Genes Are Like Sentences, Genomes Are Like Books

I lose track sometimes of exactly what the common genetic terms mean and how the genetic pieces work together. What’s the difference between a chromosome and a strand of DNA? A gene and a genome? What are those three-letter sets in a DNA diagram called and what do they do? I’m not a scientist, but since I was an English teacher, connecting the names of genetic units to the units of written language—words, sentences, and so on—makes the picture a little clearer.  Maybe it will do the same for the reader.

Let’s start small.  The spiraling rungs on diagrams of a DNA (deoxyribonucleic acid) molecule are each marked with two of four specific letters: A, C, G, and T.  The four DNA letters stand for the four nucleotides—Adenine, Cytosine, Guanine, and Thymine—that make up DNA. Like the letters of the full alphabet, these letters–or rather the four molecules they indicate–are the smallest building blocks of their language.

codons

moodle.clsd.k12.pa.us

In DNA, combinations of the letters for the four nucleotides make up the three-letter codons that are DNA’s version of words. Each three-letter codon/word specifies one amino acid. And most codons are “synonyms” in that several different codons refer to the same amino acid because there are many more codons than there are amino acids. The codons are “read” by a ribosome, a cellular reader/assembly-machine that produces the required amino acid and attaches it to the chain of amino acids that will form a protein.

Groups of these codons make up a gene, much as words make up a sentence. The genes/sentences are long because most proteins are complex; human proteins consist of anywhere from several hundred to several thousand amino acid molecules.  The gene/sentence for red hair says something like “Put this together with that and that and that….”

Genes also include a codon at the start that says “Start the gene here” and another at the end that says “Stop here; gene complete.” Within the gene, however, no actual spaces separate the codons, but since all codons are triplets, it’s always clear where codons themselves begin and end.  (Somewhat similarly, writing in the ancient world often lacked spaces between words.  As long as one could read slowly and figurethewordsoutspacesweren’tessential.)

chromosome (mayoclinic.org)

mayoclinic.org

So, to recap.  The four nucleotides are basic components much like the letters of our alphabet. Groups of three nucleotides spell out codons that can be thought of as words, which in this case are actual amino acid molecules.  And a sequence of codons/amino acids forms a gene that resembles a sentence in a protein recipe for some aspect of the organism.

Finally there are chromosomes and genomes.

A molecule of DNA is very long, a continuous strand of anywhere from a couple of hundred to more than a thousand genes, many of them about related aspects of the organism. Each molecule is a chromosome which, because its genes concern similar aspects of the body, can be compared to a chapter in a book.  But it is a strange book in that each chapter appears twice, in anticipation of the day when the molecule/chapter reproduces itself. Each human cell contain 23 such paired chromosomes, duplicate copies of the assembly instructions for an entire human being. Only the chromosome pair that determines sex contains chromosomes that are different from each other about half the time: females have two identical female chromosomes while males carry one female and one male chromosome.

Finally, our genome is like the book itself, the totality of all our genes on all our chromosomes. The book might be called Me And Us. Your genome book is almost exactly like mine except for about one tenth of one percent of our 20,000 genes that are different. That’s similar to two copies of the same long book that differ only in a few sentences.

Simplified though the comparison is, it’s startling what genetics and written language have in common considering that the second is a recent human invention and the first represents the formation of life almost four billion years ago. Both are composed of the smallest building blocks, then the groupings created from the building blocks, then the meaningful statements/instructions/recipes coded in the groupings, and finally the conversion of the code into organic construction/action/speech.

Our Actual “Eve”

She lived about 150,000 years ago in southern Africa. These days she is known as Mitochondrial Eve. The “Eve” part is a little misleading since unlike the Biblical Eve, Mitochondrial Eve wasn’t the first or only woman alive at the time, and there were also plenty of men around. Still, Mitochondrial Eve was an actual person to whom every human today, male as well as female, can be traced back on his or her mother’s side—from mother to mother’s mother and so on.

But interesting as such a linkage may be to scientists, how significant is Mitochondrial Eve for us? See what you think.

Mitochondria in a cell (Flickr)

Mitochondria in a typical cell. The long thread of genetic DNA in the nucleus is shown, but the unrelated DNA inside the mitochondria is not. (Flickr)

Mitochondria (my-de-KAHN-dree-ah) are particles inside of cells that produce energy for the cell. Originally independent cells themselves, mitochondria were engulfed by larger cells long ago, proved useful, and made themselves at home.

When they did so, mitochondria brought with them their own bits of DNA. These strands are not related to, and are much smaller than, the complex DNA in a cell’s nucleus that make up our genes. But like all DNA molecules, as mitochondrial DNA makes copies of itself, it sometimes mutates; copying errors occur and the DNA changes slightly. As a result, mitochondrial DNA, handed down through generations of female humans, forms a record of our ancestry separate from our genes.

If this is difficult to visualize, a rough analogy is the battery in a car. These 12-volt energy-units that power the starter motor come in different brands with serial numbers and other codes on them. Over the years, independently of changes in cars themselves, battery manufacturers make changes to car batteries. Now imagine that you had no other way of telling the age of a car that had, say, been crushed beyond recognition. One option w ould be to dig out what was left of the car battery to find its codes or numbers. The car battery would date the car.

But if a particular version of mitochondrial DNA is passed down through women, how is it that males also carry it?  Because this DNA comes in the cell that each human grows from, and that cell is our mother’s. Fathers, through their sperm, contribute some of the genetic DNA that creates the new person, but the cell that begins to divide and multiply is mom’s, complete with her formulation of mitochondria DNA.

At the time that Mitochondrial Eve lived, of course, other mothers were passing along their own mitochondrial DNA to their own children, to their daughters’ children, etc. What happened to all those versions? Why is it that today’s humans everywhere carry the same version, the same mutation, of mitochondrial DNA? Apparently all those other lines of mitochondrial DNA fizzled out. Some mothers bore only sons, with no daughters to carry on their cell line. Other women had no children at all. The single remaining “brand” of mitochondrial DNA has been traced back to an approximate place and time five thousand generations ago. It is as if over the years all brands of car batteries went out of production except one, and that one is now installed in all cars.

What are we to make of all this? Compared to the Biblical Eve and her list of firsts—first woman, first human to be curious, first mother—Mitochondrial Eve wasn’t a forerunner of any of our significant traits. It’s that other  DNA, the genetic DNA from our mother and father, that plays a role in the color of our eyes and our musical aptitude.

Still, as biomedical historian Siddhartha Mukherjee puts it The Gene: An Intimate History:  “I find the idea of such a founding mother endlessly mesmerizing.”

It is mesmerizing to know that a small identifier in each of us can be traced back to a single human mother long ago. In theory, any diverse group of living things has a common ancestor after whom its descendants branched off. But that common ancestor may be difficult to “relate” to. The ancestors of all primates (not only humans but also monkeys, baboons, and chimps) lived about 60 million years ago and looked something like a squirrel with large eyes. I don’t feel the warmth.

On the other hand, I like the idea of being descended from a mother a long time ago from whom all other humans today are matrilineally descended as well, and whom we could, if we saw her, recognize as one of us.