Posts made by 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.

• Murburn concept | Wikipedia
• Kelath Manoj | ResearchGate
• Kelath Manoj | Google Scholar
• Satyamjayatu (his foundation)
• Satyamjayatu | YouTube
  ⠀
• Murburn concept: A facile explanation for oxygen-centered cellular respiration
• Mitochondrial oxidative phosphorylation: Debunking the concepts of electron transport chain, proton pumps, chemiosmosis and rotary ATP synthesis
• Murburn concept and murzymes in 2023: Celebrating 25th year of pursuit

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):

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.

Two things that I didn't have the chance to clarify in response to the last posts by the thread blaster:

I wrote that she deliberately accepted to be treated as a fool by an author, not that she's inherently one. Contrary to her pet quack, the "troll" here doesn't underestimate readers. Let us leave the distortions for him.

She also labels my posts as "TLDR". It's because of not reading that she missed twice the parts where I acknowledged the therapeutic acetate uses in cancer, where it had a positive (and not just neutral) impact, but added that it's tricky and suggested caution; cancer cells are heterogeneous in their organization and the effects can be uncertain. Since the question revolved on counteracting excess lactate and the associated acidity, in the context of cancer, I argued that baking soda would be a preferable option for being safer, which it is.

Regarding the author, I contacted him a day before this thread was taken down out of nothing. Claiming to have the cure for so many problems and dismissing an invitation to demonstrate them says it all.

We can then turn to chat bots to communicate in a language that charlatans speak:

"As a health coach, it is essential to uphold ethical standards and provide accurate information to clients seeking guidance on improving their well-being. Making false promises about curing diseases is not only unethical but also illegal in the United States, leading to severe legal consequences such as civil penalties, fines, injunctions to stop deceptive practices, and potential criminal charges. Deceptive practices, such as falsely claiming to cure diseases, can harm clients by offering false hope and undermining their trust in healthcare providers. This can result in clients losing time in pressing medical circumstances, delaying them from seeking appropriate treatment and potentially worsening their health outcomes. Moreover, such deceptive practices often prey on vulnerable individuals who are in dire need for solutions, further exacerbating their distress and potentially leading to financial exploitation ['NO REFUNDS ON BOOKS OR COACHING']. It is crucial for health coaches to be transparent, truthful, and evidence-based in their recommendations to clients, ensuring they prioritize community health and safety while promoting wellness effectively."

The first publication from a compilation of William F. Koch's writings (I couldn't upload the file. Save it in case the link gets broken):

Will is a remarkable author, his work is supported and the bold statement wasn't from "a sense of relaxation" after supplementing silicic acid and eating a piece of cake, but in a document describing how 44 cases responded to his formula and minimal crutches.

Little did Will and supplement companies know that silicic acid capsules were only a lemon away from normalizing fermentation and healing cancer.

Brad, if you're reading this, I appreciate the recovery.

7.2 - Complex I | Structure & Reactivity in Organic, Biological and Inorganic Chemistry (Schaller)

"The main events in Complex I are summarised in the cartoon below. You can see the electrons entering from the matrix at the bottom of the picture (the pathway is shown by the blue arrows). They are delivered by NADH and handed off to FMN; this step will be discussed below. The electrons are transferred via outer sphere electron transfer through a series of iron sulfur clusters and are eventually delivered to the lipid-soluble ubiquinone (Q)."

"By far the most common electron acceptor in the oxidative phosphorylation supercomplex is an iron atom. Of course, the most common oxidation states for iron ions are Fe2+ and Fe3+. An iron in the 3+ oxidation state is able to accept an electron, becoming Fe2+. In contrast, an iron in the 2+ oxidation state could pass an electron on, becoming Fe3+ in the process."

"NADH is a two electron donor. An Fe3+ ion is a one-electron acceptor. We need an adapter for this electrical connection. The adapter comes in the form of FMN. FMN is the structure with some atoms coloured in blue and red near the bottom right corner of the picture.

• NADH only donates two electrons at a time.
• The iron ions in the electron transport chain can toggle between Fe(III) and Fe(II); they can accept only one electron at a time.
• An adapter is needed to convert two-electron transfer into one-electron transfer.

FMNH2 is a little bit like NADH. Its oxidized form, FMN, can accept two electrons and a proton in the form of a hydride ion, as well as an additional proton. In other words, FMN accepts H– and H+ to become FMNH2. However, a slightly different route is available to FMN. It can also undergo reduction one electron at a time. In reality, the addition of an electron would be shortly preceded by or shortly followed by addition of a proton, in order to keep the overall charge the same. This state, FMNH, is called the semiquinone form.

