Genes Are Like Sentences

I admit that I lose track sometimes of how the common genetic terms relate to each other. What’s the difference between a chromosome and a strand of DNA, for example? a gene and a genome? Are each of those three-letter sets in DNA a gene? I’m not a scientist, but I was an English teacher, so comparisons between genetic terms and units of written language—words, sentences, and so on—are helpful. Maybe they will be for you also.

Let’s start small. Diagrams of DNA include four letters: A, C, G, and T. These letters and the letter we write with are similar in some ways not in others. In both cases, they are the smallest units of their respective languages. But the four DNA letters stand for the four nucleotides—Adenine, Cytosine, Guanine, and Thymine—that are present in DNA, while the letters of our language stand mainly for the sounds we would pronounce if we were reading aloud.

In DNA, those four nucleotides, abbreviated as letters, make up the three-letter codons that are the DNA version of words. A difference is that the letters and words I am writing with don’t do the whole job. I also use punctuation marks, spaces, and capital letters to show where words and sentence begin and end.

In DNA, however, the three-letter codon-words are more efficient. They represent all the content—amino acids—and all the necessary divisions and instructions. No actual spaces separate the codons in a gene. Since all codons are three letters long, where they begin and end is automatic. (And in fact early writing in the ancient world lacked space between words also. As long as one could read slowly and figurethewordsoutspacesweren’tessential.)

chromosome (

Groups of these codons make up a gene, which can be compared to a written sentence. These gene-sentences say something like, “The hair will be red.” The sentence can also be read as a recipe: “Put this together with this and this to get red hair.” The codons for this and all genes include one that indicates where to switch on the gene and when, and another that says “Stop here; gene complete.”

Sometimes a spelling error occurs in one of the letters-nucleotides in a codon. Such a mutation may change the meaning of the gene to, “The hair will be white.”

To recap: the four nucleotides are the basic components much as the letters of our alphabets are; codons are DNA words; and a group of codons form a gene that is a sentence/recipe.

Now we come to chromosomes, genomes, and DNA itself.

The 23 pairs of chromosomes in each of our cells are like chapters in a strange book in which each chapter appears twice.  The number of genes in a chromosome runs from a couple of hundred to over a thousand, many of them about similar matters, like sentences in a chapter. In the 23rd chromosome pair, which determines sex, the two chromosomes are very different from each other about half the time: females have two X chromosomes, but males have an X and a much shorter Y chromosome.

Finally, your genome is like the book itself, the totality of all your genes on all your chromosomes. Your genome book is almost exactly like mine, since we are both humans, but about one tenth of one percent of our 20,000 or so genes are different. That’s similar to two copies of the same long book that differ only in a few sentences.

Finally, DNA itself. I think of DNA as similar to our writing system as a whole with all its symbols, spaces, and graphic conventions. DNA is not a unit as these other genetic terms are; it is the stuff that all these units are composed of. The same goes for our writing system.

And it’s interesting that writing itself, developed a few thousand years ago, is structured roughly like the genetic code that appeared with the first cells over three billion years ago. In communicating information over distance and time, whether it’s an email about a meeting next month or the genetic instructions for building a baby organism, it seems the key is a method to preserve the necessary groupings and sequencing of components.

The Pioneers: Archaea and Bacteria

For many years I shared the common belief that living things fall into three or four basic categories. Besides plants and animals, there are, I thought, one or two others groups that consisted of creatures too small to see, with names that varied over the years—Bacteria, Protists, Prokaryotes.

phylogenetic tree wikipedia

In this evolutionary genetic tree, animals and plants, in the upper right corner, are not the main limbs.         (Wikipedia)

Today there are still three categories, called Domains, but they are all too small to see. The only familiar name is Bacteria. Plants and animals are now small print in another Domain called Eukaryotes (you-CARRY-oats), meaning cells with a nucleus.

The third Domain is the Archaea. Archaea are like Bacteria in that they have no nucleus and are simpler, smaller and older than Eukaryotes. I’ve known so little about Archaea that I wasn’t even sure how to say the word. Either AR-kee-ah or ar-KY-a is acceptable. That noun is plural; the singular is AR-kee-on, an Archaeon, sounding faintly of Star Wars.

So how are these Archaea so different from Bacteria that they get their own subdivision? Biologist Carl Woese in 1977 argued they are indeed a different form of life. He showed that in much of their chemical make-up and their genetic sequencing, Archaea not only are distinct from Bacteria but are in some ways closer relatives than Bacteria to the Eukaryotic cells that form plants and animals.

