What’s really mind blowing is how fast the gluons inside the protons inside those molecules are moving.

How fast are those moving?

Speed of light.

That's really fast.

More importantly, this means that any given molecule will, in a very short time, bump into almost every other molecule in the cell. Thus, the answer to the question, how does protein X find fuel, or resource Y, or a protein Z it needs? Simple: it doesn't - it eventually just bumps into it. Similarly, in simple cells, there may be no need to transport stuff from place to place - chemical diffusion is fast enough!

Meanwhile larger cells massively benefit by speeding up those processes. So there exists lot of structures to group and or transport where different molecules are.

https://en.wikipedia.org/wiki/Golgi_apparatus

Similarly, organelles group related process together. So for example DNA related proteins are in a nucleus not inefficiently bouncing off the cell wall.

Which helps explain why mitochondria were so beneficial. Keeping a bunch of related machinery all tightly clustered together it makes more efficient use of each individual protein and can quickly replace anything that gets damaged. ATP however can diffuse through the cell just fine because so many processes use it that extra copies isn’t a major issue.