chapte NUCLEOTIDES AND NUCLEIC ACIDS 8.1 Some basics 273 quence in the cells DNA. A segment of a DNA molecule 8.2 Nucleic Acid structure 279 that contains the information required for the synthes of a functional biological product, whether protein or 8.3 Nucleic Acid Chemistry 291 RNA, is referred to as a gene. a cell typically has many 8.4 Other Functions of Nucleotides 300 thousands of genes, and DNA molecules, not surpris- ingly, tend to be very large. The storage and transmis- sion of biological information are the only known func A structure this pretty just had to exist ons of dna. -lames Watson. The Double helix. 1968 RNAs have a broader range of functions, and sev- eral classes are found in cells. Ribosomal rnas (rRNAs) are components of ribosomes, the complexes cleotides have a variety of roles in cellular metab- that carry out the synthesis of proteins. Messenger olism. They are the energy currency in metabolic RNAs(mRNAs)are intermediaries, carrying genetic transactions, the essential chemical links in the re- information from one or a few genes to a ribosome sponse of cells to hormones and other extracellular stim- where the corresponding proteins can be synthesized uli, and the structural components of an array of en- Transfer RNAs(tRNas) are adapter molecules that zyme cofactors and metabolic intermediates. And, last faithfully translate the information in mRNA into a but certainly not least, they are the constituents of nu- specific sequence of amino acids. In addition to these cleic acids: deoxyribonucleic acid(DNA)and ribonu- major classes there is a wide variety of RNAs with spe- cleic acid(RNA), the molecular repositories of genetic cial functions, described in depth in Part Ill information. The structure of every protein, and ulti- mately of every biomolecule and cellular component, is Nucleotides and Nucleic Acids Have Characteristic a product of information programmed into the nu- Bases and Pentoses cleotide sequence of a cells nucleic acids. The ability to store and transmit genetic information from one gener Nucleotides have three characteristic components ation to the next is a fundamental condition for life (1)a nitrogenous(nitrogen-containing) base, (2)apen This chapter provides an overview of the chemical se, and(3)phosphate(Fig. 8-1). The molecule with nature of the nucleotides and nucleic acids found in out the phosphate group is called a nucleoside. The most cells: a more detailed examination of the function nitrogenous bases are derivatives of two parent com- of nucleic acids is the focus of part ill of this text. pounds, pyrimidine and purine. The bases and pentoses of the common nucleotides are heterocyclic compounds 8. 1 Some basics The carbon and nitrogen atoms in the parent structures are conventionally numbered to facilitate the naming Nucleotides,Building Blocks of Nucleic Acids The amino acid and identification of the many derivative compounds sequence of every protein in a cell, and the nucleotide The convention for the pentose ring follows rules out sequence of every rNA, is specified by a nucleotide se- lined in Chapter 7, but in the pentoses of nucleotides
chapter Nucleotides have a variety of roles in cellular metabolism. They are the energy currency in metabolic transactions, the essential chemical links in the response of cells to hormones and other extracellular stimuli, and the structural components of an array of enzyme cofactors and metabolic intermediates. And, last but certainly not least, they are the constituents of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), the molecular repositories of genetic information. The structure of every protein, and ultimately of every biomolecule and cellular component, is a product of information programmed into the nucleotide sequence of a cell’s nucleic acids. The ability to store and transmit genetic information from one generation to the next is a fundamental condition for life. This chapter provides an overview of the chemical nature of the nucleotides and nucleic acids found in most cells; a more detailed examination of the function of nucleic acids is the focus of Part III of this text. 8.1 Some Basics Nucleotides, Building