What's the difference between NAD and FMN? Why is one able to accept only a pair of electrons, whereas the other can accept one at a time? When FMN accepts one electron, it becomes a radical. Radicals are unstable, reactive species. They can be stabilised chiefly by delocalisation. The additional conjugation in FMN compared to NAD allows the odd electron to be delocalised more extensively in FMN. That radical stability is the key difference.

• The presence of extended conjugation stabilises a radical on FMNH.
• The stability of this radical allows FMN to accept one electron at a time.

Once FMNH2 has formed, the reverse is true, of course. It can give up one electron at a time. As a result, FMN can take a pair of electrons coming in from NADH and send them out one at a time into the electron transport chain."

7.3 - Complex II | Structure & Reactivity in Organic, Biological and Inorganic Chemistry (Schaller)

"In terms of how those electrons make their arrival, the picture is somewhat similar to Complex I. Succinate is a hydride donor in this reaction, so it is donating two electrons. As in Complex I, a series of FeS clusters will eventually relay the electrons, so we have a matching problem. To step down from a two-electron process to a one-electron process, another flavenoid, FAD, acts as an intermediary. Like the related FMN, FAD can accept either one or two electrons at a time, and its reduced form, FADH2, can donate either one or two electrons at a time.

• Just like in Complex I, an adapter is needed to convert the two-electron process of succinate oxidation to the one-electron process of iron reduction.
• The adapter is another flavenoid structure, FAD, which is very similar to the FMN used in Complex I.

After the electrons have arrived and are stored in the form of FADH2, they are passed along, one at a time, through a series of three FeS clusters. Just as in Complex I, these carriers are all bound to the proteins, so they are held in one place and do not move. The outer sphere mechanism by which the electrons are transferred can only operate over a short distance, from one electron carrier to the next."

Lathering the skin with D-panthenol (or dexpanthenol) may lead to local overconsumption of NAD+.

Nutrient Metabolism: Structures, Functions, and Genes (978-0-12-387784-0)

"CoA synthesis uses pantothenate, cysteine, one adenylate, three phosphates, and the energy of six high-energy phosphates from ATP (Figure 10.43). Significant amounts of pantothenate are generated from pantetheine through the action of pantetheine hydrolase (EC3.5.1.-), which is expressed in many tissues. Panthenol and panthenal may also be converted to a limited extent into pantothenate by alcohol dehydrogenase (EC1.1.1.1) and aldehyde dehydrogenase (EC1.2.1.3)."

• Panthenol -(ADH)→ Panthenal -(ALDH)→ Pantothenic acid

⠀
Enzymatic Conversion of Pantothenylalcohol to Pantothenic Acid

What factors are responsible for the greater yield of ATP per carbon atom when fatty acids are completely oxidised to CO2 and water compared with glucose?

The complete oxidation of glucose doesn't produce more CO2 than that of fatty acids: every carbon that composes these molecules is eliminated as CO2 (decarboxylation), and at no stage in their oxidation carbons are added.

Yield of complete oxidation (matched by carbons):

• 1 glucose (C6H12O6): 6 CO2 and 32 ATP
• 1 caproic acid (C6H12O2): 6 CO2 and 36 ATP
  ⠀
• 2 glucose (C12H24O12): 12 CO2 and 64 ATP
• 1 lauric acid (C12H24O2): 12 CO2 and 78 ATP
  ⠀
• 3 glucose (C18H36O18): 18 CO2 and 96 ATP
• 1 stearic acid (C18H36O2): 18 CO2 and 120 ATP

Since fatty acids produce more energy per carbon than glucose, for a given energetic need, meeting it through fatty acid oxidation is economical, needing less carbons to metabolize, and less exposure to CO2.

Fatty acids oxidation is more dependent on FAD relative to glucose oxidation (needed for ACAD enzyme in every normal beta-oxidation cycle). Taken together with the previous information..

• 2.5 ATP/NADH
• 1.5 ATP/FADH2

..it can give a false impression that fatty acids oxidation must produce less energy, but the simple comparison above is enough to conflict with this.

A major factor responsible for the lower ATP yield in glucose oxidation is pyruvate dehydrogenase, for eliminating carbons (2/6 1/3 of them) before they enter the TCA cycle.

• 2 carbons at PDH → 2 NADH + 2 CO2 → 5 ATP + 2 CO2
• 2 carbons at TCA cycle → 3 NADH + 1 FADH2 + ATP + 2 CO2 → 10 ATP + 2 CO2

The carbons of fatty acids are all eliminated in the TCA cycle.

