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B
'''Blebbistatin''' is a widely used muscle and non-muscle myosin II-specific inhibitor that block contractile activity. Blebbistatin shows selectivity and high affinity for multiple class II myosins. Blebbistatin is commonly employed in respirometric experiments with permeabilized muscle fibers (pfi). Permeabilized muscle fibers are sensitive to low oxygen supply due to diffusion restrictions that limit mitochondrial respiration at the core of the fiber bundle. Therefore, hyperoxic conditions are required to counteract this limitation. Further studies have shown that the addition of blebbistatin in the respiration medium prevents fiber contraction, reduces the oxygen sensitivity and allows the study of ADP kinetics in pfi at normoxic oxygen levels. However, other studies described that the presence of blebbistatin does not prevent the oxygen dependence in pfi. Moreover, several limitations of blebbistatin i.e. low solubility in water, cytotoxicity and phototoxicity have been described. +
The '''block temperature''' of the [[Oroboros O2k]] is the continuously measured temperature of the copper block, housing the two glass chambers of the O2k. The block temperature is recorded by [[DatLab]] as one of the O2k system channels. +
'''Blood cell preparation''' (bcp) is one of the key steps in diagnostic protocols. +
'''Blood plasma''' is the non-cellular component of the blood. Plasma lacks cellular components of the blood, [[red blood cell]]s, [[white blood cell]]s, and [[platelet]]s. However, there are many proteins in plasma, i.e. fibrinogen, albumin and globulin. Both blood plasma and [[platelet-rich plasma]] maintain clotting activity after whole blood separation. +
'''Blood serum''' is a purified plasma in which the coagulant components were removed from the [[blood plasma]]. It contains other substances, i.e. antibodies, antigens and hormones. Serum can be obtained by collecting the liquid phase after blood or plasma coagulation. +
In the [[healthy reference population]] (HRP), there is zero '''body fat excess''', BFE, and the fraction of excess body fat in the HRP is expressed - by definition - relative to the reference body mass, ''M''°, at any given [[height of humans |height]]. Importantly, body fat excess, BFE, and [[body mass excess]], BME, are linearly related, which is not the case for the body mass index, BMI. +
The '''body mass''' ''M'' is the mass ([[kilogram]] [kg]) of an individual (object) [x] and is expressed in units [kg/x]. Whereas the body weight changes as a function of gravitational force (you are weightless at zero gravity; your floating weight in water is different from your weight in air), your mass is independent of gravitational force, and it is the same in air and water. +
The '''body mass excess''', BME, is an index of obesity and as such BME is a lifestyle metric. The BME is a measure of the extent to which your actual [[body mass]], ''M'' [kg/x], deviates from ''M''° [kg/x], which is the reference body mass [kg] per individual [x] without excess body fat in the [[healthy reference population]], HRP. A balanced BME is BME° = 0.0 with a band width of -0.1 towards underweight and +0.2 towards overweight. The BME is linearly related to the [[body fat excess]]. +
The '''body mass index''', BMI, is the ratio of body mass to height squared (BMI=''M''·''H''<sup>-2</sup>), recommended by the WHO as a general indicator of underweight (BMI<18.5 kg·m<sup>-2</sup>), overweight (BMI>25 kg·m<sup>-2</sup>) and obesity (BMI>30 kg·m<sup>-2</sup>). Keys et al (1972; see 2014) emphasized that 'the prime criterion must be the relative independence of the index from height'. It is exactly the dependence of the BMI on height - from children to adults, women to men, Caucasians to Asians -, which requires adjustments of BMI-cutoff points. This deficiency is resolved by the [[body mass excess]] relative to the [[healthy reference population]]. +
[[File:Table Physical constants.png|left|400px|thumb|]] The '''Boltzmann constant''' ''k'' has the SI unit [J·K<sup>-1</sup>] (IUPAC), but more strictly the units for energy per particles per temperature is [J·x<sup>-1</sup>·K<sup>-1</sup>].
''k'' = ''f''·''e''<sup>-1</sup>, the [[electrochemical constant]] ''f'' times the [[elementary charge]] ''e''.
''k'' = ''R''·''N''<sub>A</sub><sup>-1</sup>, the [[gas constant]] ''R'' divided by the [[Avogadro constant]] ''N''<sub>A</sub>. +
'''Bongkrekik acid''' is a selective and potent inhibitor of the [[adenine nucleotide translocator]] (ANT). Bka binds to the matrix (negative) site of ANT, opposite of [[carboxyatractyloside]]. +
The '''bound energy''' change in a closed system is that part of the ''total'' [[energy]] change that is always bound to an exchange of [[heat]],
d''B'' = d''U'' - d''A'' [Eq. 1]
∆''B'' = ∆''H'' - ∆''G'' [Eq. 2]
The ''free'' energy change (Helmoltz or Gibbs; d''A'' or d''G'') is the ''total'' energy change (total inner energy or enthalpy, d''U'' or d''H'') of a system minus the ''bound'' energy change.
