RNA polymerase: The cell machine that transcribes. What is a gene?

The cellular machine responsible for transcription is a protein enzyme called RNA polymerase.

RNA: because it catalyzes the creation of RNA

Polymerase: because it joins RNA nucleotides (ribonucleotides) together into a string. Polymer is a general chemistry term to describe a chemical string of one or more reoccurring building blocks.

Just as RNA polymerase is involved in expressing the genes that were produced by your engineered E. coli, RNA polymerase itself is expressed from a gene in the genome of the cell. That means RNA polymerase is involved in creating itself!

As you’ll see later in this chapter, RNA polymerase is able to bind to a DNA strand (Figure 4-21). It can then ride along the DNA like a train on tracks, and simultaneously create (transcribe) an RNA molecule.

Figure 4-21. Artist view of RNA polymerase protein (blue green) bound to a DNA strand (orange) and transcribing RNA (red)

Compared to the width of the DNA strand, RNA polymerase is much wider and is able to surround the strand of DNA. In Figure 4-22, the RNA polymerase (pink) surrounds a piece of DNA (orange/blue). Unlike the artist’s depiction in Figure 4-21, Figure 4-22 is a mathematical model based on real data of RNA polymerase bound to DNA. So while you don’t see a full DNA strand passing through the RNA polymerase, this illustration provides a very real perspective on the size of RNA polymerase compared to DNA.

Figure 4-22. Crystal structure of RNA polymerase (pink) bound to a DNA helix (orange/blue). When operating within the cell, the DNA continues through RNA polymerase, and an RNA strand protrudes out the surface

In coming sections, we will go into much deeper detail about how RNA polymerase knows where and when to start and stop transcribing.

What is a gene? A gene is one of the most talked about, but least understood, topics in education. A gene is a length of DNA that has all the DNA sequence the cell needs to read and begin the Three Steps to Microfacturing. In other words, a gene is a length of DNA that results in the creation of an end-product that has a function, like RNA or a protein.

This means a gene must have information embedded in the DNA sequence to start and stop the Three Steps to Microfacturing and to create a cellular product with a function. In other words, a gene is a length of DNA that can tell the cell machinery (RNA polymerase) when and where to start the Three Steps to Microfacturing as well as what to make. Let’s look deeper at how it works.

Just like a sentence has a structure or “syntax”, such as a subject-verb-object, genes have a grammatical order. Two kinds of information are stored in a gene’s DNA sequences. They are called “non-coding sequences” and “coding sequences” (Figure 4-23). These are both just plain old DNA. The RNA polymerase is able to distinguish between them.

A non-coding DNA sequence is a segment of DNA that acts as a switch, controlling when and how much product is made from the gene. The non-coding sequence has the right characteristics to bind ‘transcription machinery’, and it acts as the starting point of transcription. Consider The Four B’s of Cell Operation: Bump, Bind, Burst, Bump. If the non-coding DNA sequence is unable to bind the transcription machinery, then transcription doesn’t happen. Conversely, if the DNA sequence has the right shape and charge to bond to the transcription machinery, RNA polymerase binds to the DNA more frequently, and transcription can occur.

In the hands-on exercise, you engineered your cells by adding a DNA plasmid that contains a gene for creating protein color pigments. Within that gene is a non-coding sequence designed to bind with a cell’s transcription machinery -12 hours after the cells start growing and keep transcribing it thereafter.

A coding DNA sequence is a sequence situated immediately next to the non-coding DNA. It is read and transcribed by the transcription machinery into RNA. The coding DNA sequences are like the designs for the functional end-product that will be made from the gene. The non-coding DNA sequences are like the switch telling the cell where and how frequently to transcribe the coding DNA sequence.