Hypothetical Structure for Energy Transformation

Illustrations - v2

CD model catalogue for publication in the Journal of
Scientific Research and Reports, Page 30-44,
DOI: 10.9734/jsrr/2021/v27i730409 Published: 9 August 2021

Recently, a hypothetical structure, the Structure for Energy Transformation (SET), was described and submitted for publication with the title “Hypothetical Structure for Energy Transformation. Evolution of Cellular Structures for Energy Transformation”. SET might be responsible for the proper energy transformation steps leading to the continuous production of H+ and ATP in living cells.

The hypothesis is based on the properties of the atoms of the protonated adenine molecule and docking computations of molecular mechanics involved, suggesting that two ascorbate molecules may occupy the empty NADPH pocket, preferably binding to the adenine binding site.

Our hypothesized SET consists of the well-known Complexes I, II, III, IV, and V, completed with two adenine, two L-vitamin C, and two D-glucose molecules. We believe that the tetra uric acid/adenine octo phosphate ring (TAR) is the engine of the five multienzyme complexes in the mitochondria.

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Illustration 6A

Two aminated uric acid and two H2PO4e-molecules in one [Fe2S2 (SCH2CH3)]e2- cluster.

One of the four connecting points of TAR is presented in Illustration 5. In each connecting point, two electrons are transferred through the N1, and N7 atoms of the UA originated adenine molecules. I think that when adenine molecules form the TAR, the electrons pass the molecule in the direction of the N10 and N9 atoms.

Illustration 6A Watch the model

Illustration 6B

Two adenine, one Fe-S cluster.
Four Oe2- are prepared for the oxidation of two carbon atoms.

After the electrons transfer through N1 and N7 atoms of the UA/adenine molecules, the oxygen and the sulfur atoms are changed back in the Fe-S cluster. In this way, four Oe2- radicals are prepared. They will oxidize the 6th carbon atoms of the 5-phospho-glucose molecules.

Illustration 6B Watch the model

Illustration 6C

FE-S cluster oxidizing two carbon atoms (circled) of two 5-phospho-D-gluconate.

One ADP, one ribose, and two CO2 molecules will remain after the oxidation of the 6th carbon atoms of the 5-phospho-glucose molecules.

Illustration 6C Watch the model

Illustration 8A

Four ribose molecules bonded to one tetra adenine octo phosphate ring.

Before the electron flow starts, the unit is completed by six D-glucose molecules. Four 5-phospho-D-gluconate molecules are bound to the adenine molecules via a β-N9-glycosidic bond (Illustration 7A), one 5-phospho-D-gluconate (5) to the nicotinamide, and one (6) to the flavin molecule (Illustration 7B).

Illustration 8A Watch the model

Illustration 8B

One Flavin adenine dinucleotide (FAD), one nicotinamide adenine dinucleotide (NAD), and two ascorbic acid molecules within the electron flow device.

Pictures 8A and 8B illustrate the same unit of the SET.

Illustration 8B Watch the model

Illustration 9

Nicotinamide, Flavin and two ascorbic acid molecules within the electron flow device.

The N10 atoms (circled) of the aminated UA molecules connect to nicotinamide, flavin, and two L-ascorbic acid molecules with the help of dehydrogenases. The double bond between the N10 atoms of adenine and these molecules allows the electron flow. It provides the ability to connect and separate these molecules quickly.

Illustration 9 Watch the model

Each SET unit is a three-stroke rotating nano-machine.

In the "loose" state (phase 1), essential molecules enter the unit. The enzymes force these molecules together, with the active state (phase 2) creating the newly produced ATP molecules. Finally, the intense site cycles back to the open state (phase 3), releasing ATP. The coordinated operation of three units ensures that one of the three units is always active, resulting in continuous membrane potential and ATP production.

The simplified illustrations of SET - containing three units are presented in pictures 9A, 9B and 9C. The yellow, grey, and red rings are showing the silhouettes of the three units. Yellow circles represent the unit in loose (phase 1) state when molecules are entering the unit. Grey rings show the unit in the active state, while red rings are illustrating the unit in the open state when ATP is leaving the SET.

Maintenance of life requires constant electron flow. Cells provide this through permanent glycolysis. In cells, glucose is transformed into the ATP molecule, while CO2, energy, and H+ are produced, which provides a continuous membrane potential.

Twofold energy supply of the eukaryotic cells

The first eukaryotic cells arose from the symbiosis of an ancient cell (originally living in an O2-free environment) with an O2-using cell, now known as the mitochondrion. The ancient cell used peroxisome localized SET-AG, while mitochondria used SET-OP. Correspondingly; eukaryote cells use SET-AG and SET-OP. Thus, they can live in an oxygen-rich and anoxic environment.

All cells are powered by one synchronous, three-stroke twin-engine system. The ADP Producing Unit (ADP-PU) is the primary determining unit of all SETs. The SET of aerobic glycolysis (SET-AG) consists of three ADP-PUs. These units work in a synchronized way with the Complex V, which makes ATP from ADP + PO3 (Illustration 12).

Structure for Energy Transformation of Aerobic Glycolysis

ADP-PU

Mitochobdrium processes the SET-OP, containing 3 SET-AG + one pyruvate dehydrogenase and three high molecular weight Cytochromes, resulting in higher energy production, high membrane potential, and more effective defense against ROS (Illustration 13).

SET OP

ADP-PU: Adenosine diphosphate producting unit