8 DNA Structure & Chemistry To understand the structure Proteins, as we have seen, are the workhorses of the cell; they exhibit Goal and chemistry of DNA and extraordinarily varied structures, which enable them to perform myriad the significance of the double tasks. This is in sharp contrast todeoxyribonucleic acid (DNA) molecules, helix. which with few exceptions exhibit a single, common structure: the double Objectives helix. This makes sense because DNA has just one function, information storage. Just as a compact disc can contain the blueprint for building a After this chapter, you should be able to house, DNA is a storage depot for the information needed to make the • explain the structural basis for the diverse proteins of the cell. The instructions for specifying the primary directionality of polynucleotide chains. structure of a protein are stored in a stretch of DNA known as a gene. • describe how hydrogen bonding and Almost all of the carbon-containing molecules in living systems are either geometry dictate base pairing. proteins that are directly encoded by DNA or non-protein molecules that • describe the forces that stabilize the are generated by the actions of enzymes, which like other proteins are DNA double helix. themselves specified by DNA. In Chapters 8-12 we will learn how the cell replicates DNA molecules and does so faithfully, how it retrieves genetic • explain the significance of the grooves in the DNA double helix. information to direct the synthesis of proteins, and how it regulates this flow of genetic information from DNA to protein. But first, in this chapter • describe how DNA is compacted into chromosomes. we look closely at the structure and chemistry of DNA in order to learn how its double-helical architecture allows information to be stored, duplicated, and accessed. Each DNA strand is an alternating copolymer of phosphates and deoxyribose sugars As its name implies, the double helix is composed of two polynucleotide chains that are wrapped around each other as helices. We focus first on the Chapter 8 DNA Structure & Chemistry 2 Figure 1 DNA is an alternating Base Base polymer of deoxyribose and phosphate P Deoxyribose P Deoxyribose chemical nature of the individual chains. Each is a copolymer composed alternately of phosphate groups and sugar units (Figure 1). The sugar units HO 5’ are pivotal to the chains, as the four nucleobases (or more simply bases), O OH which we will consider soon, are attached to the sugars. The sugars are 4’ 1’ pentose sugars, meaning that they contain five carbon atoms. The positions 3’ 2’ of the carbons in the sugars are labeled with apostrophes, which are referred HO to as primes (1’-5’), to distinguish them from the numbering of positions in the bases (Figure 2). The bases are attached to the sugars at the 1’ (“one- 2’-deoxyribose prime”) position via a glycosidic linkage (simply meaning that the base is bonded to a sugar). Notice that the sugars are five-membered rings in Figure 2 The carbon atoms in which an oxygen atom links the 1’ and 4’ carbons. Notice also that the 5’ deoxyribose are numbered 1’ to 5’ carbon is off the ring, being attached to it via the 4’ carbon. Thus, only four of the five carbons contribute to the five-membered ring. The sugars in DNA are2’-deoxyribose sugars in that the carbon at position 2’ lacks a hydroxyl group and instead has two hydrogen atoms. RNA, which we will consider in a later chapter, is a similar copolymer, but its sugars are ribose sugars, which contain a hydroxyl group at the 2’ position in place of one of the two hydrogen atoms. Importantly, the phosphates in the alternating copolymer are joined to the sugars at the 3’ and 5’ positions via phosphate ester linkages (in which a phosphorous atom double-bonded to oxygen is joined to a carbon- containing group via a second oxygen atom) (Figure 3). Because the phosphates are joined to the sugars through two ester linkages, these are said to be phosphodiester bonds. Figure 3 Phosphodiester linkages O 5’ connect the 3’ carbon of one O Base deoxyribose sugar to the 5’ carbon 3’ of the adjacent sugar in the DNA O polymer O P O O 5’ O Base 3’ O O P O O 5’ O Base 3’ O Chapter 8 DNA Structure & Chemistry 3 Box 1 Nucleotides are tripartite repeating units in polynucleotides We have so far presented the polynucleotide chain as an alternating copolymer of phosphates and deoxyribose sugars to which bases are attached. An alternative way to think about the chain is as a simple polymer of units consisting of a phosphate, a sugar, and a base. Such tripartite units are referred to as