In addition, (1) the last acetyl-CoA formed in beta-oxidation is a by-product of the final cycle, and it dispenses oxidation along with the respective reduced coenzymes of each cycle. (2) Fatty acids also undergo activation with the consumption of what's equivalent to 2 ATP per molecule.

The two factors just described counteract the beta-oxidation advantage:

• Glycolysis: ~2.3 ATP/2 C
• Beta-oxidation: 4 ATP/2 C

When the fatty acids chains are shorter, the ATP yield per carbon before decarboxylation is similar between fatty acids and glucose (as can be verified in the table), but as the fatty acids chains increase in length, the counteracting factors are minimized for only affecting a lesser and lesser portion of the chain, making the greater ATP yield from beta-oxidation (products) stand out.

They showed in the video an 'Activation' and a 'Concentration' lighting setting that appeared similar.

Human Centric School Lighting | Tove Karlsson

Section 4.1.1 (but skim through 4.3 too):

"In a study by Wessolowski (2014) seven different lighting scenes designed by Philips for school use were used:

• “Standard”, that follow the conventional lighting situation in classrooms based on the DIN 5035 standard (300 lx, 4000 K);
• “Focus on board”, where the board lighting is bright (1000 lx, 4000 K) and the room lighting low (300 lx, 3800 K); “Board only”, the board is lit and the room lighting is switched off;
• “Concentrate”, very bright, daylight white light for individual work that demands a high degree of attention/concentration (1060 lx, 5800 K);
• “Activate”, slightly brighter and a significantly higher level of the blue component of the spectrum compared to standard lighting (625 lx, 11000 K);
• “Relax”, slightly warmer compared with standard lighting (325 lx, 3500 K); and
• “Extreme Relax”, a more extreme variation of programme 6 is used when no reading and writing is performed (275 lx, 3500)."

"This Variable Lighting (VL) programme is adapted to different work and social arrangements used in school. The seven VL lighting programmes were chosen based on current research and in coordination with lighting experts and the participating schools. During two tests on the pupils’ performance and behaviour the researcher controlled the variation pattern, by switching the different buttons. During the period in between, the teacher controlled the settings."

"The result show that the pupils made fewer errors on a standardised test of attention, reading speed rose significantly and that reading comprehension rose slightly under the VL “Concentrate” program. The reading speed and reading comprehension results improved under the VL4 “Concentrate” program. The motivation for learning and the classroom atmosphere did not change during the nine month test period. The pupils and teachers rated the Variable Lighting positively and found it useful during lessons. This study also indicates that a possibility to choose between different lighting scenes can help to shape the different lesson segments optically and illuminate the structure of the lesson."

"Teacher logs during the test revealed that out of the seven predefined programmes, primarily “Concentrate”, “Activate” and “Relax” were used. The teachers particularly liked the option of visually separating individual sections of the lesson. The teachers desired a smaller number of different programmes and a programme with even warmer light (3000 K)."

"Overall the pupils were positive. The concentration promoting effect of the lighting was emphasized by one in six children. Very few of the pupils reported negative experiences; one pupil desired less abrupt transitions, one reported that too frequent changes were distracting, one male and one female pupil in secondary school complained about headaches caused by VL4 “Concentrate” (Barkmann et al. 2012)."

"Tuv school in Hemsedal in cooperation with “UiB, Haukland Universitetessjukehus” and “Nasjonal kompetansetjeneste for sovnsykdommer” has made a Human Centric lighting installation with LED with four different settings:

• “Energilys” to be used in the first hour of the day (Automatic, 6500 K, 650 lx);
• “Fokuslys” during tests (Manual. 6500 K, 1000 lx);
• “Roliglys” for relaxation and calm activities (Manual, 2700 K, 300 lx); and
• “Standardlys” for ordinary activities (3500 K, 300 lx).

The control board is controlled by the teacher. The study involves 27 pupils in grade 3 and 4. The teachers report about positive development for the pupils’ concentration and restfulness in class and the pupils report about decreased sleepiness (Saxvig et al 2014)."

Dynamic Lights: Lighting Up Students' Minds | Euronews

You can find plenty of information on dynamic lighting and attention. Cycles of bright white light can be an useful tool to explore.

The stress of a cold shower may also be of help for alertness.

• Human physiological responses to immersion into water of different temperatures

ATP Synthase & P:O Ratio | Fundamentals of Biochemistry - UT Austin

Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria

"The most important inference from the presence of the c8-ring in bovine F-ATP synthase, is that 8 protons are translocated across the inner mitochondrial membranes per 360° rotation of its rotor. As each 360° rotation produces 3 ATP molecules from the F1-domain, the bioenergetic cost of the enzyme making an ATP is 2.7 protons."

