8.1 Some Basic Definitions and Conventions in Chapter 8 Nucleotides and Nucleic Acids

8.1 Some Basic Definitions and Conventions

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 of biological information and the transmission of that information from one generation to the next 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 information for the synthesis of a protein from one or a few genes to a ribosome. 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 are many RNAs (noncoding or ncRNAs) with a wide variety of special functions, described in depth in Part III.

Nucleotides and Nucleic Acids Have Characteristic Bases and Pentoses

A nucleotide has three characteristic components: (1) a nitrogenous (nitrogen-containing) base, (2) a pentose, and (3) one or more phosphates (Fig. 8-1). The molecule without a 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.

A two-part figure, a and b, includes part a that shows the basic structure of a nucleotide and part b that shows the basic structure of a purine and a pyrimidine. — FIGURE 8-1 Structure of nucleotides. (a) General structure showing the numbering convention for the pentose ring. This is a ribonucleotide. In deoxyribonucleotides the —OH group on the $2^{'}$ $2 prime$ carbon (in red) is replaced with —H. (b) The parent compounds of the pyrimidine and purine bases of nucleotides and nucleic acids, showing the numbering conventions.

FIGURE 8-1 Structure of nucleotides. (a) General structure showing the numbering convention for the pentose ring. This is a ribonucleotide. In deoxyribonucleotides the —OH group on the $2^{'}$ $2 prime$ carbon (in red) is replaced with —H. (b) The parent compounds of the pyrimidine and purine bases of nucleotides and nucleic acids, showing the numbering conventions.

Part a shows a five-membered ring in a box labeled pentose with O at the top vertex, between C 1 prime and C 4 prime. C 1 prime is bonded to a purine or pyrimidine base above the ring and outside the box and to H below the ring. C 1 prime is labeled with Greek letter beta. C 2 prime is bonded to H above the ring and highlighted O H below the ring; C 3 prime is bonded to H above the ring and O H below the ring; C 4 is bonded to C 5 prime above the ring and H below the ring; C 5 prime is bonded to 2 H and to O that is further bonded to P of a phosphate group that lies outside the box. P is bonded to O minus above, bonded to O minus to the left, and double bonded to O below. Part b shows a pyrimidine and a purine. The pyrimidine is a six-membered ring with N substituted for C at position 1 at the bottom, and positions numbered clockwise. It has C H at positions 2, 4, 5 and 6, N at position 3, and double bonds between positions 1 and 2, 3 and 4, and 5 and 6. The purine has a six-membered ring joined with a five-membered ring by its right side. The six-membered ring is numbered counterclockwise beginning with N at the top left vertex in position 1. The five-membered ring is numbered clockwise. The six-membered ring has N at positions 1 and 3, C H at positions 2 and 6, and double bonds between positions 2 and 3, 1 and 6, and 4 and 5. The bond between C 4 and C 5 is shared with the five-membered ring, which has N in position 7 at the top right vertex, C H in position 8 at the right side vertex, N H at position 9 at the bottom right vertex, and a double bond between positions 7 and 8.

Key Convention

The carbon atoms 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 and nucleosides the carbon numbers are given a prime ( $^{'}$ $prime$ ) 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-β-glycosyl bond to the $1^{'}$ $1 prime$ carbon of the pentose, and the phosphate is esterified to the $5^{'}$ $5 prime$ carbon. The N-β-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.

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 common pyrimidine is not the same in both: it is thymine (T) in DNA and uracil (U) in RNA. Only occasionally 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.

A figure shows the structures of the nitrogenous bases found in nucleic acids, including the major purine bases of adenine and guanine and the major pyrimidine bases of cytosine, thymine, and uracil. — 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.

