DNA and Chromosomes

CHAPTER FIVE DNA and Chromosomes Life depends on the ability of cells to store, retrieve, and translate the genetic instructions required to make and maintain a living organism. These instructions are stored within every living cell in its genes—the information-bearing elements that determine the characteristics of a species as a whole and of the individuals within it. At the beginning of the twentieth century, when genetics emerged as a science, scientists became intrigued by the chemical nature of genes. The information in genes is copied and transmitted from a cell to its daughter cells millions of times during the life of a multicellular organism, and passed from generation to generation through the reproductive cells—eggs and sperm. Genes survive this process of replication and transmission essentially unchanged. What kind of molecule could be capable of such accurate and almost unlimited replication, and also be able to direct the development of an organism and the daily life of a cell? What kind of instructions does the genetic information contain? How are these instructions physically organized so that the enormous amount of information required for the development and maintenance of even the simplest organism can be contained within the tiny space of a cell? The answers to some of these questions began to emerge in the 1940s, when it was discovered from studies in simple fungi that genetic information consists primarily of instructions for making proteins. As described in the previous chapter, proteins perform most of the cell’s functions: they serve as building blocks for cell structures; they form the enzymes that catalyze the cell’s chemical reactions; they regulate the activity of genes; and they enable cells to move and to communicate with one another. With hindsight, it is hard to imagine what other type of instructions the genetic information could have contained. 5 The other crucial advance made in the 1940s was the recognition that deoxyribonucleic acid (DNA) is the carrier of the cell’s genetic information. But the mechanism whereby the information could be copied for transmission from one generation of cells to the next, and how proteins might be specified by instructions in DNA, remained completely mysterious until 1953, when the structure of DNA was determined by James Watson and Francis Crick. The structure immediately revealed how DNA might be copied, or replicated, and it provided the first clues about how a molecule of DNA might encode the instructions for making proteins. Today, the fact that DNA is the genetic material is so fundamental to our understanding of life that it can be difficult to appreciate what an enormous intellectual gap this discovery filled. In this chapter, we begin by describing the structure of DNA. We see how, despite its chemical simplicity, the structure and chemical properties of DNA make it ideally suited for carrying genetic information. We then consider how genes and other important segments of DNA are arranged in the single, long DNA molecule that forms each chromosome in the cell. Finally, we discuss how eukaryotic cells fold these long DNA molecules into compact chromosomes inside the nucleus. This packing has to be done in an orderly fashion so that the chromosomes can be apportioned correctly between the two daughter cells at each cell division. At the same time, chromosomal packaging must allow DNA to be accessed by the large number of proteins that replicate and repair it, and that determine the activity of the cell’s many genes. single chromosome (A) dividing cell (B) nondividing cell This is the first of five chapters that deal with basic genetic mechanisms— the ways in which the cell maintains and makes use of the genetic information carried in its DNA. In Chapter 6, we discuss the mechanisms by which the cell accurately replicates and repairs its DNA. In Chapter 7, we consider gene expression—how genes are used to produce RNA and protein molecules. In Chapter 8, we describe how a cell controls gene expression to ensure that each of the many thousands of proteins encoded in its DNA is manufactured at the proper time and place. In Chapter 9, we discuss how present-day genes evolved, and, in Chapter 10, we consider some of the ways that DNA can be experimentally manipulated to study fundamental cell processes. An enormous amount has been learned about these subjects in the past 60 years. Much less obvious, but equally important, is the fact that our knowledge is very incomplete; thus a great deal still remains to be discovered about how DNA provides the instructions to build living things. 10 μm Figure 5–1 Chromosomes become visible as eukaryotic cells prepare to divide. (A) Two adjacent plant cells photographed using a fluorescence microscope. The DNA, which is labeled with a fluorescent dye (DAPI), is packaged into multiple chromosomes; these become visible as distinct structures only when they condense ECB5 e5.01/5.01 in preparation for cell division, as can be seen in the cell on the left. For clarity, a single chromosome has been shaded (brown) in the dividing cell. The cell on the right, which is not dividing, contains the identical chromosomes, but they cannot be distinguished as individual entities because the DNA is in a much more extended conformation at this phase in the cell’s division cycle. (B) Schematic diagram of the outlines of the two cells and their chromosomes. (A, courtesy of Peter Shaw.) THE STRUCTURE OF DNA Long before biologists understood the structure of DNA, they had recognized that inherited traits and the genes that determine them were associated with chromosomes. Chromosomes (named from the Greek chroma, “color,” because of their staining properties) were discovered in the nineteenth century as threadlike structures in the nucleus of eukaryotic cells that become visible as the cells begin to divide (Figure 5–1). As biochemical analyses became possible, researchers learned that chromosomes contain both DNA and protein. But which of these components encoded the organism’s genetic information was not immediately clear. We now know that the DNA carries the genetic information of the cell and that the protein components of chromosomes function largely to package and control the enormously long DNA molecules. But biologists in the 1940s had difficulty accepting DNA as the genetic material because of the apparent simplicity of its chemistry (see How We Know, pp. 