8. Central Dogma -- Part I (1,048)

If DNA is locked away in the nucleus, how does its information get out and turned into something the cell can use--namely, a protein?

Francis Crick of Watson and Crick double helix fame tackled this question and, in 1958, came up with an answer and a simple drawing to go along with it. He called his idea molecular biology's central dogma.

Central dogma

Crick originally presented central dogma as a law-like generalization or regularity. At it's core, it's a diagram of how information flow in cells. But remember that what looks like a simple diagram has to work inside a crowded, constantly moving cell. 

The figure below shows my version of Crick's central dogma diagram.

Moving from left to right, the first arrow represents replication, the copying of a DNA molecule, or chromosome. We’ll return to later, as it's the focus of the last half of this book.

The next arrow represents transcription, in which a cell makes an RNA copy of DNA (specifically, an mRNA copy) using the enzyme RNA polymerase. This, too, occurs in the nucleus. Most of the resulting mRNAs are exported through pores in the nuclear membrane into the cytoplasm.

When the mRNAs get to the cytoplasm, the cell uses them to make proteins in a process called translation. Large protein-RNA complexes called ribosomes perform this feat. They're found both diffusing in the cytoplasm and embedded in the ER membrane. 

The "why" of transcription

Every human cell has two copies of the nuclear genome (one from each parent). These are master copies, well-protected inside its nucleus. But the cell must access the information in these genomes constantly.

It does so using mRNAs. These photocopies of genes are generated in the nucleus and then exported to the cytoplasm where they are used to synthesize proteins. mRNAs are effectively an intermediary between the genome and protein synthesis. But why go through an intermediary at all? Why not use the DNA directly?

Using mRNA as an intermediary has significant benefits. It allows the cell to separate information storage in the nucleus from information use in the cytoplasm. Also, mRNAs are short-lived. Thus the number of mRNAs in the cytoplasm can be regulated depending on the cell's needs. The cell just ramps transcription up or down in the nucleus.

In fact, to ramp up, a single gene might be covered with polymerases, each at a different stage, producing a steady stream of transcripts. Think of beads moving along a thread.

mRNAs can also be edited, or spliced, before being used, which increases the number of different proteins that can be generated from one gene. We'll cover the magic of splicing toward the end of this chapter.

The "how" of transcription

Like everything else that occurs in the cell, transcription is tightly controlled and coordinated with other cellular activities. 

To begin the process, RNA polymerase and helper proteins assemble at the promoter, open the DNA, and begin transcription.

The promoter marks where transcription begins. Promoters sit within a broader regulatory landscape that includes nearby and distant DNA elements.

As the polymerase moves, it builds a complementary mRNA strand onto the DNA template strand. No one directs this process. It simply emerges from the interactions between the polymerase, the DNA, and surrounding molecules.

One detail is easy to miss: RNA polymerase doesn't move along the strand that codes for the protein. It moves along the opposite strand--the template strand--in the 3′ to 5′ direction. As it does, it builds the mRNA in the 5′ to 3′ direction.

As the RNA polymerase moves along the DNA, the mRNA gradually peels away and the double-stranded DNA re-anneals behind it.

Eventually the RNA polymerase reaches a set of signals that lead to termination. They tell theRNA polymerase to stop copying and release the RNA transcript into the nucleoplasm. 

The process of transcribing a gene takes from seconds to minutes.

Processing the mRNA

Up to now, we’ve treated the mRNA as if it were ready to use once it's transcribed. 

It isn’t.

The mRNA first generated by RNA polymerase is a pre-mRNA. A pre-mRNA must be acted on to create the final processed mRNA that's used to make a protein. 

Processing has three steps.

First, the cell adds a 5′ cap to protect the mRNA from degradation. 

Second, post-transcription most human mRNAs have a poly(A) tail—usually 50–250 adenines long--added to their 3′ ends to stabilize the molecules and help them leave the nucleus. 

The poly A tail shrinks little by little as the mRNA is used to synthesize proteins. When the polyA tail gets too short, the cell degrades the mRNA.

Third, and finally, there is mRNA splicing, or editing.

Up to this point, we've assumed that the transcribed region of a gene is simply a long string of codons. But, again, it's not that simple. 

Within the transcribed region of a gene are sequences that don't actually code for the protein. The coding portions of a gene are exons; the intervening sequences are introns.

The mRNA that's produced by the RNA polymerase--the pre-mRNA--contains all the gene's exons and all its introns. Then, post-synthesis, the mRNA is processed. The introns are removed and all or some of the exons are spliced together. 

The final mRNA, then, consists of exons connected to each other and no introns.

Why does the cell do this? 

It enables the cell to construct many different proteins from a single gene. It accomplishes this by mixing and matching exons in a modular manner. A quick example:

Imagine a gene with a transcribed region that consists of six exons separated by five introns. In one case, a protein might be produced by splicing together all the exons (exons 1-6). But another protein with a slightly different activity might be made by combining exons 1, 3, 4, and 6, etc.

Most human genes contain introns, and many can be spliced in different ways. And the cell selectively produces the variants it needs in a given context. 

Realize that the splicing of the exons to each other must be incredibly precise. Even a one-base error would shift how the three-letter codons would be read and scramble everything that follows. Yet this process works reliably.

By the time transcription and processing are complete, a usable message has emerged from a much longer and more complex sequence of events--without any central plan. 

In the next chapter, we’ll remain focused on central dogma to see how that message is turned into a working protein.