The Mysterious World of the Human Genome

by Frank Ryan

  It was now becoming increasingly likely that if DNA was the stored code for heredity, and somehow was translated into the amino acid sequences that made up proteins, RNA had something to do with the actual manufacture of those translated proteins. It was easy to see how a stretch of DNA could make an RNA copy—all it would take is for the thymine, or T, of DNA to be replaced by uracil, or U, during the copying. As early as 1947, two Strasbourg-based scientists, André Boivin and Roger Vendrely, had already proposed that the GACT-based sequences of a DNA gene would be copied in this way to the GACU-based RNA messenger, which would ferry the coding out into the cytoplasm where the corresponding proteins would be manufactured at the ribosomes. All that was left was to figure out how the four letters of GACU could translate to the 20-letter amino acid code of the proteins.

  Crick was intrigued by a letter from a Russian theoretical physicist, George Gamow, which arrived out of the blue in the summer of 1953, soon after Crick and Watson had published their first iconoclastic paper on the structure of DNA. Gamow, who was part of the group who had come up with the “big bang” theory for the origin of the universe, had been intrigued by the double helix. In his letter he proposed a way in which the four-letter code of DNA might translate to the amino acid primary sequences of proteins: triplets of the four nucleotides—G, A, C, and T—might code for single amino acids. But to Crick this didn't add up. Sixty-four different triplet assortments would result from the random mixing derived from four coding letters, whereas there were only 20 amino acids found in natural proteins. Gamow had thought this through, proposing an ingenious overlap of the triplets, so that what coded for one amino acid might in part code for another. Crick didn't buy it, but he and Watson took Gamow's letter with them when they retired, as usual, to the Eagle for lunch. If nothing else, Gamow's intervention provoked the DNA pioneers into a renewed debate on how the DNA-to-protein mystery might be cracked.

  There would be little further opportunity for them to swap ideas that year once Watson left Cambridge for America. In fact, there would be little progress in the mystery for a number of years.

  In the summer of 1954, Crick and Watson teamed up again for three weeks at Woods Hole, Massachusetts. Gamow and his wife were there. Most afternoons, Crick and Watson would join the Gamows down by the water's edge, watching the Russian physicist do card tricks and chatting about the same mystery. In the interim, since writing the letter, Gamow had collected together the names of a number of people interested in solving the problem. Somehow or other, and it was likely that both Watson and Delbrück were at the heart of the joke, a “whisky, twisty RNA party” was called for, with invitations presumably addressed to parties interested in the enigma. This became the inspiration for what came to be called the RNA Tie Club, limited to 20 members, to parallel the number of amino acids. In addition to Crick, Watson, and Gamow, the club members included Martynas Ycas, Alex Rich, and an Oxford-educated South African, Sydney Brenner. In the spring of 1953, Brenner had been one of a party of young scientists who had driven over from Oxford to Cambridge to see Watson and Crick's 3-D model of DNA. At the time, Brenner was conducting a bacteriophage project for his PhD in molecular biology. In a garden stroll with Watson, Brenner had learned about the Hershey–Chase experiment. These days he was working as a post-doc at the Medical Research Council's Molecular Biology Laboratory in Cambridge, but he had maintained that early interest in DNA and genetics. Each member of the club received a tie, made to Gamow's design by a haberdasher in Los Angeles. The ties in turn were pinned by individually designed short forms of each specific amino acid—Crick's pin read “tyr” for tyrosine. It was all a fantasy; the club never met, but, like the phage group, it acted as a rallying focus for the group, who would circulate any papers or news of common interest to members. In the words of British journalist and author, Matt Ridley, who wrote a biography of Francis Crick, the English scientist was “the dominant theoretical thinker…the conductor of the scientific orchestra.”

  Brenner showed, mathematically, that the overlapping triplet idea was a non-starter. Crick and Leslie Orgel were joined by Crick's friend and collaborator, the young Welsh mathematician John Griffith, who tried his hand at ruling out specific triplets of the four letters that simply would not work. For example, they ruled out AAA because it would cause confusion if positioned next to another identical letter, A. By excluding triplets that would cause confusion, they calculated that it only left 20 “sense” permutations. This was duly published as a paper in the Proceedings of the National Academy of Sciences in 1957. Unfortunately, it was utterly wrong.

  Nevertheless, by now some useful ideas were beginning to emerge.

  A gene, with its long thread-like molecule, made up of a specific sequence of G, A, C, and T, often a thousand or more letters long, coded for a specific protein whose primary structure was again a long thread, made up of the 20 amino acids in a very specific sequence. They even knew by now that sickle-cell disease, in which there was an abnormal oxygen-carrying hemoglobin in the red cells, was caused by a mutation in the gene that coded for the beta globin. The mutation in the gene had translated into a faulty coding for the hemoglobin protein. Crick now focused on ideas that were coalescing from several different quarters, which boiled down to the fact that there were likely to be two quite different forms of RNA involved in the translation from nuclear-based DNA genes to the coding for protein assembly in the ribosomes. One form—now called messenger RNA, or mRNA—copied the code from the entire gene in the chromosomes within the nucleus and carried the code out of the nucleus to the ribosomes. Interestingly, messenger RNA was found by a group of researchers at Harvard, working in Watson's new laboratory there. Meanwhile, a second form of RNA, called transport RNA, or tRNA, picked up single amino acids and, guided by the coding carried on the messenger RNA, added the right amino acids, one by one, to the assembling protein chain. In this way, the nucleic acid coding of the gene translated to, and was ferried into, the ribosomes to construct the corresponding protein chain.