Therefore, if a process occurs at [[equilibrium]], when d''G'' = 0 (at constant gas pressure), then d''H'' = d''B'', and at d<sub>e</sub>''W'' = 0 (d''H'' = d<sub>e</sub>''Q'' + d<sub>e</sub>''W''; see [[energy]]) we obtain the definition of the bound energy as the heat change taking place in an equilibrium process (eq),
d''B'' = ''T''∙d''S'' = d<sub>e</sub>''Q''<sub>eq</sub> [Eq. 3] +
Bovine serum albumin is a membrane stabilizer, oxygen radical scavenger, and binds Ca<sup>2+</sup> and free fatty acids, hence the rather expensive essentially free fatty acid free BSA is required in mitochondrial isolation and respiration media. Sigma A 6003 fraction V. +
'''Mitochondrial respiration medium, Buffer Z''', described by [http://bioblast.at/index.php/Perry_2011_Biochem_J Perry 2011 Biochem J]
For composition and comparison see: [[Mitochondrial respiration media: comparison]] +
C
The CDGSH iron-sulfur domain (CISDs) family of proteins uniquely ligate labile 2Fe-2S clusters with a 3Cys-1His motif. CISD1 and CISD3 have been demonstrated to localize to the outer mitochondrial membrane and mitochondrial matrix respectively, however their relationship to mitochondrial physiology remains ill-defined [1]. The best characterized member of the CISD family, CISD1, has been demonstrated to be involved in respiratory capacity, iron homeostasis, and ROS regulation +
'''CE''' marking is a mandatory conformity marking for certain products sold within the European Economic Area (EEA). +
'''CHNO-fuel substrates''' are reduced carbon-hydrogen-nitrogen-oxygen substrates which are oxidized in the [[exergonic]] process of [[cell respiration]]. Mitochondrial pathways are stimulated by CHNO-fuel substrates feeding electrons into the [[ETS]] at different levels of integration and in the presence or absence of inhibitors acting on specific enzymes which are gate-keepers and control various pathway segments. +
''See'' '''[[N/NS pathway control ratio]]''' +
''See'' '''[[S/NS pathway control ratio]]''' +
'''COPE core practices for research''' are applicable to all involved in publishing scholarly literature. +
'''Ca<sup>2+</sup>''' is a major signaling molecule in both prokaryotes and eukaryotes. Its cytoplasmic concentration is tightly regulated by transporters in the plasma membrane and in the membranes of various organelles. For this purpose, it is either extruded from the cell through exchangers and pumps or stored in organelles such as the endoplasmic reticulum and the mitochondria. Changes in the concentration of the cation regulate numerous enzymes including many involved in ATP utilizing and in ATP generating pathways and thus ultimately control metabolic activity of mitochondria and of the entire cell. Measuring changes in Ca<sup>2+</sup> levels is thus of considerable interest in the context of [[high-resolution respirometry]]. +
'''Calcium Green'''<sup>TM</sup> (CaG) denotes a family of [[extrinsic fluorophores]] applied for measurement of Ca<sup>2+</sup> concentration with [[mitochondrial preparations]]. This dye fluoresces when bound to Ca<sup>2+</sup>. When measuring mitochondrial calcium uptake it is possible to observe the increase of the CaG signal upon calcium titration, followed by the decrease of CaG signal due to the uptake. +
Calcium retention capacity (CaRC) is a measure of the capability of mitochondria to retain calcium (Ca<sup>2+</sup>), primarily in the form of calcium phosphates, in the mitochondrial matrix. By storing calcium in the form of osmotically inactive precipitates the mitochondria contribute to the buffering of cytosolic free Ca<sup>2+</sup> levels and thereby to the regulation of calcium-dependent cellular processes. Alterations of CaRC are important in stress phenomena associated with energy limitation and have been linked to neurodegenerative diseases [[Starkov 2010 FEBS J |(Starkov 2013 FEBS J).]]
