Chapter Introduction

2: DNA: The Repository of Biological Information

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  • 2.1 Mendelian Genetics

  • 2.2 Cytogenetics: Chromosome Movements during Mitosis and Meiosis

  • 2.3 The Chromosome Theory of Inheritance

  • 2.4 Foundations of Molecular Genetics

MOMENT OF DISCOVERY

James Berger

The first time I had an “Aha!” moment in science was when I was a graduate student. The question that intrigued me was related to the mechanism proposed for topoisomerases, which are essential enzymes that coil or uncoil DNA during DNA synthesis in all cells. Topoisomerase II–type enzymes (called Topo II) pass DNA strands through each other by cutting and rejoining DNA without marking or changing the genome in any way. In textbooks, the enzyme was shown as a sphere that bound to one segment of DNA, cut it, and then split in half to pass a second DNA segment through the split. But what held the DNA ends together during the passage of the DNA duplex through the double-stranded break? There had to be something else going on.

Francis Crick once said that you can’t understand how an enzyme works unless you see its structure, and I wanted to see the structure of Topo II. I spent the next couple of years trying to crystallize the enzyme with no success, and eventually reached the point where I wondered if my project would ever work, and whether I had what it took be a scientist. I made one last preparation of the enzyme, and after working overnight in the lab, I put the purified enzyme on ice and went home to bed. When I came back the next day, the protein in the tube had turned white, and I was crushed, thinking it had precipitated into a useless aggregate. But when I looked at a sample under the microscope, I saw crystals growing in the tube! At that moment I knew I had a project. I spent the next nine months solving the molecular structure of the enzyme, and I’ll never forget the thrill of seeing the structure for the first time.

It was instantly clear how Topo II must work. The enzyme has two jaws, one of which grabs and cleaves the DNA duplex and holds it while the other jaw passes a different segment of DNA through the gap. I experienced the intense joy of discovering this fundamental mechanism of DNA metabolism, and of knowing that at that moment I was the first person in the world to have this understanding of the natural world.

—James Berger, on his discovery of the structure and mechanism of topoisomerase II

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Genetics is the science of heredity and the variation of inherited characteristics. Today, we know that biological information is stored and transmitted from generation to generation by deoxyribonucleic acid, or DNA, but this understanding arose only gradually. DNA was not widely accepted as the chemical of heredity until the 1940s, and its structure was not determined until 1953, when James Watson and Francis Crick introduced the world to the DNA double helix. (The structure of DNA is described in Chapter 6.) Our knowledge of the beautiful double-helical DNA structure has transformed the way that science is performed, to the extent that it is tempting to think of the field of genetics in terms of before and after DNA structure. But genetics has a wonderfully rich and varied history, every bit as exciting in the decades before the double helix as afterward.

The beginnings of modern genetics can be traced to the 1850s, when Gregor Mendel studied the inheritance of traits in the garden pea. He deduced that organisms contain particles of heredity (what we now call genes) that exist in pairs and that the paired particles split up when gamete cells (sex cells, the ovum and pollen in peas) are formed; pairs of hereditary particles are reformed on the union of two gametes during fertilization. Mendel was absolutely correct, but decades ahead of his time. His marvelous work went unnoticed for more than 30 years, until well after his death.

In contrast, a contemporary of Mendel’s, Charles Darwin, was exceedingly famous in his lifetime. Darwin’s theory of evolution started an awakening, one that continues to this day (see Chapter 1). For evolutionary theory to work, there must be diversity among individuals within a species, and variants more suited to the environment are selected and survive to produce offspring. Darwin’s evolutionary theory, as wonderful as it is, completely lacks an explanation for how this diversity is produced. In fact, Darwin spent considerable time pondering this problem. He espoused the theory of pangenesis, first proposed by the ancient Greeks, in which genetic traits are shaped by life experience and transferred by “pangenes” to gamete cells, via the blood, enabling the traits to be inherited. In principle, the mistaken pangenesis theory is a variation of Jean-Baptiste Lamarck’s theory of inheritance of acquired characteristics (see the How We Know section at the end of Chapter 1).

Darwin’s theory of evolution became widely known, but Mendel’s work fell into obscurity. During the late 1800s, advances in microscopy pushed the optical limits, enabling scientists to visualize subcellular structures. Of particular interest to geneticists were chromosomes, structures found in the nuclei of cells. A rash of intense studies documented chromosome behavior during cell division, fertilization, and the formation of gamete cells. New discoveries revealed that the number of chromosomes in somatic cells (all cells in a multicellular organism other than sex cells) is constant for a given species and that the total number of chromosomes is halved to form gametes. When Mendel’s work was rediscovered in 1900, his principles of heredity and particles of inheritance fit nicely with the behavior of chromosomes observed under the microscope.

Proof that genes reside on chromosomes soon followed, from a series of wonderful studies on fruit flies started in 1908 by Thomas Hunt Morgan. Central to Morgan’s work were mutants, flies displaying physical traits not found in the average fly. The variety of mutant flies accumulated by Morgan’s lab during 15 years of study—generations of flies reared in milk bottles—was amazing, including flies with bodies of different shapes and sizes, a variety of wing patterns, legs of different sizes, and a whole spectrum of eye colors. These fly mutants simply appeared spontaneously over generations of growth in Morgan’s lab. Here was the answer to the variation required to make Darwin’s theory of evolution work. Spontaneous mutants are infrequent, but given the expanse of evolutionary time, sufficient numbers and types of mutants are produced for nature to select and mold new species.

Genes and mutations explain heredity and illuminate evolutionary theory. But what are genes made of, and how is the information within them translated into the physical traits of an organism? Chromosomes were known to consist of both DNA and protein—but which of these is the genetic material? Several elegant and now classic experiments identified DNA as the molecule of heredity and found that DNA contains a code to direct the synthesis of RNA and proteins. The structure of the DNA double helix intuited by Watson and Crick revealed an architecture more beautiful than anyone could have imagined. The DNA molecule consists of two long strands twisted about each other, each chain a series of repeating units called nucleotides.

Watson and Crick immediately realized that the cell must have a mechanism to untwist the two strands in order to duplicate the DNA molecule and pass the genetic information to the next generation. Indeed, as we shall see in Chapter 9, the cell contains a complex arsenal of enzymes devoted to untwisting and altering the topology of DNA. These enzymes, called topoisomerases, are important targets of anticancer drugs, and their mechanisms of action are still actively investigated by James Berger and many other researchers. By extension, it is also critical to have a thorough understanding of the DNA molecule itself, and that is the subject of this and several other chapters in this textbook.

Despite the intrinsic beauty of the newly discovered double helix, the process by which a sequence of nucleotides could code for a sequence of amino acids in a protein remained a mystery. In a rapid series of advances in the 10 years following Watson and Crick’s breakthrough, mRNA, tRNA, and rRNA were discovered and the workings of the directional flow of biological information, DNA→RNA→protein, were understood.

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The field of molecular biology developed from these great discoveries. It seeks a detailed explanation of how biological information brings order to living processes. Molecular biology—the subject of this book—is a rapidly evolving scientific pursuit. The fundamental discoveries described in this chapter provided the groundwork for all subsequent studies in the field.