Cytoplasm, Glycolysis, NADH and storage

I previously initiated a poll on whether to evolve cytoplasm for your species

The vote

It seems that many people doesn’t really like it. After all, compared to aerobic respiration, the efficiency of glycolysis is extremely low, especially now there is no shortage of oxygen. Compared to the increase in ATP and storage, the decrease in movement speed (The cytoplasm is as heavy as the Metabolosomes) and increase in reproductive costs brought about by increasing cytoplasm reduces its cost-effectiveness. Cytoplasm should have lower weight and reproductive costs.

There is a problem that the current game does not distinguish between cytoplasm and cytoplasmic matrix (or cytosol).But the current placeable protein is vague (Aggregation of similar proteins in the cytoplasmic matrix?), they belong to cytoplasmic matrix. In addition, Cytoplasmic matrix and organelles belong to cytoplasm. It would be better to rename the cytoplasm in the game to cytosol, even if it is still not accurate enough.

The glycolysis and aerobic respiration in the current game are fragmented, it is difficult to reflect that glycolysis is a prerequisite for aerobic respiration. My idea is to add pyruvate as an intermediate substance in cell metabolism, which serves as a product of glycolysis and a material for aerobic respiration. It would prevent the cells from becoming a large number of organelle aggregation at the later stage and serve as ATP buffer for possible endurance systems. The accumulation of excessive pyruvate(Exactly NADH, which is also a product of glycolysis) can cause problems for cells. It need enzyme to consume it. For example, basic metabolosomes metabolize pyruvate to lactic acid and so on (anaerobic respiration), and It can be upgraded to the current metabolosomes (aerobic respiration).

There is still potential for further development of pyruvate. For example, Separating ammonia and amino acids, Ammonia serve as environmental compounds and amino acids serve as cloud.Initially, cells were able to collect amino acids in the original soup; when the amino acids in the environment decrease, cells use ammonia and pyruvate to synthesized amino acids or hunt other cells; When the ammonia content in the environment also decreases, nitrogen fixation will take effect. In emergency situations, amino acids can also be converted into pyruvate.

I don’t know much about cell biology, but you make some interesting suggestions. There would be issues with making the processes in game too technical, and adding in too many compounds the player has to keep track of. Amino acids are at least well-known and ubiquitous enough that maybe they should be made explicit in the game.

I’m not sure what you mean, here. Are you suggesting there should be an incentive for cells with a nucleus to have cytoplasm as well as organelles?

1 Like

Mainly, it’s difficult for me to simulate the situation that a large eukaryotic predator engulfs various small prokaryotic cells. I lack something that can fill cell and make it bigger without being a burden.

At first I was going to say that cells should not just be filled with only organelle, but now I realized that the endoplasmic reticulum and golgi apparatus in eukaryotic cell should not be so small, It’s also not right to directly fill with only cytosol.

And the size of some organelle is too small(Mitochondria and chloroplasts should be larger than most prokaryotes, but many prokaryotes in the game are bigger than my eukaryotes). And many organelle have a lot of storage, It is unnecessary to use cytoplasm to increase storage space.

Some key and representative compounds like amino acids should not be ignored, but there’s no need to be too detailed about specific amino acids. Pyruvate is an important and fundamental intermediate metabolite that deserves to be reflected.

I think we should add a dynamic amothphere

Is that related to this topic specifically?

1 Like

A vacuole hex isn’t too different from a cytoplasm hex

1 Like

From a storage perspective, the current cytoplasm has little advantage in terms of capacity. Most importantly, the current storage space size is severely overflowing. Even if there is no cytoplasm, just the glucosestorage brought by various organelle is enough for photosynthetic cells to spend the night, and even the glucose synthesized by photosynthesis is insufficient for storage(This means that even more advanced storage is unnecessary.). However, Ammonia and Phosphate basically enter the evolution bar (especially large cells) directly upon acquisition, and storage is only prepared for the next evolution, which makes it unnecessary to increase the storage of Ammonia and Phosphate.

At present, the storage space of all compounds is increasing synchronously, and one idea is to separate them. In addition to the general storage of cytoplasm and vacuoles, the increased storage of various organelle should be less and related to their metabolic raw materials: for example, Rustacyanin improves iron storage, Metabolosomes (or considering pyruvate) and Thylakoids improve glucose storage. Add glycogen, starch, and leucoplast (eukaryotic organisms) to store glucose.

One idea for Ammonia and Phosphate is to allow cells to enter a dormant phase and stop growing and reproducing. If environmental compounds are achieved, during this period, cells can accumulate Ammonia and Phosphate. This requires the addition of a new ATP consumption: growth and reproduction, depending on the cost or speed of cell reproduction (or can speed gears be controlled?).

