On Cellular Organization and Respiration
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The following simplified reactions may give an impression that the hydrogens accepted by ubiquinone (UQ) to become ubiquinol (UQH2) are derived from 'NADH + H+' or 'FADH2'.
- [NADH] + H+ → [NAD+ + H–] + H+
- NADH + H+ → NAD+ + (H– + H+)
- NADH + H+ → NAD+ + (2H)
⠀ - FADH2 → FAD + (2H)
⠀ - UQ + 2H → UQH2
The first issue is that the lone proton released by dehydrogenases in the production of NADH is lost to the medium. When NADH reaches complex I to be oxidized, it won't have its original pairing proton, and it can only donate the incorporated hydrogen.
FMN in Complex I accepts it as a hydride ion (H– ⇄ H+ + 2e–) from NADH:
- NADH + FMN → NAD+ + FMNH–
Even though this hydrogen could land on ubi(semi)quinone after a series of reactions, it doesn't seem to.
You may focus on the dark blue to track the proton and red to track electrons, knowing that the top of the rectangle is NAD and the bottom is FMN. Note that when NAD dissociates, the rectangle only shows FMN. The proton is eventually released into the medium.
Protons appear to enter respiratory complexes laterally, near the innermost surface, as electrons are channeled.
More specifically:
Water route for proton pumping in mitochondrial complex I
Therefore, the protons liberated in the oxidation of NADH and FADH2 can reach ubiquinone, but likely indirectly when they add to the pool of protons in the matrix. Since the number of free protons is low, they might be buffered or metabolized as fast as they appear.
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A summary of proton movement in oxidative phosphorylation:
Matrix IMS IMS Matrix → ← 2H⁺ 
+ 4H⁺ →Complex I 4H⁺ Complex II 
2H⁺2H⁺ 2H⁺2H⁺ → Complex III 4H⁺ 4H⁺ Complex III ← 2H⁺ 2H⁺ + 2H⁺ →Complex IV 2H⁺ 2H⁺ Complex IV ← 2H⁺ + 2H⁺← → H₂O ← ½O₂ + 2H ↲ ↳ 2H + ½O₂ → H₂O 10H⁺ ← Complex V 10H⁺ 6H⁺ Complex V → 6H⁺ The arrows weren't supposed to be stylized.
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The metabolic steps responsible for the ATP difference in the breakdown and synthesis of dextructose:
Glycolysis (↓) Enzyme Gluconeogenesis (↑) –1 ATP HK N/A–1 ATP PFK N/A+2 ATP PGK –2 ATP +2 ATP PK N/AN/APEPCK –2 ATP (⇄ 2 GTP) N/APC –2 ATP Total Total +2 ATP (–4 ATP/↺) –6 ATP With the exception of PGK, these are the irreversible steps; the others not included are reversible.
If forming and unforming lactate occurred in the same cell, it would have a neutral effect. However, for pyruvate to reappear elsewhere, NADH is consumed in the origin and NAD⁺ in the destination.
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"The IMM consists of subcompartments called cristae and inner boundary membrane (IBM) (Palade, 1953). Cristae are invaginations protruding into the mitochondrial matrix, whereas the IBM runs parallel to the outer mitochondrial membrane (OMM). Cristae and IBM are connected via narrow tubular or slit‐like structures, known as crista junctions (CJs). In recent years, studies show that components of the electron transport chain (ETC) are confined to the lateral surfaces of the cristae rather than equally distributed along the IMM (Vogel et al, 2006; Wilkens et al, 2013). Moreover, dimers of F1F0 ATP Synthase assemble in rows along the edges of the cristae (Dudkina et al, 2005; Strauss et al, 2008; Davies et al, 2011). The CJs can be kept in a closed state by oligomers of the inner‐membrane dynamin‐like GTPase, OPA1 (Frezza et al, 2006; Pham et al, 2016), as well as components of the mitochondrial contact site and cristae organizing system (MICOS complex) (John et al, 2005; Rabl et al, 2009; Barrera et al, 2016; Glytsou et al, 2016)."