The purines are adenine and guanine. Adenine has a six-membered ring joined with a five-membered ring by its right side. The six-membered ring has N at positions 1 and 3, C H at position 2, C bonded to N H 2 at position 6, and double bonds between positions 2 and 3, 1 and 6, and 4 and 5. The bond between C 4 and C 5 is shared with the five-membered ring, which has N in position 7 at the top right vertex, C H in position 8 at the right side vertex, N H at position 9 at the bottom right vertex, and a double bond between positions 7 and 8. Guanine has a similar structure to adenine except that N at position 1 is bonded to H, C at position 2 is bonded to N H 2 instead of H, C at position 6 is double bonded to O, and there is a single bond between C 1 and C 6. The pyrimidines are cytosine, thymine (D N A), and uracil (R N A). Cytosine has a six-membered ring with N in position 1 at the top left vertex, C 2 double bonded to O, N H in position 3 at the bottom vertex, C H in position 4 double bonded to C H at position 5, C 6 bonded to N H 2 at the top vertex, and a double bond between the N at position 1 and the C at position 6. Thymine (D N A) has a similar structure to cytosine except that N at position 1 is bonded to H and has a single bond to C at position 6, C 5 is bonded to C H 3 instead of H, and C 6 is double bonded to O. Uracil (R N A) has a similar structure to thymine except that C 5 is bonded to H instead of to C H 3.

TABLE 8-1 Nucleotide and Nucleic Acid Nomenclature
Base	Nucleoside	Nucleotide	Nucleic acid
Purines
Adenine	Adenosine Deoxyadenosine	Adenylate Deoxyadenylate	RNA DNA
Guanine	Guanosine Deoxyguanosine	Guanylate Deoxyguanylate	RNA DNA
Pyrimidines
Cytosine	Cytidine Deoxycytidine	Cytidylate Deoxycytidylate	RNA 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.

Nucleic acids have two kinds of pentoses. The recurring deoxyribonucleotide units of DNA contain $2^{'}$ $2 prime$ -deoxy-d-ribose, and the ribonucleotide units of RNA contain d-ribose. In nucleotides, both types of pentoses are in their β-furanose (closed five-membered ring) form (Fig. 8-3a). As Figure 8-3b shows, the pentose ring is not planar but occurs in one of a variety of conformations generally described as “puckered.”

A two-part figure, a and b, shows conformations of ribose with a linear structure and Haworth ring in part a and with two ball-and-stick models in part b. — FIGURE 8-3 Conformations of ribose. (a) In solution, the straight-chain (aldehyde) and ring (β-furanose) forms of free ribose are in equilibrium. RNA contains only the ring form, β-d-ribofuranose. Deoxyribose undergoes a similar interconversion in solution, but in DNA it exists solely as *β- $2^{'}$ $2 prime$* -deoxy-d-ribofuranose. (b) Ribofuranose rings in nucleotides can exist in four different puckered conformations. In all cases, four of the five atoms are nearly in a single plane. The fifth atom (C- $2^{'}$ $2 prime$ or C- $3^{'}$ $3 prime$ ) is on either the same (endo) side or the opposite (exo) side of the plane relative to the C- $5^{'}$ $5 prime$ atom.

Part a shows an aldehyde that can undergo a reversible reaction to produce Greek letter beta furanose. Aldose is a five-membered vertical chain numbered from top to bottom with C 1 bonded to H above and double bonded to O on the right; C 2, C 3, and C 4 all bonded to O H on the right and H on the left; and C 5 bonded to 2 H O H. Greek letter beta furanose is a numbered five-membered ring with O at the top vertex between C 4 and C 1; C 1 is bonded to O H above the ring and H below the ring; C 2 and C 3 are bonded to H above the ring and O below the ring; C 4 is bonded to C 5 above the ring and H below the ring; and C 5 is bonded to 2 H and O H. Part b shows two ball-and stick models of ribofuranose rings. The left-hand ring has a red O at the top right vertex with a stick pointing down, forward, and to the right to a gray atom labeled 1 prime. Atom 1 prime has a stick pointing up and to the right to a box labeled base. It has a stick pointing slightly up and to the left to a gray atom labeled C 2 prime endo and also a faded, dotted stick pointing slightly down and to the left to a dotted gray atom labeled C 2 prime exo. A stick extends down and to the left from C 2 prime endo to a gray atom labeled 3 prime at the bottom left vertex. A faded, dotted stick extends up from faded, dotted C 2 prime exo to 3 prime. A stick extends up, back, and slightly to the right to the gray atom labeled 4 prime, from which a stick extends to the right to the red O and a second stick extends up and slightly to the left to an atom labeled 5 prime. To the right of this molecule, a similar structure is shown with a stick from 1 prime to 2 prime in the exo position, which is no longer faded and dotted. C 2 prime endo is no longer shown. This produces a more open appearance to the ring. From 2 prime, a stick extends up and to the left to an atom labeled C 3 prime endo, which appears almost on top of C 4 prime. A stick extends back and to the right from C 3 prime endo to 4 prime. A faded, dotted stick extends to the left from C 2 prime to a faded, dotted atom labeled C 3 prime exo that is almost directly below C 3 prime endo. Another faded, dotted line extends from C 3 prime exo to 4 prime.

