Key to Life
The ABCs of DNA
What do a patch of lichen struggling to survive on a dry boulder, a giant squid swimming two miles undersea, a grizzly bear munching blueberries in the Canadian Rockies and you, a book-reading mammal, all have in common? The answer, of course, is life. And that crucial quality of aliveness, that shared something that makes the lichen, the squid and you different from a rock, a button or an automobile, is DNA. In a very real sense, DNA is the key to life. And also, to each particular life.
In the classic movie version of The Wizard of Oz, Bert Lahr asks "What makes the Hottentot so hot? What puts the ape in apricot? What have they got that I ainÕt got?" The answer, for LahrÕs Cowardly Lion, is "courage". But for modern biologists, the key to specialness is more likely to be "DNA".
What do all mammals have in common? Most of us will answer: hair, warm-bloodedness and lactation. But thatÕs not all. All mammals share mammalian DNA, the genetic wherewithal that distinguishes us from birds , reptiles or fish. And what makes you and me human is Ñ you guessed it Ñ human DNA. Human beings share about 90% of their DNA with the rest of the living world, and approximately 99% with our closest non-human relatives, the chimpanzees. Whatever it is that makes us uniquely human thus resides in that less-than-1% of our DNA that we share only with other human beings. And what makes us individually unique Ñ our personal claim to biological specialness Ñ must therefore exist by virtue of even smaller snippets that we can call our own. Our DNA, our selves.
"If the property of complexity could somehow be transformed into visible brightness," wrote molecular biologist John Platt in The Step to Man, "the biological world would become a walking field of light compared to the physical world . . . an earthworm would be a beacon . . . human beings would stand out like blazing suns of complexity, flashing bursts of meaning to each other through the dull night of the physical world between."
Although it is possible to imagine alternative worlds in which lifeÕs complexity has developed around other classes of molecules, at this point, DNA and its allies have cornered the market on aliveness. It is DNA that determines why roses are red and violets blue, what it is that makes humans human, and hummingbirds hum. (Whether it also puts any ape in apricot is subject to debate.)
DNA is important, however, not only for its basic role in defining and creating life, but also as a star player in current and future events. If there is a single molecule that stands for all that is new and exciting Ñ as well as confusing and troublesome Ñ in modern biology, it is DNA. It is the closest we have to a master molecule, one that must be understood if we are to understand ourselves and the life around us, as well as some of the most dynamic frontiers of science.
In this chapter, we begin our close-up scrutiny of human biology by seeking to answer a few basic questions about DNA: What is it? What does it do? How does it do it? What have biologists been doing with it? And what are they likely to be doing in the future?
What Is DNA? The Transforming Principle
It doesnÕt take a geneticist to know that like begets like. This is one of the basic rules of living things, so obvious that it can easily go unnoticed Ñ and unappreciated. Salamanders give rise to other salamanders, bald eagles to other bald eagles, and human beings to other human beings. When a chicken egg hatches, out comes another chicken, not a condor. Moreover, different strains of chickens breed "true", just as tall parents are likely to have tall children, and blue-eyed parents, blue-eyed children. Why?
Something, it seems clear, is transmitted from parent to offspring, something that carries the basic information that says, in the case of chickens, "Make a bird, with weak wings, sharp nails, and a tendency to cluck." This something, which makes each generation a chip off the old block, is what is loosely referred to as "genes," and more precisely, as DNA. For a long time people thought that the hereditary material was carried in the blood: hence such expressions as "full-blooded," "blood relatives," "blood lines." Now we know better.
A major clue came from some simple yet perplexing experiments with bacteria that cause pneumonia. There are two different forms of Streptococcus pneumoniae: one makes smooth-looking colonies when grown in the laboratory, while the other produces a rough appearance. The two forms breed true, with smooth forms giving rise only to new, smooth colonies, and rough, only to rough. In 1928 Frederick Griffith made some puzzling observations. When he injected the smooth form of Streptococcus pneumoniae into rats, the animals died of pneumonia. When he injected the rough form, they did not. When he killed the bacteria by heating them before injecting them, neither form caused their hosts to die. So far, so good.
