5. What's Inside a Cell?

In the last chapter, I likened a human cell to a factory and then extended the analogy to the major components of a cell. In this chapter, I'll be more direct and literal in describing the cell's contents. Again, what I'll be describing are the contents of a generic human cell.

I'll proceed from larger to smaller cell components, starting with organelles. And I won't go over organelles in detail since I already introduced them them in the last chapter. Then I'll introduce macromolecules (read: large molecules) in relative detail followed by metabolites (smaller molecules) and finally, ions and water.

Organelles

Organelles are often described as the cell’s "small organs." They are medium to large sized membrane-bound structures that do, in fact, function like small organs in that they carry out specialized tasks. Let's quickly run through the ones we covered in the last post.

Organelles include the nucleus (which holds almost all the cell's genetic material, or DNA), the mitochondria (which generates energy mainly from sugars), the endoplasmic reticulum (ER) and Golgi apparatus (both of which are involved in lipid and protein folding, chemical modification, and trafficking), vesicles (storerooms for molecules) and lysosomes (sites where molecules are broken down; the recycling centers of the cell.) Given the focus of this book on genome replication, the most important organelle for us going forward will be the nucleus.

Macromolecules (large molecules)

I'll spend most of this chapter discussing macromolecules, or "large molecules." First, let's name them. There are four kinds of large molecules inside the cell: proteins, DNA, carbohydrates, and lipids. These are often referred to as "the molecules of life" since they are the essential building blocks of all living cells. Three of the four kinds of macromolecules are categorized as "polymers" so we need to define this term.

A polymer is just a long molecule made of repeating smaller molecule subunits. Let's start with a non-biological example: Let's say we had a string and beads of six different colors. We could knot up one end of the string and then slide beads down one after another. We'd end up with a polymer ("poly-" means "many") made of monomers ("mono-" means "one") called "beads." Note that the beads are not identical. They're of different colors. But they're similar enough that they can be threaded next to each other linearly to create a "bead polymer" (also known as a bracelet).

Macromolecules: monomers combine to create polymers

Let's take a closer look at our four kinds of macromolecules.

Proteins: Mini Machines

Proteins are polymers made of monomers called amino acids. In the same way that there were six differently colored beads, there are 20 different amino acids. To create a protein, the cell adds amino acids onto a growing chain in a specific order. It's almost that simple!

As the amino acids are added, the chain begins to fold up on itself (think of a wadded up piece of string). This most often occurs spontaneously but sometimes it requires the assistance of so-called "chaperone proteins."

It is the shape of the folded protein determines what the protein can do (i.e., what kind of mini machine it is). As we will see as we get farther into this chapter, proteins--these mini machines--do most of the physical work in the cell.

As I noted earlier, though, while most proteins are very much mini machines, some aren't. Some play structural roles, serving as something akin to building materials in the cell.

DNA: Operating Instructions

DNA and its close relative RNA (both are "nucleic acids") are polymers made of monomers called nucleotides. While there are six bead colors and 20 different amino acids, there are four different kinds of nucleotide monomers. To be exact, DNA takes the form of a double helix. So, each strand of the double helix is a polymer. DNA is really two entwined polymers. RNA isn't double-stranded. It's a single long polymer.

I'll be covering DNA in more detail in later chapters. For now, and as we did in a previous chapter, just think of DNA as operating instructions for the cell. More precisely, the main role of DNA is to provide the codes needed to build diverse proteins. But DNA also encodes information about when and how much of a given protein to make, and at what specific time and place. More on DNA soon.

RNA is used by the cell as kind of a photocopy of a stretch of DNA. When DNA information is needed about the structure of a protein, the cell makes an RNA "photocopy" of the DNA information. The RNA photocopy is used by the cell to make the protein (rather than using the invaluable DNA directly).

Carbohydrates: Mainly a Food Source

Large carbohydrates are called polysaccharides. They're polymers of monosaccharides (simple sugars) such as glucose and fructose. A large polysaccharide might be made up of a few hundred to a few thousand monosaccharides.

In animal cells, polysaccharide carbohydrates are mainly used for food storage. The most prevalent one in animals is glycogen, a polysaccharide made of glucose monomers. Glycogen is found in muscle and liver cells, where it can be broken down into easy-to-digest glucose monomers when energy is needed.

In plants, polysaccharides play both a food storage function (the plant polymer of glucose monomers is called starch) and a structural function (the polysaccharide cellulose is the main component of the relatively hard cell walls that enclose plant cells.

Lipids: At Home in Membranes

Of the four macromolecule types, lipids (or "fats") are the one that's not strictly a polymer. Lipids do have repeating units called fatty acids. But lipids include other elements in addition to those repeating units, so formally they aren't simple polymers. Also, they don't tend to be as large as the other three kinds of macromolecules. So let's just say that they are "borderline" macromolecules.

The one commonality of lipids is that they mix poorly with water. They are hydrophobic (water-hating) This makes them ideal components of cell membranes: both the membranes that surround the cell and those that are internal to the cell. I won't say much more about lipids or cell membranes. That's a shame, but neither are key players in our topic of genome replication.

Metabolites (small molecules)

Not surprisingly, given that I defined large molecules as a cell component, I will also define small molecules, or "metabolites", as a category. A metabolite is a substance either generated by or used in metabolism. For example, the monomers we've discussed so far--amino acids, nucleotides, and monosaccharides--are all metabolites. In addition, chemical intermediates in the pathways for both synthesizing and breaking down those monomers are considered metabolites.

Ions and Water

Below the level of molecules we have elements: the chemicals from which molecules are built, including the monomers of the polymers we just discussed. These include carbon, nitrogen, oxygen. These are the things on that periodic table poster in your high school chemistry class.

Most free chemical elements inside cells exist as ions rather than as neutral atoms, carrying either a positive or negative electric charge. Ions play critical roles in cells, but not roles that are central to our story of genome replication, so we'll save that discussion for another day.

Finally, there's water. Everything in the cell swims in water, which makes up about 70% of the cell by wet weight. The water molecules are in constant motion--called Brownian motion. It is the motion of all of the water molecules that pushes other cell components--mainly ions, metabolites and macromolecules--around the cell.