nucleotides, hence the name polynucleotide. Nucleotides in DNA have a single phosphate, but free nucleotides can have two or three (and sometimes more) phosphate groups. Nucleotides bearing three phosphates at the 5’ position of deoxyribose will become important in subsequent chapters when we consider the biosynthesis of polynucleotide chains. A bipartite structure consisting of a sugar and a base but no phosphates is referred to as a nucleoside. Figure 4 Polynucleotides are also polymers of nucleotides Shown is a single nucleotide within a DNA 5’ double helix and its three-dimensional stick representation as well as a corresponding 4’ 1’ 3’ standard line drawing. Atoms in the 2’ three-dimensional structure are colored as follows: carbon, green; oxygen, red; nitrogen, blue; phosphorus, orange. Base O NH2 O P O N Phosphate N O O N N Sugar O Polynucleotide chains have a 5’-to-3’ directionality and align in an anti- parallel orientation in the double helix A fundamental feature of the polynucleotide chain is that its ends are dissimilar. Thus, the 3’ hydroxyl is displayed at one terminus, the 3’ end, and the 5’ hydroxyl at the other terminus, the 5’ end. This means that polynucleotide chains have an intrinsic directionality. This is analogous to the directionality of polypeptide chains, which, as we have seen, have an N-terminus and a C-terminus. Since the double helix consists of two polynucleotide strands, what is the orientation of the two helical strands relative to each other? The answer is that the two strands are oriented such that the 5’-to-3’ directionality of one strand aligns with the 3’-to-5’ directionality of the other strand. That the directionality of the two strands is anti-parallel is an invariant rule that governs the interaction of polynucleotide chains (RNA as well as DNA) with each other. Chapter 8 DNA Structure & Chemistry 4 3’ 5’ 5’ O 3’ O O Base Base O O O P O O O O P O 5’ 3’ O O Base Base T A O O O P O C G O O O P O A T O Base Base O C G O O 3’ 5’ O P O O DNA strands are antiparallel O O P O O O Base Base O O O 3’ 5’ 3’ 5’ Figure 5 Polynucleotide chains are antiparallel in the double helix A:T and C:G are abbreviations for the bases and their pairing (adenine paired with thymine and cytosine paired with guanine), as we come to next. As we will consider in detail in later chapters, the directionality of polynucleotides and of polypeptides is the basis for three foundational rules that govern the duplication and retrieval of genetic information. These are that: (1) the synthesis of polynucleotide chains always proceeds in a 5’-to-3’ direction, (2) the synthesis of polypeptide chains always proceeds in an N-to-C-terminal direction, and (3) the information for amino acid sequences from the N-terminal amino acid to the C-terminal amino acid is specified sequentially in a 5’-to-3’ direction in polynucleotide chains. The two strands of the double helix interact with each other via two pairs of complementary bases Each deoxyribose in the polynucleotide chain is attached to one of four bases that mediate interactions between the two strands of the double helix. Bases are flat rings consisting of carbon and nitrogen atoms; they are said to be heterocyclic because they are composed of rings containing other atoms than just carbon. There are two kinds of bases, pyrimidines and purines. Pyrimidines are single, six-membered heterocyclic rings, whereas purines have a bicyclic structure consisting of five- and six-membered heterocyclic rings. The positions of carbon and nitrogen atoms in the pyrimidine and purine rings are numbered as shown in Figure 6. Pyrimidines are joined Chapter 8 DNA Structure & Chemistry 5 7 6 4 5 N 1 5 3 8 N N 2 4 6 2 9 N N N H 3 1 Purine Pyrimidine O NH2 NH2 O N NH N N N NH N N NH N N N O N O H 2 H H H Guanine Adenine Cytosine Thymine Figure 6 The bases are purines and pyrimidines The four bases in DNA belong to two families whose numbering systems are shown. via a glycosidic linkage to the 1’ position of deoxyribose via the nitrogen at position 1, whereas purines are attached via the nitrogen at position 9. The pyrimidines are cytosine (C) and thymine (T), and the purines are adenine (A) and guanine (G) (Figure 6). Base pairs consist of a pyrimidine and a purine such that cytosine pairs uniquely with guanine (C:G) and thymine specifically with adenine T:A( ) (Figure 7). (As we will see in Chapter 10, RNA contains the pyrimidine uracil in place of thymine; like thymine, uracil pairs with adenine.) Compared to the 20 disparate side chains of amino acids, the four bases are relatively similar-looking.