Key Convention

Although DNA and RNA seem to have two distinguishing features — different pentoses and the presence of uracil in RNA and thymine in DNA — it is the pentoses that uniquely define the identity of a nucleic acid. If the nucleic acid contains $2^{'}$ $2 prime$ -deoxy-d-ribose, it is DNA by definition, even if it contains uracil. Similarly, if the nucleic acid contains d-ribose, it is RNA, regardless of its base composition. The presence of uracil or thymine is not a defining characteristic.

Figure 8-4a gives the structures and names of the four major deoxyribonucleotides, the structural units of DNAs, and Figure 8-4b shows the four major ribonucleotides, the structural units of RNAs. Deoxyribonucleotides are also referred to as deoxyribonucleoside $5^{'}$ $5 prime$ -monophosphates, deoxynucleotides, and deoxynucleoside triphosphates; ribonucleotides are also called ribonucleoside $5^{'}$ $5 prime$ -monophosphates.

A two-part figure, a and b, shows the nucleosides and symbols for four deoxyribonucleotides in part a and for four ribonucleotides in part b. — 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 (a) DNA and (b) RNA are shown. For each nucleotide, the more common name is given, followed by the complete name in parentheses and symbols used to represent them. All abbreviations assume that the phosphate group is at the $5^{'}$ $5 prime$ position. The nucleoside portion of each molecule is shaded in light red. In this and the following illustrations, the ring carbons are not shown.

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 (a) DNA and (b) RNA are shown. For each nucleotide, the more common name is given, followed by the complete name in parentheses and symbols used to represent them. All abbreviations assume that the phosphate group is at the $5^{'}$ $5 prime$ position. The nucleoside portion of each molecule is shaded in light red. In this and the following illustrations, the ring carbons are not shown.

