Chpater10The Structure and Function of DNA

Chapter 10: The Structure and Function of DNA Biology and Society Sabotaging HIV Discovery Channel Video Clip Emerging Diseases Vaccines AIDS, acquired immunodeficiency syndrome, is one of the most significant health challenges facing the world today. The cause of AIDS is infection by HIV, the human immunodeficiency virus. Since it was first recognized in 1981, HIV has infected an estimated 40 million people worldwide and caused 3 million deaths. While there is no cure for AIDS, its spread can be slowed by anti-HIV drugs. One such drug, AZT, has proved to be the most effective weapon yet found in the fight against AIDS.    How does AZT stop HIV? To answer this question, we have to think on the molecular level. Like all viruses, HIV must infect a host cell because it cannot reproduce on its own. After gaining entry into a human immune cell, HIV depends on a special viral enzyme to convert its RNA genome into a molecule of DNA. As you learned in Chapter 3, all DNA is made from four chemical building blocks called nucleotides: A, T, C, and G. The special viral enzyme uses nucleotides from the cytoplasm of the infected cell to build a DNA molecule.    The key to AZT’s effectiveness is its shape (another example of the connection between form and function in biology). The shape of a molecule of AZT is very similar to the shape of part of the T (thymine) nucleotide (Figure 10.1). In fact, AZT’s shape is so similar to the T nucleotide that AZT binds to the viral enzyme instead of T. But unlike thymine, AZT cannot be incorporated into a growing DNA chain. Thus, AZT “gums up the works”; it acts as a molecular saboteur that interferes with the synthesis of HIV DNA. Because this synthesis is an essential step in the reproductive cycle of HIV, AZT may block the spread of the virus. HYPERLINK "javascript:bigFig('3684110001.jpg',%20'../fig/big/3684110001.jpg','3684110001.jpg');" INCLUDEPICTURE "http://wps.pearsoncustom.com/wps/media/objects/5319/5447672/ebk/fig/thm/3684110001.jpg" \* MERGEFORMATINET (Click image to enlarge) Figure 10.1  AZT and the T nucleotide.  The anti-HIV drug AZT (left) has a chemical shape very similar to part of the T (thymine) nucleotide of DNA.    AZT is a good example of how a detailed understanding of biological molecules can help improve human health. In this chapter, you will learn about molecular biology[The study of the molecular basis of genes and gene expression; molecular genetics], the study of heredity at the molecular level. You will learn in detail how the DNA of genes exerts its effects on the cell and on the whole organism. You’ll learn, too, how DNA replicates—the molecular basis for the similarities between parents and offspring—and how it can mutate. And because viruses have played key roles in the history of molecular biology, and continue to be important as both research organisms and disease-causing pathogens, these tiny entities are also a major topic of this chapter DNA: Structure and Replication DNA was known to be a chemical in cells by the end of the 19th century, but Mendel and other early geneticists did all their work without any knowledge of DNA’s role in heredity. By the late 1930s, experimental studies had convinced most biologists that a specific kind of molecule, rather than some complex chemical mixture, was the basis of inheritance. Attention focused on chromosomes, which were already known to carry genes. By the 1940s, scientists knew that chromosomes consisted of two types of chemicals: DNA and protein. And by the early 1950s, a series of discoveries had convinced the scientific world that DNA acts as the hereditary material.    What came next was one of the most celebrated quests in the history of science: the effort to figure out the structure of DNA. A good deal was already known about DNA. Scientists had identified all its atoms and knew how they were covalently bonded to one another. What was not understood was the specific three-dimensional arrangement of atoms that gave DNA its unique properties—the capacity to store genetic information, copy it, and pass it from generation to generation. A race was on to discover how the structure of this molecule could account for its role in heredity. We will describe that momentous discovery shortly. First, let’s review the underlying chemical structure of DNA and its chemical cousin RNA. DNA and RNA Structure Recall from Chapter 3 that both DNA and RNA are nucleic acids, which consist of long chains (polymers) of chemical units (monomers) called nucleotides[(nū′-klē-ō-tīd) An organic monomer consisting of a five-carbon sugar covalently bonded to a nitrogenous base and a phosphate group. Nucleotides are the building blocks of nucleic acids]. (For an in-depth refresher, see the information on nucleic acids in Chapter 3, particularly Figures 3.26–3.29.) A very simple diagram of a nucleotide polymer, or polynucleotide[(pol′-ē-nū′-klē-ō-tīd) A polymer made up of many nucleotides covalently bonded together], is shown in Figure 10.2. This sample polynucleotide chain shows only one of many possible arrangements of the four different types of nucleotides (abbreviated A, C, T, and G) that make up DNA. Polynucleotides tend to be very long and can have any sequence of nucleotides, so a great number of polynucleotide chains are possible. HYPERLINK "javascript:bigFig('3684110002.jpg',%20'../fig/big/3684110002.jpg','3684110002.jpg');" INCLUDEPICTURE "http://wps.pearsoncustom.com/wps/media/objects/5319/5447672/ebk/fig/thm/3684110002.jpg" \* MERGEFORMATINET (Click image to enlarge) Figure 10.2  The structure of DNA.  