4. What's Inside a Cell? (1,077) DONE

Imagine shrinking down until you're inside a human cell. If all the molecules and ions were to slow down from their rapid random movement, would you see?

First you'd be struck by the large, membrane-bound compartments all around you--the organelles. After that, you might notice an enormous variety of molecular machines doing different jobs both funcvtionaland structural. These are the macromolecules. And finally, there will be countless smaller molecules and ions crashing about.

Organelles

Inside the cell are compartments where specific jobs are performed--energy production, molecule assembly, recycling, and storage.

We covered organelles in the last chapter. But in the spirit of completeness, the cell's organelles include the nucleus (holds almost all of the cell's DNA), the mitochondria (generates energy by breaking molecular bonds), the endoplasmic reticulum (ER) and Golgi apparatus (involved in lipid and protein synthesis and folding, their chemical modification, and protein trafficking), vesicles (storerooms for molecules) and lysosomes (where molecules are broken down and recycled).

Given the focus of this book is genome replication, the most important organelle for us going forward will be the nucleus.

Macromolecules

I'll spend most of this chapter on the four kinds of macromolecules (large molecules) found in the cell: proteins, DNA (and RNA), carbohydrates, and lipids. These are often referred to as "the molecules of life." They're the essential building blocks needed to make and manage a cell.

Three of the four kinds of macromolecules are polymers--long molecules made of repeating smaller molecule subunits.

Let's start with a non-biological example of a polymer. Consider 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 individual subunits or monomers ("mono-" means "one") called beads.

Note the beads are not identical. They're of six different colors. But they're similar enough that they can be connected up next to each to create a bead polymer.

Macromolecules: monomers combine to create polymers

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

Proteins: mini machines

I'll have more to say about proteins in the next chapter. For now, know that proteins are polymers made of monomers called amino acids.

In the same way there were six different 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.

As the amino acids are added, the chain begins to fold up on itself. This usually occurs spontaneously but sometimes requires the help of chaperone proteins.

It is the shape of the folded protein determines what it can do (i.e., what kind of mini machine it is). As we'll see in the next chapter, protein mini machines do most of the work 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 were six different bead colors and 20 different amino acids, there are four different kinds of nucleotide monomers that we know by the first letters of their chemical names: A, G, C, and T.

To be exact, DNA takes the form of a double helix. So, really, each strand of the double helix is a polymer. DNA is two entwined polymers. RNA isn't double-stranded so it's a single polymer.

I'll be covering DNA in more detail in later chapters. Proteins and DNA are the stars of this book.

For now, think of DNA as the cell's operating instructions. Or, more precisely, the primary role of DNA is to provide the codes needed to build tens of thousands of different proteins. But DNA also encodes other information, including information about when and how much of a given protein to make.

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 code. This RNA photocopy is used by the cell to make the protein (rather than using the precious DNA master code directly).

Carbohydrates: a food source

Large carbohydrates--polysaccharides--are also polymers. The monomers are monosaccharides. These are simple sugars like glucose and fructose. A polysaccharide might contain a few hundred to a few thousand monosaccharides.

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

Lipids: the stuff of membranes

Lipids (or "fats") are not strictly-speaking polymers. They do have repeating units called fatty acids. But they include other elements, too, so they aren't true polymers. Let's just say that they are "borderline" polymers.

Lipids are hydrophobic. They mix poorly with water. This makes them the ideal components of membranes--both those that surround the cell as well as those that form organelles.

I won't say any more about carbohydrates or lipids because, as critical as they are to the cell, neither plays a significant role in genome replication.

Smaller molecules, ions and water

In addition to the large macromolecules we’ve discussed, cells are filled with smaller molecules known as metabolites. These include the basic building blocks of macromolecules—amino acids, nucleotides, and simple sugars—as well as the many intermediate molecules involved in synthesizing and breaking them down.

These small molecules are constantly being made, modified, and consumed. They are the raw materials and intermediates that keep the cell’s chemical reactions moving forward.

Ions and water

At an even smaller scale are ions—individual atoms or small molecules carrying an electric charge. Elements such as sodium, potassium, calcium, and chloride exist in cells primarily in this charged form. Though small, ions play essential roles in maintaining the cell’s internal environment and enabling many cellular processes.

And then there is water.

Water makes up about 70% of a cell by weight, and everything inside the cell exists within this watery environment. But this environment is anything but still. Water molecules are in constant motion—so-called Brownian motion—and this motion continually jostles ions, metabolites, and macromolecules alike.

As a result, the interior of the cell is not a quiet, orderly space. It is a crowded, dynamic environment where molecules are constantly moving, colliding, and reacting.

In the next chapter we take a deeper dive into proteins, the amazing mini machines (or factory workers) of the cell.