Difference between revisions of "MitoPedia: Terms and abbreviations"
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Revision as of 14:17, 19 October 2022
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MitoPedia: Terms and abbreviations
The MitoPedia terminology is developed continuously in the spirit of Gentle Science.
SI, IUPAC and MitoEAGLE recommendations
- 'The International System of Units, the SI, has been used around the world as the preferred system of units, the basic language for science, technology, industry and trade since it was established in 1960'[1]. IUPAC guidelines are followed for general terms of physical chemistry[2],[3],[4], extended by concepts of mitochondrial physiology and nonequilibrium thermodynamics[5],[6],[7].
- According to BEC guidelines, 'manuscripts must adhere to SI units and IUPAC recommendations. MitoEAGLE recommendations on terms and symbols are to be implemented'.
Harmonization
- Harmonization of some terms in mitochondrial physiology links separate 'subcultures' in publication. Ambiguities are pointed out for clarification of concepts. A platform-independent terminology is preferred. See also Table 2. Harmonization of terminology on respiratory states[8].
- Table 1. Some platform-independent and platform-specific or outdated terms in mitochondrial physiology
Symbol Platform-independent terms Platform-specific or outdated terms ce living cells intact cells R ROUTINE respiration, in ROUTINE state basal respiration, in basal state P OXPHOS capacity, in OXPHOS state of mt-preparations State 3 L LEAK respiration proton leak; State 4 E ET capacity, electron transfer capacity maximum respiration; State 3u L/E L/E coupling-control ratio 1/UCR = L/E (ambiguous) L/P L/P coupling-control ratio 1/RCR = L/P R/E R/E control ratio 1/UCR = E/R R-L R-L net ROUTINE capacity, net ROUTINE respiration ATP production, ATP-linked respiration E-R E-R reserve capacity spare capacity Rox residual oxygen consumption, in ROX state nonmitochondrial respiration; State 2
- Bioblast links: Coupling control - >>>>>>> - Click on [Expand] or [Collapse] - >>>>>>>
1. Mitochondrial and cellular respiratory rates in coupling-control states
Respiratory rate | Defining relations | Icon | |
---|---|---|---|
OXPHOS capacity | P = Pยด-Rox | mt-preparations | |
ROUTINE respiration | R = Rยด-Rox | living cells | |
ET capacity | E = Eยด-Rox | ยป Level flow | |
ยป Noncoupled respiration - Uncoupler | |||
LEAK respiration | L = Lยด-Rox | ยป Static head | |
ยป LEAK state with ATP | |||
ยป LEAK state with oligomycin | |||
ยป LEAK state without adenylates | |||
Residual oxygen consumption Rox | L = Lยด-Rox |
2. Flux control ratios related to coupling in mt-preparations and living cells
FCR | Definition | Icon | |
---|---|---|---|
L/P coupling-control ratio | L/P | ยป Respiratory acceptor control ratio, RCR = P/L | |
L/R coupling-control ratio | L/R | ||
L/E coupling-control ratio | L/E | ยป Uncoupling-control ratio, UCR = E/L (ambiguous) | |
P/E control ratio | P/E | ||
R/E control ratio | R/E | ยป Uncoupling-control ratio, UCR = E/L | |
net P/E control ratio | (P-L)/E | ||
net R/E control ratio | (R-L)/E |
3. Net, excess, and reserve capacities of respiration
Respiratory net rate | Definition | Icon |
---|---|---|
P-L net OXPHOS capacity | P-L | |
R-L net ROUTINE capacity | R-L | |
E-L net ET capacity | E-L | |
E-P excess capacity | E-P | |
E-R reserve capacity | E-R |
4. Flux control efficiencies related to coupling-control ratios
- ยป Flux control efficiency jZ-Y
- ยป Background state
- ยป Reference state
- ยป Metabolic control variable
Coupling-control efficiency | Definition | Icon | Canonical term | ||
---|---|---|---|---|---|
P-L control efficiency | jP-L | = (P-L)/P | = 1-L/P | P-L OXPHOS-flux control efficiency | |
R-L control efficiency | jR-L | = (R-L)/R | = 1-L/R | R-L ROUTINE-flux control efficiency | |
E-L coupling efficiency | jE-L | = (E-L)/E | = 1-L/E | E-L ET-coupling efficiency ยป Biochemical coupling efficiency | |
E-P control efficiency | jE-P | = (E-P)/E | = 1-P/E | E-P ET-excess flux control efficiency | |
E-R control efficiency | jE-R | = (E-R)/E | = 1-R/E | E-R ET-reserve flux control efficiency |
5. General
- ยป Basal respiration
- ยป Cell ergometry
- ยป Dyscoupled respiration
- ยป Dyscoupling
- ยป Electron leak
- ยป Electron-transfer-pathway state
- ยป Hyphenation
- ยป Oxidative phosphorylation
- ยป Oxygen flow
- ยป Oxygen flux
- ยป Permeabilized cells
- ยป Phosphorylation system
- ยป Proton leak
- ยป Proton slip
- ยป Respiratory state
- ยป Uncoupling
- Bioblast links: Uncoupling - >>>>>>> - Click on [Expand] or [Collapse] - >>>>>>>
- Specific
- ยป Artefacts by single dose uncoupling
- ยป ATP synthase
- ยป CCCP
- ยป Coupling-control protocol
- ยป DNP
- ยป Dyscoupled respiration
- ยป FCCP
- ยป Is respiration uncoupled - noncoupled - dyscoupled?
