10.3 DNA Consists of Two Complementary and Antiparallel Nucleotide Strands That Form a Double Helix

DNA, though relatively simple in structure, has an elegance and beauty unsurpassed by other large molecules. It is useful to consider the structure of DNA at three levels of increasing complexity, known as the primary, secondary, and tertiary structures of DNA. The primary structure of DNA refers to its nucleotide structure and how the nucleotides are joined together. The secondary structure refers to DNA’s stable three-dimensional configuration, the helical structure worked out by Watson and Crick. In Chapter 11, we will consider DNA’s tertiary structures, which are the complex packing arrangements of double-stranded DNA in chromosomes.

The Primary Structure of DNA

The primary structure of DNA consists of a string of nucleotides joined together by phosphodiester linkages.

Nucleotides

DNA is typically a very long molecule and is therefore termed a macromolecule. For example, within each human chromosome is a single DNA molecule that, if stretched out straight, would be several centimeters in length, thousands of times longer than the cell itself. In spite of its large size, DNA has a quite simple structure: it is a polymer—that is, a chain made up of many repeating units linked together. The repeating units of DNA are nucleotides, each comprised of three parts: (1) a sugar, (2) a phosphate, and (3) a nitrogen-containing base.

The sugars of nucleic acids—called pentose sugars—have five carbon atoms, numbered 1′, 2′, 3′, and so forth (Figure 10.9). The sugars of DNA and RNA are slightly different in structure. RNA’s sugar, called ribose, has a hydroxyl group (—OH) attached to the 2′-carbon atom, whereas DNA’s sugar, or deoxyribose, has a hydrogen atom (—H) at this position and therefore contains one oxygen atom fewer overall. This difference gives rise to the names ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). This minor chemical difference is recognized by most of the cellular enzymes that interact with DNA or RNA, thus yielding specific functions for each nucleic acid. Furthermore, the additional oxygen atom in the RNA nucleotide makes it more reactive and less chemically stable than DNA. For this reason, DNA is better suited to serve as the long-term repository of genetic information.

Figure 10.9: A nucleotide contains either a ribose sugar (in RNA) or a deoxyribose sugar (in DNA). The carbon atoms are assigned primed numbers.

The second component of a nucleotide is its nitrogenous base, which may be of two types—a purine or a pyrimidine (Figure 10.10). Each purine consists of a six-member ring attached to a five-member ring, whereas each pyrimidine consists of a six-member ring only. Both DNA and RNA contain two purines, adenine and guanine (A and G), which differ in the positions of their double bonds and in the groups attached to the six-member ring. Three pyrimidines are common in nucleic acids: cytosine (C), thymine (T), and uracil (U). Cytosine is present in both DNA and RNA; however, thymine is restricted to DNA, and uracil is found only in RNA. The three pyrimidines differ in the groups or atoms attached to the carbon atoms of the ring and in the number of double bonds in the ring. In a nucleotide, the nitrogenous base always forms a covalent bond with the 1′-carbon atom of the sugar (see Figure 10.9). A deoxyribose or a ribose sugar and a base together are referred to as a nucleoside.

Figure 10.10: A nucleotide contains either a purine or a pyrimidine base. The atoms of the rings in the bases are assigned unprimed numbers.

The third component of a nucleotide is the phosphate group, which consists of a phosphorus atom bonded to four oxygen atoms (Figure 10.11). Phosphate groups are found in every nucleotide and frequently carry a negative charge, which makes DNA acidic. The phosphate group is always bonded to the 5′-carbon atom of the sugar (see Figure 10.9) in a nucleotide.

Figure 10.11: A nucleotide contains a phosphate group.

The DNA nucleotides are properly known as deoxyribonucleotides or deoxyribonucleoside 5′-monophosphates. Because there are four types of bases, there are four different kinds of DNA nucleotides (Figure 10.12). The equivalent RNA nucleotides are termed ribonucleotides or ribonucleoside 5′-monophosphates. RNA molecules sometimes contain additional rare bases, which are modified forms of the four common bases. These modified bases will be discussed in more detail when we examine the function of RNA molecules in Chapter 14. The names for DNA bases, nucleotides, and nucleosides are shown in Table 10.2. TRY PROBLEM 26

Figure 10.12: There are four types of DNA nucleotides.