Each nucleotide is shown with its symbols and nucleoside. All nucleoside names are highlighted. All of the molecules have the sugar and nitrogenous base enclosed in a shaded box with phosphate outside of the box. Part a shows four deoxyribonucleotides. Deoxyadenylate (deoxyadenosine 5 prime monophosphate) has the symbols uppercase A; lowercase d uppercase A; and lowercase d uppercase A uppercase M uppercase P; and it has the nucleoside deoxyadenosine. It has a five-membered sugar ring with O at the top vertex; C 1 prime bonded to N at position 9 of adenine above the ring and H below the ring; C 2 prime bonded to H above and below the ring; C 3 prime bonded to H above the ring and O H below the ring; C 4 prime bonded to C 5 prime above the ring and H below the ring, and C 5 prime bonded to 2 H and to an O outside of the shaded box that is further bonded to P that is bonded to O minus above, double bonded to O below, and bonded to O minus to the left. Adenine has a six-membered ring joined by its right side to a five-membered ring. The six-membered ring has N at positions 1 and 3, C at position 6 bonded to N H 2, double bonds between positions 2 and 3 and positions 1 and 6, and a double bond between positions 4 and 5 that is shared with the five-membered ring. The five-membered ring has N at position 7, N at position 9 that is bonded to C 1 prime of the sugar below, and a double bond between position 1 and position 2. Deoxyguanylate (deoxyguanosine 5 prime monophosphate) has the symbols uppercase G, lowercase d uppercase G, and lowercase d uppercase G uppercase M uppercase P; and it has the nucleoside deoxyguanosine. It has a similar structure to deoxyadenylate except that the six-membered ring of the base has N bonded to H at position 1, C bonded to N H 2 at position 2, and C double bonded to O at position 6. Deoxythymidylate (deoxythymidine 5 prime monophosphate) has the symbols uppercase T, lowercase d uppercase T, and lowercase d uppercase T uppercase M uppercase P; and it has the nucleoside deoxythymidine. It has a similar structure to deoxyadenylate except that the base has a single six-membered ring with N at position 1 bonded to C 1 prime of the sugar ring below, C 2 at the bottom right vertex double bonded to O, N H at position 3 at the top right vertex, C at position 4 double bonded to O at the top vertex, C at position 5 at the left top vertex bonded to C H 3, and a double bond between positions 5 and 6. Deoxycytidylate (deoxycytidine 5 prime monophosphate) has the symbols uppercase C, lowercase d uppercase C, and lowercase d uppercase C uppercase M uppercase P; and it has the nucleoside deoxycytidine. It has a similar structure to deoxythymidylate except that the base has N at position 3 that is double bonded to C at position 4, a single bond from C at position 4 to N H 2, and no C H 3 bonded to C at position 5. Part b shows four ribonucleotides. Adenylate (adenosine 5 prime monophosphate) has the symbols uppercase A and uppercase A uppercase M uppercase P and has the nucleoside adenosine. It has a similar structure to deoxyadenylate except that C 2 prime of the sugar is bonded to H above the ring and O H below the ring. Guanylate (guanosine 5 prime monophosphate) has the symbols uppercase G and uppercase G uppercase M uppercase P and has the nucleoside guanosine. It has a similar structure to deoxyguanylate except that C 2 prime of the sugar is bonded to H above the ring and O H below the ring. Uridylate (uridine 5 prime monophosphate) has the symbols uppercase U and uppercase U uppercase M uppercase P and has the nucleoside uridine. It has a similar structure to deoxythymidylate except that C 2 prime of the sugar is bonded to H above the ring and O H below the ring and the nitrogenous base does not have C H 3 bound to C in position 5 at the upper right vertex. Cytidylate (cytidine 5 prime monophosphate) has the symbols uppercase C and uppercase C uppercase M uppercase P and has the nucleoside cytidine. It has a similar structure to deoxycytidylate except that C 2 prime of the sugar is bonded to H above the ring and O H below the ring.

Although nucleotides bearing the major purines and pyrimidines are most common, both DNA and RNA also 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. Hundreds of different modified bases are also found in RNAs, especially in rRNAs and tRNAs (see Fig. 8-25 and Fig. 26-22). The modifications are usually introduced by enzymes that act after the RNA or DNA is synthesized.

A two-part figure, a and b, shows the structures of the minor purine bases 5-methylcytidine, N superscript 6 methyladenosine, N superscript 2-methylguanosine, and 5-hydroxymethylcytidine in part a and of the minor pyrimidine bases inosine, pseudouridine, 7-methylguanosine, and 4-thiouridine in part 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, $N^{6}$ $upper N Superscript 6$ -methyladenosine in bacterial DNA, and 5-hydroxymethylcytidine in the DNA of animals and 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, uracil is attached through C-5.

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, $N^{6}$ $upper N Superscript 6$ -methyladenosine in bacterial DNA, and 5-hydroxymethylcytidine in the DNA of animals and 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, uracil is attached through C-5.