  The coding triplets were eventually discovered through trial and error by scientists including Marshall Nirenberg, Gobind Khorana, and Severo Ochoa. Today, we know that triplets of nucleotides, now called “codons,” code for specific amino acids, but a single amino acid can have more than one corresponding codon. For example, the amino acid leucine has six different triplet codons: CTT, CTC, CTA, CTG, TTA, and TTG; phenylalanine has two, TTT and TTC; while methionine has just one, ATG. Moreover, there are specific triple permutations—TAA, TAG, and TGA—that code not for amino acids at all but for the genetic equivalent of a full stop. These halt the production of a protein at the full stop, and so are known as “stop codons.”

  This was another major step in understanding, but, once again, it raised new questions. The factory-like mechanisms of protein production had to be controlled. How did a cell decide which protein to make? How did it decide when to make the specific protein in the life of the cell? How did it turn protein production on and off?

  We might recall the group who had earlier contributed to the Watson–Crick discovery (a world-based cooperative of scientists working with the viruses that infect bacteria), the phage group. A trio of Paris-based scientists, André Michel Lwoff, Jacques Monod, and François Jacob, were conducting research on phages and their host bacteria at the Pasteur Institute. They focused on the bacterium that was the host for all of the phage experiments, a bug called Escherichia coli—E. coli for short—which is the bacterium most commonly found in the human intestine. What interested them, to begin with, was a discovery made by their American colleagues Joshua Lederberg and Edward Tatum, which suggested that, contrary to the prevailing ideas, bacteria had a kind of sex life. Normally bacteria reproduce asexually through a daughter bacterium simply budding off the maternal strain—rather like one sausage being squeezed off in the middle to form two—but now and then a bacterium would fashion a penis-like extrusion through which it would inject its genetic material into another bacterium. The
scientists jokily referred to it as “coitus.”

  In 1955, Jacob, working with a colleague called Élie Wollman, explored the way in which genetic information was passed on from one bacterium to another. Realizing that bacteria had genes made up of DNA, just like all other life-forms, they also knew that the bacterial genes were threaded along a single lengthy chromosome that took the form of a ring, which had a point of attachment to the inside of the bacterial wall. Jacob and Wollman now discovered that during coitus the chromosome was very slowly extruded from the “male” and through the cell wall into the body of the “female” bacterium. While bacterial reproduction by budding took only twenty minutes, bacterial sex lasted for roughly two hours. This allowed Jacob and Wollman to conduct a series of “coitus interruptus” experiments in which they halted the process at timed intervals along the two-hour process. Since the bacterial chromosome always came through in the same order of genes, they could, through looking for the effects of specific mutated genes, plot where along the course of the bacterial chromosome the genes for various different properties were located.

  But now the French scientists took the experiment a step further; they set out to discover how those genes were controlled within the bacterium.

  They focused on three genes that allowed the bacterium to transport the sugar, lactose, into the body of the bacterium and there digest it into its two smaller component sugars, glucose and galactose. It would be wasteful for the bacterium to activate these genes all the time, even when there was no lactose in its environment. What they discovered was that the genetic chemistry operated a system of control. When there is no lactose around, this triggered the activation of a “repressor,” which halted the production of the three relevant genes. When lactose was present, the repressor was removed and a genetic area alongside the genes, known as the “promoter,” activated the expression of the genes.

  We don't need to worry about the precise genetic details. All we need to grasp is that there are regulatory systems that switch genes on and off in every life-form. Moreover, these systems have ways of detecting key signals coming from outside the genome—in the above case they are capable of detecting the presence of the sugar, lactose, in the bacterial environment. This was the first scientific demonstration of what we now call genetic “regulatory” control. It would result in Lwoff, Monod, and Jacob sharing the Nobel Prize in Physiology or Medicine in 1965.

  The time has come to introduce a little magic. What I have in mind is a maiden voyage in a mystery train. Imagine that we have shrunk to ultramicroscopic size—a thousand times smaller than a retrovirus, so that a human cell would appear the size of a major city and where the individual nucleotides that make up DNA are easily discernible. We can, in the blink of an eye, climb aboard the most exciting part of it, the chugging engine.

  With a toot on the whistle, we are off. Up ahead we see a glowing spiraling shape, a spectacularly beautiful double helix, spinning away through the ether from left to right. As we approach, the double helix flattens out, still glowing, still running across the dream-like landscape in horizontal fashion, from left to right. We now see that it takes the form of a railway line, with twin rails spaced by closely set horizontally placed sleepers. For a dizzy moment or two, we gaze on the extraordinary structure of DNA from this close. Then I slow the engine down to a halt. We are now hovering in a steam-filled stillness immediately above the railway line. We hop out so we can take a good look at where we are.

