Keywords-MitoPedia BEC 2020.1"
From Bioblast
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| adenosine triphosphate || [[ATP]] || ATP || - || Fig. 2, 5 | | adenosine triphosphate || [[ATP]] || ATP || - || Fig. 2, 5 | ||
|- | |- | ||
| adenylates || [[ | | adenylates || [[Adenine nucleotides]] || AMP, ADP, ATP || - || Section 2.5.1 | ||
|- | |- | ||
| amount of substance ''X'' || [[Amount]] || ''n''<sub>''X''</sub> or ''n''(''X'') || [mol] || SI | | amount of substance ''X'' || [[Amount]] || ''n''<sub>''X''</sub> or ''n''(''X'') || [mol] || SI | ||
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| ATP yield per O<sub>2</sub> || [[ATP yield]] || ''Y''<sub>P»/O<sub>2</sub></sub> || 1 || P»/O<sub>2</sub> ratio measured in any respiratory state | | ATP yield per O<sub>2</sub> || [[ATP yield]] || ''Y''<sub>P»/O<sub>2</sub></sub> || 1 || P»/O<sub>2</sub> ratio measured in any respiratory state | ||
|- | |- | ||
| catabolic reaction || [[ | | catabolic reaction || [[Respirometry]] || k || - || Fig. 1, 3 | ||
|- | |- | ||
| catabolic rate of respiration || [[ | | catabolic rate of respiration || [[Respirometry]] || ''J''<sub>kO<sub>2</sub></sub>; ''I''<sub>kO<sub>2</sub></sub> || ''varies'' || Fig. 1, 3; ''see'' flux ''J'' and flow ''I'' | ||
|- | |- | ||
| cell count || [[Count]] || ''N''<sub>ce</sub> || [x] || Tab. 4; Fig. 5; ''see'' number of cells | | cell count || [[Count]] || ''N''<sub>ce</sub> || [x] || Tab. 4; Fig. 5; ''see'' number of cells | ||
|- | |- | ||
| cell mass || [[ | | cell mass || [[Body mass]] || ''m''<sub>ce</sub> || [kg] || Tab. 5; Fig. 5 | ||
|- | |- | ||
| cell mass, mass per cell || [[ | | cell mass, mass per cell || [[Body mass]] || ''M''<sub>''N<sub>ce</sub></sub> || [kg∙x<sup>-1</sup>] || Tab. 5; Fig. 5 | ||
|- | |- | ||
| cell-mass concentration || [[Concentration]] || ''C''<sub>''m''<sub>ce</sub></sub> || [kg∙L<sup>-1</sup>] || ''see'' ''C''<sub>''m''<sub>s</sub></sub>: Tab. 4; ''C''<sub>''m''<sub>ce</sub></sub> = ''m''<sub>ce</sub>∙''V''<sup>-1</sup> | | cell-mass concentration || [[Concentration]] || ''C''<sub>''m''<sub>ce</sub></sub> || [kg∙L<sup>-1</sup>] || ''see'' ''C''<sub>''m''<sub>s</sub></sub>: Tab. 4; ''C''<sub>''m''<sub>ce</sub></sub> = ''m''<sub>ce</sub>∙''V''<sup>-1</sup> | ||
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| mass format || [[Format]] || <u>''m''</u> || [kg] || Tab. 4 | | mass format || [[Format]] || <u>''m''</u> || [kg] || Tab. 4 | ||
|- | |- | ||
| mass of diluted sample || [[ | | mass of diluted sample || [[Body mass]] || ''m''<sub>s</sub> || [kg] || SI: mass of pure sample ''m''<sub>S</sub> | ||
|- | |- | ||
| mass per single object || [[ | | mass per single object || [[Body mass]] || ''M<sub>N<sub>X</sub></sub>'' || [kg∙x1] || Fig. 5; Tab. 4; SI: m(X); compare molar mass ''M''(''X'') | ||
|- | |- | ||
| mass, dry mass || [[ | | mass, dry mass || [[Body mass]] || ''m''<sub>d</sub> ||[kg] || Fig. 5 (dry weight) | ||
|- | |- | ||
| mass, wet mass || [[ | | mass, wet mass || [[Body mass]] || ''m''<sub>w</sub> || [kg] || Fig. 5 (wet weight) | ||
|- | |- | ||
| MITOCARTA || [https://www.broadinstitute.org/scientific-community/science/programs/metabolic-disease-program/publications/mitocarta/mitocarta-in-0 MITOCARTA] || || || | | MITOCARTA || [https://www.broadinstitute.org/scientific-community/science/programs/metabolic-disease-program/publications/mitocarta/mitocarta-in-0 MITOCARTA] || || || | ||
|- | |- | ||
| mitochondria or mitochondrial || [[Mitochondria]] || mt || - || Box 1 | | mitochondria or mitochondrial || [[Mitochondria]] || mt || - || Box 1 | ||
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|- | |- | ||
| mitochondrial yield || [[Mitochondrial yield]] || ''Y<sub>mtE</sub>''/''m''<sub>s</sub> || [mtEU∙kg<sup>-1</sup>] || mt-yield in imt-stock per mass of tissue sample; ''Y<sub>mtE</sub>''/''m''<sub>s</sub>=''Y<sub>mtE</sub>''∙''D<sub>mtE</sub>'' | | mitochondrial yield || [[Mitochondrial yield]] || ''Y<sub>mtE</sub>''/''m''<sub>s</sub> || [mtEU∙kg<sup>-1</sup>] || mt-yield in imt-stock per mass of tissue sample; ''Y<sub>mtE</sub>''/''m''<sub>s</sub>=''Y<sub>mtE</sub>''∙''D<sub>mtE</sub>'' | ||
