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Modern Genetic Analysis Chapter 2. The Structure of Genes and Genomes
The Nature of DNA

How do we know that genomes are composed of DNA? Using histochemical and physical techniques, it is relatively simple to demonstrate this fact for eukaryotic nuclear chromosomes. DNA-binding dyes such as Feulgen or DAPI primarily stain the nuclear chromosomes in cells and to a lesser extent also stain the mitochondria and chloroplasts. Furthermore if a mass of cells is ground up and its components fractionated, it becomes clear that the bulk of DNA can be isolated from the nuclear fraction, and the remainder from mitochondria and chloroplasts.

That DNA is the hereditary material has now been demonstrated in many prokaryotes and eukaryotes. Cells of one genotype (the recipient) are exposed to DNA extracted from another (the donor), and donor DNA is taken up by the recipient cells. Occasionally a piece of donor DNA integrates into the genome of the recipient and changes some aspect of the phenotype of the recipient into that of the DNA donor. Such a result demonstrates that DNA is indeed the substance that determines genotype and therefore is the hereditary material (see Genetics in Process 2-1).

The Three Roles of DNA

Even before the structure of DNA was elucidated, genetic studies clearly indicated several properties that had to be fulfilled by hereditary material.

One crucial property is that essentially every cell in the body has the same genetic makeup; therefore, the genetic material must be faithfully duplicated at every cell division. The structural features of DNA that allow such faithful duplication will be considered later in this chapter.

Secondly, the genetic material must have informational content, since it must encode the constellation of proteins expressed by an organism. How the coded information in DNA is deciphered into protein will be the subject of Chapter 3.

Finally, although the structure of DNA must be relatively stable so that organisms can rely on its encoded information, it must also allow the coded information to change on rare occasion. These changes, called mutations, provide the raw materialgenetic variationthat evolutionary selection operates on. We will discuss the mechanisms of mutation in Chapter 7.

The Building Blocks of DNA

DNA has three types of chemical component: phosphate, a sugar called deoxyribose, and four nitrogenous basesadenine, guanine, cytosine, and thymine. Two of the bases, adenine and guanine, have a double-ring structure characteristic of a type of chemical called a purine. The other two bases, cytosine and thymine, have a single-ring structure of a type called a pyrimidine. The chemical components of DNA are arranged into groups called nucleotides, each composed of a phosphate group, a deoxyribose sugar molecule, and any one of the four bases. It is convenient to refer to each nucleotide by the first letter of the name of its base: A, G, C, and T. Figure 2-1 shows the structures of the four nucleotides in DNA.

How can a molecule with so few components fulfill the roles of a hereditary molecule? Some clues came in 1953 when James Watson and Francis Crick showed precisely how the nucleotides are arranged in DNA (see Genetics in Process 2-2). DNA structure is summarized in the next section.

DNA Is a Double Helix

DNA is composed of two side-by-side chains ("strands") of nucleotides twisted into the shape of a double helix. The two nucleotide strands are held together by weak associations between the bases of each strand, forming a structure like a spiral staircase (Figure 2-2). The backbone of each strand is a repeating phosphatedeoxyribose sugar polymer. The sugar-phosphate bonds in this backbone are called phosphodiester bonds. The attachment of the phosphodiester bonds to the sugar groups is important in describing the way in which a nucleotide chain is organized. Note that the carbons of the sugar groups are numbered 1 through 5. One part of the phosphodiester bond is between the phosphate and the 5 carbon of deoxyribose, and the other is between the phosphate and the 3 carbon of deoxyribose. Thus, each sugar-phosphate backbone is said to have a 5-to-3 polarity, and understanding this polarity is essential in understanding how DNA fulfills its roles. In the double-stranded DNA molecule, the two backbones are in opposite, or antiparallel, orientation, as shown in Figure 2-2. One strand is oriented 5 3; the other strand, though 5 3, runs in the opposite direction, or, looked at another way, is 3 5.