A molecule of DNA contains two polynucleotides, each a chain of nucleotides. Each nucleotide consists of a nitrogenous base, a sugar (blue), and a phosphate group (gold). The chemical structure at the right shows the details of a DNA nucleotide.    The nucleotides are joined to one another by covalent bonds between the sugar of one nucleotide and the phosphate of the next. This results in a sugar-phosphate backbone[The alternating chain of sugar and phosphate to which DNA and RNA nitrogenous bases are attached], a repeating pattern of sugar-phosphate-sugar-phosphate. The nitrogenous bases are arranged like ribs that hang off this backbone. Zooming in on our polynucleotide in Figure 10.2, we see that each nucleotide consists of three components: a nitrogenous base, a sugar (blue), and a phosphate group (gold). Examining a single nucleotide even more closely (Figure 10.2, right), we see the chemical structure of its three components. The phosphate group, with a phosphorus atom (P) at its center, is the source of the acid in nucleic acid. (The phosphate has given up a hydrogen ion, H+, leaving a negative charge on one of its oxygen atoms.) The sugar has five carbon atoms (shown in red): four in its ring and one extending above the ring. The ring also includes an oxygen atom. The sugar is called deoxyribose because, compared to the sugar ribose, it is missing an oxygen atom. The full name for DNA[Deoxyribonucleic acid (dē-ok′-sē-rī′-bō-nū-klā′-ik). The genetic material that organisms inherit from their parents; a double-stranded helical macromolecule consisting of nucleotide monomers with deoxyribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and thymine (T). See also gene.] is deoxyribonucleic acid, with the nucleic part coming from DNA’s location in the nuclei of eukaryotic cells. The nitrogenous base (thymine, in our example) has a ring of nitrogen and carbon atoms with various functional groups attached. In contrast to the acidic phosphate group, nitrogenous bases are basic; hence their name.    The four nucleotides found in DNA differ only in their nitrogenous bases (see Figure 3.27 for a review). At this point, the structural details are not as important as the fact that the bases are of two types. Thymine[(thī′-min) A single-ring nitrogenous base found in DNA] (T) and cytosine[(sī′-tuh-sin) A single-ring nitrogenous base found in DNA and RNA] (C) are single-ring structures. Adenine[(ad′-uh-nēn) A double-ring nitrogenous base found in DNA and RNA] (A) and guanine[(gwa′-nēn) A double-ring nitrogenous base found in DNA and RNA] (G) are larger, double-ring structures. (The one-letter abbreviations can be used for either the bases alone or for the nucleotides containing them.) Recall from Chapter 3 that RNA has the nitrogenous base uracil[(yū′-ruh-sil) A single-ring nitrogenous base found in RNA] (U) instead of thymine (uracil is very similar to thymine). And, as already mentioned, RNA contains a slightly different sugar than DNA (ribose instead of deoxyribose). Other than that, RNA and DNA polynucleotides have the same chemical structure. Watson and Crick’s Discovery of the Double Helix The celebrated partnership that resulted in the determination of the physical structure of DNA began soon after a 23-year-old American named James D. Watson journeyed to Cambridge University, where Englishman Francis Crick was studying protein structure with a technique called X-ray crystallography (Figure 10.3a). While visiting the laboratory of Maurice Wilkins at King’s College in London, Watson saw an X-ray crystallographic photograph of DNA, produced by Wilkins’s colleague Rosalind Franklin (Figure 10.3b). To Watson’s trained eye, the photograph clearly revealed the basic shape of DNA to be a helix (spiral). On the basis of Watson’s later recollection of the photo, he and Crick deduced that the diameter of the helix was uniform. The thickness of the helix suggested that it was made up of two polynucleotide strands—in other words, a double helix[The form of native DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape]. HYPERLINK "javascript:bigFig('3684110003.jpg',%20'../fig/big/3684110003.jpg','3684110003.jpg');" INCLUDEPICTURE "http://wps.pearsoncustom.com/wps/media/objects/5319/5447672/ebk/fig/thm/3684110003.jpg" \* MERGEFORMATINET (Click image to enlarge) Figure 10.3  Discoverers of the double helix.  (a) James Watson (left) and Francis Crick, who deduced the structure of DNA, are shown in 1953 with their model of the double helix. (b) By generating X-ray images of DNA (right), Rosalind Franklin provided Watson and Crick with some key data about the structure of DNA.    Using wire models, Watson and Crick began trying to construct a double helix that would conform both to Franklin’s data and to what was then known about the chemistry of DNA. After failing to make a satisfactory model that placed the sugar-phosphate backbones inside the double helix, Watson tried putting the backbones on the outside and forcing the nitrogenous bases to swivel to the interior of the molecule. It occurred to him that the four kinds of bases might pair in a specific way. This idea of specific base pairing was a flash of inspiration that enabled Watson and Crick to solve the DNA puzzle.    At first, Watson imagined that the bases paired like with like—for example, A with A, C with C. But that kind of pairing did not fit with the fact that the DNA molecule has a uniform diameter. An AA pair (made of two double-ringed bases) would be almost twice as wide as a CC pair (made of two single-ringed bases), causing bulges in the molecule. It soon became apparent that a double-ringed base on one strand must always be paired with a single-ringed base on the opposite strand. Moreover, Watson and Crick realized that the individual structures of the bases dictated the pairings even more specifically. Each base has chemical side groups that can best form hydrogen bonds with one appropriate partner (to review hydrogen bonds, see Figure 2.10). Adenine can best form hydrogen bonds with thymine, and guanine with cytosine. In the biologist’s shorthand, A pairs with T, and G pairs with C. A is also said to be “complementary” to T, and G to C.    You can picture the model of the DNA double helix proposed by Watson and Crick as a rope ladder having rigid, wooden rungs, with the ladder twisted into a spiral (Figure 10.4). Figure 10.5 shows three more detailed representations of the double helix. The ribbonlike diagram in Figure 10.5a symbolizes the bases with shapes that emphasize their complementarity. Figure 10.5b is a more chemically precise version showing only four base pairs, with the helix untwisted and the individual hydrogen bonds specified by dashed lines; you can see that the double helix has an antiparallel arrangement—that is, the two sugar-phosphate backbones are oriented in opposite directions. Figure 10.5c is a computer graphic showing part of a double helix in atomic detail. HYPERLINK "javascript:bigFig('3684110004.jpg',%20'../fig/big/3684110004.jpg','3684110004.jpg');" INCLUDEPICTURE "http://wps.pearsoncustom.com/wps/media/objects/5319/5447672/ebk/fig/thm/3684110004.jpg" \* MERGEFORMATINET (Click image to enlarge) Figure 10.4  A rope-ladder model of a double helix.  The ropes at the sides represent the sugar-phosphate backbones. Each wooden rung stands for a pair of bases connected by hydrogen bonds. HYPERLINK "javascript:bigFig('3684110005.jpg',%20'../fig/big/3684110005.jpg','3684110005.jpg');" INCLUDEPICTURE "http://wps.pearsoncustom.com/wps/media/objects/5319/5447672/ebk/fig/thm/3684110005.jpg" \* MERGEFORMATINET (Click image to enlarge) Figure 10.5  Three representations of DNA.     Although the base-pairing rules dictate the side-by-side combinations of nitrogenous bases that form the rungs of the double helix, they place no restrictions on the sequence of nucleotides along the length of a DNA strand. In fact, the sequence of bases can vary in countless ways.    In April 1953, Watson and Crick shook the scientific world with a succinct, two-page paper proposing their molecular model for DNA in the British scientific journal Nature. Few milestones in the history of biology have had as broad an impact as their double helix, with its AT and CG base pairing. In 1962, Watson, Crick, and Wilkins received the Nobel Prize for their work. (Franklin might have received the prize as well, but she had died from cancer in 1958.)    In their 1953 paper, Watson and Crick wrote that the structure they proposed “immediately suggests a possible copying mechanism for the genetic material.” In other words, the structure of DNA also points toward a molecular explanation for life’s unique properties of reproduction and inheritance, as we see next. DNA Replication When a cell or a whole organism reproduces, a complete set of genetic instructions must pass from one generation to the next. For this to occur, there must be a means of copying the instructions. Watson and Crick’s model for DNA structure immediately suggested to them that DNA replicates by a template mechanism, with each DNA strand serving as a mold, or template, to guide reproduction of the other strand. The logic behind the Watson-Crick proposal for how DNA is copied is quite simple. If you know the sequence of bases in one strand of the double helix, you can very easily determine the sequence of bases in the other strand by applying the base-pairing rules: A pairs with T (and T with A), and G pairs with C (and C with G). For example, if one polynucleotide has the sequence ATCG, then the complementary polynucleotide in that DNA molecule must have the sequence TAGC.    