3. A Small Factory

Analogies are ubiquitous in molecular biology. Traditionally, two analogies have been used to describe the cell: the cell as a factory and the cell as a city. Some will say these analogies are overused. I disagree. They are heavily used. But that's because they are effective. We’ll use the factory analogy.

Think about a factory. It's a physical facility that brings in raw materials and uses human workers, tools and technologies, and energy to produce a finished product. Factories need workers, a source of power, an assembly line, and instructions on how to build the product and how to keep all the company’s internal processes running smoothly. They also need facilities to store the finished product and they need some kind of trash and recycling function. Cells have analogs for every one of these factory elements.

Physical Facility

Human cells are enclosed in a wrapper called a cell membrane, which creates an enclosed space, which is a prerequisite for the emergent property called "life" to happen. The cell membrane serves as the outer barrier, or outer "walls" of the factory (even though the cell membrane is a dynamic, flexible structure). This cell membrane holds the cell's water-based, gelatinous cytosol and the various organelles, or "small organs," contained in it.

Other membranes form inside the cell to create what are effectively partitioned "rooms" where specific cellular activities take place. I'm thinking of organelles like the endoplasmic reticulum (ER), Golgi apparatus, mitochondria, lysosomes, and vesicles, all of which I'll say something about in this chapter.

Cells also have a cytoskeleton, which is a network of rigid--but also dynamically generated and maintained--fibers inside the cell that provides additional support. The cytoskeleton's fibers are constructed mainly of long molecular structures called microtubules. We can think of the cytoskeleton as "support beams" that give the cell its shape.

In addition to outer and inner walls, 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. And the shipping and receiving department makes sure only the right materials enter and the right products exit the facility.

In cell, it is the membranes I just described that perform this gatekeeper function. The membranes include embedded proteins, pores, and ion pumps that control what enters and exits the cell. In fact, the membranes are so selective that most molecules cannot cross them at all unless the cell actively provides a specific doorway or transport mechanism.

Factory Workers

Factories can’t function without employees (or robots, I suppose). Likewise, the cell needs workers to perform the specialized function of the cell and to just keep it running. The cell’s main equivalents of factory workers are its functional proteins--that is, the proteins that perform tasks like catalyzing chemical reaction or copying DNA. I'm excluding proteins in the cell 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.

Thus, proteins perform most of the jobs necessary for the cell to live, grow, and divide. They perform thousands of different chemical reactions, unwind DNA, break up old proteins and organelles for recycling, transport materials to specific destinations in the cell… the list goes on. Proteins are central to the cell's functioning so I cover them in more depth later.

One other "worker" in our cellular factory is the ribosome. These are large macromolecular machines made of specific protein and RNA molecules. Their job is to build all the other protein "workers." Ribosomes can be free-floating in the cytoplasm or they can be 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 other aspects of 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 particular factory uses internal power generators rather than electricity supplied by an outside utility company.

“The mitochondrion is the powerhouse of the cell” might be the oldest biology trope around. But… it’s true. Mitochondria take in large molecules and break them down, borrowing the energy held in their chemical bonds to build smaller energy-laden molecules—most importantly adenosine triphosphate (ATP), which is 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 is highly variable 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, illustrating how tightly mitochondrial number is matched to cellular function.

Assembly Line

The cell’s assembly line consists of two organelles that both take the form of membrane-bound passageways. They are the endoplasmic reticulum (ER) and the Golgi apparatus. The ER, in fact, accounts for over 50% of the total membrane in eukaryotic cells. Many macromolecules get built in the ER and Golgi apparatus.

For example, lipid synthesis (including the lipids that make up the cell’s membranes) occurs in the ER. Also, proteins—especially those that tend to be secreted by the cell—are synthesized by the ER. The ER is referred to as "rough" or "smooth" depending on whether there are ribosomes attached to the outer membrane surface.

Some proteins synthesized in the ER travel to the Golgi apparatus. Think of the Golgi as 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. Once received, they travel through passageways (being chemically modified along the way if appropriate) toward the other face, which sends proteins to other sites in the cell.

The Golgi apparatus places molecular identification tags on proteins that act like zip codes on mailing labels. It can also package proteins in membrane-bound transport vesicles that it marks—again, chemically—for delivery to specific 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.

Document control

How does a factory “know” how to build its product(s) or how to run its many departments? Yes, knowledge lives in the heads of employees, but they aren't failsafe. Employees come and go. Thus, companies typically have formal, version-controlled Standard Operating Procedures (SOPs) that represent a permanent record. These are typically maintained by a Document Control department.

In the cell, the Document Control department lives in the nucleus. And the equivalent of the SOPs are the all of the cell’s genes: in other words, its genomic DNA. Among countless other things, the DNA effectively tells the cell when and how to generate energy, when and how to build its products, when and how to divide, when and how to replicate its genome, and when and how to produce every protein in the cell.

Storage, trash and recycling

Both the ER and Golgi apparatus take the form of membrane-bound passageways. Other membrane-bound structures or sacs can be found in the cell as well. These include vesicles that store nutrients, ions, and other small molecules. Other sacs specialize in isolating, breaking down and expelling waste products.

Lysosomes represent a specific kind of vesicle that maintains a low internal pH (a highly acidic environment) conducive to the action of enzymes that break macromolecules down into smaller components. These are then released into the cytosol where they serve as nutrients. Some lysosomes, complete with their internal digestive enzymes, are believed to arise from budding of the trans face of the Golgi apparatus.

So when you think of a cell, think of a small factory. The cell takes in raw materials and processes them to create a finished product or activity. A real example of a finished product would be the insulin synthesized and secreted from pancreatic cells. A real example of an activity would be the contractions of muscle cells that combine to cause gross muscle movement. Every cell is a productive environment and the factory metaphor captures this.