Experimentally, CaRC has been indirectly assessed by determination of respiratory rates of isolated mitochondria which were exposed to continuously increasing doses of Ca<sup>2+</sup> by use of the [[TIP2k-Module| Titration-Injection microPump TIP2k]]. The upper limit of CaRC was observed as a sudden decrease of respiration presumed to reflect opening of the permeability transition pore [[Hansson_2010_J_Biol_Chem |(Hansson 2010 J Biol Chem).]] +
The calorimetric/respirometric or '''calorespirometric ratio''' (CR ratio) is the ratio of calorimetrically and respirometrically measured heat and oxygen flux, determinded by [[calorespirometry]]. The experimental CR ratio is compared with the theoretically derived [[oxycaloric equivalent]], and agreement in the range of -450 to -480 kJ/mol O<sub>2</sub> indicates a balanced [[aerobic]] energy budget ([[Gnaiger_1987_PhysiolZool|Gnaiger and Staudigl 1987]]). In the transition from aerobic to [[anaerobic | anaerobic metabolism]], there is a [[Limiting pO2|limiting ''p''<sub>O2</sub>]], ''p''<sub>lim</sub>, below which CR ratios become more exothermic since anaerobic energy flux is switched on. +
'''Calorespirometry''' is the method of measuring simultaneously metabolic heat flux ([[calorimetry]]) and oxygen flux ([[respirometry]]). The [[calorespirometric ratio]] (CR ratio; heat/oxygen flux ratio) is thus experimentally determined and can be compared with the theoretical [[oxycaloric equivalent]], as a test of the aerobic energy balance. +
The candela, symbol cd, is the SI unit of luminous intensity in a given direction. It is defined by taking the fixed numerical value of the luminous efficacy of monochromatic radiation of frequency 540 × 10<sup>12</sup> Hz, ''K''<sub>cd</sub>, to be 683 when expressed in the unit lm W<sup>−1</sup>. +
A '''canonical ensemble''' is the group of compartments enclosed in an isolated system '''H''', with a smaller compartment A<sub>1</sub> in thermal equilibrium with a larger compartment A<sub>2</sub> which is the heat reservoir at temperature ''T''. When A<sub>1</sub> is large in the canonical sense, if its state can be described in terms of macroscopic thermodynamic quantities of ''V'', ''T'', and ''p'' merging with the state described as a probability distribution. +
'''Carbohydrates''', also known as '''saccharides''', are molecules composed of carbon, hydrogen and oxygen. These molecules can be divided by size and complexity into monosaccharides, disaccharides, oligosaccharides, and polysaccharides. [[Glucose]] is a monosaccharide considered the primary source of energy in cells and a metabolic intermediate. This carbohydrate undergoes glycolysis, with the generation of [[pyruvate]], that can enter the [[TCA cycle]].
Carbohydrates such as glucose and fructose may also be involved in the [[Crabtree effect]]. +
'''Carbonyl cyanide m-chlorophenyl hydrazone''', CCCP (U; C<sub>9</sub>H<sub>5</sub>ClN<sub>4</sub>; ''F''<sub>W</sub> = 204.62) is a protonophore (H<sup>+</sup> ionophore) and is used as a potent chemical [[uncoupler]] of [[oxidative phosphorylation]]. Like all uncouplers, CCCP concentrations must be titrated carefully to evaluated the optimum concentration for maximum stimulation of mitochondrial respiration, particularly to avoid inhibition of respiration at higher CCCP concentrations. +
'''Carboxy SNARF® 1''' is a cell-impermeant pH indicator dye. The pKa of ~7.5 makes it useful for measuring pH in the range of pH 7 to pH 8. The emission shifts from yellow-orange at low pH to deep red fluorescence at high pH. Ratiometric fluorometry, therefore, is applied at two emission wavelengths,such as 580 nm and 640 nm.
Relative molecular mass: ''M''<sub>r</sub> = 453.45 +
'''Carboxyatractyloside''' CAT is a highly selective and potent inhibitor of the [[adenine nucleotide translocator]] (ANT). CAT stabilizes the nucleoside binding site of ANT on the cytoplasmic (positive) side of the inner membrane and blocks the exchange of matrix ATP and cytoplasmic ADP. It causes stabilization of the ''c'' conformation of ANT leading to permeability transition pore (PTP) opening, loss of mitochondrial membrane potential, and apoptosis. +
'''Cardiolipin''', CL, is a double phospholipid (having 4 fatty acyl chains) in the mitochondrial inner membrane (mtIM) which plays an important role in mitochondrial bioenergetics. CL is involved in the mitochondria-dependent pathway of apoptosis, participates in the function and stabilization of mitochondrial respiratory complexes and supercomplexes and also contributes to mitochondrial integrity.