Figure 10.6 shows how the template model can account for the direct copying of a piece of DNA. The two strands of parental DNA separate, and each becomes a template for the assembly of a complementary strand from a supply of free nucleotides. The nucleotides are lined up one at a time along the template strand in accordance with the base-pairing rules. Enzymes link the nucleotides to form the new DNA strands. The completed new molecules, identical to the parental molecule, are known as daughter DNA molecules (no gender should be inferred from this name). HYPERLINK "javascript:bigFig('3684110008.jpg',%20'../fig/big/3684110008.jpg','3684110008.jpg');" INCLUDEPICTURE "http://wps.pearsoncustom.com/wps/media/objects/5319/5447672/ebk/fig/thm/3684110008.jpg" \* MERGEFORMATINET (Click image to enlarge) Figure 10.6  DNA replication.  The two strands of the original (parental) DNA molecule (blue) serve as templates for making new (daughter) strands (orange). Replication results in two daughter DNA molecules, each consisting of one old strand and one new strand. The parental DNA untwists as its strands separate, and the daughter DNA rewinds as it forms.    Although the general mechanism of DNA replication is conceptually simple, the actual process is complex and requires the cooperation of more than a dozen enzymes and other proteins. The enzymes that make the covalent bonds between the nucleotides of a new DNA strand are called DNA polymerases[(puh-lim′-er-ās) An enzyme that assembles DNA nucleotides into polynucleotides using a preexisting strand of DNA as a template]. As an incoming nucleotide base-pairs with its complement on the template strand, a DNA polymerase adds it to the end of the growing daughter strand (polymer). The process is both fast and amazingly accurate; typically, DNA replication proceeds at a rate of 50 nucleotides per second, with only about one in a billion incorrectly paired. In addition to their roles in DNA replication, DNA polymerases and some of the associated proteins are also involved in repairing damaged DNA. DNA can be harmed by toxic chemicals in the environment or by high-energy radiation, such as X-rays and ultraviolet light (Figure 10.7). HYPERLINK "javascript:bigFig('3684110009.jpg',%20'../fig/big/3684110009.jpg','3684110009.jpg');" INCLUDEPICTURE "http://wps.pearsoncustom.com/wps/media/objects/5319/5447672/ebk/fig/thm/3684110009.jpg" \* MERGEFORMATINET (Click image to enlarge) Figure 10.7  Damage to DNA by ultraviolet light.  The ultraviolet (UV) radiation in sunlight can damage the DNA in skin cells. Fortunately, the cells can repair some of the damage, using enzymes that include some that catalyze DNA replication. You can protect yourself from UV radiation by wearing protective clothing and sunscreen.    DNA replication begins at specific sites on a double helix, called origins of replication. It then proceeds in both directions, creating what are called replication “bubbles” (Figure 10.8). The parental DNA strands open up as daughter strands elongate on both sides of each bubble. The DNA molecule of a eukaryotic chromosome has many origins where replication can start simultaneously, shortening the total time needed for the process. Eventually, all the bubbles merge, yielding two completed double-stranded daughter DNA molecules. HYPERLINK "javascript:bigFig('3684110010.jpg',%20'../fig/big/3684110010.jpg','3684110010.jpg');" INCLUDEPICTURE "http://wps.pearsoncustom.com/wps/media/objects/5319/5447672/ebk/fig/thm/3684110010.jpg" \* MERGEFORMATINET (Click image to enlarge) Figure 10.8  Multiple “bubbles” in replicating DNA.     DNA replication ensures that all the body cells in a multicellular organism carry the same genetic information. It is also the means by which genetic information is passed along to offspring. Checkpoint 1. Compare and contrast the chemical components of DNA and RNA. 2. Along one strand of a DNA double helix is the nucleotide sequence GGCATAGGT. What is the sequence for the other DNA strand? 3. How does complementary base pairing make the replication of DNA possible? 4. What is the function of DNA polymerase in DNA replication? Click here for answersAnswers: 1. Both are polymers of nucleotides. A nucleotide consists of a sugar + a nitrogenous base + a phosphate group. In RNA, the sugar is ribose; in DNA, it is deoxyribose. Both RNA and DNA have the bases A, G, and C; for a fourth base, DNA has T and RNA has U. 2. CCGTATCCA 3. When the two strands of the double helix separate, each serves as a template on which nucleotides can be arranged by specific base pairing into new complementary strands. 4. This enzyme covalently connects nucleotides one a