The bases are attached to the 1 carbon of each deoxyribose sugar in the backbone of each strand. Interactions between pairs of bases, one from each strand, hold the two strands of the DNA molecule together. The bases of DNA interact according to a very straightforward rule, namely, that there are only two types of base pairs: A·T and G·C. The bases in these two base pairs are said to be complementary. This means that at any "step" of the stairlike double-stranded DNA molecule, the only base-to-base associations that can exist between the two strands without substantially distorting the double-stranded DNA molecule are A·T and G·C.

The association of A with T and G with C is through hydrogen bonds. The following is an example of a hydrogen bond:

Each hydrogen atom in the NH2 group is slightly positive ( d +) because the nitrogen atom tends to attract the electrons involved in the NH bond, thereby leaving the hydrogen atom slightly short of electrons. The oxygen atom has six unbonded electrons in its outer shell, making it slightly negative ( d ). A hydrogen bond forms between one slightly positive H and one slightly negative atomin this example, O. Hydrogen bonds are quite weak (only about 3 percent of the strength of a covalent bond), but this weakness (as we shall see) is important to the DNA molecule's role in heredity. One further important chemical fact: the hydrogen bond is much stronger if the participating atoms are "pointing at each other" (that is, if their bonds are in alignment), as shown in the sketch.

Note that because the G·C pair has three hydrogen bonds, whereas the A·T pair has only two, one would predict that DNA containing many G·C pairs would be more stable than DNA containing many A·T pairs. In fact, this prediction is confirmed. Heat causes the two strands of the DNA double helix to separate (a process called DNA melting or DNA denaturation); it can be shown that DNAs with higher G+C content require higher temperatures to melt them.

Although hydrogen bonds are individually weak, the two strands of the DNA molecule are held together in a relatively stable manner because there are enormous numbers of these bonds. It is important that the strands be associated through such weak interactions, since they have to be separated during DNA replication and during transcription into RNA.

The two paired nucleotide strands automatically assume a double-helical configuration (Figure 2-3), mainly through interaction of the base pairs. The base pairs, which are flat planar structures, stack on top of one another at the center of the double helix. Stacking (Figure 2-3c) adds to the stability of the DNA molecule by excluding water molecules from the spaces between the base pairs. The most stable form that results from base stacking is a double helix with two distinct sizes of grooves running around in a spiral. These are the major groove and the minor groove, which can be seen in the models. A single strand of nucleotides has no helical structure; the helical shape of DNA depends entirely on the pairing and stacking of the bases in antiparallel strands.

DNA Structure Reflects Its Function

How does DNA structure fulfill the requirements of a hereditary molecule? First, duplication. With the antiparallel orientation of the DNA strands, and the rules for proper base pairing, we can envision how DNA is faithfully duplicated: each strand serves as an unambiguous template (alignment guide) for the synthesis of its complementary strand. If, for example, one strand has the base sequence AAGGCTGA (reading in the 5-to-3 direction), then we automatically know that its complementary strand can have only the sequence (in the 3-to-5 direction) TTCCGACT. Replication is based on this simple rule. The two DNA strands separate, and each serves as a template for building a new complementary strand.

An enzyme called DNA polymerase is responsible for building new DNA strands, matching up each base of the new strand with the proper complement on the old, template strand. Thus, the complementarity of the DNA strands underlies the entire process of faithful duplication. This process will be described more fully in Chapter 4.

The second requirement for DNA is that it have informational content. This informational requirement for DNA is fulfilled by its nucleotide sequence, which acts as a kind of written language. The third requirement, mutation, is simply the occasional replacement, deletion, or addition of one or more nucleotide pairs, resulting in a change of the encoded information.

MESSAGE
Double-stranded DNA is composed of two antiparallel, interlocked nucleotide chains, each consisting of a sugar-phosphate backbone with bases hydrogen-bonded with complementary bases of the other chain.

© 1999 by W. H. Freeman and Company. All rights reserved.