From an exchange with cool people:

Vitamin D (978-0-12-809965-0) - David Feldman

"It is now widely believed the enzyme [CYP27B1; calcidiol → calcitriol] exists in nonrenal tissues to boost local production of cellular 1,25(OH)2D3 in a paracrine/intracrine system. Such a role would suggest that cellular 1,25(OH)2D3 concentrations in extrarenal CYP27B1 tissues might be higher than in the tissues of the classical endocrine system, which depend on renally synthesized blood-derived 1,25(OH)2D3 at a concentration around 10^−10 to 10^−9 M (e.g., intestine, bone, parathyroid gland). In turn, the genes regulated in extrarenal tissues (e.g., macrophage, colon, prostate) might be a less-sensitive cell differentiation and antiproliferative subset, known to be regulated in cancer cell lines at 1,25(OH)2D3 concentrations of 10^−8 to 10^−7 M under cell culture conditions. A role for the extrarenal CYP27B1 is also consistent with the finding that serum 25(OH)D levels are associated with various health outcomes from bone health to cardiovascular health. In particular, low serum 25(OH)D levels are associated with increased mortality for colon, breast, and prostate cancer; increased autoimmune diseases and greater susceptibility to tuberculosis; increased cardiovascular diseases and hypertension. The presence of CYP27B1 in cells of the colon, breast, prostate, monocyte/macrophage, and vasculature could explain why serum 25(OH)D levels are so critical to the normal functioning of these tissues."

"Patients with hyperthyroidism (high serum levels of thyroxine, T4 and/or triiodothyronine hormone, T3) have been reported to have low circulating levels of 1,25(OH)2D [55,56]. Recent studies in mice with T3-induced hyperthyroidism showed markedly suppressed serum levels of 1,25(OH)2D and renal expression of Cyp27b1 [26]. Functional studies using PCT cells demonstrated the presence of a negative thyroid hormone response element (TRE) −50 to −20 bp upstream of the transcriptional start site of the CYP27B1 gene with this TRE overlapping the sterol regulatory element (1α-SRE) and TATA box [26]. Data in this study indicated that SRE-binding protein 1c acts as a transcriptional inducer of CYP27B1, but this effect is compromised following treatment with T3. Transcriptional repression effects of T3 on CYP27B1 appear to be due to thyroid hormone receptor (TR)α, and TRβ1 heterodimerizing with retinoid X receptor (RXR)α, to prevent binding of SRE-binding protein to its DNA target. In this way, T3 indirectly suppresses expression of CYP27B1 [26]."

"The serum phosphate concentration is another major regulator of renal 1,25(OH)2D production. In adult humans, dietary phosphorus restriction causes an increase in circulating concentrations of 1,25(OH)2D to 80% above control values, an increase not due to accelerated metabolic clearance of this hormone [38]. Dietary phosphorous supplementation has the opposite effect. Although the mechanism by which decreased serum phosphate increases renal 1,25(OH)2D production remains uncertain [39], it is clear that in humans the calcium-phosphorous-PTH axis cooperates to regulate the conversion of 25(OH)D to 1,25(OH)2D in the kidney. For example, decreased serum calcium concentrations are immediately registered by the parathyroid chief cell calcium-sensing receptors, which, in turn, relax inhibition of PTH production and secretion. The resulting rise in circulating PTH levels directly stimulates the renal 1α-OHase, while a PTH-mediated phosphaturic response and a subsequent decrement in the serum phosphate concentrations indirectly promotes 1,25(OH)2D production (Fig. 8.1)."

↳ [38] https://raypeatforum.com/community/threads/is-vitamin-d-supplementation-even-neccessary.23844/post-797842

Hypophosphatemia: the common denominator of all rickets

"In contrast to its renal counterpart, the macrophage 1α-OHase is unaffected by the stimulatory effects of PTH and phosphate [95,102]. The macrophage plasma membrane is not enriched with PTH receptors [103], and there is no evidence macrophages are responsive to PTH or PTH-related protein in terms of stimulating the protein kinase signaling pathways that are associated with induction of renal 1α-OHase. Similarly, the macrophage enzyme appears to be uninfluenced by changes in the extracellular phosphate concentration [95]. Moreover, exposure of activated macrophages expressing 1α-OHase to a calcium ionophore stimulates the hydroxylation reaction [104], while increasing the extracellular calcium concentration has the opposite inhibitory effect on the renal 1α-OHase [105]."

"Although effects of extracellular phosphate and serum FGF23 on macrophage 1α-OHase activity have yet to be documented, decreased expression of the enzyme has been shown in peripheral blood monocytes treated with FGF23 in vitro [106]. However, the general conclusion is that the key extracellular signaling systems for renal 1α-OHase activity are not heeded by the macrophage enzyme. This provides an explanation for why 1,25(OH)2D production by the macrophage in diseases such as sarcoidosis is not subject to the same negative feedback control that is mediated by a drop in the serum PTH concentration and an increase in the circulating calcium and phosphate level. By contrast, macrophage 1α-OHase activity is potently inhibited by antiinflammatory agents such as glucocorticoids which have little or no effect on the renal enzyme. In vivo this is likely to be due in part to the effects of glucocorticoids on macrophage differentiation and apoptosis. However, studies in vitro suggest that there is also direct inhibition of macrophage 1α-OHase activity by glucocorticoids [74]."