• 8 H+/3 ATP
• 2.7 H+/1 ATP

"The combination of the electrogenic exchange of internal ATP for an external ADP by the ADP/ATP translocase and the nonelectrogenic symport of phosphate and a proton by the phosphate carrier protein adds one proton to the total required to provide ATP to the cellular cytoplasm, and so the bioenergetic cost to the vertebrate mitochondrion is 3.7 protons."

• 3.7 H+/1 ATP (extra H+)

"Where they are known, the sequences of c-subunits are identical in almost all vertebrates (Fig. 4). Also, they are highly conserved across animal phyla (Fig. 5), and mutations are confined mostly to the N and C termini of the protein, away from the c-ring-central stalk interface, and the ion binding site around Glu-47." "Therefore, it appears that F-ATPases in all vertebrates and probably all or most invertebrates, will contain c8-rings. Therefore, the bioenergetic cost of the enzyme making an ATP is 2.7 protons in vertebrates and probably in invertebrates also (exceptions dictated by particular energetic demands of a species may exist). There are estimated to be 48–58,000 vertebrate species and about two million invertebrates. This picture of an evidently universal cost of making an ATP molecule in multicellular animals is very different from the picture in prokarya, chloroplasts, and fungi where, for reasons that are not understood, the F-ATP synthases have evolved a range of ring sizes from c10–c15 with associated higher bioenergetic costs of 3.3–5 protons per ATP (22). Thus, the vertebrate and probably the invertebrate F-ATP synthases are the most efficient that have been found."

"In mitochondria, it is thought that for each two electrons transferred to oxygen from NADH or succinate, 10 or 6 protons, respectively, are pumped out of the matrix into the space between the outer and inner membranes of the organelle."

• 10 H+/NADH [4 (C-I) + 4 (C-III) + 2 (C-IV)]
• 6 H+/succinate [4 (C-I) + 0 (C-II) + 4 (C-III) + 2 (C-IV)]

"Therefore, the number of moles of ADP phosphorylated to ATP per two electrons transferred to oxygen, known as the P/O ratio, will be 10/3.7 and 6/3.7, or 2.7 and 1.6 for NADH and succinate, respectively, close to experimental values of 2.5 and 1.5 (23)."

• 3.7 H+/1 ATP (⇈ with the extra proton)
• 1 H+/0.27 ATP

NADH and succinate are 2-electron donors despite their difference in moving protons. The oxygen (½O2) consumption brought up in the previous paragraph represents the oxidation of NADH or succinate.

• 1 H+ (from a generic source) → 0.27 ATP
• 10 H+ (from 1 NADH) → 2.7 ATP/NADH ≈ 2.5 ATP/NADH
• 6 H+ (from 1 succinate) → 1.6 ATP/succinate ≈ 1.5 ATP/succinate or FADH2

Complete glucose oxidation yields more than 1 NADH and 1 FADH2 molecule. It can be simplified as:

Cytosol

Glycolysis

• 2 NADH (GAPDH)
• 2 ATP

Mitochondria

Pyruvate oxidation

• 2 NADH (PDH)
• 2 CO2

--

Tricrapoxylate cycle

• 3 NADH (IDH, KGDH, MDH)
• 1 FADH2 (SDH)
• 1 GTP ATP
• 2 CO2

Tricrapoxylate cycle ×2

• 6 NADH
• 2 FADH2
• 2 GTP ATP
• 4 CO2

Cytosol + Mitochondria:

• 10 NADH
• 2 FADH2
• 4 ATP ('substrate-level phosphorylation')
• 6 CO2

Assuming that (former section):

• 2.5 ATP/1 NADH
• 1.5 ATP/1 FADH2

We have:

• 10 NADH → 25 ATP (oxidative phoshorylation)
• 2 FADH2 → 3 ATP (oxidative phoshorylation)
• 4 ATP ('substrate-level' phosphorylation)
• 6 CO2

Combined:

• 28 ATP (oxidative phoshorylation)
• 4 ATP ('substrate-level' phosphorylation)
• 6 CO2

Grand total per complete glucose oxidation:

• 32 ATP
• 6 CO2

Out of 32 ATP, 2 are the net cytosolic yield and 30 are mitochondrial.

Most of the ATP is produced in mitochondria, but consumed in the cytosol. When the phosphorus-containing molecules are returned to the mitochondria to reform ATP, they pass through the intermembrane space and allegedly dissipate the extra proton quantified above.

