Biological metabolism, matter and energy, carbon and hydrogen

This topic is about what I want to share about biological metabolism as a biology enthusiast, including what I have recently learned. Welcome everyone to supplement what you have learned. If possible, I hope a theorist to point out the shortcomings of my understanding.

ATP synthesis

Starting from ATP synthesis. The three ATP synthesis methods I learned about: Substrate level phosphorylation, Oxidative phosphorylation and Photophosphorylation. Among them, Oxidative phosphorylation and Photomorphophylation require ATP synthase and are membrane dependent, It utilizes proton-motive force to synthesize ATP. Substrate level photosynthesis does not need ATP synthase and does not depend on membrane. It is represented by Glycolysis.


When cells leave the proton-motive force environment provided by the hydrothermal vent, they begin to obtain ATP through Glycolysis. EMP (Embden Meyerhof Parnas pathway) is the most familiar Glycolysis pathway. It is the most common way for cells to produce energy in an anaerobic environment. In addition, there are HMP (Hexose Monophase Pathway), ED (Entner Doudoroff), HK. Their products and efficiency vary.

For each molecule of glucose: (glyceraldehyde-3-phosphate enter EMP, Ignore water and NAD (P)+)

Pathway Net material consumption Net output
EMP 1x glucose 2x NADH2
2x pyruvate
2x ATP
HMP 1x glucose
1x ATP
3x CO2
1x glyceraldehyde-3-phosphate
HMP+EMP 1x glucose 1x NADH2
3x CO2
1x pyruvate
1x ATP
ED 1x glucose
1x ATP
1x pyruvate
1x glyceraldehyde-3-phosphate
ED+EMP 1x glucose 1x NADH2
2x pyruvate
1x ATP
HK 1x glucose 1x lactic acid
1.5x acetic acid
2.5x ATP
Carbon fixation

The natural presence of organic matter in the environment is limited, and cells fix carbon from inorganic matter.

The Wood Ljungdahl pathway is considered the earliest carbon sequestration pathway used by Luca. It uses hydrogen and carbon dioxide to synthesize acetyl-CoA or acetic acid.And acetyl-CoA can enter TCA cycle or enter gluconeogenesis to synthesize glucose.(It is worth mentioning that Gluconeogenesis consumes not only ATP but also NADPH)

In addition to utilizing hydrogen, Carbon fixation can utilize ATP and NADPH from a wider range of sources as raw materials.

In addition to the Wood Ljungdahl pathway, the rTCA cycle also exists in both bacteria and archaea. It is the reverse of the TCA cycle, where acetyl CoA undergoes synthesis into Pyruvate at high levels of carbon dioxide concentration. At the same time, this pathway can use NADPH for hydrogen source supply without relying on hydrogen.

When it comes to carbon sequestration, we have to mention RubisCO enzyme. The Calvin cycle is the most extensive carbon fixation pathway in the world, and RubisCO enzyme is its key enzyme.

However, Calvin cycle does not exist in archaea, which does not mean RubisCO enzyme does not exist in archaea. Four forms of RubisCO have been identified, with forms I-III being true carboxylating RubisCO enzymes Form IV is referred to as RubisCO like protein (RLP) and is found in many bacteria and archea. Although structurally related to the true RubisCOs, RLPs do not function as RubisCO enzymes, but instead catalyse different reactions in sulphur metabolism.
Form III RubisCO is only found in archaea, it is currently known and recognized as the earliest branch of RubisCO enzyme, which may reflect the form of RubisCO enzyme in early biological evolution. It is quite heat-resistant but not suitable for room temperature, and is highly sensitive to oxygen. It catalyzes the carbon sequestration pathway: Pentose diphosphate pathway( Thermococcus kodakaraensis) or PRPP-RuBP-PGA pathway.


Chemosynthesis is a good source of energy for life born from the deep sea before it enters the light layer. The reducing substances continuously released from hydrothermal vents are good electron donors, and the abundant sulfates in the primitive ocean can be used as oxidants to synthesize ATP through oxidative phosphorylation. Furthermore, NAD (P) H is synthesized from hydrogen in inorganic materials for carbon sequestration.

Triple state simplification considering complexity.


Perhaps initially it was just to avoid ultraviolet radiation.

Photoelectric autophy may be a precursor to photosynthesis, Cells absorb and utilize photoelectrons on mineral surfaces to drive proton pumps through photosynthetic chains, forming proton-motive force between inside and outside the membrane to finish Photophosphorylation to synthesize ATP and use Hydrogen source to synthesize NADPH.

Later, organisms evolved that photosynthetic pigments no longer rely on mineral photoelectrons. Bacteria evolved a Photosystem with porphyrin pigments as the reaction center (chlorophyll).

This is the evolution diagram of bacterial Photosystem. Proto RC has been specialized into RC I and RC II in evolution, and some bacteria have lost one of the Photosystem in evolution.

Archaea evolved a Bacteriorhodopsin with Carotenoid pigments as the reaction center (Retinal). The proton pump operation of Bacterorhodopsin depends on the photoinduced isomerization deformation of Retinal molecule without involving electron transfer. The decomposition of photosynthetic hydrogen sources in archaea may take the same form as chemoautotrophic.

Hydrogen source

HMP Pathway is an important source of NADPH. However, using organic compounds as hydrogen sources to synthesize organic compounds has inherent limitations, and it is still necessary to place the hydrogen source on inorganic materials.

Before the Great Oxidation Event, Hydrogen sulfide is the most widelyhydrogen source used by autotroph, and hydrogen sulfide was widely present in the primitive ocean. In that era, photosynthetic archaea was the main force for carbon fixation.

Until blue-green algae evolved oxygen evolution complexes (OECs),which are the only protein complexes in nature that can decompose water at ordinary temperature. It meant the birth of oxygen producing photosynthesis.

Although it requires more light energy, water is a more extensive source of hydrogen than hydrogen sulfide, and the byproduct oxygen gradually eliminates reducing substances in the primitive ocean until hydrogen sulfide can only exist on the seabed with low oxygen dissolution, and organisms that rely on hydrogen sulfide can only distribute on the seabed.

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