"Of the various bioactive cytokines concentrated in the alveolar space of patients with active sarcoidosis [77,78,130,131], interferon γ (IFNγ) was found to be the principal stimulator of the sarcoid macrophage 1α-hydroxylation reaction, with IFNα having minimal affect only at higher concentrations [74]. However, it is now clear that many other cytokines are also able to stimulate macrophage 1α-OHase. Recent studies have shown that interleukin-15 (IL-15) [132] and IL-32 [133] play pivotal roles in the induction of macrophage CYP27B1 during innate immune responses to bacterial infection. Elevated expression of IL-15 is frequently associated with inflammatory diseases, notably sarcoidosis [134]; as such, IL-15-mediated induction of 1α-OHase activity may provide a link between the regulation of 1α-OHase in normal innate immunity and the dysregulated 1,25(OH)2D production associated with granulomatous disease. Other cytokines such as tumor necrosis factor α (TNFα) [43,79] and IL-2 [102] are also know to stimulate macrophage 1α-OHase. As all of these factors have been implicated in the maturation of macrophage responsiveness within the innate immune system, it seems likely that upregulated 1α-OHase activity is a common feature of activated, but not quiescent, macrophages. More recently and in contrast to the effects of type 2 IFN, IFN-γ, it has been shown that type 1 IFN, IFN-β, negatively regulates the expression of 1α-OHase in human monocytes through increasing the expression of IL-10, which, in turn, inhibits CYP27B1 expression. This results in attenuated 1,25(OH)2D synthesis and consequent reduction in the antimicrobial peptide cathelicidin [135]. Similar observations have also been made for IL-4 that potently suppresses 25(OH)D-induced antibacterial responses in macrophages [136]. In this case, the precise effects of IL-4 on CYP27B1 are unclear, and may involve indirect effects via CYP24A1 [136]."

"Signaling via cytokines such as IFNγ may also lead to the activation of other calcium-dependent pathways in the macrophage, specifically the PKC [143] and phospholipase A2 (PLA2) pathways [144,145]. Because the macrophage 1α-OHase was not influenced by attempts to directly stimulate or inhibit PKC, attention has focused on the PLA2 pathway and the endogenous arachidonic acid metabolic cascade as the signal transduction pathway of most influence over the macrophage enzyme. Further dissection of the intracellular arachidonate metabolic pathway in this cell demonstrated that signal transduction through the 5-lipoxygenase pathway, specifically with the generation of leukotriene C4, was most critical to an increase in 1,25(OH)2D synthesis [146]. These studies were extended to investigate another compound with potential actions in the PLA2-arachidonic acid pathway, the 4-amino quinoline derivative chloroquine. Synthesis of 1,25(OH)2D by macrophages was completely inhibited by exposure to chloroquine in vitro [86]. Furthermore, this effect is independent of chloroquine’s apparent ability to alter the pH of intracellular organelles. When given orally to a hypercalcemic patient with sarcoidosis, chloroquine [83,86] or its analog hydroxychloroquine [84] can effectively reduce the serum 1,25(OH)2D and calcium concentration within 36 hours."

"Pathogen-associated molecular patterns such as the bacterial LPS are potent inducers of macrophage 1α-OHase expression and activity [95,102]."

"As outlined above, LPS and IFNγ commonly activate different signal transduction pathways but, as outlined previously, there is potential for cross talk between these pathways, which may have a significant impact on transactivation of CYP27B1. Notably, IFNγ and LPS are also the two most effective stimulators of nitric oxide (NO) synthesis in macrophages, and this has supported the hypothesis that production of NO and 1,25(OH)2D in macrophage-like cells may be functionally linked [151–153]."

"It is therefore interesting that two of the major stimulators of the human macrophage 1α-OHase, IFNγ, and LPS, are also key transcriptional regulators of the iNOS gene (NOS2) [156,157], which is itself a CYP-linked oxidase [158]. These observations coupled with the fact that NO has established inhibitory effects on other CYPs [159,160] suggest a possible link with the enzymes involved in vitamin D metabolism."

---

Cytochrome P450 Vitamin D Hydroxylases in Inflammation and Cancer

"Regulation of CYP27B1 expression is tissue dependent.

• In the kidney, the main regulators are PTH, serum calcium and phosphate, FGF-23, and 1,25(OH)2D3 (Armbrecht, Boltz, & Hodam, 2003; Perwad & Portale, 2011). Inhibition of CYP27B1 expression by 1,25(OH)2D3 involves complex epigenetic regulation of its promoter through VDR (Kim et al., 2009). However, there are tissues where 1,25(OH)2D3 either induces CYP27B1 expression or has no effect.
• In extrarenal tissues, CYP27B1 expression and activity are independent of circulating PTH. In prostate epithelial cells, the epidermal growth factor (EGF) induces, while 1,25(OH)2D3 inhibits CYP27B1 expression (Wang, Flanagan, et al., 2004). In macrophages and keratinocytes, the expression is increased by different cytokines, e.g., interferon gamma (IFN-γ), or tumor necrosis factor α (TNF-α) (Hewison et al., 2007), while nuclear factor kappa B (NFκB) is a potent inhibitor of CYP27B1 expression (Fig. 4)."

"There is evidence from in vitro studies that inflammatory cytokines influence expression of vitamin D metabolizing enzymes. While renal CYP27B1 expression is tightly controlled by PTH and 1,25(OH)2D3, in extra-renal tissues, CYP27B1 is regulated independently of those factors in a tissue-specific manner (Fig. 4). Soluble factors like cytokines and growth factors from the microenvironment affect cellular levels of this enzyme. IL1, IFN-γ, and TNF-α increase CYP27B1 expression in immune cells (van Etten, Stoffels, Gysemans, Mathieu, & Overbergh, 2008). TNF-α stimulated activity of CYP27B1 in untransformed cells such as human keratinocytes, endothelial cells (Zehnder et al., 2002), and peripheral blood monocytes (Gyetko, Hsu, Wilkinson, Patel, & Young, 1993). In cells of the human placenta, TNF-α induced expression of both CYP27B1 and CYP24A1, the latter to a greater extent (Noyola-Martínez et al., 2014). In the alveolar macrophages of patients with sarcoidosis, an inflammatory granulomatous disorder, CYP27B1 is expressed at a very high level, leading to pathologic increase of systemic 1,25(OH)2D3 levels and to hypercalcemia (Inui et al., 2001; Jones, 2008). In addition to the high CYP27B1 expression and activity, 1,25(OH)2D3-induced upregulation of CYP24A1 leads to the expression of a splice variant that lacks the mitochondrial targeting sequence thereby blunting the negative feedback regulation (Zehnder et al., 2002), contributing to the high circulating 1,25(OH)2D3 levels. CYP27B1 expression in macrophages is controlled by immune signals, such as IFN-γ, LPS, or by viral infections (van Etten et al., 2008)."