"Measurement of ΔΨm in individual cristae reveals that crista junctions provide electrical insulation and sustain polarization of individual mitochondrial cristae within a single mitochondrion even when neighbouring cristae are damaged.
- Cristae have higher ΔΨ compared to their adjoining inner mitochondrial membranes.
- Cristae are electrically insulated, allowing individual cristae within any given mitochondrion to have different membrane potentials.
- Cristae can remain polarized despite depolarization of neighbouring ones.
- Disruption of crista junctions impairs the electrical insulation of cristae, equilibrating their ΔΨ with those of inner mitochondrial membranes."
"This study raises interesting questions as to why mitochondria organize the ΔΨm in this way. One advantage, for example, could be related to the fact that ΔΨm constitutes the main energy available to drive protons through F1F0 ATP Synthase to produce ATP. As such, the localization of F1F0 ATP Synthase at the cristae rims appears to be advantageous in terms of proximity to the batteries. Another possible advantage could be compartmentalization of ΔΨm in each crista may serve as a safeguard mechanism restricting the impact of localized damage. In the case of the equipotential model, where the inner membrane of the entire mitochondrion represents a single capacitor, a breach in membrane integrity in one crista would cause a collapse in voltage in all cristae and compromise the function of the whole organelle. If, on the other hand, the IMM could maintain numerous, discrete electrochemical gradients, like a group of batteries, then failure of one or more would not invariably jeopardize the entire mitochondrion. This may be of particular relevance in cells harboring a highly interconnected mitochondrial network as opposed to cells with less elongated and/or branched mitochondria. Furthermore, the hetero‐potential model suggests that cristae with higher ΔΨCr‐IBM could compensate for cristae with impaired function."
"Hyperpolarized and depolarized IMM potentials are associated with different states of respiration. While both uncoupling and an increased rate of ATP synthesis dissipate ΔΨm, a decrease in ATP synthesis may result in hyperpolarization and increased ROS production. The hetero‐potential model of the mitochondrion allows for different cristae to serve different functions. In this model, some cristae could be more dedicated to ATP synthesis, whereas neighboring cristae could play a role in ROS signaling. The hetero‐potential model further allows for the consideration that different cristae may engage in primarily complex II vs. complex I respiration, which are associated with different membrane potentials and could be driven by different fuels."
Protonic Capacitor: Elucidating the biological significance of mitochondrial cristae formation
"[..]excess protons (positive charges) in an aqueous liquid on one side of a membrane will repel each other to become electrostatically localized along the membrane surface, attracting an equal number of excess hydroxyl anions (negative charges) to the other side of the membrane and thus resulting in a “protonic capacitor structure” (Fig. 2)."
Consequences of Folding the Mitochondrial Inner Membrane
"The greater the energy requirements of a cell, the more inner membrane surface area it contains. Because there are practical limits to the volume fraction that cells can reserve for mitochondria, crista packing is maximized where energy demand is greatest, e.g., in cardiomyocytes the surface area of the inner membrane is more than tenfold that of the outer membrane."
"Although internalizing the chemiosmotic membrane is essential for mass production of ATP, it creates a complex and potentially risky situation for the cell. In particular, conditions that swell the matrix will cause the inner membrane to unfold and, eventually, rupture the outer membrane. In fact, cells use this demolition mechanism when death is the intended outcome. For example, inner membrane “herniation” of the outer membrane is observed in late stages of programmed cell death (extrinsic apoptosis) in FAS-activated liver (
Figure 1). Crista contents, including cytochrome c, spill into the cytosol, resulting in irreversible loss of membrane potential and ATP production (Mootha et al., 2001). Matrix swelling in this case was attributed (Feldmann et al., 2000) to the mitochondrial permeability transition pore, MPTP, the opening of which can drive an osmotic influx of water sufficient to unfold the inner membrane and rupture the outer membrane (e.g., Rasola and Bernardi, 2011).""Extreme crista swelling is as perilous to the cell as uncontrolled matrix swelling, e.g., the total volume of a few fully expanded cristae in a single muscle mitochondrion easily exceeds the volume enclosed by the outer membrane. In fact, rupture of the outer membrane by crista (not matrix) swelling occurs in insect flight muscle as a prelude to apoptosis (Walker and Benzer, 2004). Clearly, the process of unfolding the inner membrane is as important to cell survival as generating the crista folds and likely is regulated as carefully."
