DNA Function

My last post covered the structure of DNA: what DNA is. In this post, I move on to function: what DNA does, or, maybe better, how DNA works.

I'll start, though, by quickly reviewing some points about structure. Recall that DNA is a polymer made of monomers called nucleotides. There are four different nucleotides that we refer to by their initials: A, T, G, and C. I also clarified that the double helix form of DNA is really two DNA molecules (polymers) intertwined and connected to each other by weak hydrogen bonds between complementary bases (that is, A bound to T and G bound to C).

Given complementary base pairing, if we were to walk down a stretch of DNA we could announce the letters as we passed: "ACCTCGGATAGATGC" etc. A code is embedded in these letters. But if we really think about it, there's no conscious entity inside a cell to read a code. The code works by shape. That's all there is, shape. It's the shape of the nucleotide bases that makes DNA work. Admittedly, this is a tough concept to get one's head around.

What's the purpose of the code? In short, making proteins. We've covered proteins. They're polymers, too, made of amino acids monomers. A protein is simply a linear array of amino acids. DNA is just a linear array of nucleotides. The two kinds of molecules are somewhat similar in design, which makes the one (DNA) coding for the other (proteins) possible.

The genetic code: Multiple three letter codi=os correspond to each amino acid. Note that the code is written with uracil (U) rather than thymine (T). This is because U is used instead of T in RNA. And when the code is actually put into use, it is "written" in RNA rather than DNA. Amino acids are listed using their shortened names (e.g. at the top left of the table, "Phe" stands for the amino acid phenylalanine.

If a cell wants to make some protein, it needs to know the order of amino acids. Fortunately, the cell's genomic DNA tells it the order. How? Using a genetic code that assigns every possible three-letter combination of nucleotide bases (called a codon) to a specific amino acid. The genetic code uses these three letter codons to build proteins.

A bit of an aside: Given that there are four different nucleotides and three different code positions, there are four to the third--that is, 64--different possible codons. If the goal is to have exactly one codon correspond to each of the 20 amino acids, then we have too many codons. But that ends up not being a problem. Most amino acids are identified by more than one codon. So there is what's called "redundancy" to the genetic code. Anyway, a two letter codon wouldn't work. It would only generate four squared--or 16--different codons, which isn't enough to identify all 20 amino acids.

With the genetic code, we likened a three letter codon to a word. Continuing the analogy, we can liken a gene to a sentence. A gene (sentence) is a linear string of codons (words) that has meaning. For example, if we have a piece of DNA 450 bases long, that would equate to 150 codons (450 bases divided by three bases per codon). And with a 150 codon gene, the cell can make a protein that's 150 amino acids long!

Now that we've moved on to genes, I need to make a few points. First, every gene starts with the same codon. It's called the start codon and it's ATG (AUG in the language of RNA). It's indicated in blue in the code table. The start codon also codes for the amino acid methionine (Met). So the first amino acid in many proteins is methionine, although in some cases that first methionine is removed after the protein has been synthesized.

Genes also have stop codons that identify their termini. Also from the table, we can see that there are three stop codons: UAA, UAG, and UGA. Once the code reader (a protein called an RNA polymerase that I'll discuss in the next post) reaches a stop codon, protein synthesis terminates.

Another important point: genes also have sequences close to them that regulate it--turn the gene on or off. These sequences are called promotors and they are typically near the start codon. So-called "regulatory proteins" (mentioned in a previous post) attach to promotor sequences not only to turn the gene on (i.e., make the protein it codes for) but also to control the degree to which the gene will be turned on .

Let me recap. A given gene codes for a given protein using three-letter codons made up of four different nucleotides that correspond to each of the 20 amino acids. Genes start with the codon ATG (the start codon) and end with one of three stop codons. Genomic DNA also includes sequences near gene start sites called promotors that play a regulatory role.

So far, I haven't talked about the process by which a gene makes a protein. That's the topic of the next blog post. Get ready to learn about transcription and translation. Both are amazing processes.