"In DCs, as in other extrarenal tissues, the level of the precursor 25(OH)D3 is often the limiting factor in the synthesis of the active metabolite (Jeffery et al., 2012). LPS, the ligand for TLRs, increased gene expression of CYP27B1 in DCs and human macrophages (Liu et al., 2006). 1,25(OH)2D3 synthesis in monocyte-derived DC is impaired due to a truncated, less active CYP27B1, while catabolism is not affected. Regulation of VDR targets in these cells seems to occur in a paracrine manner. It is the 1,25(OH)2D3 produced by macrophages that induces expression of vitamin D target genes in the neighboring DCs, inhibits maturation of DC, and reduces DC-dependent T-cell responses (Kundu, Chain, Coussens, Khoo, & Noursadeghi, 2014)."

"T-cell-derived cytokines regulate expression of the activating enzyme CYP27B1 in monocytes via TLR 2/1. IFN-γ increased the activity of CYP27B1 and decreased that of CYP24A1 (Noyola-Martínez et al., 2014). Mechanistic studies using promoter–reporter constructs in monocytes revealed that IFN-γ-induced increase of CYP27B1 is mediated via JAK– STAT, NFκB, and p38-MAPK pathways (Stoffels et al., 2006). Activation of TLR1 and 2 by Mycobacterium tuberculosis or IFN-γ increases expression of VDR and CYP27B1, (Adams et al., 2009; Liu et al., 2006). The resultant, locally synthesized 1,25(OH)2D3 induces the expression of antimicrobial peptides, such as cathelicidin (Gombart, 2009; Hoyer-Hansen, Nordbrandt, & Jaattela, 2010) or defensin 4β (Wang, Nestel, et al., 2004)."

@LetTheRedeemed

From what I can remember in posting about it on the Ray Peat Forum, supplementation is safe. In support:

• Sub-chronic (13-week) oral toxicity study with d-ribose in Wistar rats

Hi, Miguel. I hope that you're well.

I recall an episode where professor Garrett admitted to be a faddist, adding that such days were finally over now that he found the ultimate culprit of health problems: poison A. Some months afterwards, he was onto the next target, and this time it was bile (then niacin, pyridoxin, methylene blue..).

But the diversion of attention was quite clever. Before waiting for his poison A depletion program to fail and customers to protest, he sneakily recentered his approach on liver and bile, broadening it to the lowering of toxins—an abstract concept, with perpetual exposure and many confounders—guaranteeing for him a safe and sustainable business in a foggy picture.

Grant set the wrong tone, but both are responsible for misleading and the extremism. A group of people already addressed the majority of their arguments in the past.

We have covered a lot in exhaustive discussions on macabrotenoids and poisonoids, with the origin and biosynthesis in plants and microbes (potential suppliers to a host), their differentiation (including colorless ones), occurrence in foods, digestion and release, interactions with meal components, interception by microbiota, absorption factors, conversion efficiency, regulatory controls, transport, storage (inside and outside the liver), their specific distribution in liver, size of organs and capacity, recirculation, historical levels in tissues, population status, conditions associated with lack or excess, metabolic pathways and backup routes, methods of elimination and the clearance rate depending on body load, change in excretion rate for conservation in scarcity, total reserves and estimates of their lasting, transformed and intact excretion, conjugation, nutrients involved in their metabolism and in defending against adverse effects from excess, the criteria for the RDA, the management in livestock and hypomobilization states, lab experiments and their limitations, natural and unnatural isotretinoin levels, nuclear receptors and their (alternative) ligands with respective concentrations and affinities, interaction between receptors, genomic and non-genomic effects, enzymatic and non-enzymatic reactions, anti- and pro-oxidant activity, their relative orientation in lipids of cells and recycling, the undetectable serum levels (that applies to other toxins too, kilcidiol is an example), the idiotic “aposematism” objection (colorful macabrotenoids signal threat, similar to strawberries), response to supplements in varying forms…

It was in vain for the poison A crowd. Their only take-away was to continue to take it away from the plate.

To treat macabrotenoids and poisonoids as poisons helps to be at ease with prolonged avoidance. Why own the intolerance and investigate the internal issue when we can reclassify a nutrient as a toxin? Who worries about a lead shortage? If anything, we have some stored for life.

People who benefit from the avoidance of poisons will continue to dismiss refutations until a practical measure is offered, one with good results that dispenses restriction.

The issue appears immunological in nature, likely involving disturbances at the lining of tissues (in special gut, lungs, and skin), that can be manipulated by limiting the availability of poisons. In Grant's case, he associates his exaggerated immune responses to poison A, as it’s involved in gene expression and not invariably tolerogenic, which is why he suspects that any food that provokes these responses in him has hidden poisonoic acid.

Of course, if we're going to invalidate the interpretation of an experiment by pointing out a dietary factor that was common to both groups, we can't accept adverse reactions to macabrotenoids as a mere consequence of malnutrition or the unintentional elimination of allergens as a satisfactory explanation. After all, we have a lot of malnourished people who tolerate poisons just fine (for example, Ray suggested that the addition of this toxin can have a sparing effect on protein), and exclusion diets that have in common the elimination of one component can be challenged, which they likely were.

Extra information..

Phosphate species distribution

The change in phosphate species as it passes from serum to urine contributes to eliminate H⁺:

• Serum (pH ~7.4)
  • 20% dihydrogen phosphate (H₂PO₄⁻)
  • 80% monohydrogen phosphate (HPO₄⁻⁻)
• Urine (pH ~6.8)
  • 50% dihydrogen phosphate (20% 50%)
  • 50% monohydrogen phosphate (80% 50%)

(10.1002/9780470048672.wecb641)

So, for a given quantity of phosphate, the species redistribution represents additional protons being accepted by phosphates and taken out.