Contributed by [[Sparagna G]] 2016-04-18 +
[[File:CERG.gif|200px|left|CERG]]
The '''Cardiovascular Exercise Research Group''' (CERG) was established in January 2008 and their research focuses on identifying the key cellular and molecular mechanisms underlying the beneficial effects of physical exercise on the heart, arteries and skeletal muscle in the context of disease prevention and management through experimental, clinical and epidemiological studies.
Since 2003 this research group organizes the biennial seminar [http://www.ntnu.edu/cerg/seminar-2013 "Exercise in Medicine"] in Trondheim, Norway. +
'''Carnitine''' is an important factor for the transport of long-chain fatty acids bound to carnitine ([[carnitine acyltransferase]]) into the mitochondrial matrix for subsequent β-oxidation. There are two enantiomers: D- and L-carnitine. Only the L-isomer is physiologically active. +
'''Carnitine O-octanoyltransferase''' is a mitochondrial enzyme that transfers [[carnitine]] to octanoyl-CoA to form [[Coenzyme A]] and [[octanoylcarnitine]]: Octanoyl-CoA + L-carnitine ↔ CoA + L-octanoylcarnitine. +
'''Carnitine acetyltransferase''' (CrAT) is located in the mitochondrial matrix and catalyses the formation of acetyl-carnitine from acetyl-CoA and L-carnitine and thus regulates the acetyl-CoA/free CoA ratio which is essential for [[pyruvate dehydrogenase]] complex (PDC) activity. +
'''Carnitine acyltransferases''' mediate the transport of long-chain fatty acids across the inner mt-membrane by binding them to carnitine. First, long-chain fatty acids are activated by an energy-requiring step in which the fatty acid ester of CoA is formed enzymatically at the expense of ATP. The fatty acids then pass through the inner mt-membrane and enter the mitochondria as carnitine esters ([[acylcarnitine]]s). The fatty acyl group is then transferred from carnitine to intramitochondrial CoA and the resulting fatty acyl CoA is used as a substrate in the fatty acid oxidation (FAO) cycle in the mt-matrix. +
'''Carnitine palmitoyltransferase I''' (CPT-I, also known as carnitine acyltransferase I) is a regulatory enzyme in mitochondrial long-chain acyl-CoA uptake and further oxidation. CPT-I is associated with the mt-outer membrane mtOM and catalyses the formation of [[acylcarnitine]]s from acyl-CoA and L-carnitine. In the next step, acyl-carnitines are transported to the mitochondrial matrix via [[carnitine-acylcarnitine translocase]] in exchange for free [[carnitine]]. In the inner side of the mtIM [[carnitine palmitoyltransferase II]] converts the acyl-carnitines to carnitine and acyl-CoAs. There are three enzyme isoforms: CPT-1A (liver type), CPT-1B (muscle type), CPT-1C (brain type). Isoforms have significantly different kinetic and regulatory properties. Malonyl-CoA is an endogenous inhibitor of CPT-I. +
'''Carnitine palmitoyltransferase II''' (CPT-II, also known as carnitine acyltransferase II) is part of the carnitine shuttle which is responsible for the mitochondrial transport of long-chain fatty acids. CPT-II is located on the inner side of the mtIM and converts the [[acylcarnitine]]s (produced in the reaction catalyzed by [[carnitine palmitoyltransferase I]]) to carnitine and acyl-CoAs, which undergo ß-oxidation in the mitochondrial matrix. Free carnitines are transported out of the mitochondrial matrix in exchange for acyl-carnitines via an integral mtIM protein [[carnitine-acylcarnitine translocase]] (CACT). Short- and medium-chain fatty acids do not require the carnitine shuttle for mitochondrial transport. +
'''Carnitine-acylcarnitine translocase''' (CACT) is part of the carnitine shuttle which mediates the mitochondrial transport of long-chain fatty acids where the [[fatty acid oxidation]] occurs.
CACT is an internal mt-IM protein and transports [[acylcarnitine]]s into the mitochondrial matrix in exchange for free [[carnitine]]. +
Most of the nonpolar compounds have to be diluted in organic solvents such as DMSO or acetonitrile in order to use them for the titrations in the SUIT protocols. However, the solvent (carrier) itself could affect the mitochondrial physiology and promote alterations that we need to take into account. For this reason, it is necessary to run in parallel to our treatment experiment a control experiment on which we will add a '''carrier control titration''' to test if it affects our sample or not. +
'''Catalase''' catalyzes the dismutation of [[hydrogen peroxide]] to water and [[oxygen]]. Perhaps all cells have catalase, but mitochondria of most cells lack catalase. Cardiac mitochondria are exceptional in having mt-catalase activity (rat heart mitochondria: Radi et al 1991; mouse heart mitochondria: Rindler et al 2013). [[Hydroxylamine]] is an inhibitor of catalase, which is also inhibited by [[cyanide]] and [[azide]].