Blocks of Nucleic Acids The amino acid sequence of every protein in a cell, and the nucleotide sequence of every RNA, is specified by a nucleotide sequence in the cell’s DNA. A segment of a DNA molecule that contains the information required for the synthesis of a functional biological product, whether protein or RNA, is referred to as a gene. A cell typically has many thousands of genes, and DNA molecules, not surprisingly, tend to be very large. The storage and transmission of biological information are the only known functions of DNA. RNAs have a broader range of functions, and several classes are found in cells. Ribosomal RNAs (rRNAs) are components of ribosomes, the complexes that carry out the synthesis of proteins. Messenger RNAs (mRNAs) are intermediaries, carrying genetic information from one or a few genes to a ribosome, where the corresponding proteins can be synthesized. Transfer RNAs (tRNAs) are adapter molecules that faithfully translate the information in mRNA into a specific sequence of amino acids. In addition to these major classes there is a wide variety of RNAs with special functions, described in depth in Part III. Nucleotides and Nucleic Acids Have Characteristic Bases and Pentoses Nucleotides have three characteristic components: (1) a nitrogenous (nitrogen-containing) base, (2) a pentose, and (3) a phosphate (Fig. 8–1). The molecule without the phosphate group is called a nucleoside. The nitrogenous bases are derivatives of two parent compounds, pyrimidine and purine. The bases and pentoses of the common nucleotides are heterocyclic compounds. The carbon and nitrogen atoms in the parent structures are conventionally numbered to facilitate the naming and identification of the many derivative compounds. The convention for the pentose ring follows rules outlined in Chapter 7, but in the pentoses of nucleotides NUCLEOTIDES AND NUCLEIC ACIDS 8.1 Some Basics 273 8.2 Nucleic Acid Structure 279 8.3 Nucleic Acid Chemistry 291 8.4 Other Functions of Nucleotides 300 A structure this pretty just had to exist. —James Watson, The Double Helix, 1968 8 273
274 Chapter 8 Nucleotides and Nucleic Acids NH: pyrimidin CH Phaphate-0-P-Io-cH Adenine Oum ine Purines H OH HN aCH grimme FurT towne FIGURE 8-1 Structure of nucleotides. (a) General structure showing (RNAy Pyrimidines the numbering convention for the pentose ring. This is a ribonu- cleotide In deoxyribonucleotides the -OH group on the 2' carbon FIGURE 8-2 Major purine and pyrimidine bases of nucleic acids (in red) is replaced with-H. (b) The parent compounds of the pyrim- Some of the common names of these bases reflect the circumstances idine and purine bases of nucleotides and nucleic acids, showing the of their discovery Guanine, for example, was first isolated from guano (bird manure), and thymine was first isolated from thymus tissue and nucleosides the carbon numbers are given a prime long sequences of A, T, G, and C nucleotides in DNA are ()designation to distinguish them from the numbered the repository of genetic information. atoms of the nitrogenous bases. Although nucleotides bearing the major purines and The base of a nucleotide is joined covalently(at N-1 pyrimidines are most common, both DNA and rNa also of pyrimidines and N-9 of purines) in an N-B-glycosyl bond to the 1' carbon of the pentose, and the phosphate is esterified to the 5 carbon. The M-B-glycosyl bond is formed by removal of the elements of water (a hydroxyl group from the pentose and hydrogen from the base as in Glycosidic bond formation(see Fig. 7-31) H-C-OH Both DNA and RNa contain two major purine bases adenine(A)and guanine(G), and two major pyrim dines. In both DNA and RNa one of the pyrimidines is cytosine(C), but the second major pyrimidine is not CHOH the same in both: it is thymine(t)in DNA and uracil (a) Aldehyde 各 Furanose (U)in RNA. Only rarely does thymine occur in RNA or uracil in DNA. The structures of the five major bases corresponding nure 8-2, and the nomenclature of their shown in fi nucleotides and nucleosides is summa. C-s end rized in table 8-1 Nucleic acids have two kinds of pentoses. The urring deoxyribonucleotide units of DNA contain 2 deoxy-D-ribose, and the