But here was the surprise: when Griffith injected rats with living rough bacteria (the kind that doesnÕt cause disease) along with dead smooth bacteria (the lethal kind), the rats died. Moreover, when Griffith took samples from these dead rats and "cultured" them in his laboratory (that is, grew the cells under artificial conditions), lo and behold, there were plenty of smooth colonies, as though they had risen from the dead. His conclusion? Something had been given off by the dead smooth bacteria that transformed the innocuous, rough form into killer smoothies. Griffith called it the "transforming principle".
Nearly twenty years later, three scientists, O.T. Avery, C. M. Macleod, and M. McCarty, were finally able to purify enough of this transforming principle to identify it as a long, chainlike chemical known as deoxyribonucleic acid, or DNA.
Still, some scientists were unconvinced that DNA was the molecule of heredity. DNA, after all, was a newcomer on the biologistsÕ block; many believed that genetic information was carried by proteins , molecules that were relatively well known and, in a way, well loved.
But in 1952 a crucial experiment by Alfred Hershey and Martha Chase supplied strong additional evidence that DNA was indeed the crucial transforming principle. Hershey and Chase worked with a kind of virus known as bacteriophages ("bacteria eaters"). In particular, they worked with a strain that attacks the common intestinal bacteria Escherichia coli, taking over the metabolic machinery of each infected bacterium and turning it into a microminiaturized virus factory that produces hundreds more phage particles. Bacteriophages consist of just two kind of chemicals: protein and DNA. So when bacteria were infected, one of these chemicals was passed from phage to bacteria. Which one was the culprit, responsible for transforming an E. coli cell into lots of little phages?
To answer this question, Hershey and Chase took advantage of the fact that protein contains sulfur, which is not present in DNA, whereas DNA contains phosphorus, which is present only in very small quantities in protein. They incubated one batch of phage particles in a solution labeled with radioactive sulfur, and another with radioactive phosphorus. Then they exposed E. coli to each type. When the resulting mixtures were mashed up in a kitchen blender and then spun around in a centrifuge, the heavier parts (containing the E. coli cells plus whatever parts of the phage had entered them) were found at the bottom of the centrifuge test tubes while the lighter parts (containing those components of the phage that did not enter the cells) floated on the top.
The results? When E. coli cells were infected with phage whose proteins had been radioactively labeled, radioactivity was not found in the cells but only in the lightweight fluid; this showed that the protein had not entered the cells. On the other hand, when E. coli cells were infected with phage whose DNA had been radioactively labeled, radioactivity was found inside the cells. DNA had been caught red-handed, responsible for transforming normal E. coli into infected E. coli and ultimately into more bacteriophages.
Subsequent research has confirmed that DNA is the ultimate transformer: it makes the difference between life and nonlife.
The Structure of DNA
LetÕs examine the structure of DNA, not just because figuring it out was one of the great scientific detective stories of the twentieth century, but because its physical makeup is the key to how this molecule of heredity does its job.
When DNA is analyzed chemically, it is found to consist of three building blocks: a phosphate group, a type of sugar (deoxyribose), and a variety of so-called nitrogenous bases. These bases are the most interesting part. They come in four kinds: adenine, thymine, cytosine, and guanine (referred to as A, T, C, and G, respectively.)
Every cell of every animal and plant contains DNA. These DNAs differ somewhat from one species to the next, although in all cases this complicated chemical has been found in the nucleus of cells, never in the surrounding cytoplasm. In 1950, Erwin Chargaff made two important discoveries. First, he showed that the DNA of different species is different; specifically, it differs in the proportion of those nitrogenous bases, A, T, C, and G. This was crucial because for DNA to be the hereditary material, it could not very well be the same from one species to another. Second, Chargaff purified DNA from a number of sources and found that regardless of its origin, the amount of adenine (A) equaled that of thymine (T), and the amount of cytosine (C) always equaled that of guanine (G). This turned out to be portentous for revealing the structure of the DNA molecule.
Three years later, the now-famous double-helix structure of DNA was announced. Rosalind Franklin and M. H. F. Wilkins had bombarded DNA crystals with X rays, and by studying the scattering pattern that resulted, they obtained actual measurements of the spatial arrangement of the atoms comprising each molecule. It remained for two young researchers, American James Watson and Englishman Francis Crick, to put this information together and propose a structure for the enigmatic molecule. DNA, they showed, is like a ladder, whose structural sides are composed of the phosphate and sugar groups, and whose rungs are made up of nitrogenous bases, weakly joined together by so-called hydrogen bonds. These bases, furthermore, are organized so that A and T or C and G always pair up to make each rung. ThatÕs why the amounts of A and T are always equal, as with C and G. These base pairs are complementary; it is only when A is paired with T and C with G that a given rung of the DNA molecule is completed, and made structurally whole.