Part a shows four structures. 5-methylcytidine has a six-membered ring with N at position 1, C double bonded to O at position 2, N at position 3 bonded to ribose below, a double bond between positions 4 and 5, C 5 labeled with a number 5 and bonded to C H 3, C 6 bonded to N H 2, and a double bond between positions 6 and 1. N superscript 6 end superscript methyladenosine has a six-membered ring joined with a five-membered ring. The six-membered ring has N at position 1, a double bond between positions 2 and 3, N at position 3, a double bond at positions 4 to 5 shared with the five-membered ring, C at position 6 labeled with a number 6 and bonded to N H that is further bonded to C H 3, and a double bond between C 1 and C 6. The five-membered ring has N at position 7, a double bond between positions 7 and 8, and N at position 9 that is bonded to ribose below. N superscript 2 end superscript -methylguanosine has a similar structure to N superscript 6 end superscript -methyladenosine except that N at position 1 is bonded to H, C 2 is labeled with a number 2 and bonded to N H that is further bonded to C H 3, C 5 is not labeled, and C 6 is double bonded to O. 5-hydroxymethylcytidine has a similar structure to 5-methylcytidine except that C 5 is bonded to C H 2 O H. Part b also shows four structures. Inosine has a six-membered ring joined with a five-membered ring. The six-membered ring has N H at position 1, a double bond between positions 2 and 3, N at position 3, a double bond at positions 4 to 5 shared with the five-membered ring, and C at position 6 that is double bonded to O. The five-membered ring has N at position 7, a double bond between positions 7 and 8, and N at position 9 that is bonded to ribose below. 7-methylguanosine has a similar structure to inosine except that the six-membered ring has C at position 2 that is bonded to N H 2 and the five-membered ring has N plus at position 7 that is labeled with the number 7 and bonded to C H 3. Pseudouridine has a six-membered ring with N H at position 1, C 2 double bonded to O, N H at position 3, a double bond between C 4 and C 5, C 5 labeled with a number 5 and bonded to ribose, and C 6 double bonded to O. 4-thiouridine has a similar structure to pseudouridine except that N at position 1 is at the bottom vertex and bonded to ribose below, there is a double bond between C 2 and C 3, C 4 is labeled with a number 4 and double bonded to S, there is an N H at position 5, and C 6 is double bonded to O.

Key Convention

The nomenclature for the minor bases can be confusing. Like the major bases, many minor bases have common names — hypoxanthine, for example, shown as its nucleoside inosine in Figure 8-5. When an atom in the purine ring or the 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 (i.e., 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 $N^{6}$ $upper N Superscript 6$ ; similarly, the carbonyl oxygen and amino nitrogen at C-6 and C-2 of guanine are $O^{6}$ $upper O Superscript 6$ and $N^{2}$ $upper N squared$ , respectively. Examples of this nomenclature are $N^{6}$ $upper N Superscript 6$ -methyladenosine and $N^{2}$ $upper N squared$ -methylguanosine (Fig. 8-5).

Cells also contain nucleotides with phosphate groups in positions other than on the $5^{'}$ $5 prime$ carbon (Fig. 8-6). Ribonucleoside $2^{′}$ $bold 2 bold prime$ , $3^{′}$ $bold 3 bold prime$ -cyclic monophosphates are isolatable intermediates, and ribonucleoside $3^{'}$ $bold 3 prime$ -monophosphates are end products of the hydrolysis of RNA by certain ribonucleases. Other variations are adenosine $3^{'}$ $3 prime$ , $5^{'}$ $5 prime$ -cyclic monophosphate (cAMP) and guanosine $3^{'}$ $3 prime$ , $5^{'}$ $5 prime$ -cyclic monophosphate (cGMP), considered at the end of this chapter.

A figure shows four adenosine monophosphates: adenosine 5 prime-monophosphate, adenosine 2 prime-monophosphate, adenosine 3 prime-monophosphate, and adenosine 2 prime, 3 prime-cyclic monophosphate. — FIGURE 8-6 Some adenosine monophosphates. Adenosine $2^{'}$ $2 prime$ -monophosphate, $3^{'}$ $3 prime$ -monophosphate, and $2^{'}$ $2 prime$ , $3^{'}$ $3 prime$ -cyclic monophosphate are formed by enzymatic and alkaline hydrolysis of RNA.