ribonucleotide units of RNA CA,ao ontain D-ribose. In nucleotides, both types of pentoses (b) C2 exe are in their B-furanose(closed five-membered ring FIGURE 8-3 Conformations of ribose(a)In solution, the straight form. As Figure 8-3 shows, the pentose ring is not pla- chain(aldehyde)and ring(B-furanose) forms of free ribose are in equi. nar but occurs in one of a variety of conformations gen- librium. RNA contains only the ring form, B- D-ribofuranose. Deoxy erally described as"puckered. ribose undergoes a similar interconversion in solution, but in DNA Figure 8-4 gives the structures and names of the exists solely as B-2 -deoxy-D-ribofuranose. (b)Ribofuranose rings in four major deoxyribonucleotides(deoxyribonucleo- nucleotides can exist in four different puckered conformations In all side 5'-monophosphates), the structural units of DNAS, cases, four of the five atoms are in a single plane. The fifth atom major ribonucleotides(ribonucleoside 5. (C-2' or C-3) is on either the same (endo) or the opposite(exo)side monophosphates), the structural units of RNAs. Specific of the plane relative to the C-5'atom
and nucleosides the carbon numbers are given a prime () designation to distinguish them from the numbered atoms of the nitrogenous bases. The base of a nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines) in an N--glycosyl bond to the 1 carbon of the pentose, and the phosphate is esterified to the 5 carbon. The N--glycosyl bond is formed by removal of the elements of water (a hydroxyl group from the pentose and hydrogen from the base), as in O-glycosidic bond formation (see Fig. 7–31). Both DNA and RNA contain two major purine bases, adenine (A) and guanine (G), and two major pyrimidines. In both DNA and RNA one of the pyrimidines is cytosine (C), but the second major pyrimidine is not the same in both: it is thymine (T) in DNA and uracil (U) in RNA. Only rarely does thymine occur in RNA or uracil in DNA. The structures of the five major bases are shown in Figure 8–2, and the nomenclature of their corresponding nucleotides and nucleosides is summarized in Table 8–1. Nucleic acids have two kinds of pentoses. The recurring deoxyribonucleotide units of DNA contain 2- deoxy-D-ribose, and the ribonucleotide units of RNA contain D-ribose. In nucleotides, both types of pentoses are in their -furanose (closed five-membered ring) form. As Figure 8–3 shows, the pentose ring is not planar but occurs in one of a variety of conformations generally described as “puckered.” Figure 8–4 gives the structures and names of the four major deoxyribonucleotides (deoxyribonucleoside 5-monophosphates), the structural units of DNAs, and the four major ribonucleotides (ribonucleoside 5- monophosphates), the structural units of RNAs. Specific long sequences of A, T, G, and C nucleotides in DNA are the repository of genetic information. Although nucleotides bearing the major purines and pyrimidines are most common, both DNA and RNA also 274 Chapter 8 Nucleotides and Nucleic Acids FIGURE 8–1 Structure of nucleotides. (a) General structure showing the numbering convention for the pentose ring. This is a ribonucleotide. In deoxyribonucleotides the OOH group on the 2 carbon (in red) is replaced with OH. (b) The parent compounds of the pyrimidine and purine bases of nucleotides and nucleic acids, showing the numbering conventions. (b) (a) FIGURE 8–2 Major purine and pyrimidine bases of nucleic acids. Some of the common names of these bases reflect the circumstances of their discovery. Guanine, for example, was first isolated from guano (bird manure), and thymine was first isolated from thymus tissue. FIGURE 8–3 Conformations of ribose. (a) In solution, the straightchain (aldehyde) and ring (-furanose) forms of free ribose are in equilibrium. RNA contains only the ring form, -D-ribofuranose. Deoxyribose undergoes a similar interconversion in solution, but in DNA exists solely as -2-deoxy-D-ribofuranose. (b) Ribofuranose rings in nucleotides can exist in four different puckered conformations. In all cases, four of the five atoms are in a single plane. The fifth atom (C-2 or C-3) is on either the same (endo) or the opposite (exo) side of the plane relative to the C-5 atom