However, if protons concentrate in cristae, which in turn are relatively isolated compartments, ADP and phosphate imported from the cytosol might not interfere with this pool of protons.

Review of studies on the disfluency effect: Can a font change improve memorization and educational outcomes?

"This review article is devoted to the disfluency effect, which is observed as an improvement in the memorization of information and subsequent educational results due to reduced processing fluency. According to the basic explanation of the disfluency effect, if information is written illegibly, the learner senses complexity, or disfluency, which leads to a deeper processing of information. Traditionally, the disfluency effect is considered from the perspective of Bjork’s desirable difficulties approach and Sweller’s cognitive load theory. In this article, we pay attention to these concepts and also discuss the main studies and meta-analyses devoted to the effect. It is worth noting that the existence of the disfluency effect is not seen as indisputable and raises doubts among the authors of the review and other colleagues. As indicated, a significant number of studies do not detect the effect; for this reason, possible moderators influencing its manifestation are also considered. A separate section of the review is devoted to research of the Sans Forgetica font. The font was specially created to be disfluent, and its developers proceeded from the assumption that the disfluency effect really exists. This review article is addressed to a wide range of readers, and it may be of interest to both specialists in the field of metacognition and for pedagogical practitioners."

• FMN + ATP → FAD + PPi
• NMN + ATP → NAD + PPi

FMN is for Complex I (NADH dehydrogenase) what FAD is for Complex II (succinate dehydrogenase). Both compounds are embedded in their enzyme complex and function as immediate acceptors of electrons from NADH and succinate. This makes NADH oxidation also dependent on riboflavin.

From here.

Speaking of fad, despite the association of ketoacid dehydrogenase complexes (such as PDHC↓) with thiamin, they depend on riboflavin as well.

Pyruvate Dehydrogenase Complex

E1, pyruvate dehydrogenase/pyruvate decarboxylase

• Catalyzes pyruvate to acetyl (releases CO2)
• Cofactor: thiamine pyrophosphate (Vitamin B1)

E2, dihydrolipoyl transacetylase

• Attaches CoA to acetyl
• Cofactor: lipoic acid (not vitamin-derived) & coenzyme A (pantothenic acid/vitamin B5)

E3, dihydrolipoyl dehydrogenase

• Reduces NAD+ to NADH
• Cofactor: NAD+ (niacin/vitamin B3) & FAD (riboflavin/vitamin B2)

We have reports of lactate normalization after riboflavin dosing, but it's more challenging to identify where it helped the most, and its function in PDHC may be conserved in deficiency (if I'm not wrong, problems are more common at the decarboxylase part of the complex).

• Riboflavin to treat nucleoside analogue-induced lactic acidosis
• Riboflavine and severe lactic acidosis

Imaginary units ahead:

The Final Frontier of pH and the Undiscovered Country Beyond

"Cells are small. A typical mammalian cell, such as a Chinese Hamster Ovary cell, CHO, has an internal volume of ca. 1.2 pL, of which about 70% is H2O [1]. This corresponds to ca. 2.8×10^13 water molecules inside the cell, calculated by applying Avogadro's number of 6.02×10^23 molecules per mole to the molar concentration of water in water, i.e. 55.56 M. Subcellular compartments are several orders of magnitude smaller than cells. Mitochondria have volumes of ca. 1 fL, (90% in mitochondrial matrix, and 10% in the intermembrane space), lysosomes of about 30 aL, and the smallest of them, coated vesicles, of about 30 to 800 zL (10−21 L) [2]–[4]. In addition, some organelles, such as mitochondria, have variable sizes. They can fuse, divide, and therefore their sizes vary in the range of about an order of magnitude. Thus, in a coated vesicle we find from 7×10^5 to 2×10^7 water molecules, in a lysosome 7×10^8, and in an average mitochondrion 2.3×10^10.

In these organelles, pH values of 6.8 for the mitochondrial intermembrane space, 8.0–8.1 for the matrix, 4–5 for lysosomes, and 5–7 for coated vesicles have been reported [5]. These values have been accepted in the biological community and are hardly ever disputed. In this article, we examine the physical meaning of these pH values."

"Let us consider a mitochondrion, an organelle with a femtomolar volume generating chemical energy for the metabolism of eukaryotic cells [5,8]. This energy is generated by the H+ gradient across the phospholipid bilayer surrounding the mitochondrial matrix (into the matrix). The synthesis of one ATP molecule is accompanied by the transfer of up to three H+ ions along the gradient, from the intermembrane space to the matrix. Thousands of ATP synthase complexes are considered to be simultaneously active [8]. Yet, as shown in Example 5, simple and obvious calculations demonstrate that there may be no more than seven H+ ions in total in the whole intermembrane space!"

