5. Tiny Machines (824) DONE

A typical human cell contains tens of millions of protein molecules, each carrying out a specific task. Some proteins cut DNA. Others build new molecules, transport cargo, or send signals from one part of the cell to another. Many are literal molecular machines—motors, pumps, switches, and clamps—operating at a scale far too small to see but performing the work that keeps the cell alive.

To get some perspective, proteins account for about 50% of the cell's dry weight. That's much more than DNA, which accounts for about 1-2%. It's also more than RNA, which accounts for about 20%.

The exact numbers vary by cell type, but the big picture is simple: about half of the cell's dry weight is proteins

But it isn't just their quantity. As I described, proteins are the workhorses of the cell. RNAs can play functional roles, too. But even when RNAs act directly, they usually do so as part of protein-RNA machines.

To keep our model of the cell simpler, we'll focus only on proteins.

Types of proteins

There are two broad types of proteins based on their purpose. Functional proteins perform tasks. They include enzymes, motors, receptors, and regulators. Functional proteins tend to be globular, or somewhat spherical in shape.

Structural proteins provide physical support. They give cells their shape. Structural proteins often take the form of elongated fibers. But there are exceptions.

Most proteins adopt a globular shape, even though they are actually long, linear molecules.

Many different proteins

The variety of different kinds of proteins in the cell is staggering.

A human cell can produce tens of thousands of different proteins, each folded into its own unique shape with its own unique task.

Much of protein diversity is due to the many kinds of functional proteins. There are roughly ten times as many kinds of functional proteins as structural proteins.

Functional protein roles

Functional proteins will be the focus of this book--more so than structural proteins. Many fall into larger categories. Here are a few.

Enzymes perform (speed up, really) specific chemical reactions.

Motor proteins walk along molecular tracks carrying molecular cargo from one part of the cell to another.

Signaling proteins attach to receptors on the surface of cells to, in effect, tell them to behave in a certain way--including to grow and divide.

Transcription factors attach to DNA near genes to activate them, or turn them on.

Nucleases act like scissors that cut DNA. Some--exonucleases--chew DNA from the end inward. Others--endonucleases--cut DNA at an internal position.

These are just a few of the roles performed by poroteinsin the cell. But what, actually, is a protein?

A chain of amino acids

How does the cell create thousands of completely different protein machines efficiently?

By using a limited set of subcomponents and mixing and matching them liberally.

Only 20 different amino acids--the subcomponents of proteins--are needed to build every protein in the human body. These 20 amino acids are all chemically different from each other, but also similar in that they all capable of attaching to each other in linear fashion.

On average, a human protein might be composed of 300-400 amino acids all lined up and connected. But they can range from 50 to thousands of amino acids long.

Beads on a string as an analogy for a protein's primary structure.

Imagine 20 different colored beads threaded onto a string. Any number of beads can be on the string. They can be in any order.

Each of the differently colored beads represents a different amino acid.

We'll call the protein's linear order of amino acids its linear structure.

From chains to tiny machines

A newly made protein chain doesn’t stay linear for long. Within milliseconds the chain twists, bends, and snaps into a precise three-dimensional shape.

This automatic folding occurs because different amino acids have different chemical properties. Some are positively charged; others are negatively charged. Some are large; others are small. Some are hydrophilic (attracted to water); others are hydrophobic (repelled by water).

Each amino acid responds to other amino acids in its local environment differently. This is what drives the folding.

We'll call the protein's folded form its folded structure.

This is the functional three-dimensional form of the protein--the form capable of doing the kinds of jobs just described.

Multi-protein complexes

Finally, in some cases, multiple folded protein structures assemble to form a multi-protein complex.

Multi-protein complexes can contain two, three, four, or five proteins. These are referred to as "dimers," "trimers," "tetramers," and "pentamers," respectively.

We'll be introduced to many very talented multi-protein complexes and individual proteins once we get into genome replication.

Thus, proteins are the tiny machines that perform most of the work inside cells.

But like machines in a factory, they do not operate in empty space. They work within a carefully organized environment filled with membranes, compartments, and other molecules.

To understand how protein machines operate, we first need to explore the components of the cellular factory itself.