NH C -0--P-0--cH O 0-P-0-CH OH H OH H A dA dAMP G dG, dGMP T d. dTMP C, dC, dCMP (a) Deoxyribonucleotides HaN 0-P-0-CH 0→P-0—CH 0-P-0 0-P-0 OHOH OH OH Nucleotide: Cytidylate(cytidine monophosphate) 5′· monophosphate) 5b包 A, AMP G GMP U UMP C, CMP Uridine (b) Ribonucleotides FIGURE 8-4 Deoxyribonucleotides and ribonucleotides of nucleic GMP, UMP, and CMP. For each nucleotide, the more common name cids. All nucleotides are shown in their free form at pH 70. The nu- is followed by the complete name in parentheses. All abbreviations cleotide units of DNA (a)are usually symbolized as A, G, T, and C, assume that the phosphate group is at the 5 position. The nucleoside sometimes as dA, dG, dT, and dC: those of RNA (b)as A, G, U, and portion of each molecule is shaded in light red. In this and the fol- C In their free form the deoxyribonucleotides are commonly abbre. lowing illustrations, the ring carbons are not shown viated dAMP dgMP dTMP and dCMP. the ribonucleotides AMP lE 8-1 Nucleotide and Nucleic Acid Nomenclature Nucleoside Nucleotide Nucleic acid Adenine Adenosine Note: 'Nucleoside and '" are Deoxyadenosine genenic terms that include both ribo- and Guanine Guanosine ribonucleotides are here desimated simpl as nucleosides and nucleotides(eg, nibo- adenosine as adenosine), and deox- Cytidylate nucleosides and daarynibonucleotides as Deoxycytidir Deoxycytidylate Thymidine or deoxythymidine Thymidylate or deoxythymidylate DNA Uridine RNA able, but the shortened names are more mmonly used Thymine is an exception
8.1 Some Basics 275 O CH2 O OH H P CH3 O HN N H H H H O T, dT, dTMP Deoxythymidine Nucleotide: Deoxyadenylate (deoxyadenosine 5-monophosphate) Deoxyguanylate (deoxyguanosine 5-monophosphate) Deoxythymidylate (deoxythymidine 5-monophosphate) Deoxycytidylate (deoxycytidine 5-monophosphate) Symbols: A, dA, dAMP Nucleoside: Deoxyadenosine O G, dG, dGMP Deoxyguanosine O C, dC, dCMP Deoxycytidine (a) Deoxyribonucleotides O O CH2 N O O OH H P NH2 O N N N H H H H O O O CH2 O OH H P HN H2N O N N N H H H H O O O CH2 O OH H P NH2 O N N H H H H O O O O CH2 N O O OH H P NH2 O N N N H H H O O O CH2 O OH H P HN H2N O N N N H H H O O O CH2 O OH H P O N N H H H O O (b) Ribonucleotides U, UMP C, CMP Uridine Nucleotide: Adenylate (adenosine 5-monophosphate) Guanylate (guanosine 5-monophosphate) Uridylate (uridine 5-monophosphate) Cytidylate (cytidine 5-monophosphate) Symbols: A, AMP Nucleoside: Adenosine G, GMP Guanosine Cytidine O CH2 O OH H P NH2 O N N H H H O O O OH OH OH OH H O O FIGURE 8–4 Deoxyribonucleotides and ribonucleotides of nucleic acids. All nucleotides are shown in their free form at pH 7.0. The nucleotide units of DNA (a) are usually symbolized as A, G, T, and C, sometimes as dA, dG, dT, and dC; those of RNA (b) as A, G, U, and C. In their free form the deoxyribonucleotides are commonly abbreviated dAMP, dGMP, dTMP, and dCMP; the ribonucleotides, AMP, GMP, UMP, and CMP. For each nucleotide, the more common name is followed by the complete name in parentheses. All abbreviations assume that the phosphate group is at the 5 position. The nucleoside portion of each molecule is shaded in light red. In this and the following illustrations, the ring carbons are not shown. TABLE 8–1 Nucleotide and Nucleic Acid Nomenclature Base Nucleoside Nucleotide Nucleic acid Purines Adenine Adenosine Adenylate RNA Deoxyadenosine Deoxyadenylate DNA Guanine Guanosine Guanylate RNA Deoxyguanosine Deoxyguanylate DNA Pyrimidines Cytosine Cytidine Cytidylate RNA Deoxycytidine Deoxycytidylate DNA Thymine Thymidine or deoxythymidine Thymidylate or deoxythymidylate DNA Uracil Uridine Uridylate RNA Note: “Nucleoside” and “nucleotide” are generic terms that include both ribo- and deoxyribo- forms. Also, ribonucleosides and ribonucleotides are here designated simply as nucleosides and nucleotides (e.g., riboadenosine as adenosine), and deoxyribonucleosides and deoxyribonucleotides as deoxynucleosides and deoxynucleotides (e.g., deoxyriboadenosine as deoxyadenosine). Both forms of naming are acceptable, but the shortened names are more commonly used. Thymine is an exception; “ribothymidine” is used to describe its unusual occurrence in RNA.