1 Like

I just now noticed the existence of this post.
Ironically, this is the very day I have a test on this entire process (energy transitions, glycolysis, Krebs cycle, electron chain, membrane, and fat storage) as part of my undergraduate biology academic studies.
So I can contribute a thing or two about this:

Glycolysis, as you mentioned, is energetically inefficient - produces a total of only 2 ATP (in total) and 2 NADH as a byproduct.
But here there is a slight problem with this process and it is not due to the ATP, it is another substance that I just mentioned: NAD+. It is a very important substance that takes 2 electrons and 2 protons from glucose during its conversion to pyruvate. If the cell runs out of this substance, glycolysis will not work and must find a solution.
In cells that use oxygen, the oxygen is the solution as part of the electron chain process that occurs in the mitochondria, together with the FADH2 molecule that is formed in the Krebs cycle.
But in cells that do not consume oxygen as part of anaerobic respiration, without oxygen recycling these molecules, the cell needs to find another way to return NADH to NAD+ (which is a strong reduction).

Here two processes come into play - lactic fermentation and alcoholic fermentation. Start to see in the picture here that I copied from my study material:

This is more or less an extension of your words, which are mostly true, but as strange as it is, glycolysis is one of the earliest ways to break down glucose as we know it. It is almost impossible to find evidence of another process capable of doing anything similar to this process.
But we have other ways to produce energy, but it all comes down to one very simple thing -
ATP synthase (and its bacterial counterpart F-ATPase) and proton transfer in it. After all, it all boils down to electron transitions and proton transitions as a way to produce energy and a connection between ADP and a phosphate molecule to ATP.

Because of this complexity, I’m actually quite against adding the Pyrowatt to the game, because it would make the game simply too complex to understand. After all, the game focuses on life “as we know it” and theories that have proven to be possible. Adding an in-between material that is a by-product is something very important in my opinion, but this material is not a suitable candidate just for the reason I mentioned above - because it is immediately disintegrated, essentially making its role unnecessary for the presentation.

That’s my opinion at least on this topic. And all this material, with a summary of 46 pages (if I were to translate it into English, it would take something like almost 20 pages more to learn (almost 70)) that I worked on for a week already gave me a headache just looking at it.
I will repeat myself again as the semester test from import in a few months.

If there are any questions about this, I can help answer it with the material I have.

According to many studies (which I won’t find now because I don’t have much time until the test starts). Phosphate is a major limiting factor regarding the spread of life on Earth, as its main source comes from the rocks that weather slowly until it reaches the sea. As strange as it is, the cell does not have an efficient phosphate storage system in particular the vacuole. Thus, what is currently represented in the game, quite corresponds to reality. In multicellular organisms like us and vertebrates, phosphate is stored in bones and teeth as a solid substance. Role of vacuoles in phosphorus storage and remobilization - PubMed
The cell is not really capable of storing anything separately, as these are individual substances. If it did this, the cell would be much larger, reducing the surface area it required to function efficiently. So I’m quite against the idea. (I’m talking here about inorganic materials in unicellular production, There are exceptions such as substances found in the lysosome or this substance participates as a control process of something else such as in calcium stores in muscle cells, but in the end, everything according to diffusion is stored within the cytoplasm itself)


As for NADH, as I was talking about the use of NADPH as an intermediate in autotroph,

I originally intended to use NADH as an intermediate in glycolysis and aerobic respiration. They should be similar to ATP. The reason why I changed to pyruvate is that I have discovered that pyruvate can synthesize amino acids (I hope to distinguish ammonia and amino acids to achieve ammonia nutrition), but now I have found this:

Consider synthesizing amino acids or using glucose as the substrate directly.

From a gaming perspective, NADH is just an indicator of the intensity of glycolysis, limiting the intensity of aerobic respiration that can proceed next. During stable preparation, NADH should be fully utilized by aerobic respiration. If there is surplus NADH, it should be used for fermentation (it seems that there is no need for a separate organelle for fermentation, perhaps the fermentation type can consider the passive protein system that has not yet been realized?).

For individual storage, if glycogen adds the same amount of storage space to glucose and iron, isn’t that right. Regarding storage, cells enrich substances into semi permeable membranes by active transport and synthesize macromolecular substances, like starch to store glucose separately. The main reason is that there is no need to treat all storage methods as separate compounds unless they have further special uses. For cytoplasm and vacuoles, it is a universal storage device that still works as it does now. Separate storage should appear in the corresponding organelle, which represents the buffer effect of substances.

Compared with the storage of phosphate, the direct storage of ammonia seems more absurd, which can only be said to be a abstraction. Ammonia should be further abstracted as nitrogen to add nitrate. At that time, nitrogen is used to synthesize amino acids and enter the breeding strip. Ammonia (ammonium) and nitrate, respectively, can be absorbed and converted into nitrogen as environmental compounds. It is allowed to add nitrifying bacteria and denitrification bacteria.

SRB(Sulfate-reducing bacteria) can use pyruvic acid and other organic substances as electron donor to reduce sulfate to hydrogen sulfide, and obtain survival energy from redox reaction. Sulfates are widely present in primitive oceans and hot springs, and can serve as a good anaerobic pathway for glucose metabolism. Should direct oxidation of hydrogen, hydrogen sulfide, and ammonia by sulfate be feasible?


I just found some information that NADH can serve as a hydrogen donor for nitrogenase nitrogen fixation. In fact, NADPH is also. In addition to ammonia, nitrogenase also has the ability to catalyze the synthesis of hydrogen gas, which is hydrogen fermentation.

1 Like