Depending on the charge, an ion can pair with more or less counterions to maintain neutrality. The Equivalent unit (Eq) accounts for these charge differences.

Predictable values would be:

• 100% as dihydrogen phosphate (H₂PO₄⁻): mEq = 1
• 100% as hydrogen phosphate (HPO₄⁻⁻): mEq = 2

For example, if sodium ions were to pair with them, one ion would be needed for dihydrogen phosphate (NaH₂PO₄) and two for hydrogen phosphate (Na₂HPO₄).

However, it's always a combination of these species in the body, that calls for an approximate mEq value somewhere between 1-2:

• Phosphorus, phosphorous, and phosphate

• Serum

  • 20% (dihydrogen phosphate) * 1 mEq
  • 80% (monohydrogen phosphate) * 2 mEq
  • mEq = 0.2 + 1.6 = 1.8

• Urine

  • 50% (dihydrogen phosphate) * 1 mEq
  • 50% (monohydrogen phosphate) * 2 mEq
  • mEq = 0.5 + 1.0 = 1.5

So, when you spot this unit applied to phosphate in medicine, it should be an approximation based on mixed charges.

(10.3390/nu14214468)

For a victim that excretes 20 mmol of phosphate in a day, we would have in total:

Serum:

• 4 mmol H₂PO₄⁻ (20%)
• 16 mmol HPO₄⁻⁻ (80%)

Urine:

• 10 mmol H₂PO₄⁻ (50%)
• 10 mmol HPO₄⁻⁻ (50%)

The change:

• 10 − 4 mmol = 6 mmol H⁺/day

Therefore, out of 20 mmol eliminated in a day, 6 mmol would represent acid excretion and the rest of phosphates are excreted without accepting more protons because they were already loaded.

You can search for calculators that 'convert pH to molar concentrations' for precise values, but at the extreme condition of urine pH of 4.4, the proton concentration would be something like 0.04 mmol H⁺/L (0.00004 mol H⁺/L).

Protons elimination:

• Through phosphate: 6 mmol H⁺/day
• Free: 0.06 mmol H⁺/day (from: 0.04 mmol H⁺/L urine × 1.5 L urine/day)

But there's a problem..

The original form of phosphorus

Most of the attention is on renal metabolism and excretion, whereas the ingested form is usually neglected.

When we know how a compound entered and left the body, it's possible to have a better idea if there was overall gain or loss of protons.

(10.1038/ki.1983.217)

If the ingested phosphate is derived from acidic foods or those that yield dihydrogen phosphate after phosphocompounds are broken down, minimal net loss of protons from the body occurs in the grand picture, as the phosphates in question wouldn't accept more hydrogens for having the respective sites are already occupied. That is, unless the urine is acidified (allowing phosphates to accept more protons). However, beyond the relevant buffering range of phosphate, the body must resort to other buffers or mobilize stored phosphate.

(10.1007/978-1-4614-3770-3_7)

In extreme situations, ketones (mainly hydroxybutyrate) become significant urinary buffers as well.

For an animal in normal conditions, whose diet after digestion yielded similar phosphate species as that of urine, the net effect on protons would be neutral. It may seem an obvious statement, but if we only compare the compounds in urine to those in serum, it could mislead, making it seem to represent acid excretion.

Bone as a buffer

The hydrogens are released as protons to prepare the phosphates to be incorporated in (hydroxy)apatite. The protons released result in acidification.

• Metabolism and Acid-base Physiology

Two representations of hydroxyapatite:

• 3[Ca₃(PO₄)₂]⋅Ca(OH)₂ (calcium phosphate 3:1 calcium hydroxide)
• Ca₁₀(PO₄)₆(OH)₂

10 parts of calcium for 6 parts of phosphorus is the synthetic molar ratio, which can be simplified:

• Ca 10:6 P
• Ca 1.67:1 P

In bone formation, phosphorus (as phosphate) is derived from circulation for deposition, where have the phosphate species in the expected proportions because of pH (and other factors):

Serum

• 20% dihydrogen phosphate × 6 = 1.2 dihydrogen phosphate
• 80% monohydrogen phosphate × 6 = 4.8 monohydrogen phosphate

The reaction can be represented as follows:

• 10 [Ca²⁺] + 1.2 [H₂PO₄⁻] + 4.8 [HPO₄²⁻] + 2 [H₂O] ⇄ [Ca₁₀(PO₄)₆(OH)₂] + 9.2 [H⁺]

Protons	Source
2 × 1.2 H⁺	H₂PO₄⁻
4.8 H⁺	HPO₄²⁻
2 H⁺	2H₂O: 2H⁺ + 2OH⁻
9.2 H⁺	← Total released per hydroxyapatite formed

The result is acidification in bone formation or alkalinization in bone dissolution, when the reaction above is reversed (right to left), consuming an equivalent amount of protons.

Therefore, bone synthesis and break down can help to regulate acidity (as drugs) when other systems are not enough. Unlike dietary phosphate that's preloaded with hydrogen atoms, bone phosphate is not, and can take up a substantial amount as protons for excretion. However, note that it's a short-term effect, and we return to the same issue: phosphate was once derived from the diet with the respective release of protons.

Immobilization can lead to a marked loss of bone, independent of diet, in particular during the initial period. The amount of calcium lost may double.

• Nephrolithiasis as a Complication of Immobilization Induced Hypercalcemia

More toxins on the scene. What are the remaining nutrients? Magnesium?

• Phosphate is a vascular toxin
• Phosphate Is a Uremic Toxin
• Phosphate Is a Cardiovascular Toxin
• Dietary phosphorus as a nutritional toxin: the influence of age and sex

The outer shell of phosphorus contains 5 electrons.

When we connect them, the message is clear.

What authorities are trying to accomplish by recommending its consumption?