76 Chapter 8 Nucleotides and Nucleic Acids here)is simply to indicate the ring position of the sub- stituent by its number-for example, 5-methylcytosine 7-methylguanine, and 5-hydroxymethylcytosine(shown as the nucleosides in Fig. 8-5). The element to which the substituent is attached (N, C, O)is not identified. The convention changes when the substituted atom is exocyclic(not within the ring structure), in which case s-Alchyleytidno N Methy ladanoame the type of atom is identified and the ring position to which it is attached is denoted with a superscript. The amino nitrogen attached to C-6 of adenine is N, simi- CH OH arly, the carbonyl oxygen and amino nitrogen at C-6 and C-2 of guanine are O' and N, respectively. Examples of this nomenclature are N-methyladenosine and methylguanosine(Fig. 8-5) Riase Cells also contain nucleotides with phosphate (a) N2Mcthylgunasine groups in positions other than on the 5 carbon(Fig 8-6). Ribonucleoside 2, 3 -cyclic monophosphates are isolatable intermediates. and ribonucleoside 3 monophosphates are end products of the hydrolysis of rna by certain ribonucleases. Other variations are adenosine 3, 5'-cyclic monophosphate(CAMP)and guanosine 3, 5'-cyclic monophosphate(cGMP), consid ed at the end of this chapte Inosine Pseudouridine Phosphodiester Bonds Link Successive Nucleotides Nucleic acids The successive nucleotides of both dna and rna are HN N covalently linked through phosphate-group"bridges, "in Ribose which the 5-phosphate group of one nucleotide unit is Thicurdine Adenine FIGURE 8-5 Some minor purine and pyrimidine bases, shown as the HO→CH nucleosides. (a)Minor bases of DNA. 5-Methylcytidine occurs in the DNA of animals and higher plants, N"-methyladenosine in bacterial Adne DNA, and 5-hydroxymethylcytidine in the DNA of bacteria infected"o-p-o with certain bacteriophages. (b)Some minor bases of tRNAS Inosine H contains the base hypoxanthine. Note that pseudouridine, like uridine contains uracil; they are distinct in the point of attachment to the ribose-in uridine, uracil is attached through N-1. the usual attach- ent point for pyrimidines: in pseudouridine, through C-5 Adnasna 6monophosphate idanasne 2-mm ophasphako contain some minor bases( Fig. 8-5). In DNa the most Aden ng common of these are methylated forms of the major bases: in some viral DNAs, certain bases may be hy- droxymethylated or glucosylated. Altered or unusual bases in DNA molecules often have roles in regulating or protecting the genetic information. Minor bases of -p0 many types are also found in RNAs, especially in tRNAs (see Fig. 26-24) The nomenclature for the minor bases can be con- Adenosine s'-mmophosphat Adenoxine 2 3'syelie fusing, Like the major bases, many have common names- hypoxanthine, for example, shown as its nucleoside ino- FIGURE 8-6 Some adenosine monophosphates. Adenosine 2" sine in Figure 8-5. When an atom in the purine or monophosphate, 3-monophosphate, and 2 3 -cyclic monophosphate pyrimidine ring is substituted, the usual convention(used are formed by enzymatic and alkaline hydrolysis of RNA
contain some minor bases (Fig. 8–5). In DNA the most common of these are methylated forms of the major bases; in some viral DNAs, certain bases may be hydroxymethylated or glucosylated. Altered or unusual bases in DNA molecules often have roles in regulating or protecting the genetic information. Minor bases of many types are also found in RNAs, especially in tRNAs (see Fig. 26–24). The nomenclature for the minor bases can be confusing. Like the major bases, many have common names— hypoxanthine, for example, shown as its nucleoside inosine in Figure 8–5. When an atom in the purine or pyrimidine ring is substituted, the usual convention (used here) is simply to indicate the ring position of the substituent by its number—for example, 5-methylcytosine, 