Finally, Watson and Crick suggested that the whole business is twisted, so that instead of a ladder, each DNA molecule is more like a spiral staircase.
Organization and Genes
Imagine a human DNA molecule, containing about 3 billion "nucleotides." (A nucleotide consists of a nitrogenous base Ñ A, T, G, or C Ñ combined with a sugar and a phosphate group; each nucleotide is a link in the spiral DNA chain.) If such a chain was arranged simply as a spiral staircase, it would be over a meter long; yet all those "rungs " manage to fit into a cell that is measured in microns (millionths of a meter). How does it do this? The answer lies in the way DNA is organized: wound around itself and some proteins in an exquisitely com-plicated structure.
First, DNA molecules do not normally stand naked to the world. Even within a cell, they are integrated into parts of physical structures inside the nucleus: the chromosomes. A typical bacterium such as E. coli has "only" about 5 million nucleotides and therefore has them organized as a single chromosome. Human beings, on the other hand, have a grand total of nucleotides that is about 700 times greater. These are distributed onto 46 chromosomes, each carrying about 50 to 250 million nucleotides (the notable exception is the Y chromosome, which confers maleness and has substantially less genetic information than its "sister" X chromosome). In any event, each of the other chromosomes would still be at least 1 centimeter long if it wasnÕt further organized into a substructure that is yet more complex and dense than the DNA molecule itself.
The enormous compaction that occurs, allowing all genetic information to be contained in a tiny package, occurs through the use of pebblelike helper proteins called histones. The long, stringy DNA molecules wrap themselves around nodules of these hugely helpful histones, rather like thread tightly wound on many tiny spools. The result is that a strand of DNA looks like a number of beads (the histones) on a string (the DNA between and around the histones). Beads and string are then further wound into a dense, complicated pattern, twisted around itself in various ways; this DNA packing must eventually be undone in order for it to exert its crucial biological role. Sometimes part of this unpacking doesnÕt occur, in which case that part remains biochemically and genetically inactive.
For all these twistings and turnings, however, the true importance of DNA is contained in its internal, linear sequence, the ordering of the nucleotide bases. Here lies all the information needed to create a functional being, provided the DNA gets a little help from its friends, as we will see. In general, more complex creatures need more DNA than their simpler counterparts. Mammals in general have more DNA than any fungus or bird and more than most insects, fish, and reptiles. It is easy, nonetheless, to wax indignant over the claim that a person is only 700 times more complicated than a bacterium.
However, there are some amphibians and plants that have more than 30 times the amount of DNA that a human has. One of the main reasons for this seeming discrepancy is that much of the DNA in a cell is junk, useless batches of meaningless jabberwocky (as in Lewis CarrollÕs "ÕTwas brillig and the slithey toves did gyre and gimble in the wabe . . . "). It appears that the only useful parts of a DNA strand are those carrying the instructions needed to form a functional molecule called RNA, described below. Every such useful section of DNA is a gene. A gene, therefore, is not just a unit of heredity but also a packaging unit, by which we identify useful DNA as opposed to "slithey toves". To be "useful", the information contained in the nucleotide sequences of DNA must eventually direct the development and manufacture of something. Add up all those somethings, and you get a cell. Add up all those cells, and you get a porcupine, a porpoise, or a person.
What Does DNA Do? Replication
What does a molecule of heredity have to do? First, it must be able to make accurate copies of itself, or replicate. This is why Gertrude SteinÕs observation "A rose is a rose is a rose" rings true, not only poetically but genetically, from generation to generation. For a rose to make a rose, which in turn makes yet more roses, rose DNA must create rose DNA, which in turn makes more rose DNA, every time each rose reproduces. In the biological world, DNA is unique in that it has the ability to direct its own replication.