Polynucleotide Strands

DNA is made up of many nucleotides connected by covalent bonds, which join the 5′-phosphate group of one nucleotide to the 3′-hydroxyl of the next nucleotide (Figure 10.13); note that the structures shown in Figure 10.13 are flattened into two dimensions while the molecule itself is three dimensional, as shown in Figure 10.14). These bonds, called phosphodiester linkages, are strong covalent bonds; a series of nucleotides linked in this way constitutes a polynucleotide strand. The backbone of the polynucleotide strand is composed of alternating sugars and phosphates; the bases project away from the long axis of the strand. The negative charges of the phosphate groups are frequently neutralized by the association of positive charges on proteins, metals, or other molecules.

Figure 10.13: DNA and RNA are composed of polynucleotide strands. DNA is usually composed of two polynucleotide strands, although single-stranded DNA is found in some viruses.

An important characteristic of the polynucleotide strand is its direction, or polarity. At one end of the strand, a free (meaning that it’s unattached on one side) phosphate group is attached to the 5′-carbon atom of the sugar in the nucleotide. This end of the strand is therefore referred to as the 5′ end. The other end of the strand, referred to as the 3′ end, has a free OH group attached to the 3′-carbon atom of the sugar.

RNA nucleotides also are connected by phosphodiester linkages to form similar 5 to 3 polynucleotide strands (see Figure 10.13).

Secondary Structures of DNA

The secondary structure of DNA refers to its three-dimensional configuration—its fundamental helical structure. DNA’s secondary structure can assume a variety of configurations, depending on its base sequence and the conditions in which it is placed.

The Double Helix

A fundamental characteristic of DNA’s secondary structure is that it consists of two polynucleotide strands wound around each other—it’s a double helix. The sugar–phosphate linkages are on the outside of the helix, and the bases are stacked in the interior of the molecule (see Figure 10.13). The two polynucleotide strands run in opposite directions—they are antiparallel, which means that the 5′ end of one strand is opposite the 3′ end of the other strand.

The strands are held together by two types of molecular forces. Hydrogen bonds link the bases on opposite strands (see Figure 10.13). These bonds are relatively weak compared with the covalent phosphodiester bonds that connect the sugar and phosphate groups of adjoining nucleotides on the same strand. As we will see, several important functions of DNA require the separation of its two nucleotide strands, and this separation can be readily accomplished because of the relative ease of breaking and reestablishing the hydrogen bonds.

The nature of the hydrogen bond imposes a limitation on the types of bases that can pair. Adenine normally pairs only with thymine through two hydrogen bonds, and cytosine normally pairs only with guanine through three hydrogen bonds (see Figure 10.13). Because three hydrogen bonds form between C and G and only two hydrogen bonds form between A and T, C–G pairing is stronger than A–T pairing. The specificity of the base pairing means that, wherever there is an A on one strand, there must be a T in the corresponding position on the other strand, and, wherever there is a G on one strand, a C must be on the other. The two polynucleotide strands of a DNA molecule are therefore not identical but are complementary DNA strands. The complementary nature of the two nucleotide strands provides for efficient and accurate DNA replication, as will be discussed in Chapter 12.

The second force that holds the two DNA strands together is the interaction between the stacked base pairs in the interior of the molecule. Stacking means that adjacent bases are aligned so that their rings are parallel and stack on top of one another. The stacking interactions stabilize the DNA molecule but do not require that any particular base follow another. Thus, the base sequence of the DNA molecule is free to vary, allowing DNA to carry genetic information. TRY PROBLEMS 32 AND 37

Different Secondary Structures

As we have seen, DNA normally consists of two polynucleotide strands that are antiparallel and complementary (exceptions are single-stranded DNA molecules in a few viruses). The precise three-dimensional shape of the molecule can vary, however, depending on the conditions in which the DNA is placed and, in some cases, on the base sequence itself.

The three-dimensional structure of DNA described by Watson and Crick is termed the B-DNA structure (Figure 10.14). This structure exists when plenty of water surrounds the molecule and there is no unusual base sequence in the DNA—conditions that are likely to be present in cells. The B-DNA structure is the most stable configuration for a random sequence of nucleotides under physiological conditions, and most evidence suggests that it is the predominant structure in the cell.

Figure 10.14: B-DNA consists of a right-handed helix with approximately 10 bases per turn. (a) Space-filling model of B-DNA showing major and minor grooves. (b) Diagrammatic representation.