All of the molecules have a five-membered sugar ring with O at the top vertex. Adenosine 5 prime-monophosphate has C 1 prime bonded to adenine above the ring and H below the ring; C 2 prime and C 3 prime bonded to H above the ring and O H below the ring; C 4 prime bonded to C 5 prime above the ring and H below the ring; and C 5 prime bonded to 2 H and further bonded to O that is bonded to P that is bonded to O minus above, bonded to O minus to the left, and double bonded to O below. C 1 prime, C 2 prime, C 3 prime, C 4 prime, and C 5 prime are all labeled with numbers. Adenosine 2 prime-monophosphate has a similar structure to adenonsine 5 prime-monophosphate except that C 2 prime is bonded to H above the ring and to O below the ring that is further bonded to P that is bonded to O minus on the right, double bonded to O below, and bonded to O minus on the left; and C 5 prime is bonded to 2 H and O H. C 2 prime is labeled as 2 prime. Adenosine 3 prime-monophosphate has a similar structure to adenonsine 2 prime-monophosphate except that the phosphate group is bonded to C 3 prime below the ring instead of to C 2 prime, which is bonded to O H below the ring. C 3 prime is labeled as 3 prime. Adenosine 2 prime, 3 prime-cyclic monophosphate has a similar structure to adenosine 3 prime-monophosphate except that C 2 prime is bonded to O that is further bonded to P to the left that is bonded to O minus to the lower right, double bonded to O to the lower left, and bonded to O to the upper right that is further bonded to C 3 prime above.

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 $5^{'}$ $5 prime$ -phosphate group of one nucleotide unit is joined to the $3^{'}$ $3 prime$ -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 $p K_{a}$ $p upper K Subscript a Baseline$ 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.

A figure shows the phosphodiester linkages in the covalent backbones of D N A and R N A. — 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 $5^{'}$ $5 prime$ and $3^{'}$ $3 prime$ ends of the macromolecule may be free or may have an attached phosphoryl group.

D N A and R N A are each shown as a vertical chain of 3 nucleotides with the 5 prime end at the top and the 3 prime end at the bottom. A vertical arrow points from 5 prime above to 3 prime below. The top nucleotide unit of D N A is adenine. It has a five-membered ring with O at the top vertex between C 4 prime and C 1 prime; C 1 prime bonded to A above the ring and H below the ring; C 2 prime bonded to H above and below the ring; C 3 prime bonded to H above the ring and to O in a shaded box below that is further bonded; C 4 prime bonded to C 5 prime above and H below, and C 5 prime bonded to 2 H and to O above that is further bonded to P that is double bonded to O on the right, bonded to O minus above, and bonded to O minus to the left. The O bonded to C 3 prime of this nucleotide is part of a phosphate group that is enclosed in a shaded box labeled phosphodiester linkage. The O is bonded to P below that is double bonded to O on the right, bonded to O below that is further bonded to C 5 prime of a sugar below that is not in the box, and bonded to O minus on the left. The nucleotide unit below has a similar structure to the top nucleotide unit except that it has T instead of A bonded to C 1 prime and the O bonded to C 3 prime is not in a shaded box. The O bonded to C 3 prime is bonded to a P below that is double bonded to O on the right, O below that is bonded to C 5 prime of the nucleotide unit below, and to O minus on the left. The third nucleotide unit below is similar except that it has G instead of T or A bonded to C 1 prime, and C 3 prime is bonded to H above and to O below that is further bonded to H. The R N A molecule is similar to the D N A molecule except that the nucleotides, from top to bottom, have U, G, and C instead of A, T, and G and each nucleotide unit has C 2 prime bonded to H above and O H below instead of being bonded to H above and below.