But mere replication isnÕt enough. As the logicians might say, it is necessary but not sufficient. Living things, after all, are made up of pretty much the same atoms: carbon, hydrogen, nitrogen, phosphorus, sulfur, calcium, and so on. The immense difference between, say, roses and rhinoceroses is due to the way these atoms are put together to comprise the cells, tissues, and organs of individuals. And it is the job of heredity Ñ of DNA Ñ to organize this putting together and to keep each individual running smoothly. It is because of this organizational and maintenance role of DNA that a rose by any other name smells as sweet as it does. It is also why roses have sharp thorns and lovely petals. In short, it is what accounts for a rose being a rose, for its ineffable rosiness. And for a chickenÕs chickenness, and a human beingÕs humanness.
This, then, is the other great task of DNA: to organize and maintain cells and bodies, making them what they are. This is done by conveying information for the production of proteins. As we have seen, proteins are not the hereditary material; but they are the initial stuff upon which heredity acts. Proteins comprise the basic structural building blocks of living things; in addition (in their enzyme form), they direct the various chemical reactions, such as digestion, respiration, etcetera, by which life sustains itself.
First things first, however. How does DNA replicate itself?
Recall that the rungs of the spiral DNA ladder are made up of paired halves: when A appears in one strand, it is always matched with T in the other, and similarly T with A, G with C, and C with G. The copying process relies on the fact that these complementary pairings are highly specific: a chunk of DNA carrying G will match up only with another chunk containing the complementary molecule, C. Once you know one half of a pair of bases (for example, A), you know the other half (it must be T).
The first step in replication, then, is for DNA to uncoil and then unzip, with the various A-T, T-A, G-C, and C-G bonds breaking apart, right at the hyphen, which represents comparatively weak hydrogen bonds. Each half of the old DNA molecule remains intact. It then proceeds to reassemble itself because each of the nitrogenous bases will pair up with only one type of partner; again, G with C, A with T, and so forth. Extra supplies of all four bases are floating about, needing only to be activated by particular enzymes, notably one known as DNA polymerase. A polymer is any long molecule, such as DNA, that is made up of many smaller component molecules, all lined up in repeated sequence. The suffix ase indicates an enzyme, which is a molecule (almost always a protein) that serves to speed up a chemical process that is biologically important. DNA polymerase, then, is an enzyme that helps DNA replicate by stringing unattached nucleotides together to recreate a new, full-fledged DNA molecule, using each half of the original DNA molecule as a template.
Through this process, a DNA molecule becomes two molecules, with each half identically copied, based on the structural information (the sequence of the A, T, G, and C bases) present within itself. Each strand Ñ more precisely, each of the nitrogenous bases associated with each strand Ñ provides the information needed for the manufacture of its complementary half.
So far so good. But simply making copies of itself is not good enough. To be useful, and to count as a gene and a relevant unit of life and of heredity, DNA must in a sense step outside of itself, get beyond its own selfish replication, and be pertinent to the affairs of the cell of which it is part. It does this by directing the production of proteins.
DNAÕs nitrogenous bases in their linear sequence do double duty: they carry not only the information needed for DNA to replicate itself but also precise instructions about how various proteins are to be put together. (These proteins, in turn, are the cellular handymen that go on to perform many of the functions of being alive.)
HereÕs how itÕs done.
Transcription
Each DNA molecule is a vast source of information, a kind of encyclopedic cookbook, chock full of recipes and instructions for the making of proteins. But these hereditary volumes, comprising the genetic library of each individual, do not circulate. Rather, they remain inside the central repository of each cell: the nucleus. (This is not surprising, since each one is precious and could be lost or damaged if it circulated freely; reference books that are especially valuable usually cannot be taken out from public libraries, either.) Somehow, then, the information contained within the DNA Ñ the linear sequence of its nitrogenous bases Ñ must be made available. In technical terms, it must be "transcribed" from its master repository, the DNA molecule, into a form that allows it to be conveyed to the cellÕs protein-building machinery and then deciphered. Enter DNAÕs henchman: ribonucleic acid, or RNA.
There are several kinds of RNA. Of special interest for the process of transcription is messenger RNA, known as mRNA. As its name suggests, mRNAÕs role is to carry a message: namely, the order in which the various bases are arranged to form the rungs of the DNA ladder. (This, as we shall see, is then "translated" into the order of amino acids making up each protein.) For the sequence of nitrogenous bases to be transcribed from DNA to mRNA, the DNA molecule must once again unzip, exposing those bases lined up alon
