Which Is True Of The Secondary Structure Of Dna? ? A Physical Structure

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Griffiths AJF, Gelbart WM, Miller JH, et al. Modern Genetic Analysis. New York: W. H. Freeman; 1999.

By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

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

That DNA is the hereditary material has now been demonstrated in many prokaryotes andeukaryotes. Cells of one genotype (the recipient) are exposed to DNA extracted fromanother (the donor), and donor DNA is taken up by the recipient cells. Occasionallya piece of donor DNA integrates into the genome of the recipient and changes someaspect of the phenotype of the recipient into that of the DNA donor. Such a resultdemonstrates that DNA is indeed the substance that determines genotype and thereforeis the hereditary material (see Genetics inProcess 2-1).

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Genetics In Process 2-1: Oswald Avery’s demonstration that the hereditarymaterial is DNA.

The Three Roles of DNA

Even before the structure of DNA was elucidated, genetic studies clearlyindicated several properties that had to be fulfilled by hereditarymaterial.

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

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

Finally, although the structure of DNA must be relatively stable so thatorganisms can rely on its encoded information, it must also allow the codedinformation to change on rare occasion. These changes, calledmutations, provide the raw material—genetic variation—thatevolutionary selection operates on. We will discuss the mechanisms of mutationin Chapter 7.

The Building Blocks of DNA

DNA has three types of chemical component: phosphate, a sugar calleddeoxyribose, and four nitrogenous bases—adenine,guanine, cytosine, and thymine. Two of the bases, adenine and guanine, have adouble-ring structure characteristic of a type of chemical called apurine. The other two bases, cytosine and thymine, have asingle-ring structure of a type called a pyrimidine. Thechemical components of DNA are arranged into groups callednucleotides, each composed of a phosphate group, a deoxyribosesugar molecule, and any one of the four bases. It is convenient to refer to eachnucleotide by the first letter of the name of its base: A, G, C, and T. Figure 2-1 shows the structures of the fournucleotides in DNA.

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Figure 2-1

Chemical structure of the four nucleotides (two with purine bases andtwo with pyrim-idine bases) that are the fundamental building blocksof DNA. The sugar is called deoxyribose because it is a variation ofa common sugar, ribose, which has one more (more…)

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

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Genetics In Process 2-2: James Watson and Francis Crick propose thecorrect structure for DNA.

DNA Is a Double Helix

DNA is composed of two side-by-side chains (“strands”) of nucleotides twistedinto the shape of a double helix. The two nucleotide strands are held togetherby weak associations between the bases of each strand, forming a structure likea spiral staircase (Figure 2-2). Thebackbone of each strand is a repeating phosphate–deoxyribose sugar polymer. Thesugar-phosphate bonds in this backbone are called phosphodiesterbonds. The attachment of the phosphodiester bonds to the sugar groupsis 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 partof the phosphodiester bond is between the phosphate and the 5′ carbon ofdeoxyribose, and the other is between the phosphate and the 3′ carbon ofdeoxyribose. Thus, each sugar-phosphate backbone is said to have a 5′-to-3′polarity, and understanding this polarity is essential in understanding how DNAfulfills its roles. In the double-stranded DNA molecule, the two backbones arein opposite, or antiparallel,orientation, as shown in Figure 2-2. Onestrand is oriented 5′ → 3′; the other strand, though 5′ → 3′, runs in theopposite direction, or, looked at another way, is 3′ → 5′.

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Figure 2-2

The arrangement of the components of DNA. A segment of the double helix has been unwound to show the structures more clearly. (a) Anaccurate chemical diagram showing the sugar-phosphate backbone inblue and the hydrogen bonding of bases in the center (more…)

The bases are attached to the 1′ carbon of each deoxyribose sugar in the backboneof each strand. Interactions between pairs of bases, one from each strand, holdthe two strands of the DNA molecule together. The bases of DNA interactaccording to a very straightforward rule, namely, that there are only two typesof base pairs: A·T and G·C. The bases in these two base pairs are said to becomplementary. This means that at any “step” of the stairlikedouble-stranded DNA molecule, the only base-to-base associations that can existbetween the two strands without substantially distorting the double-stranded DNAmolecule 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(δ+) because the nitrogen atom tends to attract the electronsinvolved in the N–H bond, thereby leaving the hydrogen atom slightly short ofelectrons. The oxygen atom has six unbonded electrons in its outer shell, makingit slightly negative (δ−). A hydrogen bond forms between one slightlypositive H and one slightly negative atom—in this example, O. Hydrogen bonds arequite weak (only about 3 percent of the strength of a covalent bond), but thisweakness (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 theparticipating atoms are “pointing at each other” (that is, if their bonds are inalignment), as shown in the sketch.

Note that because the G·C pair has three hydrogen bonds, whereas the A·T pair hasonly two, one would predict that DNA containing many G·C pairs would be morestable than DNA containing many A·T pairs. In fact, this prediction isconfirmed. Heat causes the two strands of the DNA double helix to separate (aprocess called DNA melting or DNAdenaturation); it can be shown that DNAs with higher G+C contentrequire higher temperatures to melt them.

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

The two paired nucleotide strands automatically assume a double-helicalconfiguration (Figure 2-3), mainlythrough interaction of the base pairs. The base pairs, which are flat planarstructures, stack on top of one another at the center of the double helix.Stacking (Figure 2-3c) adds to thestability of the DNA molecule by excluding water molecules from the spacesbetween the base pairs. The most stable form that results from base stacking isa 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 themodels. A single strand of nucleotides has no helical structure; the helicalshape of DNA depends entirely on the pairing and stacking of the bases inantiparallel 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 rulesfor proper base pairing, we can envision how DNA is faithfully duplicated: eachstrand serves as an unambiguous template (alignment guide) for the synthesis of its complementarystrand. If, for example, one strand has the base sequence AAGGCTGA (reading inthe 5′-to-3′ direction), then we automatically know that its complementarystrand 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 eachserves as a template for building a new complementary strand.

An enzyme called DNA polymerase is responsible for building newDNA strands, matching up each base of the new strand with the proper complementon the old, template strand. Thus, the complementarity of the DNA strandsunderlies the entire process of faithful duplication. This process will bedescribed more fully in Chapter4.

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

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Double-stranded DNA is composed of two antiparallel, interlockednucleotide chains, each consisting of a sugar-phosphate backbone withbases hydrogen-bonded with complementary bases of the otherchain.

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