  We take a short stroll along the glowing DNA molecule in the direction that the now-stationary train is pointing.

  What we took to be rails are actually banded structures, made up of alternating four-pointed stars and pentagons at right angles to the sleepers. The sheer gorgeousness of it is overwhelming. The stars and pentagons are made up of glowing spheres connected by lines of force.

  “So,” you gaze a little closer, in what I imagine to be the same wonder that I am feeling, “the spheres are the atoms that make up the component molecules?”

  “Yes.”

  “The crosses and pentagons…?”

  “The pentagons are the deoxyribose sugars. The stars are the supporting phosphate molecules.”

  “Between them they make the rails?”

  “The phosphate stars make up the external spine that Watson and Crick argued about. Each sugar connects the phosphate spine to a sleeper.”

  “The lines of force between the atoms are the stable covalent bonds?”

  “Yes. The phosphates hold the whole thing together. The sugars are the connection between the spine and the sleepers. Time, perhaps, to take a closer look at the sleepers.”

  I allow you the leisure of a stroll along the track, examining sleeper after sleeper.

  “The sleepers are attached to the inner angles of every sugar pentagon?”

  “Take a closer look at them…”

  “There are two shapes, joined together in the middle.”

  “Two complementary nucleotides, yes—but the join is not exactly in the middle.”

  “It has to be a trifle eccentric since the complementary nucleotides are unequal. This join here is closest to the upper rail. In the following sleeper it is closer to the lower rail.”

  “The purines, guanine and adenine—G and A—are wider because they contain two contiguous atomic rings. The pyrimidines, thymine and cytosine, are shorter because they only contain a single ring.”

  “So, one way or another, the sleeper is always made up of a purine and a pyrimidine?”

  “Yes. It has everything to do with shapes. Take a good look at the junction in the middle of the sleepers. Look at how the shapes of the nucleotides meet. Does it remind you of anything?”

  “It's like the meeting of two pieces of a jigsaw puzzle.”

  “Exactly.”

  “So that's why they are complementary?”

  “Absolutely. And now you know why the molecule has to be constructed exactly as it is.”

  “So the real DNA—the nucleotides—is like beads on the string of phosphates and sugars?”

  “No. Another scientist, I think a mathematician, said exactly that to Crick. But he was wrong. Crick told him that DNA was itself the string.”

  “The DNA has to include the phosphates and sugars, as well as the nucleotides?”

  “The construction has to be the whole thing, exactly as it is. Can you see why?”

  You take another short stroll, getting the hang of this idea. “So, the nucleotides, the bases, don't make contact along the thread?”

  “Their only meeting point is one-to-one within the sleepers. And always with their complementary partner, A to T, and G to C, or vice versa.”

  You gaze down at this wonder, blinking for a moment or two. “So the code lies in the sleepers?”

  “That's right. And the sleepers also explain how the code replicates to form a new daughter strand of DNA. They also explain how code of protein-coding genes translates to proteins. What you need to grasp is the code is contained in just a single rail. In this case, if we take the uppermost of the two rails, the code is in the sequence of the uppermost portions of the sleepers. You can read it off if you stroll along the rail and name each nucleotide as you come to them, like a series of letters.”

  “I'm reading them: A, A, C, T, G, C…I think I'm getting the picture. But why then is there a second rail?”

  “The code has already copied itself to a daughter thread. What you see on the opposite rail is this copy.”

  “Ah! So—the double helix is actually two copies of the coding DNA?”

  “Yes, two complementary sequences. Would you like to see it copy itself?”

  “I'd love to see that.”

  We stand back and our engine evaporates. The line begins to vibrate.

  “What's happening?”

  “To copy itself the double helix must part into its two component halves. This normally happens through the action of an enzyme, but it can be done just by heating the system up. Heat adds enough r
andom energy to break open the bonds within the sleepers.”

  “So those bonds holding the sleepers together are not stable?”

  “No. These are the relatively weak hydrogen bonds we came across when talking about Linus Pauling and his study of chemical bonds.”

  As we watch, the sleepers come apart, like pieces of a jigsaw separating. A cloud-like mass appears out of the distance and it begins to move over the now-separated upper rail, with its exposed half sleepers.

  “What's that?”

  “The cloud is an enzyme—a protein called a synthetase that helps DNA to replicate.”

  We watch as the cloud moves along the detached rail, from east to west. It appears to discover the nucleotides it needs from the teeming background, and as it passes along, it attaches the complementary nucleotides, A to T, C to G, T to A, G to C, then some other element in the cloud, perhaps another enzyme, or enzymes, grabs the necessary phosphates and sugars to make up the spine.

  You're too dazzled by the speed at which the cloud is shuttling along to say a word. In what seems no more than a few moments, the hive of activity has long passed us by, and the new twin track is there before us and gleaming into the distance.

  “That's it?”

  “Almost. I have one more point to make before we head for home. First we need to take a journey along this new stretch of track.”