I’ll describe a few features that Archaea and Bacteria have in common and then some features that are unique to Archaea. The information, from Wikipedia and elsewhere, is quite specialized and my renderings of it are admittedly general and selective.

Both Archaea and Bacteria are small, unstructured, and simple compared to the Eukaryotes that came after them. But one achievement they both share has been to try out nearly every possible chemical or environmental source to get their energy. Sunshine, salty water, temperatures ranging from volcanic to polar, even radioactive settings—varieties of Bacteria and especially Archaea have found ways to draw energy from, and live off of, these and many other environments.

Another similarity is that Archaea and Bacteria don’t reproduce sexually; two cells don’t mingle their genes to form a new individual that is slightly different from the parents. Instead, individual cells just multiply themselves by two and then divide to form identical clones. But despite their reproductive sameness, they had—and have—a different trick for switching up their DNA. A Bacterium or Archaeon can pump some of its DNA into another cell. Or a cell can just pick up a bit of DNA floating near it. No merging, no swapping, just fresh ingredients. It’s one reason that antibiotic-resistant bacteria in hospitals can spread their immunity to other bacteria so quickly.

archaea hot springs yellowstone nationa park (

Archaea at home in a Yellowstone hot spring.       (

This gene-sharing is called lateral gene transfer, and it has an interesting feature. It doesn’t have to take place between members of the same species. For animals and plants, sexual reproduction, to be productive, almost always takes place within one species. But DNA can be transferred from any Bacterium or Archaeon to any other variety in those Domains if the conditions are right. If plants and animals could do that, the mind boggles. You might see squirrels transferring some of their DNA into dandelions. Or vice-versa. Such promiscuity makes it easier, I think, to imagine how Bacteria and Archaea have evolved in so many different kinds and colors in so many different environments.

Despite their similarities, though, Archaea are distinct from Bacteria in notable ways. Archaea were first discovered in extreme settings where Bacteria fear to tread: geysers, intensely salty water, even thermal vents at 251 degrees F, the hottest place any organism has been found living. Another feature is that, while some varieties of both Archaea and Bacteria get their energy from light, Archaea do it their own way, through a process unrelated to the photosynthesis that Bacteria passed on to plants. Importantly, too, only Archaea produce methane, essential to organic decomposition. Finally, while many Bacteria can make us sick—think Lyme, Cholera, Syphilis—Archaea may be nicer; no pathogenic Archaea have been discovered, so far.

Archaea and Bacteria had the Earth to themselves for well over a billion years. Then about 2 billion years ago, Eukaryotes appeared, evolving from their single-celled predecessors but larger and internally more developed. By then, Archaea, like Bacteria, had carried out much of the groundwork for living, pioneering what it takes to survive in different conditions, experimenting with energy sources, trying out each other’s genetic parts.

And they succeeded. They didn’t fade away after the sophisticated Eukaryotes began evolving into countless large species. Today, the total mass of Archaea and Bacteria on earth is at least equal to the mass of all the plants, animals and other organisms together. They got the basics right.

Is DNA Alive?

No, it’s not alive…mostly. The only sense in which a DNA molecule is a living thing is that it makes copies of itself, although it can’t even do that on its own. Otherwise, DNA fails all the tests: it doesn’t process any kind of fuel in order to maintain its state, it doesn’t grow and develop, so it has no energized activity that starts or ends—in other words, it’s not born and it doesn’t die.

Somewhere along the line in reading general science I picked up the impression, even though I think I knew differently, that DNA strands are alive. They are such vital keys to living organisms, and I’d read so many descriptions of what DNA does and of “selfish” genes, that although I knew they were blueprints of a sort, they came to seem like living blueprints.

DNA and seed (

DNA and seed

One image that took shape in the back of my mind was that DNA was a kind of seed, and seeds, I thought, are alive. But no, seeds are not fully alive either. They are not active and, until they germinate, they don’t change or develop. (Another familiar item that may seem alive but that doesn’t meet all the criteria are viruses. Viruses are bundles of DNA that become active only when they are inside a cell, at which point they take over the cell and give us the flu.)

It shouldn’t be surprising that some familiar biological components do not, by themselves, meet all the criteria for the complex condition we call “being alive.” Still, surprised I was about DNA. Perhaps because we humans are so fully aware that we are alive, it is easy to think that there must be a fully living seed or even a soul at the root. It is almost more than we can imagine that the liveliness we feel is the product of a complexity of non-living parts. It’s an astounding thing.