3. A Small Factory (1,126) DONE

Two analogies are commonly used to describe cells: the cell as a factory and the cell as a city. In this chapter, we’ll use the factory analogy.

Think about a factory. It brings in raw materials and uses workers, tools, and energy to produce a product or service. To do that, it needs power, an assembly line, instructions, storage facilities, and systems for waste disposal.

Cells have analogs for all these.

Structure

Factories are enclosed buildings. Cells have a cell membrane that also creates an enclosed space--a prerequisite for the emergent property called "life" to happen. The cell membrane is analogous to the outer walls of a factory.

Other membranes form inside the cell to create organelles--effectively, partitioned rooms where specific cellular activities take place. These include the endoplasmic reticulum (ER), Golgi apparatus, mitochondria, lysosomes, and vesicles, all of which I'll comment on in this chapter.

Cells also contain a cytoskeleton—a network of protein fibers that supports the cell and helps maintain its shape. It's like the factory's support beams. The cytoskeleton is made up of microtubules and a few other kinds of protein fibers.

Factories also have systems for controlling the entry and exit of people, materials, and products in and out of the facility. A receptionist greets visitors. Employees use card keys to enter buildings. The shipping and receiving department makes sure the right materials enter and the right products exit the facility.

In cells, membranes perform these gatekeeper functions.

Membranes contain embedded proteins, pores, and pumps that control what enters and exits the cell. Most molecules can't cross a membrane unless a specific doorway, or transport mechanism, is provided.

Workers

Factories can’t function without employees (or robots). Likewise, a cell needs workers--both to perform its specific function and to just keep the cell running.

The cell’s analog for factory workers are its functional proteins--that is, the proteins that perform tasks like catalyzing chemical reaction or copying DNA. I'm excluding proteins that play structural roles.

I must note that RNAs also play critical functional roles in cells. But most of what we know about cellular mechanism—enzymes, motors, checkpoints, repair—has been uncovered through the study of proteins.

This book follows that tradition, using proteins as the main actors in the story of how cells work. And, in fact, proteins do perform most of the work in the cell. They catalyze chemical reactions, move molecules, copy DNA, and recycle worn-out components… the list goes on.

One other worker in our cellular factory is the ribosome. These are large molecular machines made of protein and RNA.

Ribosomes build all the other proteins the cell needs. Ribosomes can be free-floating in the cytoplasm or attached to one of the organelles that I'll introduce shortly, the endoplasmic reticulum (ER).

Energy

Factories need power to build their products and run their operations. With most factories, power lines deliver electricity generated by an outside utility company.

Cells also need energy to run their operations. But in a cell, energy is generated internally--mainly by organelles called mitochondria. Thus, for the sake of our analogy, we’ll assume that our factory uses internal power generators rather than electricity supplied by a utility company.

“The mitochondrion is the powerhouse of the cell” might be the oldest biology trope around. But… it’s true.

Mitochondria use energy derived from the breakdown of of the chemical bonds in nutrients to produce adenosine triphosphate (ATP), the main energy currency used by proteins to fuel their activities

There are typically a few hundred to a couple thousand mitochondria per cell. But this number varies enormously by cell type. Cells with the greatest energy demands—such as heart muscle and neurons—contain thousands of mitochondria, while red blood cells contain none at all.

Manufacturing and shipping

The cell’s assembly line consists of two organelles that take the form of membrane-bound passageways: the endoplasmic reticulum (ER) and the Golgi apparatus. The ER, in fact, accounts for over 50% of the total membrane in human cells.

Many proteins and lipids--especially those destined for membranes or secretion--are produced through the ER-Golgi system.

The ER is referred to as "rough" or "smooth" depending on whether there are ribosomes attached to the outer membrane surface or not. The ribosomes of the rough ER manufacture proteins. The smooth ER is focused on lipid production.

Some proteins synthesized in the rough ER travel to the Golgi apparatus. The Golgi is a facility for receiving, modifying (through chemical addition), sorting and shipping proteins to specific destinations in the cell.

The Golgi apparatus has two faces. One receives proteins from the rough ER. Once received, they travel through the Golgi passageway toward the other face.

Along the way, they're modified with molecular identification tags that act like zip codes on mailing labels. At the other face, they are sent to the appropriate sites in the cell.

Not all proteins pass through the Golgi. And different proteins use different targeting signals. But for many cellular shipments the Golgi functions as the main sorting and dispatch center.

Information storage

How does a factory even know how to build its products and run its departments? Yes, knowledge lives in the heads of the employees. But that information isn't failsafe. Employees come and go.

Thus, companies typically keep a permanent record: formal, version-controlled standard operating procedures (SOPs). These are typically maintained by a document control department.

In the cell, the document control department is the nucleus. The SOPs are the cell’s genomic DNA. The nucleus stores the genome--the master set of instructions for building and running the cell.

Among countless other things, this genomic DNA determines when and how to produce every macromolecule in the cell, when and how to generate energy and to build products, and when and how to replicate its genome and divide.

Waste and recycling

Both the ER and Golgi apparatus are membrane-bound passageways. Other membrane-bound structures exist in the cell, too. These include vesicles that store nutrients, ions, and other small molecules.

Lysosomes are a specific kind of vesicle that maintains a highly acidic environment conducive to the action of enzymes that break large molecules down into smaller components. These are released into the cytosol where they serve as nutrients.

So when you think of a cell, think of a small factory.

Like factories, cells take in raw materials and process them to deliver a finished product or activity. A real-life example of a product would be the insulin synthesized and secreted by pancreatic cells. An example of an activity would be the contractions of muscle cells that combine to cause gross muscle movement.

Every cell is a tiny factory—one that continuously builds, repairs, and regulates itself using an intricate network of molecular machines.

Next we'll take a more literal tour of the cell to get a feel for its contents.