On Cellular Organization and Respiration

Amazoniac

NADPH Oxidases (NOX): An Overview from Discovery, Molecular Mechanisms to Physiology and Pathology

This relates to the previous post and to the next information.

If you want to question your current understanding of cellular respiration, check out the work of Kelath Manoj and his subversive murburn model (stands for 'mild, unrestricted burning'), where he challenges anything that crosses the way.

He treats (diffusible) reactive oxygen species (DROS) as an essential part of cellular respiration. Speculates that the projections of respiratory complexes were evolutionarily shaped to take advantage of radical generation. He identifies sites of ATP synthesis in all respiratory complexes and it's as oxidative phosphorylative as it gets: a reduction of oxygen to superoxide in respiratory complexes leads to its diffusion towards local ADP or phosphate attack, and a straightforward reaction joins them to form ATP without involving the convoluted steps of protons movement to drive ATP synthase (Complex V) subunit rotation.

Superoxide radical as electron donor for oxidative phosphorylation of ADP (referenced by him)

Aerobic respiration: Proof of concept for the oxygen-centric murburn perspective

A respirawesome or supercomplex [I(III)2IV] showing 11 ADP-binding sites within projections into the matrix:

6 in Complex I
4 in Complex III
1 in Complex IV

His team also report 'cavities or channels' that promote diffusion of oxygen species to desired targets (be them ADP, phosphorus or the known electron acceptors):

The proposed chain of reactions is shown here (omitting what occurs in between each):

AdP-O-H	ADP
P-O-H	Pi (inorganic phosphate)
AdP-O-P	ATP

When complexes cluster, the organization favors their interaction, and ADP-binding sites from one complex can make use of diffusing reactive oxygen species from another. The strategic location and shared metabolites are shown in this diagram:

He not only diminishes the importance of Complex V as a source of ATP synthesis, but suggests that it's a decomposer of ATP (an ATPase). According to him, Complex V has much higher affinity for ATP than ADP, which is odd for a protein that's intended to produce ATP. To compound the issue, he argues that ADP is available at lower concentration than ATP.

The half-affinity for ADP being close to its concentration would be a problem.

He acknowledges the meek quantity of free protons per mitochondrion, which would be another concern for a 'rotary' protein dependent on them, but rejects the buffering or hopping possibility. I haven't looked into why. He adds to the picture the following considerations:

Complexes per mitochondrion: ~10^4-10^5
Proton requirement: ~10^6 (which is ×10 the previous value, assuming 10 H+ extruded per 1 NADH oxidized in the traditional model)

There's a lot more to uncover from his work. As an example, he's familiar with Gilbert Ling's model, compares it with his proposal and the traditional approach.

Amazoniac

A while ago I came across this publication through GembaRed's articles:

Blood contains circulating cell-free respiratory competent mitochondria

However, Tony questioned its validity:

Human blood contains circulating cell-free mitochondria, but are they really functional?

"As noted by Bertero et al. (7), the evidence provided by Dache et al. (4 ⇈) was not sufficient to assess the functionality or the respiratory competence of human circulating cell-free mitochondria. By conducting a comprehensive analysis of mitochondrial bioenergetics of human circulating cell-free mitochondria in direct comparison with mitochondria extracted from platelets of the same blood samples, we found no significant support for the functionality or the respiratory competence of those cell-free mitochondria. Indeed, there was no significant evidence that cell-free mitochondria possess a functional electron transport system since they exhibited no responses to mitochondrial substrates, ADP, or inhibitors. Yet, when fueling directly complex IV with exogenous electrons (i.e., Asc + TMPD), a significant mitochondrial O2 consumption was detected [similarly to Dache et al. (4), except that no negative control was provided in their study]."

"Although fully rejecting the hypothesis that human circulating cell-free mitochondria are functional would require a way larger sample size (e.g., n > 90 for reaching a statistical power of 0.80 for OXPHOSCI + II based on data presented in Fig. 1B), our results do not support the functionality of circulating cell-free mitochondria. Further studies investigating the functionality or lack of functionality of circulating cell-free mitochondria are now required, since this appears as a critical point to elucidate their potential physiological role(s) [e.g., (8)]."

Amazoniac

NAD is used here as the generic term for NAD+ and NADH. Despite their reactive site in evidence, both have an overall negative charge because of the phosphate groups.

ATP, NAD AND FAD | Brigham Young University

In addition to being charged molecules, they're bulky.

These factors make mitochondrial matrix unable to exchange NAD with the cytosol. For similar reasons, glucose is trapped once inside the cell after phosphorylation by hexokinase.

NADH within the matrix is oxidized locally and the electrons are channeled to oxygen. However, a fraction of NADH is formed in the cytosol (GAPDH). This NADH has to be oxidized as well, to regenerate NAD+ for glycolysis to continue.

The inability to import cytosolic NADH into the matrix is circumvented by the known mitochondrial shuttles. NADH can transfer its electrons to a temporary carrier, one that's importable, and the electrons (with protons) can be recovered once inside.

The method on the left appears to be the predominant in tissues with high energy demands, although both can be important. In support:

Thyroid Hormone Regulation of the NADH Shuttles in Liver and Cardiac Mitochondria

This way, most of the NADH is reformed on the matrix side. Or else, transferring the electrons to FAD would result in less energy production, whether we go by the traditional model (10 H+/NADH versus 6 H+/FADH2) or Kekel's approach.

The external layer of the mitochondria is much more permeable than the internal. For the specific location of mGPDH:

How neutrophil metabolism affects bacterial killing

But prior to crossing comparments, pyruvate and NADH are in equilibrium with lactate and NAD+.