193–195). DNA, after all, is simply a long polymer composed of only four types of nucleotide subunits, which are chemically very similar to one another. Then, early in the 1950s, Maurice Wilkins and Rosalind Franklin examined DNA using x-ray diffraction analysis, a technique for determining the three-dimensional atomic structure of a molecule (see Panel 4−6, pp. 168–169). Their results provided one of the crucial pieces of evidence that led, in 1953, to Watson and Crick’s model of the double-helical structure of DNA. This structure—in which two strands of DNA are wound around each other to form a helix—immediately suggested how DNA could encode the instructions necessary for life, and how these instructions could be copied and passed along when cells divide. In this section, we examine the structure of DNA and explain in general terms how it is able to store hereditary information. A DNA Molecule Consists of Two Complementary Chains of Nucleotides A molecule of deoxyribonucleic acid (DNA) consists of two long polynucleotide chains. Each chain, or strand, is composed of four types of nucleotide subunits, and the two strands are held together by hydrogen bonds between the base portions of the nucleotides (Figure 5–2). As we saw in Chapter 2 (Panel 2–7, pp. 78–79), nucleotides are composed of a nitrogen-containing base and a five-carbon sugar, to which a phosphate group is attached. For the nucleotides in DNA, the sugar is deoxyribose (hence the name deoxyribonucleic acid) and the base can be either adenine (A), cytosine (C), guanine (G), or thymine (T). The (A) building blocks of DNA (B) DNA strand sugar phosphate + sugar phosphate (C) 5′ G base (guanine) G A DNA double helix 3′ 5′ G A T A G C G T 0.34 nm T A G sugar–phosphate backbone C C G C G A A T G C C A A T A A C C C G T T G 5′ (D) 5′ C T A nucleotide double-stranded DNA 3′ 3′ C G 3′ hydrogen-bonded base pairs 3′ G T 5′ Figure 5–2 DNA is made of four nucleotide building blocks. (A) Each nucleotide is composed of a sugar phosphate covalently linked to a base—guanine (G) in this figure. (B) The nucleotides are covalently linked together into polynucleotide chains, with a sugar–phosphate backbone from which the bases—adenine, cytosine, guanine, and thymine (A, C, G, and T)—extend. (C) A DNA molecule is composed of two polynucleotide chains (DNA strands) held together by hydrogen bonds between the paired bases. The arrows on the DNA strands indicate the polarities of the two strands, which run antiparallel to each other (with opposite chemical polarities) in the DNA molecule. (D) Although the DNA is shown straightened out in (C), in reality, it is wound into a double helix, as shown here. Figure 5–3 The nucleotide subunits within a DNA strand are held together by phosphodiester bonds. These bonds connect one sugar to the next. The chemical differences in the ester linkages—between the 5ʹ carbon of one sugar and the 3ʹ carbon of the other—give rise to the polarity of the resulting DNA strand. For simplicity, only two nucleotides are shown here. 5’ end of chain O –O P O base CH2 O sugar 3’ O –O P phosphodiester bond O O base 5’ CH2 4’ O sugar 3’ O 1’ 2’ 3’ end of chain ECB5 n5.200/5.06 nucleotides are covalently linked together in a chain through the sugars and phosphates, which form a backbone of alternating sugar–phosphate– sugar–phosphate (see Figure 5–2B). Because only the base differs in each of the four types of subunits, each polynucleotide chain resembles a necklace: a sugar–phosphate backbone strung with four types of tiny beads (the four bases A, C, G, and T). These same symbols (A, C, G, and T) are also commonly used to denote the four different nucleotides—that is, the bases with their attached sugar phosphates. The nucleotide subunits within a DNA strand are held together by phosphodiester bonds that link the 5ʹ end of one sugar with the 3ʹ end of the next (Figure 5−3). Because the ester linkages to the sugar molecules on either side of the bond are different, each DNA strand has a chemical polarity. If we imagine that each nucleotide has a phosphate “knob” and a hydroxyl “hole” (see Figure 5–2A), each strand, formed by interlocking knobs with holes, will have all of its subunits lined up in the same orientation. Moreover, the two ends of the strand can be easily distinguished, as one will have a hole (the 3ʹ hydroxyl) and the other a knob (the 5ʹ phosphate). This polarity in a DNA strand is indicated by referring to one end as the 3ʹ end and the other as the 5ʹ end (see Figure 5−3). The two polynucleotide chains in the DNA double helix are held together by hydrogen-bonding between the bases on the different strands. All the bases are therefore on the inside of the double helix, with the sugar– phosphate backbones on the outside (see Figure 5–2D). The bases do not pair at random, however; A always pairs with T, and G always pairs with C (Figure 5–4). In each case, a bulkier two-ring base (a purine, see Panel 2–7, pp. 78–79) is paired with a single-ring base (a pyrimidine). Each purine–pyrimidine pair is called a base pair, and this complementary base-pairing enables the base pairs to be packed in the energetically most favorable arrangement along the interior of the double helix. In this arrangement, each base pair has the same width, thus holding the sugar– phosphate backbones an equal distance apart along the DNA molecule. For the members of each base pair to fit together within the double helix, the two strands of the helix must run antiparallel to each other—that is, be oriented with opposite polarities (see Figure 5–2C and D). The antiparallel sugar–phosphate strands then twist around each other to form a double helix containing 10 base pairs per helical turn (Figure 5–5). This twisting also contributes to the energetically favorable conformation of the DNA double helix. QUESTION 5–1 Which of the following statements are correct? Explain your answers. A. A DNA strand has a polarity because its two ends contain different bases. B. G-C base pairs are more stable than A-T base pairs. As a consequence of the base-pairing arrangement shown in Figure 5–4, each strand of a DNA double helix contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand—an A always matches a T on the opposite strand, and a C always matches a G. This complementarity is of crucial importance when it comes to both copying and maintaining the DNA structure, as we discuss in Chapter 6. An animated version of the DNA double helix can be seen in Movie 5.1.