"Although, at first glance, it seems risky to fold a large membrane within an outer membrane, rupture of which is fatal, this situation actually provides the cell an advantage. When mitochondria are suspended in hypo-osmotic media, outer membranes lyse at sucrose gradients tenfold greater than liposomes or mitochondrial inner membrane vesicles of similar size, typically 20–30 mM (Douce et al., 1972; Li et al., 1986). This dramatic protection against osmotic stress directly accrues from the outer membrane being osmotically inactive, i.e., very permeable to small solutes. The chemiosmotic inner membrane is the mitochondrial osmometer. Swelling of the matrix caused by osmotic influx of water compresses the cristae before significant pressure is applied to the outer membrane by outward expansion of the inner membrane. In effect, unfolding the inner membrane absorbs significant osmotic stress and delays irreversible damage to the mitochondria. Equally important, this indirect rupture mechanism provides the cell the opportunity to regulate outer membrane lysis."
"A mechanism has been proposed that would protect mitochondria against outer membrane lysis and inner-membrane domain mixing during crista swelling: fusion of tubular cristae to form larger cristae more adaptable to volume changes. Crista fusion was suggested by the first EM tomograms of mammalian mitochondria, which revealed complex cristae with tubular and lamellar regions (Mannella et al., 1997; Perkins et al., 1997). Larger cristae are more prevalent in condensed mitochondria; decreased matrix volume brings cristae into closer proximity, favoring fusion (Mannella et al., 2001). It is likely that crista fusion in response to matrix contraction is quite extensive. Condensed liver mitochondria have large dilated cristae with multiple (up to seven) junctions (Mannella et al., 1997) and condensed yeast mitochondria may have a single dilated internal cavity with much of the inner membrane pulled away from the outer membrane and no well-defined crista junctions or cristae (Mannella et al., 2001)."
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Hydrogen economy in glycolysis (the charges may be ignored):
Out (–) In (+) HK H⁺ PFK H⁺ 2GAPDH *2H⁻ 2H⁺ 2ENO 2H₂O 2PK 2H⁺ Total 10H 2H (*2H⁻ from 2NADH)
The expectation (–10H + 2H = –8H) is different from the actual change (–6H), when we obtain the pyruvates:
Toxin Formula Glucose C6H12O6 (–8H →) Expected C6H4O6 (–6H →) 2Pyruvate C6H6O6 2Lactate C6H10O6 2Lactic acid C6H12O6 What explains the difference (between expected and actual change) is that the 2H⁺ released at the dehydrogenase level (GAPDH) are derived from inorganic phosphate rather than extracted from the glucose metabolite (
NADH + H⁺). When we disconsider these 2H⁺, we arrive on the –6H needed.
As for lactate, when it's formed, 4H are consumed from 2H⁻ + 2H⁺. Going backwards, it would be equivalent to never having produced:
- H⁺ (HK)
- H⁺ (PFK)
- 2H⁻ (2GAPDH)
Then, we're left with –2H for 2 lactates (C6H10O6) to match with a glucose molecule (C6H12O6).
Even though 2H⁺ were disconsidered previously, they still occur, just not extracted from glucose metabolites. After canceling out the 3 products listed above, we get:
Out (–) In (+) 2GAPDH 2H⁺ 2ENO 2H₂O 2PK 2H⁺ Total 6H 2H When lactate is exported from the cell, it tends to bring a H⁺ along as counter-ion. So, 2 lactates would take out the equivalent to those 2H⁺ produced at 2GAPDH.
What remains is the bottom of the original table:
- 2H₂O out (produced)
- 2H⁺ in (consumed)
Therefore, lactate synthesis and export is an alkalinizing process for the cell:
- H⁺ are consumed when pyruvates are formed (pyruvate enol-phosphate + H⁺ → pyruvate), to then become lactates to be exported. In contrast, the H₂O molecules produced are neutral.