- ยป Noncoupled respiration: Discussion
- ยป Uncoupler
- ยป Uncoupled respiration - see ยป Noncoupled respiration
- ยป Uncoupling proteins
- ยป Uncoupling protein 1
- ยป Uncoupler titrations - Optimum uncoupler concentration
- Specific
- Respiratory states and control ratios
- ยป Biochemical coupling efficiency
- ยป Coupling-control state
- ยป Electron-transfer-pathway state
- ยป Electron-transfer pathway
- ET capacity
- ยป E-L coupling efficiency
- ยป Flux control efficiency
- ยป Flux control ratio
- ยป LEAK-control ratio
- ยป LEAK respiration
- ยป Noncoupled respiration
- ยป OXPHOS
- ยป OXPHOS capacity; ยป State 3
- ยป OXPHOS-control ratio, P/E ratio
- ยป Respiratory acceptor control ratio
- ยป ROUTINE-control ratio
- ยป ROUTINE respiration
- ยป ROUTINE state
- ยป State 3u
- ยป State 4
- ยป Uncoupling-control ratio UCR
- Respiratory states and control ratios
- Gnaiger E et al โ MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. https://doi.org/10.26124/bec:2020-0001.v1
- Gnaiger E (2020) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 5th ed. Bioenerg Commun 2020.2. https://doi.org/10.26124/bec:2020-0002
- General (alphabetical order)
- Other keyword lists
- Coupling control tables - >>>>>>> - Click on [Expand] or [Collapse] - >>>>>>>
4-compartmental OXPHOS model. (1) ET capacity E of the noncoupled electron transfer system ETS. OXPHOS capacity P is partitioned into (2) the dissipative LEAK component L, and (3) ADP-stimulated P-L net OXPHOS capacity. (4) If P-L is kinetically limited by a low capacity of the phosphorylation system to utilize the protonmotive force pmF, then the apparent E-P excess capacity is available to drive coupled processes other than phosphorylation Pยป (ADP to ATP) without competing with Pยป.
References
- โ Bureau International des Poids et Mesures (2019) The International System of Units (SI). 9th edition:117-216. ISBN 978-92-822-2272-0
- โ Cohen ER, Cvitas T, Frey JG, Holmstrรถm B, Kuchitsu K, Marquardt R, Mills I, Pavese F, Quack M, Stohner J, Strauss HL, Takami M, Thor HL (2008) Quantities, Units and Symbols in Physical Chemistry, IUPAC Green Book, 3rd Edition, 2nd Printing, IUPAC & RSC Publishing, Cambridge. - ยปBioblast linkยซ
- โ International Union of Biochemistry and Molecular Biology: Recommendations for terminology and databases for biochemical thermodynamics. - ยปOpen Accessยซ
- โ International Union of Biochemistry (1981) Symbolism and terminology in enzyme kinetics. - ยปOpen Accessยซ
- โ Gnaiger Erich et al โ MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. doi:10.26124/bec:2020-0001.v1
- โ Gnaiger E (2020) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 5th ed. Bioenerg Commun 2020.2. https://doi.org/10.26124/bec:2020-0002
- โ Gnaiger E (1993) Nonequilibrium thermodynamics of energy transformations. Pure Appl Chem 65:1983-2002. - ยปBioblast linkยซ
- โ Zdrazilova L, Hansikova H, Gnaiger E (2022) Comparable respiratory activity in attached and suspended human fibroblasts. PLoS ONE 17:e0264496. https://doi.org/10.1371/journal.pone.0264496