Mitochondrial respiration medium [[MiR05]] was developed considering the intracellular conditions of mitochondria in living cells. In mitochondrial preparations, enzymes and substrates present in the cytosol (such as catalase) are diluted when the plasma membrane is removed. Therefore, the addition of catalase is recommended when working with mitochondrial preparations, to consume any H<sub>2</sub>O<sub>2</sub> generated during the assay. +
'''Catalytic activity''' of an enzyme is measured by an enzyme assay and is expressed in units of katal (kat [mol∙s<sup>-1</sup>]). More commonly (but not conforming to SI units or IUPAC recommendations) enzyme activity is expressed in units U [mol∙min<sup>-1</sup>]. +
Cataplerosis is the exit of TCA cycle intermediates from the mt-matrix space. +
[[File:SUIT-catg_MitoPathway types.jpg|right|200px]]
'''Categories of SUIT protocols''' group [[MitoPedia: SUIT |SUIT protocols]] according to all substrate types involved in a protocol (F, N, S, Gp), independent of the sequence of titrations of substrates and inhibitors which define the [[Electron-transfer-pathway state]]s. The [[N-pathway control |N-type substrates]] are listed in parentheses, independent of the sequence of titrations. ROX states may or may not be included in a SUIT protocol, which does not change its category. Similarly, the [[CIV]] assay may or may not be added at the end of a SUIT protocol, without effect on the category of a SUIT protocol.
* '''F''' - ET-pathway-level 5: [[FADH2 |FADH<sub>2</sub>]]-linked substrates (FAO) with obligatory support by the N-linked pathway.
* '''N''' - ET-pathway-level 4: [[NADH]]-linked substrates (CI-linked).
* '''S''' - ET-pathway-level 3: [[Succinate]] (CII-linked).
* '''Gp''' - ET-pathway-level 3: [[Glycerophosphate]] (CGpDH-linked).
* '''Y(X)'''- In the SUIT general protocols Y makes reference to the ET-pathway state and X to the combination os substrates added for the corresponding pathway.
» [[#Categorization of SUIT protocols: ETS pathway control states |'''MiPNet article''']] +
[[File:CellSymposiaLogo.jpg|90px]] Organized by the editors of Cell Press's leading journals, '''Cell Symposia''' bring together exceptional speakers and scientists to discuss topics at the forefront of scientific research. +
The '''cell count''' ''N''<sub>ce</sub> is the number of cells, expressed in the abstract [[unit]] [x] (1 Mx = 10<sup>6</sup> x). The ''elementary entity'' cell ''U''<sub>ce</sub> [x] is the real unit, the 'single individual cell'. A cell count is the multitude or number ''N'' of cells, ''N''<sub>ce</sub> = ''N''·''U''<sub>ce</sub> ([[Gnaiger MitoFit Preprints 2020.4]]). Normalization of respiratory rate by cell count yields oxygen [[flow]] ''I''<sub>O<sub>2</sub></sub> expressed in units [amol·s<sup>-1</sup>·x<sup>-1</sup>] (=10<sup>-18</sup> mol·s<sup>-1</sup>·x<sup>-1</sup>). +
'''Cell culture media''', like RPMI or DMEM, used for [[HRR]] of living cells. +
'''Cell respiration''' channels metabolic fuels into the chemiosmotic coupling (bioenergetic) machinery of [[oxidative phosphorylation]], being regulated by and regulating oxygen consumption (or consumption of an alternative final electron acceptor) and molecular redox states, ion gradients, mitochondrial (or microbial) membrane potential, the phosphorylation state of the ATP system, and heat dissipation in response to intrinsic and extrinsic energy demands. See also [[respirometry]].
In internal or '''cell respiration''' in contrast to [[fermentation]], redox balance is maintained by external electron acceptors, transported into the cell from the environment. The chemical potential between electron donors and electron acceptors drives the [[electron transfer pathway]], generating a chemiosmotic potential that in turn drives ATP synthesis. +
(1) Cellular substrates ''in vivo'', endogenous; '''Ce'''.
(2) Cellular substrates ''in vivo'', with exogenous substrate supply from culture medium or serum; '''Cm'''.
* ''This page needs an update.'' +