Mitochondrial lactate metabolism: history and implications for exercise and disease

Keq (equilibrium constant) = [Lactate][NAD+] / [Pyruvate][NADH]

A high ratio of lactate to pyruvate is a normal occurrence in tissues. We have authors who go to the extent of treating lactate as the final product of healthy glucose breakdown in the cytosol (but acknowledge the problems when elevated in disease).

Lactate:pyruvate	Tissue
Error	Kvothean
7:1	Liver
13:1	Skeletal muscle (rest)
23:1	Brian (not to be confused with brain)
≥25:1	Traumatic brian injury
159:1	Skeletal muscle (immediately after exhaustive exercise)

A generic ratio would be lactate 10:1 pyruvate.
⠀
NAD+/NADH and skeletal muscle mitochondrial adaptations to exercise

Cytosol

[NAD+] = 0.15 mM

[NADH] = 0.00028 mM

NAD+ ~540:1 NADH

Mitochondrial Matrix

[NAD+] = 3.15 mM

[NADH] = 0.5 mM

NAD+ ~6:1 NADH

It's an advantage to not have NAD moving freely between compartments to maintain the desired ratios in each.

From the information above, an example with skeletal muscle (assuming cytosolic ratios for both):

Lactate	13:1	pyruvate
NAD+	540:1	NADH

(Keq = 7020)

Therefore, the favored molecules are products of the LDH reaction in one direction.

Pyruvate + NADH (+ H+) -(LDH)→ Lactate + NAD+

Lactate dehydrogenase has 'very high activity', that 'exceeds glycolytic capacity', which contributes to their proportional variations respecting the ratio in the given tissue, possibly under great influence of NAD. If pyruvate and NADH levels increase, a corresponding increase in lactate and NAD+ tends to follow.

Through lactate formation, NAD+ can be regenerated without depending on the matrix (glycolysis can function independently from oxidative phosphorylation), and this lactate can be distributed to other cells if it can't be metabolized locally. It's a feature that's advantageous for cancer cells.

The Regulation and Function of Lactate Dehydrogenase A: Therapeutic Potential in Brain Tumor

You'll find two lactate shuttles being discussed by researchers:

Intercellular (cell-to-cell)
Intracellular (cytosol-to-matrix)

The redistribution of lactate between organs is a well-known phenomenon, hence the lactate (Cori) cycle. It's a wasteful cycle because glycolysis net-produces 2 ATP and 'reverse glycolysis' (gluconeogenesis) consumes 6 ATP. But lactate doesn't have to undergo reverse glycolysis to reform glucose elsewhere, to then be metabolized by other tissues from scratch.

If an equilibrium exists between pyruvate and lactate, and lactate formation is favored in non-Kvothean cells, they need to have means to recover pyruvate. The oxidative component is overlooked, but lactate dehydrogenase occurs in mitochondria for this purpose; the controversy lies in where.

Role of mitochondrial lactate dehydrogenase and lactate oxidation in the intracellular lactate shuttle

It may be present:

On the outer surface of the inner membrane (mLDH in the middle, positioned similarly to mGPDH shown earlier); or
In the matrix (mLDH at the bottom).

The benefit of it occurring in the matrix would be to function as another mitochondrial shuttle, which would take advantage of the pyruvate-lactate distribution with preferential lactate formation. However, the same distribution tendency can be problematic in the matrix for diverting pyruvate and NADH away from their expected fate when levels rise from origins other than lactate oxidation. Lactate dehydrogenase would tend to metabolize them into lactate and NAD+ in place of pyruvate dehydrogenase (PDH) and NADH dehydrogenase (Complex I).

Recall that the equilibrium between lactate and pyruvate is also dictated by NAD+ and NADH. Considering how many sources of NADH there are in the matrix, it would be concerning to have LDH competing for its oxidation.

This is a situation where the different (iso)forms of lactate dehydrogenase would be of help, so that the enzyme had a specific function:

Lactate → pyruvate: Ach, ja.
Pyruvate → lactate: Nicht, nicht.

But it doesn't seem to be the case and the location of mitochondrial LDH is deemed to be outside of the matrix to avoid these issues:

Amazoniac

Coenzyme Q-cytochrome c oxidoreductase (Complex III) | Wikipedia
↳ Q cycle | Wikipedia

I thought that improvising a stepwise animation would clarify the cycle better than text. The transfer molecules towards cytochrome c are not shown.

Q cycle.gif

Kekel is a harsh critic of the conventional model, but understanding both sides helps to form an opinion.

Amazoniac

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.

Energetics and Dynamics of Proton-Coupled Electron Transfer in the NADH/FMN Site of Respiratory Complex I

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.

Amazoniac

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.

Amazoniac

Gluconeogenesis - Waheeda Nargis | SlideShare

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/A~~
~~N/A~~	PEPCK	–2 ATP (⇄ 2 GTP)
~~N/A~~	PC	–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.

Amazoniac

Individual cristae within the same mitochondrion display different membrane potentials and are functionally independent

"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)."

Amazoniac

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?

Amazoniac

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.

Prefixes:

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
2	~~Diose~~
1	~~Monose~~

*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).

Amazoniac

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..

Glycolysis | Wikipedia

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
⠀

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.
⠀
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.

Lejeboca

@Amazoniac Thanks!
It is on my reading list now! Main goal not to side-track

Amazoniac

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-track

Спасибо за визит.

Amazoniac

Tricarboxylic Acid Cycle

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:

Alterations in Cytosolic and Mitochondrial [U- 13 C]-Glucose Metabolism in a Chronic Epilepsy Mouse Model

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.