Fundamentals: How a cell reads a DNA plasmid

The basic operating environment of a cell: The Four B’s (Bump, Bind, Burst, Bump). In a large red brick factory, raw materials are turned into products using machines that rely on workers who pull levers and push buttons, or computers that complete automated protocols through deliberate and intentional actions. Does a cell “microfactory” work like this? How does a cell know what to do?

Cells operate very differently than actual factories. There are no deliberate or intentional acts by atoms or molecules. Atoms and molecules do not think or plan out what to do! Rather, three general factors play a role in the ‘decision making’ or ‘logic’ of a cell:

- The number of molecules: Back in Chapter 1, we learned that what’s inside a cell is a bit like a ball pit - it’s packed full of molecules. These molecules range from small ones like water to large ones like a cell’s genome and protein machinery.

Even though this microfactory is very small, it will have thousands or millions of copies of these cellular machines to complete tasks. The quantity of any particular atom or molecule determines how many are available to participate in chemical reactions or other processes. The more molecules or protein machines, the more reactions happen.

- The rate at which molecules bump into other molecules: In general, atoms and molecules freely move about the cell bumping into other atoms or molecules at a very fast rate. In the world of the very small, activities happen surprisingly fast. For example, around you right now are trillions of gas molecules - oxygen, hydrogen, nitrogen and carbon dioxide - that fill the room. Do you know how fast they are moving? Hydrogen moves at more than 6,000 kilometers per hour - 60 times faster than a car on a highway! These molecules are so small that we don’t feel or notice them.

Further, the atoms that make up molecules can vibrate at up to 100,000,000,000,000 times per second (10¹⁴ Hz). The fast movement and vibrations mean that atoms and molecules can bump into other atoms or molecules very often. Within cells, molecules also move fast. Water molecules have an average velocity of 2,000 kilometers/hour.

In other words, atoms and molecules can move and vibrate at high speed over small distances.

Cells are packed full of different molecules which vibrate and bounce around into one another very rapidly. This allows for trillions or quadrillions of interactions to happen in a single cell at any given moment. A single molecule can bounce around and interact with thousands or millions of other molecules every second and, when chemical bonding is strong enough between two molecules, a chemical reaction may occur. Chemical bonding is when atoms or molecules stick together.

- The strength of chemical bonding between molecules: Cell ‘logic’ and decision making is based primarily upon chemical bonding, which is the ability of some molecules to bind specifically or not with other atoms or molecules. This is what causes certain chemical reactions that result in product-making “actions” to take place.

These factors contribute to the basic operating environment of a cell. In short, an extremely large number of “events” involving a large number of atoms and molecules in combination with bonding leads to an action or outcome.

When thinking of the operating environment of a cell, remember the Four B’s of Basic Cell Operation:
- Bump: Molecules move fast and bump into other molecules in the cell.
- Bind: When a molecule bumps into another molecule, it can result in two or more molecules being bound together if the chemical interaction is strong enough.

- Burst (optional): In the case of protein enzymes that catalyze chemical reactions, when two molecules interact, a ‘burst’ or change in energy may occur resulting in a chemical reaction.
- Bump: The molecules or products of the chemical reaction separate and continue bumping around the cell.

These are by no means scientific terms, and there are other mechanisms by which certain cellular operations occur, but the Four B’s of Basic Cell Operation are a great starting point to understanding and remember how E. coli cells work. The cells do not have a brain and do not think in the way we understand thinking. Instead, they use these Four B’s.