Contradiction between random molecular collisions and regulated cellular processes [closed]

Question

A cell is a chemical system, consisting of billions of molecules, ions, and atoms. These chemical species are constantly engaged in chemical reactions.

Physics gives the impression that chemical species concentrated in a tiny space, such as a cell, are randomly moving and colliding into one another. Any chemical reaction can occur only if the correct reactants collide with one another and get transformed into a raft of products, under exergonic conditions.

It appears that motions and reactions for biochemicals inside a cell are random and unpredictable. However, cell biology is all about highly regulated and coordinated cellular processes, including transcription, translation, vesicular transport, replication, gene regulation, and so on.

Since each of these cellular processes relies on specific biochemicals to undergo correct chemical reactions, it now appears chemical reactions inside a cell are much more predictable and controlled than what physics might suggest, and so are motions of biochemicals.

How do I reconcile these conflicting ideas about the nature of cells?

Answer 1

Short answer: Unlike the physical model you're describing above, the reality is that localisation of biomolecules in the cell isn't a passive process, instead molecules are actively concentrated where they're required to be by a variety of different mechanisms.

long answer: I think possible 'missing pieces' of this picture which may help you reconcile these ideas are compartmentalisation and intracellular localisation, which extends beyond just the nucleus and membrane-bound organelles.

It's often the case that the constituents required for biochemical reactions are concentrated locally in compartments which facilitate the "collision" of relevant components to progress the reaction. Some examples would include liquid-liquid phase separated compartments or membrane-less organelles (https://www.sciencedirect.com/science/article/pii/S0960982217311090 and https://www.frontiersin.org/articles/10.3389/fmolb.2019.00021/full are some good overviews).

Scaffold proteins also help in this regard (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117218/)

Another example would be the idea of spatially localised transcription hubs where all of the components required for gene regulation and transcription are located in proximity (https://www.scienceopen.com/document_file/6fe11e52-baf9-4ee7-97be-72f3444d1e04/PubMedCentral/6fe11e52-baf9-4ee7-97be-72f3444d1e04.pdf). A specific example would be nuclear speckles (https://academic.oup.com/nar/article/45/18/10350/4101253).

In terms of intracellular signalling it's often the case that molecules involved in cascades are localised in close proximity at the cell membrane (https://pubmed.ncbi.nlm.nih.gov/16467194/). Receptors which sit at the cell membrane but act as transcription factors when active (e.g. nuclear hormone receptors) are actively imported into the nucleus on activation and other signalling molecules are similarly trafficked in an active, directed process (https://cellandbioscience.biomedcentral.com/articles/10.1186/2045-3701-2-13).

Ultimately, most biochemical processes are compartmentalised or otherwise localised through diverse but active mechanisms to facilitate life, as opposed to molecules floating and randomly bumping into each other as you get in a cell-free solution.