7-methylguanine, and 5-hydroxymethylcytosine (shown as the nucleosides in Fig. 8–5). The element to which the substituent is attached (N, C, O) is not identified. The convention changes when the substituted atom is exocyclic (not within the ring structure), in which case the type of atom is identified and the ring position to which it is attached is denoted with a superscript. The amino nitrogen attached to C-6 of adenine is N6 ; similarly, the carbonyl oxygen and amino nitrogen at C-6 and C-2 of guanine are O6 and N2 , respectively. Examples of this nomenclature are N6 -methyladenosine and N2 - methylguanosine (Fig. 8–5). Cells also contain nucleotides with phosphate groups in positions other than on the 5 carbon (Fig. 8–6). Ribonucleoside 2,3-cyclic monophosphates are isolatable intermediates, and ribonucleoside 3- monophosphates are end products of the hydrolysis of RNA by certain ribonucleases. Other variations are adenosine 3,5-cyclic monophosphate (cAMP) and guanosine 3,5-cyclic monophosphate (cGMP), considered at the end of this chapter. Phosphodiester Bonds Link Successive Nucleotides in Nucleic Acids The successive nucleotides of both DNA and RNA are covalently linked through phosphate-group “bridges,” in which the 5-phosphate group of one nucleotide unit is 276 Chapter 8 Nucleotides and Nucleic Acids (a) (b) FIGURE 8–5 Some minor purine and pyrimidine bases, shown as the nucleosides. (a) Minor bases of DNA. 5-Methylcytidine occurs in the DNA of animals and higher plants, N6 -methyladenosine in bacterial DNA, and 5-hydroxymethylcytidine in the DNA of bacteria infected with certain bacteriophages. (b) Some minor bases of tRNAs. Inosine contains the base hypoxanthine. Note that pseudouridine, like uridine, contains uracil; they are distinct in the point of attachment to the ribose—in uridine, uracil is attached through N-1, the usual attachment point for pyrimidines; in pseudouridine, through C-5. FIGURE 8–6 Some adenosine monophosphates. Adenosine 2- monophosphate, 3-monophosphate, and 2,3-cyclic monophosphate are formed by enzymatic and alkaline hydrolysis of RNA
DNA joined to the 3-hydroxyl group of the next nucleotide, 5′End 5 End linkage(Fig. 8-7) the covalent backbones of nucleic acids consist of al o-P=0 ternating phosphate and pentose residues, and the trogenous bases may be regarded as side groups joined to the backbone at regular intervals. The backbones of 5 CH both DNA and RNa are hydrophilic. The hydroxy groups of the sugar residues form hydrogen bonds with water. The phosphate groups, with a pKa near 0. are completely ionized and negatively charged at pH 7, and Phospho- the negative charges are generally neutralized by ionic 0-P=0 0-P=0 interactions with positive charges on proteins, metal ions, and polyamines All the phosphodiester linkages have the same ori- 5 CHz 5° entation along the chain(Fig. 8-7), giving each linear nucleic acid strand a specific polarity and distinct 5'and 3ends. By definition, the 5 end lacks a nucleotide at the 5 position and the 3 end lacks a nucleotide at the 3 position. Other groups(most often one or more phos- 0P=0 phates) may be present on one or both ends The covalent backbone of DNA and RNa is subject 5 CH O 5 CH to slow, nonenzymatic hydrolysis of the phosphodiester bonds. In the test tube, RNA is hydrolyzed rapidly un der alkaline conditions, but DNA is not; the 2-hydroxyl groups in RNA (absent in DNA) are directly involved in 9 OH the process. Cyclic 2, 3-monophosphate nucleotides are the first products of the action of alkali on rNa and 3 End 3 End are rapidly hydrolyzed further to yield a mixture of 2 and 3'-nucleoside monophosphates(Fig. 8-8) FIGURE 8-7 Phosphodiester linkages in the covalent backbone of The nucleotide sequences of nucleic acids can be DNA and RNA. The phosphodiester bonds (one of which is shaded in