|- | |||
| MitoPedia || [[MitoPedia: Respiratory states]] || || || | |||
|- | |- | ||
| molar format || [[Format]] || <u>''n''</u> || [mol] || Tab. 6 | | molar format || [[Format]] || <u>''n''</u> || [mol] || Tab. 6 | ||
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| residual oxygen consumption || [[Residual oxygen consumption]] || ROX; ''Rox'' || - || state ROX; rate Rox; Tab. 1 | | residual oxygen consumption || [[Residual oxygen consumption]] || ROX; ''Rox'' || - || state ROX; rate Rox; Tab. 1 | ||
|- | |- | ||
| respiration || [[ | | respiration || [[Respirometry]] || ''J''<sub>rO<sub>2</sub></sub> || ''varies'' || rate of reaction r; Overview | ||
|- | |- | ||
| respiratory state || [[MitoPedia: Respiratory states]] || - || - || Tab. 1, 3; Fig. 2, 4 | | respiratory state || [[MitoPedia: Respiratory states]] || - || - || Tab. 1, 3; Fig. 2, 4 | ||
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| substrate concentration at half-maximal rate || [[Concentration]] || ''c''<sub>50</sub> || [mol∙L<sup>-1</sup>] || Section 2.1.2 | | substrate concentration at half-maximal rate || [[Concentration]] || ''c''<sub>50</sub> || [mol∙L<sup>-1</sup>] || Section 2.1.2 | ||
|- | |- | ||
| substrate-uncoupler-inhibitor-titration || [[Substrate-uncoupler-inhibitor | | substrate-uncoupler-inhibitor-titration || [[Substrate-uncoupler-inhibitor titration]] || SUIT || - || Section 2.2 | ||
|- | |- | ||
| tissue homogenate || [[Tissue homogenate]] || thom || - || Tab. 5 | | tissue homogenate || [[Tissue homogenate]] || thom || - || Tab. 5 |
Revision as of 10:38, 27 May 2020
Keywords—MitoPedia - >>>>>>> - Click on [Expand] or [Collapse] - >>>>>>>
Table 8. Terms, symbols, and units including the Keywords—MitoPedia. 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 | Adenine nucleotides | 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 | Respirometry | k | - | Fig. 1, 3 |
catabolic rate of respiration | Respirometry | 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 | Body mass | mce | [kg] | Tab. 5; Fig. 5 |
cell mass, mass per cell | Body 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 | 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) |
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 |
flux control ratio | Flux control ratio | FCR | 1 | background/reference flux; Fig. 5 |
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] |
living cells | Living cells | ce | - | Tab. 5 (intact cells) |
LEAK-state | LEAK-respiration | 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 | Body 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) |
mass, dry mass | Body mass | md | [kg] | Fig. 5 (dry weight) |
mass, wet mass | Body mass | mw | [kg] | Fig. 5 (wet weight) |
MITOCARTA | MITOCARTA | |||
mitochondria or mitochondrial | Mitochondria | mt | - | Box 1 |
mitochondrial DNA | Mitochondria | mtDNA | - | Box 1 |
mitochondrial concentration | Mitochondrial marker, Concentration | CmtE = mtE∙V-1 | [mtEU∙L-1] | Tab. 4 |
mitochondrial content | Mitochondrial marker | mtENX | [mtEU∙x-1] | mtENX = mtE∙NX-1; Tab. 4 |
mitochondrial density | Mitochondrial marker, 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 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: 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-state | OXPHOS-capacity | 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 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 |
rate in ET-state | ET | 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 | 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 |
uncoupling | Uncoupler titrations | - | - | Tab 2; Fig. 3 |
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 |