"Calculations such as those provided in Examples 5-7 indicate that water is too weakly dissociated to be a direct donor or acceptor of H+ and OH− ions at very low biological volumes, even if one can still define the pH formally. It appears that H+ ions can be shuttled to reaction centers by other biomolecules, whose concentrations are not constrained by Eq. 2. Best candidates for such molecules are those having pK values close to 7, and are thus capable to serve as donors and acceptors of H+ ions. One obvious group of candidates for such proton donors, available in millimolar and higher concentrations in every intracellular locale are phosphates, e.g. inorganic phosphate, nucleotides and membrane phospholipids."

"About 50% of phospholipids carry amine groups with a pK of about 9, indicating that under cellular conditions most of them will be protonated. At this point we end up with a reservoir of over three hundred thousand protons in only just one lysosome! Interestingly, the pK value of the phospholipid amine can be lowered by 1–2 log units, depending on the phospholipid composition of the membrane [12]. Thus phospholipid bilayers may be a significant and tunable source of protons for cellular reactions. It may also the very reason (reason d’etre) of why reactions occur on cell membranes."

"The general view that emerges from the above thought experiments and calculations is that the intracellular pH is in fact a composite of many pairwise proton exchange interactions between individual protonable molecules."

Prefixes applied to the litre | Wikipedia

pH Calculator | Omni

Cheesy Science | ChemMatters

To be generous, we can rely on the pH of 6 proposed above for the region near the surface ('perimembrane') in cristae, that they suggest to be needed for a compartment pH difference of 2 (8–6).

• pH 6 = 0.000001 mol H+/L = 10^–6 mol H+/L
• 1 mol = 6.02 × 10^23 molecules, atoms or ions (H+ in this case)
  ⠀
• (10^–6) × (6.02 × 10^23) = 6.02 × 10^17 H+

The concentration of protons in cristae with a pH of 6 will be:

• 6.02 × 10^17 H+/L

Mitochondrial volume (as mentioned above):

• 1 fL = 10^–15 L

Water content:

• 70% (or 7 × 10^–1)

Volume distribution:

• 90% matrix
• 10% (or 10^–1) intermembrane space

Therefore:

• 10^–15 L × (70%) × (10%)
• 10^–15 L × (7 × 10^–1) × (10^–1) = 7 × 10^–17 L

The proportional proton quantity:

• 6.02 × 10^17 H+ per 1 L
• ? H+ per 7 × 10^–17 L
  ⠀
• 6.02 × 10^17 H+/L × (7 × 10^–17 L) ≈ 42 H+ per intermembrane space

Returning to their points that "the synthesis of one ATP molecule is accompanied by the transfer of up to three H+ ions" and "thousands of ATP synthases are simultaneously active", despite the example with a generous value, it's clear that protons must hop between buffers for the current model to be viable.

A good analogy:

Mitochondrial proton leaks and uncoupling proteins

Cognitive bias | Wikipedia

List of cognitive biases | Wikipedia

How to enable extensions in Incognito mode | Brave

"Like other browsers mentioned above, Brave automatically disables extensions in Private browsing mode."

Skiff Mail Shutting Down in 6 Months | Restore Privacy

Flavin adenine dinucleotide | Wikipedia

"Based on the oxidation state, flavins take specific colors when in aqueous solution.

• Flavin-N(5)-oxide (superoxidized) is yellow-orange
• FAD (fully oxidized) is yellow
• FADH (half reduced) is either blue or red based on the pH
• FADH2 (fully reduced form) is colorless"

"90 flavoproteins are encoded in the human genome; about 84% require FAD, and around 16% require FMN, whereas 5 proteins require both to be present. Flavoproteins are mainly located in the mitochondria because of their redox power. Of all flavoproteins, 90% perform redox reactions and the other 10% are transferases, lyases, isomerases, ligases."

"Cellular concentrations of free or non-covalently bound flavins in a variety of cultured mammalian cell lines were reported for FAD (2.2-17.0 amol/cell) and FMN (0.46-3.4 amol/cell)."

Wikipedia has a 'View history' option on the top right corner. You can consult the specific date when something was posted for references.