represented schematically, as illustrated on the follow the DNA) link successive nucleotide units. The backbone of alternat. ing page by a segment of DNA with five nucleotide units ing pentose and phosphate groups in both types of nucleic acid is The phosphate groups are symbolized by and each highly polar. The 5 end of the macromolecule lacks a nucleotide at deoxyribose is symbolized by a vertical line, from C-l at the top to C-5 at the bottom(but keep in mind that deriva 00 0-H OH P- CH2oBasez FIGURE 8-8 Hydrolysis of RNA under alkaline in an intramolecular displacement. The 2, 3'-cyclic monophosphate derivative is further hydrolyzed to OH Shortened 0 OH a mixture of2·and3’, monophosphates.DNA RNA0-P=0 o-P=0 which lacks 2 hydroxyls, is stable under similar conditions
joined to the 3-hydroxyl group of the next nucleotide, creating a phosphodiester linkage (Fig. 8–7). Thus the covalent backbones of nucleic acids consist of alternating phosphate and pentose residues, and the nitrogenous bases may be regarded as side groups joined to the backbone at regular intervals. The backbones of both DNA and RNA are hydrophilic. The hydroxyl groups of the sugar residues form hydrogen bonds with water. The phosphate groups, with a pKa near 0, are completely ionized and negatively charged at pH 7, and the negative charges are generally neutralized by ionic interactions with positive charges on proteins, metal ions, and polyamines. All the phosphodiester linkages have the same orientation along the chain (Fig. 8–7), giving each linear nucleic acid strand a specific polarity and distinct 5 and 3 ends. By definition, the 5 end lacks a nucleotide at the 5 position and the 3 end lacks a nucleotide at the 3 position. Other groups (most often one or more phosphates) may be present on one or both ends. The covalent backbone of DNA and RNA is subject to slow, nonenzymatic hydrolysis of the phosphodiester bonds. In the test tube, RNA is hydrolyzed rapidly under alkaline conditions, but DNA is not; the 2-hydroxyl groups in RNA (absent in DNA) are directly involved in the process. Cyclic 2,3-monophosphate nucleotides are the first products of the action of alkali on RNA and are rapidly hydrolyzed further to yield a mixture of 2- and 3-nucleoside monophosphates (Fig. 8–8). The nucleotide sequences of nucleic acids can be represented schematically, as illustrated on the following page by a segment of DNA with five nucleotide units. The phosphate groups are symbolized by P, and each deoxyribose is symbolized by a vertical line, from C-1 at the top to C-5 at the bottom (but keep in mind that 8.1 Some Basics 277 O RNA CH2 O O H P H OH H O 3 5 U H O CH2 O O H P H H O O 3 5 G H O CH2 O O H P H H O O 3 5 H O H O 5 End O CH2 O O H P H H H O 3 5 A H O CH2 O O H P H H H O O 3 5 T H O CH2 O O H P H H H O O 3 5 G H O H O 5 End 3 End 3 End C 5 3 DNA Phosphodiester linkage OH OH FIGURE 8–7 Phosphodiester linkages in the covalent backbone of DNA and RNA. The phosphodiester bonds (one of which is shaded in the DNA) link successive nucleotide units. The backbone of alternating pentose and phosphate groups in both types of nucleic acid is highly polar. The 5 end of the macromolecule lacks a nucleotide at the 5 position, and the 3 end lacks a nucleotide at the 3 position. H P H H H O OH 2,3-Cyclic monophosphate derivative O O CH2 O H P H H H O O Base1 O O O H CH2 O H P H H H O O Base2 O O H P O O CH2 H H H H O O Base2 O H P O O OH Base1 P O O O Mixture of 2- and 3-monophosphate derivatives CH2 O O RNA Shortened RNA H2O O RNA Shortened RNA FIGURE 8–8 Hydrolysis of RNA under alkaline conditions. The 2 hydroxyl acts as a nucleophile in an intramolecular displacement. The 2,3-cyclic monophosphate derivative is further hydrolyzed to a mixture of 2- and 3-monophosphates. DNA, which lacks 2 hydroxyls, is stable under similar conditions.