B-DNA is a right-handed helix, meaning that it has a clockwise spiral. There are approximately 10 base pairs (bp) per 360-degree rotation of the helix, so each base pair is twisted 36 degrees relative to the adjacent bases (see Figure 10.14b). The base pairs are 0.34 nanometer (nm) apart; so each complete rotation of the molecule encompasses 3.4 nm. The diameter of the helix is 2 nm, and the bases are perpendicular to the long axis of the DNA molecule. A space-filling model shows that B-DNA has a slim and elongated structure (see Figure 10.14a). The spiraling of the nucleotide strands creates major and minor grooves in the helix, features that are important for the binding of some proteins that regulate the expression of genetic information (see Chapter 16).

Another secondary structure that DNA can assume is the A-DNA structure, which exists if less water is present. Like B-DNA, A-DNA is a right-handed helix (Figure 10.15a), but it is shorter and wider than B-DNA (Figure 10.15b) and its bases are tilted away from the main axis of the molecule. A-DNA has been detected in some DNA-protein complexes and in spores of some bacteria.

Figure 10.15: DNA can assume several different secondary structures.

[After J. M. Berg, J. L. Tymoczko, and L. Stryer, Biochemistry, 6th ed. (New York: W. H. Freeman and Company, 2002), pp. 785 and 787.]

A radically different secondary structure, called Z-DNA (Figure 10.15c), forms a left-handed helix. In this form, the sugar–phosphate backbone zigzags back and forth, giving rise to its name. A Z-DNA structure can result if the molecule contains particular base sequences, such as stretches of alternating C and G nucleotides. Researchers have found that Z-DNA-specific antibodies bind to regions of the DNA that are being transcribed into RNA, suggesting that Z-DNA may play some role in gene expression. Additional secondary structures of DNA (C-DNA, D-DNA, etc.) can form under specialized laboratory conditions or in DNA with specific base sequences.

CONNECTING CONCEPTS: Genetic Implications of DNA Structure

Watson and Crick’s great contribution was their elucidation of the genotype’s chemical structure, making it possible for geneticists to begin to examine genes directly, instead of looking only at the phenotypic consequences of gene action. The determination of the structure of DNA led to the birth of molecular genetics—the study of the chemical and molecular nature of genetic information.

Watson and Crick’s structure did more than just create the potential for molecular genetic studies; it was an immediate source of insight into key genetic processes. At the beginning of this chapter, four fundamental properties of the genetic material were identified. First, it must be capable of carrying large amounts of information. Watson and Crick’s model suggested that genetic instructions are encoded in the base sequence, the only variable part of the molecule.

A second necessary property of genetic material is its ability to replicate faithfully. The complementary polynucleotide strands of DNA make this replication possible. Watson and Crick proposed that in replication, the two polynucleotide strands unzip, breaking the weak hydrogen bonds between the two strands, and each strand serves as a template on which a new strand is synthesized. The specificity of the base pairing means that only one possible sequence of bases—the complementary sequence—can be synthesized from each template. Newly replicated double-stranded DNA molecules will therefore be identical with the original double-stranded DNA molecule (see Chapter 12 on DNA replication).

A third essential property of genetic material is the ability to express its instructions into the phenotype. DNA expresses its genetic instructions by first transferring its information to an RNA molecule, in a process termed transcription (see Chapter 13). The term transcription is appropriate because, although the information is transferred from DNA to RNA, the information remains in the language of nucleic acids. In some cases, the RNA molecule then transfers the genetic information to a protein by specifying its amino acid sequence. This process is termed translation (see Chapter 15) because the information must be translated from the language of nucleotides into the language of amino acids. A fourth property of DNA is that it must be capable of varying. This variation consists of differences in the sequence of bases found among different individuals.

We can now identify three major pathways of information flow in the cell (Figure 10.16a): in replication, information passes from one DNA molecule to other DNA molecules; in transcription, information passes from DNA to RNA; and, in translation, information passes from RNA to protein. This concept of information flow was formalized by Francis Crick in a concept that he called the central dogma of molecular biology. The central dogma states that genetic information passes from DNA to protein in a one-way information pathway. We now realize, however, that the central dogma is an oversimplification. In addition to the three general information pathways of replication, transcription, and translation, other transfers may take place in certain organisms or under special circumstances. Retroviruses (see Chapter 9) and some transposable elements (see Chapter 18) transfer information from RNA to DNA (in reverse transcription), and some RNA viruses transfer information from RNA to RNA (in RNA replication; Figure 10.16b).

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Figure 10.16: Pathways of information transfer within the cell.