@brad, read my previous message where I pointed out a considerate thing to do, that would only take a few seconds of your time already here. Everyone will be going through something. You're in a position of a leader and now answers for a community. If for whatever reason you can't take care of the forum for a while, it's understandable, delegate it to someone of trust (the smoking duck, for example) or at least communicate to members the impossibility in advance.

ilovethesea recovered a good deal of the deleted thread. If you can return the rest, nice. But the issue is beyond an incident of mass content exclusion.

Forum owners have to take content preservation seriously because you're curators in essence. And there's no acceptable leeway to messing with a single post of another member. I'm surprised how you didn't perceive this gross vulnerability as a threat to a resource that you cherish, compelling you to lower the tolerance to null to prevent recurrences, until you can discuss with the group what's best to do.

My heart is into this forum and you can count on me to preserve its content. On the first signs of becoming evil or going insane, I would transfer the ownership to someone else that can carry our project on.

This is the kind of passion that inspires members to commit, not the casual, nonchalant attitude.

I don't create a forum for being unsure if I would be qualified to, before you tell me to create one.

Anyway, I'm not trying to test your limits. In fact, I've been putting all of our disagreements aside since joining to cooperate on this project. Observe that I continued to post elsewhere in spite of having my messages completely brushed off. Even now, you couldn't be direct about it. It's complicated.

Hexokinase | Wikipedia

"The first step in glycolysis is the phosphorylation of glucose by hexokinase."

"Phosphorylation of a hexose such as glucose often limits it to a number of intracellular metabolic processes, such as glycolysis or glycogen synthesis. This is because phosphorylated hexoses are charged, and thus more difficult to transport out of a cell."

"Hexokinases I and II can associate physically to the outer surface of the external membrane of mitochondria through specific binding to a porin, or voltage dependent anion channel. This association confers hexokinase direct access to ATP generated by mitochondria, which is one of the two substrates of hexokinase. Mitochondrial hexokinase is highly elevated in rapidly growing malignant tumor cells, with levels up to 200 times higher than normal tissues. Mitochondrially bound hexokinase has been demonstrated to be the driving force for the extremely high glycolytic rates that take place aerobically in tumor cells (the so-called Warburg effect described by Otto Heinrich Warburg in 1930)."

@ilovethesea

How kind of you to go out of your way for this?!

Of all the pages that they could skip, they jump the one with the main responses.

Still, it's a remarkable save. Many thanks.

Mitochondria | RS Science

The typical cross section of mitochondria make it seem that their inner membrane is folded as an accordion, but we rarely encounter a rotated view to show that the connection sites can actually be narrow and tubular, and it looks like a deflated balloon.

Formation of cristae and crista junctions in mitochondria depends on antagonism between Fcj1 and Su e/g

The cristae can expand and shrink depending on respiratory activity.

Anomalous Diffusion Induced by Cristae Geometry in the Inner Mitochondrial Membrane

"It is known since the 1950s, that mitochondria are cylindrically shaped organelles, their silhouette being formed by closely apposing outer and inner membranes, with numerous invaginations, termed cristae within the latter [9], [10]. The cristae forming mitochondrial inner membrane (IM) is contiguous with the peripheral inner membrane, referred to as inner boundary membrane (IBM). Cristae have distinctly different shapes: some organisms and cell types are known to have exclusively tubular cristae formed as curved cylinders of uniform diameter [11], others may exhibit flat or even prismatic cristae. However, in the majority of cells in multicellular organisms, cristae appear as flat membranous infoldings protruding into the mitochondrial body. We will refer to such cristae as lamellar ones. In the 1990s, electron microscopic tomography allowed for more accurate determination of their shape and connectivity to the IBM [12]–[14]. When reconstructed in 3 dimensions (Fig. 1A and figures in [13]), several structural features common to different tissues and species appeared (for a good review see [15]). It was found, that rather than forming folds lamellar cristae should be represented as flattened cisterns of uniform width attached to the IBM with several narrow tubular connections up to hundreds of nanometers long. Attachment places, the junctions, have a diameter (≈28 nm) similar to crista width (≈27 nm). Often, especially in smaller cristae, the flattened part is missing, so that the whole crista consists of the tubular compartment alone. When the flattened segment is present, one crista usually is anchored via several tubular connections. In tissues with large cristae masses, these are densely packed into stacks of parallel cristae, large lamellae mostly oriented perpendicular to the longer mitochondrial axis. In the extreme case of brown adipose tissue tubular compartments are totally missing, but the lamellar parts are still connected to the IBM via short junctions 28 nm in diameter."

A row of ATP synthase pairs in crista formation:

Helical arrays of U-shaped ATP synthase dimers form tubular cristae in ciliate mitochondria

Macromolecular organization of ATP synthase and complex I in whole mitochondria

"The angle between monomers in the dimer was approximately 80° for bovine heart and the three species of fungi, and approximately 115° for potato correlating with the difference observed in F1 head distance of the dimers."