- LDH reaction consumes H⁺ directly (pyruvate + NADH + H⁺ → lactate + NAD⁺)
- Additional H⁺ tend to be eliminated with lactates as counter-ions (lactate + H⁺)
Nevertheless, lactate is associated with acidification for a few reasons that I'm aware of:
The coexport with a H⁺ alkalinizes the interior and acidifies the exterior of the cell. It's easier to monitor the outside, so that's what we associate with.
Once this lactic acid equivalent leaves the cell, the H⁺ is quickly buffered, leaving lactate to pair with available cations, such as Na⁺ ('HLac' + NaHCO3 → NaLac + H2CO3). If not by using up hydrocarbonate ions, a surge of lactate with expansion of the pool of organic anions can lead to an increase in cations to maintain ion neutrality. This tends to reflect on the concentration of free H⁺, that may rise in proportion along.
Marked ATP hydrolysis, that often coincides with excess lactate formation, is acidifying.
- ATP + H₂O → ADP + Pi + H⁺
Rather than the theoretical source from the previous section, this H⁺ can be the pair for lactate.
The following diagram has these events simplified:
Metabolic acidosis and fatigue: Where to from here?
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Observe the inconsistency in the conventional nomenclature for glycolysis metabolites:
Abbreviation Metabolite GLC Glucose G6P Glucose-6-phosphate F6P Fructose-6-phosphate F1,6BP Fructose-1,6-bisphosphate DHAP Dihydroxyacetone-3-phosphate G3P Glyceraldehyde-3-phosphate 1,3BPG 1,3-Bisphosphoglycerate 3PG 3-Phosphoglycerate 2PG 2-Phosphoglycerate PEP Phosphoenolpyruvate PYR Pyruvate I think that they put phosphate in evidence when the molecule becomes a phosphate donor, similar to creatine (phosphocreatine, which is creatine phosphate), but to relegate the core is confusing, and it's worse without bolding.
Standardizing against the norm makes it easier to grasp:
Abbreviation Metabolite GLC Glucose G6P Glucose 6-phosphate F6P Fructose 6-phosphate F1,6BP Fructose 1,6-bisphosphate DHAP Dihydroxyacetone 3-phosphate G3P Glyceral 3-phosphate 1,3BPG Glyceral 1,3-bisphosphate 3PG Glycerate 3-phosphate 2PG Glycerate 2-phosphate PEP Pyruvate Enol-phosphate PYR Pyruvate The numbers next to phosphate indicate the carbon position where phosphates are attached to the molecule.
- For a molecule with 6 carbons, we can infer that a '6-phosphate' is a a phosphate attached to one extremity.
- When we get '1,6-bisphosphate', the molecule contains phosphates on both extremities.
In working with split molecules of 3 carbons, the same approach applies.
- Bis- and tris-: separate (example: P-Molecule-P)
- Di- and tri-: in sequence (example: Molecule-PP)
High-energy phosphate | Wikipedia
"Often, high-energy phosphate bonds are denoted by the character '~'. In this "squiggle" notation, ATP becomes A-P~P~P. The squiggle notation was invented by Fritz Albert Lipmann, who first proposed ATP as the main energy transfer molecule of the cell, in 1941. Lipmann's notation emphasizes the special nature of these bonds. Stryer states:
ATP is often called a high energy compound and its phosphoanhydride bonds are referred to as high-energy bonds. There is nothing special about the bonds themselves. They are high-energy bonds in the sense that free energy is released when they are hydrolyzed, for the reasons given above. Lipmann's term "high-energy bond" and his symbol ~P (squiggle P) for a compound having a high phosphate group transfer potential are vivid, concise, and useful notations. In fact Lipmann's squiggle did much to stimulate interest in bioenergetics."
Number of carbons Saccharide (-ose*) 6 Hexose 5 Pentose 4 Tetrose 3 Triose 2Diose1Monose*As in Alberto's 'godnose'.
