What's Inside a Cell?

In the last post I likened a human cell to a factory and then I extended the analogy to characterize the major components of a cell. In this post, I'll be more direct in describing the cell's contents. And, again, what I'll be describing is the contents of a generic human cell with no specialized function.

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

Organelles

Organelles are basically small organs--large to medium sized membrane-bound structures (made of many molecules) that perform specific tasks. For completeness, let's run through the ones we covered in the last post.

Organelles include, first and foremost, the nucleus, which holds almost all the cell's genetic material (DNA), the mitochondria (generate energy from sugars), the endoplasmic reticulum (ER) and Golgi apparatus (both involved in lipid and protein production and protein transport), vesicles and vacuoles (storerooms for molecules) and lysosomes (break down molecules... basically, the recycling centers of the cell).

Since the focus of this blog is genome replication, the most relevant organelle going forward will be the nucleus.

Macromolecules (large molecules)

I'll spend most of the blog discussing macromolecules. 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 "polymers" so we need to define this term first.

A polymer is a long molecule made of repeating smaller units--units that are just smaller molecules. Let's start with a non-biological example: Let's say we had a string and some 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 are of different colors. But they are 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 beans, 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). The shape of the folded protein determines what it can do (i.e., what kind of mini-machine it is). As we will see as we get farther into this blog, proteins--these mini machines--do most of the physical work in the cell.

I must note, though, that while most proteins in the cell are very much mini-machines, some aren't. Instead, they play structural roles, serving as something akin to building materials.

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 of those two helices is a polymer. DNA is really two entwined polymers. RNA is a single long polymer.

I'll be covering DNA (and proteins) in more detail in later posts. For now, just think of DNA as operating instructions for the cell. More precisely, the main role of DNA is to provide the code needed to build specific proteins (i..e., to know the correct order of amino acids in given protein). But DNA also encodes information related to when and how much of a given protein to make at a given time and much more. 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, fructose and ribose. 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 main 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 also considered metabolites.

Ion and Water

Below the level of molecules we have elements: the chemical from which molecules are built. They include carbon, nitrogen, oxygen. These are the things that were on that periodic table poster in your high school chemistry class. Most of the chemical elements in the cell exist in the form of ions, which are simply version of those elements that have an electric charge, either positive or negative. Ions play critical roles in cells, but those roles aren't central to our story of genome replication, so I won't describe them any further.

Finally, there's water. Everything in the cell swims in water, which makes up about 70% of the cell by 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.