---

• Scientific Opinion on Dietary Reference Values for Calcium | EFSA
• Scientific Opinion on Dietary Reference Values for Phosphorus | EFSA
• Phosphorus | Institute of Medicine
• The Institute of Medicine’s “Dietary Reference Intake” for Phosphorus: A Critical Perspective

Absorption

The absorption rates of calcium and phosphorus are not proportional:

Disorders of Calcium, Phosphate, and Magnesium Metabolism

"The amount of dietary calcium intake [..] regulates the proportion of calcium absorbed through the gastrointestinal tract (Fig. 10.05)."

"Absorption is a linear, nonsaturable function of phosphate intake (Fig. 10.14) and amounts to 60% to 75% of total phosphate intake (15 to 50 mmol/day)."

But within reasonable amounts, the absorption fraction may be simplified as:

Adults

• Ca: 30%
• P: 60%
• Ca 1:2 P

Infants

• Ca: 60%
• P: 80%
• Ca 1:1.3 P

Understanding Sources of Dietary Phosphorus in the Treatment of Patients with Chronic Kidney Disease

"Inorganic P, such as P additives, are not protein bound; they are salts that more readily disassociate and are absorbed in the intestinal tract (50). Indeed, it is believed that >90% of inorganic P may be absorbed in the intestinal tract, as opposed to only 40 to 60% of the organic P present in natural foods (51,52). The major public health implication from these considerations is that the P burden from inorganic P–containing food additives is disproportionately high relative to organic P. In the early 1990s, P additives contributed approximately 500 mg/d P to the American diet, whereas today P additives may contribute as much as 1000 mg/d P to the average American diet (37,51,53,54)."

Twenty-Four-Hour Urine Phosphorus as a Biomarker of Dietary Phosphorus Intake and Absorption in CKD

"Accurate and reliable assessment of phosphorus intake is needed, but this is complicated by limitations in the tools available (9). These limitations include the nutrient databases, which are incomplete and often inaccurate for phosphorus. Differences between phosphorus content determined by nutrient database versus direct chemical analysis of foods show that databases can drastically underestimate phosphorus content of foods (approximately 15%–70%) [?] (10–16)."

Calcium and phosphorus interaction in the gut

Phosphorus Nutrition and the Treatment of Osteoporosis

"Food phosphorus binding by coingested calcium is a well-recognized and well-used approach, particularly in the management of phosphorus absorption in patients with end-stage renal disease.” “Heaney and Nordin[15] have shown that fecal phosphorus content (and therefore, inversely, absorbed phosphorus) is determined primarily by unabsorbed calcium and to a lesser extent by phosphorus intake. Together, dietary calcium and phosphorus intakes account for nearly three fourths of the variation in the quantity of phosphorus absorbed. Briefly, each 500 mg of ingested calcium binds 166 mg of diet phosphorus (95% confidence interval, 144-188 mg)."

"The degree of interference reported here (~166 mg phosphorus for every 500 mg ingested calcium—0.4 mmol phosphorus for every mmol calcium) is substantially less than might have been predicted from simple stoichiometry. A 1:1 molar ratio for CaHPO4 would predict binding of 388 mg phosphorus by 500 mg calcium and, for Ca3(PO4)2 at a Ca:P molar ratio of 1.5:1.0, 258 mg phosphorus would be bound per 500 mg calcium. A molar ratio of 1:1 seems more likely at digestate pH values below 7.0. Even at the upper end of the confidence interval for the regression model—210 mg (6.8 mmol)— binding would still be substantially less than the lowest stoichiometric prediction. This discrepancy may be partly due to rapid absorption of phosphorus in the duodenum well before calcium and phosphorus complexes can form in the chyme. In any event it undoubtedly reflects the complexity and multiplicity of the interactions within the digestive residue." (10.1080/07315724.2002.10719216)

"Under such circumstances, absorbed phosphorus may be too low to support both soft tissue phosphorus needs and new bone mineralization (which consumes mineral at a Ca:P molar ratio of ~1.6:1). Any induced phosphorus insufficiency under these circumstances, expressed as a lowering of serum inorganic phosphorus concentration, would not only limit bone gain, but enhance osteoclastic bone resorption [5]—precisely opposite to the direction toward which current anti-osteoporosis therapy is pointed. Moreover, teriparatide, specifically, exerting its inherent parathyroid hormone activity [↑PTH; ↓Pi], would itself lower the renal phosphorus threshold, thereby compounding the problem by lowering serum inorganic phosphorus levels still further." (10.1080/07315724.2002.10719216)

"Using this relationship, Figure 2 shows the amount of food phosphorus that would be available for absorption in a woman ingesting 70% [490 mg] of the phosphorus RDA [700 mg] (Table 1) under varying conditions of dietary and calcium supplementation. The calculations used in constructing Figure 2 assume that the calcium supplements are coingested with the food phosphorus.[15] At a calcium supplement intake of between 1000 and 1500 mg/d, all the food phosphorus is complexed by unabsorbed calcium and rendered nonavailable. Above that point, phosphorus absorption becomes negative (ie, phosphorus in digestive secretions and sloughed intestinal mucosa, estimated at as much as 250 mg/d,[16] will be complexed as well, blocking its reclamation by the gut; this converts the gut into a net excretory organ for phosphorus)."

"Adding a single serving of milk to the diet of such women eliminates much of the problem. Alternatively, the use of a calcium phosphate supplement provides the desired calcium, prevents the blocking of food phosphorus absorption, and ensures a generous supply of available phosphorus. Although total phosphorus intake rises nearly 3-fold with the highest of the calcium phosphate supplement scenarios, available phosphorus rises very little. Thus, basically what the calcium phosphate supplement does, in addition to providing the desired calcium, is to spare food phosphorus."