The upper part of the glycolysis list are the hexoses (until F1,6BP). After splitting (below F1,6BP), we get the trioses. A hexose or triose phosphate is self-explanatory.
When glucose (6-phosphate) is diverted from glycolysis for nucleotide synthesis, it undergoes oxidative decrapoxylation (losing a carbon), becoming a pentose. It gives name to the Pentose Phosphate Pathway (sometimes referred to as Hexose Monophosphate Shunt).
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ATP use:
- ATP + H₂O ⇉ ADP + Pi + H⁺
And 2 methods of regeneration:
'Substrate-level' phosphorylation:
- ADP + R-OP + *H⁺ → ATP + R-OH
(R for "Root")
Oxidative phosphorylation:
- ADP + Pi + H⁺ → ATP + H₂O
*Whether a H⁺ is consumed will depend on the reaction.
Creatine cycling does consume (→) and produce (←) H⁺:
- ADP + (Creatine-OP) + H⁺ ⇄ ATP + (Creatine-OH)
Throughout cellular respiration, it's tricky..
Enzyme Participants Dir. Participants HK ADP + R-OP + H⁺ ← ATP + R-OH PFK ADP + R-OP + H⁺ ← ATP + R-OH PGK ADP + R-OP + H⁺→ ATP + R-O⁻ PK ADP + R-OP + *H⁺→ ATP + R-O *But a hydrogen is incorporated elsewhere (R-CH₂ → R-CH₃):
We could argue that glycolysis metabolites become ionized as soon as phosphate is attached to them (early on in glycoylsis), and this contributes to their trapping in cells. However, the definite ionization occurs when phosphates start to be detached in PGK, where crapoxylates are formed (note in the table how H⁺ aren't consumed against expectation).
It's for the phosphorylation steps that you'll find a one-way arrow in diagrams, deeming them irreversible (except for PGK). However, if this was the case in all tissues, glucose resynthesis wouldn't be possible. As an example, the reactions of HK and PFK can be undone through phosphorylases that work as hydrolases:
- Glycolite-OP + H₂O → Glycolite-OH + Pi
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In oxidative phosphorylation, the PO₃⁺ (of inorganic phosphate; Pi) goes towards ADP, and OH⁻ (also from Pi) combines with H⁺ to form H₂O.
- ADP + Pi + H⁺ → ATP + H₂O
With substrate-level phosphorylation in mitochondria, we have a variation of it. SCS reaction (omitting the succinyl group):
- 'ADP' + Pi + CoAS⁻ → 'ATP' + CoASH
As before, the PO₃⁺ (of inorganic phosphate; Pi) goes towards ADP, but here OH⁻ doesn't combine with H⁺ to form H₂O. Rather, oxygen gets incorporated to yield succinate, and H⁺ is accepted by CoA instead of released immediately in free form. No additional H⁺ is consumed.
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Therefore, lactate formation aside, increase reliance on substrate-level phosphorylation for ATP resynthesis goes without the immediate compensatory H⁺ consumption, although complete metabolism should be an overall H⁺-consuming process.It's worth noting the complicators.
Free phosphates will occur as mixed species that take up more or less H⁺ depending on its concentration, and differences in acidity between compartments will affect the composition.
We also know that most of the ATP is produced in mitochondria and consumed in the cytosol. The synthesis of ATP with H⁺ consumption occurs in a more alkaline environment relative to where most of ATP is hydrolyzed. At some stage, the extra H⁺ taken up by phosphates in the cytosol will have to be released when the phosphates in question return to mitochondria. -
@Amazoniac Thanks!
It is on my reading list now! Main goal not to side-track
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Does Aerobic Respiration Produce Carbon Dioxide or Hydrogen Ion and Bicarbonate?