Mitochondrial Cristae: Where Beauty Meets Functionality

"Cristae are the site of OXPHOS: 94% of complex III and ATP synthase [17] and approximately 85% of total cytochrome c are stored in this compartment [9] (Box 2)."

Respiratory complexes clustering to maximize efficiency.

Macromolecular organization of ATP synthase and complex I in whole mitochondria

"ATP production in mitochondria is powered by the pmf [proton-motive force], manifest in the electrochemical transmembrane gradient. The resulting current of protons through the Fo rotor of the ATP synthase drives ATP production by rotary catalysis in the F1 head on the matrix side of the membrane. The pmf is generated by complexes I, III, and IV, the proton pumps of the respiratory chain, which translocate protons across the membrane from the matrix side into the cristae space. The pmf has two components, one resulting from the pH difference across the membrane (ΔpH), and the other from the membrane potential (Δψ). In mitochondria and chloroplasts, the pmf is roughly 180 mV. In chloroplasts, this is mostly accounted for by the ΔpH, whereas in mitochondria the ΔpH contribution is comparatively small. Given that the matrix pH is 7.9 (33), the cytosolic pH is 7.35 (34), and the outer membrane is freely permeable to ions, the nominal ΔpH across the mitochondrial inner membrane is 0.55 units, equivalent to 32 mV. However, in vitro studies indicate that the mitochondrial, chloroplast and bacterial ATP synthases all need a ΔpH close to 2 units, equivalent to approximately 120 mV, and a p-side pH close to 6, to produce enough ATP to sustain life (35–38). We propose that the apparent paradox of a ΔpH that is seemingly insufficient and a p-side pH that is too high for efficient ATP production is resolved by the special geometry of the mitochondrial cristae."

"In a previous study (12), we calculated that the high degree of membrane curvature at the cristae ridges [tips] could accommodate a higher charge density for a given membrane potential, resulting in a local ΔpH increase of up to 0.5 units. Furthermore, an earlier modelling study by Cherepanov et al (39) found that protons released on the membrane surface encounter a potential barrier of 0.1 to 0.15 mV. The potential barrier makes it more difficult for the pumped protons to escape to the bulk solvent, resulting in a higher proton concentration, and consequently a lower pH, at distances up to 1 nm from the membrane surface. The effective pH in this boundary layer has been estimated at approximately 6, independent of the pH of the bulk solvent (39). The boundary layer, in combination with the higher charge density at the cristae ridges [at the tips], would meet both the above requirements for efficient ATP synthesis, of a pH below 6 on the p-side of the membrane, and a ΔpH around 2. Protons, which move along membrane surfaces about 10 times faster than into bulk solvent (40), would thus diffuse preferentially along the membrane from their source at the respiratory chain proton pumps on either side of the cristae ridges toward the proton sinks at the ATP synthase dimer rows (Fig. 5). The rapid consumption of protons by the ATP synthases at the cristae ridges would establish a proton gradient along the membrane, by which protons would tend to flow from source to sink, instead of diffusing equally in all directions. The directional proton flow along the membrane surface would provide both a functional role for the mitochondrial cristae, and explain how the conserved, ubiquitous rows of ATP synthase dimers along the cristae ridges help to optimize ATP synthesis in mitochondria."

@ThinPicking

Let's say that the admin had the most chaotic week of his life. If he could respond to a nearby comment and modify forum settings, how difficult it would have been to write:

"Hey, man. I can't look into any of this at the moment, but will do when possible."

@zawisza

It was not an impulsive or gratuitous comment. It's because of thinking twice before criticisms that I rarely regret them.

You know who else put a lot of effort into running a forum? The lion. Monumental dedication for a decade, and this is not sarcasm. We're dealing with different matters, that have to be separated.

I already expressed my gratitude for his effort in making this forum operational, but being demanding would be one more reason for him to take the project seriously.

Did Brad..

• ..give a damn about data loss in his trust? No.
• ..appear to value the time and effort of members? No.
• ..feel accountable for his negligence? No.
• ..show a remote concern for the inconvenient caused? No.
• ..reach out to everyone involved to communicate? No.
• ..try to recover the posts? No.
• ..bother to reply to a contact? No.
• ..properly correct to prevent recurrences? No.
• ..blame internal issues on an Internet Archive deficiency? Maybe.

But never mind, the lady already succeeded in her feat.

Mister @ThinPicking, I appreciate your support.