"The timing of the calcium supplement intake is important for this relationship. As noted, the foregoing calculations are for simultaneous ingestion of calcium and phosphorus, which is in accord with the usual recommendation. Taking supplements with meals remains a sound stratagem because by slowing gastric emptying, the meal effect improves calcium utilization efficiency, and by spreading the dose throughout the day, calcium absorption is improved further. However, this same stratagem maximizes phosphorus binding and minimizes phosphorus absorption. Schiller et al[17] have shown, using a single-meal design, that separation of the calcium supplement dose from the time of the phosphorus-containing meal substantially reduces the degree of phosphorus binding. This is, of course, to be expected for a process that involves nothing more complex than simple chemical binding. Figure 3 plots some of the data from the article by Schiller et al, showing both the degree of reduction in phosphorus absorption produced by simultaneous coingestion of calcium and phosphorus and the reduction in this effect produced by giving the calcium supplement 2 hours after the meal."

Consequences of Phosphate Imbalance

"Phosphate is absorbed all along the intestinal tract, with the jejunum being the most active absorptive site (91, 184). It is excreted into the gastrointestinal tract with the digestive juices in the amount of approximately 200 mg/day (193), about two thirds of which is reabsorbed (153). Saliva and bile acids are the most important gastrointestinal secretory fluids of phosphate (194)."

"The relative amounts of Ca and P in the intestinal lumen may have another important implication. It has been hypothesized (134, 187, 188) that ionic calcium in the colonic lumen forms nonsoluble complexes with free bile acids and fatty acids. By forming these complexes, calcium can protect the colonic mucosa from the damaging effects of these acids. Free bile acids and fatty acids are thought to enhance cellular profileration in the colonic mucosa (27, 109), a process that can lead to neoplastic changes and eventually to cancer. In the presence of high concentrations of phosphate in the intestinal lumen, calcium becomes bound to phosphate in nonsoluble complexes; this decreases the amount of ionized calcium available for neutralization of free bile and fatty acids and their damaging effect on the mucosa." "Low sodium in the intestinal lumen reduces phosphate absorption (124), while high K increases it (69, 174)."

Circulation and Distribution

Calcium, Phosphorus and Magnesium Turnover

Consequences of Phosphate Imbalance

Role of transporters in regulating mammalian intracellular inorganic phosphate

"[..]physiological [Pi]in, in many but not all mammalian cells, is about 1-5 mM."

"A partial list of published MRS data on [Pi]in (Table 1, upper) shows that in mammalian cells other than erythrocytes, [Pi]in is generally equal to or higher than [Pi]ex. The MRS data indicate that [Pi]in under resting conditions is ∼4 mM in skeletal muscle (highest in slow-twitch fibers) and ∼1 mM in the heart and brain."

Phosphorus-contaminated molecules

For the 14% of phosphorus found outside of bones, these are some of the phosphorus-contaminated molecules (and their formula, taken from PubChem):

• TDP (TPP) (C12H19N4O7P2S+)
• FMN (C17H21N4O9P) and FAD (C27H33N9O15P2)
• NAD (C21H28N7O14P2+) and NADP (C21H28N7O17P3)
• CoA (C21H36N7O16P3S)
• PLP (C8H10NO6P)
• Biotinyl '5-AMP (C20H28N7O9PS)
• AdoCbl (C72H100CoN18O17P–3) and MeCbl (C63H91CoN13O14P–3)
• Nucleotide

"Nucleotides are composed of three subunit molecules: a nucleobase, a five-carbon sugar (ribose or deoxyribose), and a phosphate group consisting of one to three phosphates. The four nucleobases in DNA are guanine, adenine, cytosine, and thymine; in RNA, uracil is used in place of thymine."

"Nucleotides also play a central role in metabolism at a fundamental, cellular level. They provide chemical energy—in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP)—throughout the cell for the many cellular functions that demand energy, including: amino acid, protein and cell membrane synthesis, moving the cell and cell parts (both internally and intercellularly), cell division, etc..[2] In addition, nucleotides participate in cell signaling (cyclic guanosine monophosphate or cGMP and cyclic adenosine monophosphate or cAMP) and are incorporated into important cofactors of enzymatic reactions (e.g., coenzyme A, FAD, FMN, NAD, and NADP)." Nucleotide | Wikipedia

• Phosphocreatine
• Phospholipids
• Inositol phosphate

"Inositol phosphates play a crucial role in various signal transduction pathways responsible for cell growth and differentiation, apoptosis, DNA repair, RNA export, regeneration of ATP and more."

• 2,3-Bisphosphoglyceric acid

"D-2,3-BPG is present in human red blood cells (RBC; erythrocyte) at approximately 5 mmol/L. It binds with greater affinity to deoxygenated hemoglobin (e.g., when the red blood cell is near respiring tissue) than it does to oxygenated hemoglobin (e.g., in the lungs) due to conformational differences: 2,3-BPG (with an estimated size of about 9 Å) fits in the deoxygenated hemoglobin conformation (with an 11-Angstrom pocket), but not as well in the oxygenated conformation (5 Angstroms). It interacts with deoxygenated hemoglobin beta subunits and decreases the affinity for oxygen and allosterically promotes the release of the remaining oxygen molecules bound to the hemoglobin. Therefore, it enhances the ability of RBCs to release oxygen near tissues that need it most. 2,3-BPG is thus an allosteric effector."

• Phosphorylation
• Protein phosphorylation

"Approximately 13,000 human proteins have sites that are phosphorylated."

• Kinases

Consequences of Phosphate Imbalance

"The phosphate is needed inside the cells for phosphorylation of glucose and fructose and for ATP synthesis. It is well established that glucose load (as given in the glucose tolerance test) induces a transient reduction in the serum phosphate levels (42, 78). In feeding after starvation, hypophosphatemia can occur when insufficient phosphate is given. Again, the carbohydrate load given during feeding causes phosphate shifts into the cells, resulting in hypophosphatemia." "Glycolysis enhances utilization of phosphate and thus induces shifts from the extracellular fluid into the cell."