The majority of CO₂ in the body circulates as the hydrocarbonate ion:
Carbon dioxide and derivatives Content Hydrocarbonate ion (HCO₃⁻) ~70% Carbamates (protein-bound; R-NH-CO₂) ~23% Carbon dioxide (CO₂) ~7% Carbonic acid (H₂CO₃) <1% Organic anions are considered alkalinizing when they are hydrocarbonate precursors. However, prior to its formation, CO₂ has to be hydrated, and for every hydrocarbonate ion derived from CO₂, a H⁺ is released in the system:
- CO₂ + H₂O ⇄ H₂CO₃ ⇄ H⁺ + HCO₃⁻
The H⁺ are temporarily sequestered, but complexation doesn't negate it.
It's easy to overlook the H⁺ load for not being apparent in circulation, where normal levels are:
- [HCO₃⁻]: 22-32 mmol/L
- [H⁺]: 0.000036-0.000043 mmol/L (from pH: 7.44-7.37)
Far from a 1:1 ratio.
It can be argued that hydrocarbonate precursors alkalinize for consuming H⁺ in priming molecules for complete oxidation (into CO₂ and H₂O), which is true, but the consumption is compensated when the equivalent of carbonic acid molecules appear in the system.
Unlike non-volatile acids that can remain paired by a corresponding counter-ion until elimination (example: sodium sulfate), the occurrence of carbonic acid or variants yields CO₂ and H₂O. This CO₂ leaves the body, and the original pairing cation is left as unpaired as residue (example: sodium
citrate).To maintain ion neutrality and rebalance, the body may try to lower cations, which would affect H⁺ concentration, and conserve anions, including hydrocarbonate. Fluid redistribution from the excess cation can also dilute H⁺. The hydrocarbonate are first and foremost carbonic acid precursors, so we need explanations along these lines.
@Lejeboca said in On Cellular Organization and Respiration:
@Amazoniac Thanks!
It is on my reading list now! Main goal not to side-trackСпасибо за визит.
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Each turn of the TCA cycle eliminates 2 carbons in consecutive (oxidative) decrapoxylation steps:
- IDH: isocitrate → ketoglutarate* + CO₂
- KGDH: ketoglutarate* → succinyl(CoA) + CO₂
A peculiarity of the TCA cycle is that succinate and (its product) fumarate are symmetrical molecules (⇈). Since this property applies to both of them, we can tell that succinate dehydrogenase modifies succinate evenly.
The next reaction is the conversion of fumarate to malate, where asymmetry appears. Even though fumarate is symmetrical, it contains newer or older atoms throughout the molecule. Depending on which side of fumarate is primarily changed after fumarase, the carbon stay in the cycle will differ.
This gives an idea:
I've adapted it for ease of tracing and until completion:
Therefore, the original carbons (from a given acetyl group) aren't eliminated straight away. They remain intact on the 1st turn, and the chances of their complete elimination appear to be:
- 50% on the 3rd turn
- 25% on the 4th turn
- 12.5% on the 5th turn
- 6.25% on the 6th turn
- ...
*Ketoglutarates:
- 2-oxoglutarate = a-ketoglutarate
- 3-oxoglutarate = b-ketoglutarate
Alpha refers to the second carbon because the first is the crapoxyl group, that's disconsidered in counting (similar to beta-oxidation).
Urine Organic Acids as Potential Biomarkers for Autism-Spectrum Disorder in Chinese Children
"[..]3-oxoglutarate, a common metabolite of yeast and fungi (Thomas et al., 2010; MacFabe et al., 2011; Kocovska et al., 2012), was significantly lower in children with autism. The low concentrations of both carboxycitric acid and 3-oxoglutarate that we observed in urine from autistic patients could be due to increased uptake of these compounds across the blood-brain barrier of the brain. Our results are consistent with previous studies that showed anti-fungal treatments for children with autism can effectively reduce the amounts of corresponding organic acid indicators (Cobb and Cobb, 2010), and suggests that gastrointestinal yeast could provide a basis for dietary adjustments such as gluten/casein-free diets that are important for children’s nervous system development and could mitigate autism symptoms. 3-oxoglutarate in urine is associated with the presence of harmful gut flora such as Candida albicans (Schmidt, 1994)."
It's fine to omit the 'alpha' prefix from ketoglutarate for the same reason that we only need to clarify which Paris we're going to when it's not the one in France.