"Intracellular phosphate regulates the activity of various enzymes affecting (a) glucose metabolism: hexokinase, phosphofructokinase (98, 180); (b) amino acids: glutaminase (137); (c) nucleic acids: AMP deaminanse, 5'-nucleotidase, adenine denucleotidase (58, 93, 193); and (d) hormones: 25-OH-D hydroxylase (195)."

Healthy Nutrition And The Human Musculoskeletal System

Main forms in bone:

	Ca:P
Synthetic hydroxyapatite	2.2:1
Natural hydroxyapatite	1.9:1
Amorphous (non-crystalline) calcium phosphate	1.7:1

Their mass ratios:

	Ca:P	Range
Bone (measured)	2.2:1	(2.1-2.3):1
Whole-body (calculated*)	1.9:1	(1.8-2.0):1
Whole-body (measured)	2.1:1	(1.9-2.2):1
Whole-body (measured)	2.2:1	(2.0-2.4):1

*Calculated from bone, containing 99% of body Ca and 85% of body P.

By the way, the EFSA concluded that there are no reliable 'biomarkers of intake or status' and chose their lowest ratio (body composition) to use as reference for intake recommendations:

• Ca (1.8):1 P
• Ca 1:(0.55) P

The recommendation for kilcium is 1000 mg/day, leaving phosphorus at 550 mg/day.

As a side note, they mentioned that the inner bone structure is responsible for most of the turnover in spite of representing only 20% of the total bone mass.

Presentation #552381 | SlideShare

Serum levels

• Calcium: 2.1–2.6 mmol/L (8.5–10.5 mg/dL)
• Phosphate
• Phosphorus: 0.75 and 1.45 mmol/L (2.5–4.5 mg/dL)

---

Elimination

"Kidneys filter 180-200 liters of blood per day and each kidney contains approximately 1 million nephrons, which are often referred to as the ‘functional units’ of the kidney." (10.1016/j.pharmthera.2023.108481)

The kidneys recover multiple grams of these toxins a day from blood filtration. The values vary depending on the source, but it's something like 8-10 g of calcium and 4-6 g of phosphate filtered daily.

(10.2215/CJN.09750913)

Each pass is a chance to make adjustments and eliminate the unwanted fraction, but with limitations. These authors pointed out that the urinary excretion rate is 45 mg/h (can be increased after the effects of PTH or FGF23), and it takes many hours for the absorbed fraction to be entirely eliminated.

Complete absorption is faster than elimination, leading them to speculate that a phosphorus buffer pool exists to maintain stable levels in the blood and inside cells.

Calcium and Phosphorus Metabolism in Chronic Uremia

"It is well known that the physicochemical interrelationships between the two ions concentrations are regulated in such a way that any increase in one is followed by a proportional decrease in the other. This depends on the precipitation of calcium phosphate salts [29]. However, this relationship is not regularly evident in vivo: in fact, the calcium infusion test in normal subjects and in patients with renal osteomalacia is followed by a regular increase in plasma [PO₄] [26,50]. This apparent contradiction to the physico­chemical theory may be explained by the phosphate load coming from the cells and compensating in excess for the phosphate delivered to bones [13]."

↳ [13] Renal Excretion of Calcium by the Dog

"Howard (11) explained the phenomenon of increased serum phosphate following intravenous calcium on the basis of a decreased secretion of parathyroid hormone. He suggested that the action of the parathyroid hormone is to alter the ratio between organic and inorganic phosphorus within cells. Thus the primary effect would not be on phosphate excretion but an action increasing the level of circulating phosphate. Whatever the mechanism is for explaining the elevated serum phosphate and decreased urinary phosphate, it must be an immediate effect since in these experiments this phenomena occurred within 10 minutes after the start of the calcium infusion. While it may be dangerous to generalize on phosphorus distribution of total body cells by analysis only of red blood cells, the source of the increased inorganic serum phosphate following intravenous calcium may be assumed to be the organic phosphate esters of the red blood cells."

---

Calcium and phosphorus balance

I couldn't find the source of the diagrams below, but they give a rough idea of this balance (without showing for phosphorus the buffer pool and losses to the gut):

Recall that the approximate absorption ratio is Ca 1:2 P.

The urinary excretion ratio is about Ca 1:3 P (200:650 mg). However, if we lump the amount of calcium secreted into the gut (150 mg; to be eliminated with the unabsorbed portion) with the urinary excretion (200 mg), we arrive on the original absorption ratio of 1:2 (350:650 mg).

The body absorbs more phosphorus, but the urinary excretion makes up for it. This greater elimination of phosphorus is probably a reflect of absorption rate rather than a fixed property.

	Ca:P
Absorption/Excretion	1:2
Bone composition/decomposition	2:1
Whole-body (w/ soft tissues)	1.7:1

When tissues are not in equilibrium and the balance is tipped in favor of construction, absorption can be upregulated and excretion downregulated to compensate for the mismatch.

Infants minimize the difference by increasing the intestinal absorption rate of calcium relative to phosphorus, perhaps with further renal retention.

If the next table is right, human milk would have another advantage:

?

Sipping must also help to prevent saturation and to make adjustments.

Phosphorus Nutrition and the Treatment of Osteoporosis

"Phosphorus is vital for cellular life and activity, being involved in cell structure, information coding, energy transfer, functional activation of catalytic and signaling proteins, and, in short, virtually every aspect of cell function."

"As would be expected for a limiting nutrient, phosphorus absorption by the human intestine is relatively efficient, with net absorption typically ranging from 55% to 80% (depending on concurrent calcium intake and absorption). Moreover, because phosphorus is distributed widely in many foods, it is not likely to function as a limiting nutrient (as is calcium) in animals at the top of the food chain. Nevertheless, circumstances exist in which phosphorus intake may be insufficient to support the bone rebuilding that today may be possible in patients with osteoporosis."

"[..]as can be seen in Table 1, 5% of women older than 30 years, 10% of women older than 60 years, and 15% of women older than 80 years have intakes on any given day that are less than 70% of the RDA."

"[..]the diets of women with low phosphorus intakes are multiply inadequate. The correct solution to this problem is for health professionals first to recognize that the problem exists and then to address it, with either a change in diet or a polyvalent nutritional supplement. Unfortunately, this is not often done in medical practice, and frequently these women, particularly if they have osteoporosis, will be prescribed bone active agents and encouraged to take supplements of calcium and vitamin D."

"Simple maintenance of skeletal mass translates to zero phosphorus balance and places little or no demand on dietary phosphorus intake. This is because urinary phosphorus excretion can be reduced to extremely low levels, and phosphorus released in bone resorption can thus be efficiently reused for mineralization of newly forming bone sites."

"During any age-related decline in bone or muscle mass, phosphorus released in the process can substitute for phosphorus in the diet. Indeed, it must otherwise be excreted by the kidney. Thus, even intakes well below the RDA, whatever other nutritional effects they may have, should be able to sustain the skeletal phosphorus requirements of the typical elderly individual."

"Extremely large calcium supplement doses (eg, >1500 mg/d), particularly if taken regularly as 500 to 600 mg with every meal, could create a negative phosphorus balance situation even for women who are not undergoing antiosteoporosis therapies, particularly if their meat and dairy intakes are low. However, it is improbable that a regimen of invariable coingestion would be rigidly followed. Hence, without a bone-building demand for phosphorus, it is unlikely that phosphorus binding by calcium supplements would be sufficiently complete as to constitute a serious problem. However, once bone active agents, and particularly anabolic agents such as teriparatide, are used, the situation changes. Figure 2 shows that, with calcium carbonate or citrate supplement intakes in excess of 1200 mg/d, there is effectively no diet phosphorus available to support bone building. This supplement dose is less than that used in some teriparatide treatment studies.[18]"

"In brief, because of the likelihood of some irregularity of the coingestion of calcium supplements with foods, it may still be possible for women with low phosphorus intakes and those receiving antiresorptive therapies to realize the small increase in bone mass that these therapies are able to produce. However, it is unlikely that this would be the case with the anabolic agents, which create a phosphorus demand for bone mineralization that is approximately 10 times that of the antiresorptives. Under such circumstances, it would clearly be prudent to adjust the diet of the patient or to use a calcium phosphate salt as the calcium supplement (or both)."

"Antiresorptive therapies [..] typically produce a slow increase in bone mineral content of 0.5% to 1.0% yearly at the spine after an initial positive remodeling transient of +4.5% to +5.5% in the first year.[14] The steady-state increase in bone mineral content after 1 year creates a small tissue-level phosphorus requirement, with net phosphorus uptake by bone in the range of 4.5 to 9.0 mg/d. By contrast, new-generation anabolic therapies, capable of increasing axial bone mineral content by up to 15% yearly, call for a positive phosphorus balance of up to 45 to 90 mg/d. (The foregoing estimates assume that values measured in the axial skeleton in response to bone active agents apply to the whole skeleton and hence reflect a worst-case, or maximum likely, phosphorus demand.)"

"As reported previously,[15] effective phosphorus deficiency with respect to bone mineralization must express itself as a low value for serum inorganic phosphorus. As long as the bone-forming site is exposed to normal phosphorus concentrations, it will have sufficient phosphorus to support matrix mineralization. In many older individuals with reduced creatinine clearance, there will commonly be some elevation of serum phosphorus levels, which would be protective of the skeleton. The effect of complete or nearly complete food phosphate binding on serum phosphorus in such individuals is unknown. However, they may be protected to some extent. Greater experience with teriparatide therapy will be needed before their relative vulnerability will become clear."

Hormonal regulation of biomineralization

"A very old observation highlights the important role of extracellular phosphate concentration in the mineralization process: by mobilizing phosphate from soft tissue stores, starvation improved rickets in experimental animals[74]. An adequate phosphate level is necessary for normal growth plate development, owing to the phosphate dependent apoptosis of hypertrophic chondrocytes[75]. Infusion of calcium and phosphate in vitamin D deficient rats results in normal mineralization[76]. Furthermore, in a systemic Vdr-knockout model, rickets and osteomalacia can be prevented by a diet rich in calcium and phosphate[66,77]. Similarly, a calcium and phosphate rescue diet improves bone and cartilage in Cyp27b1 knockout mice that lack the 25 hydroxyvitamin D 1α hydroxylase[78]. However, the bone disorders of these animals are not totally normalized by providing minerals, suggesting some possible direct effect of calcitriol as well[79]."

Long-Term Cola Intake Does Not Cause Evident Pathological Alterations in the Femoral Bone Microstructure: An Animal Study in Adult Mice

Modulating phosphate consumption, a novel therapeutic approach for the control of cancer cell proliferation and tumorigenesis

@Amazoniac said in Resources for authors:

Writing in the Sciences | Kristin Sainani (highly recommended)

For convenience:

• Writing in the Sciences (YouTube)

Don't be discouraged by title, it has value for life and you will like.

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.

• How To Annotate An Article: Annotation Strategies | Software Testing Help

• How to take notes for research papers |
  Jonathan Yuan

---

It's noteworthy when two guys who are obsessed with workflow optimization are fond of a software:

• Cal Newport — The Pursuit of Craftsmanship, The Deep Life, Slow Productivity, and a 30-Day Challenge | Tim Ferris

• Cal Newport's Article Writing System

---

One of the rare instances where a book author documented and shared his process in video:

• 2 Years Of Writing A Book In 30 Minutes
• The Writer's Process: How A Book Is Made
• Ryan Holiday's Writing Process Part 1: Cracking The Structure
• Ryan Holiday's Writing Process Part 2: The First Draft Of Anything Is Sh*t
• How To Write A Book - From Research to Writing to Editing to Publishing by Ryan Holiday

---

@brad said in Resources for authors:

@Amazoniac No problem, done

Thanks, Brad.

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.

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.