Key Convention

All the phosphodiester linkages in DNA and RNA have the same orientation along the chain (Fig. 8-7), giving each linear nucleic acid strand a specific polarity and distinct $5^{'}$ $5 prime$ and $3^{'}$ $3 prime$ ends. By definition, the $5^{'}$ $bold 5 prime$ end lacks a nucleotide attached at the $5^{'}$ $5 prime$ position, and the $3^{'}$ $3 prime$ end lacks a nucleotide attached at the $3^{'}$ $3 prime$ position. Other groups (most often one or more phosphates) may be present on one or both ends. The $5^{'} \to 3^{'}$ $5 prime right-arrow 3 prime$ orientation of a strand of nucleic acid refers to the ends of the strand and the orientation of individual nucleotides, not the orientation of the individual phosphodiester bonds linking its constituent nucleotides.

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 $2^{'}$ $2 prime$ -hydroxyl groups in RNA (absent in DNA) are directly involved in the process. Cyclic $2^{'}$ $2 prime$ , $3^{'}$ $3 prime$ -monophosphate nucleotides are the first products of the action of alkali on RNA and are rapidly hydrolyzed further to yield a mixture of $2^{'}$ $2 prime$ - and $3^{'}$ $3 prime$ -nucleoside monophosphates (Fig. 8-8).

A figure shows the hydrolysis of R N A under alkaline conditions. — FIGURE 8-8 Hydrolysis of RNA under alkaline conditions. The $2^{'}$ $2 prime$ hydroxyl acts as a nucleophile in an intramolecular displacement. The $2^{'}$ $2 prime$ , $3^{'}$ $3 prime$ -cyclic monophosphate derivative is further hydrolyzed to a mixture of $2^{'}$ $2 prime$ - and $3^{'}$ $3 prime$ -monophosphates. DNA, which lacks $2^{'}$ $2 prime$ hydroxyls, is stable under similar conditions.

R N A is shown on the left as two nucleotide units arranged vertically. The top unit has a five-membered sugar ring with O at the top vertex, C 1 prime bonded to base subscript 1 end subscript above and H below, C 2 prime bonded to H above and O H below, C 3 prime bonded to H above and O below that is further bonded; C 4 prime bonded to C 5 above and H below, and C 5 prime bonded to 2 H and O that is further bonded to P that is double bonded to O on the right, bonded to O minus on the left, and further bonded above. The O beneath C 3 prime is further bonded to P that is double bonded to O on the right, bonded to O below that is further bonded to C 5 prime of the sugar below, and bonded to O minus on the left. The bottom nucleotide unit has a similar structure to the top nucleotide unit except that C 1 prime is bonded to base subscript 2 end subscript and C 3 prime is bonded to O below that is further bonded to P that is double bonded to O on the right, bonded to O minus on the left, and further bonded below. O H minus is shown near the right bottom of the top nucleotide unit with a highlighted arrow pointing from the minus to H of the O H bonded to C 2 prime of the top nucleotide unit. A highlighted arrow points from the bond between this H and the O bonded to C 2 prime to the P in the phosphodiester linkage beneath, connecting the two nucleotide units. A highlighted arrow points from the bond connecting this P to O that is bonded to C 5 prime of the bottom ring to the same O. To the right of R N A, an arrow labeled highlighted H plus points to the right, where two molecules are shown. The top molecule is labeled 2 prime, 3 prime-cyclic monophosphate derivative. It has the same structure as the top nucleotide unit on the left except that C 2 prime is bonded to O below that has a bond down and to the left to P that is double bonded to O to its lower right, bonded to O to its lower left, and bonded to O to its upper left that is further bonded to C 3 prime of the same ring. An arrow pointing to the right of this molecule shows that the addition of H 2 O produces a mixture of 2 prime- and 3 prime- monophosphate derivatives. The bottom molecule, produced from the bottom nucleotide unit, is labeled shortened R N A. It has a similar structure to the bottom nucleotide unit except that C 5 is bonded to 2 H and to O bonded to a highlighted H.

The nucleotide sequences of nucleic acids can be represented schematically, as illustrated below by a segment of DNA with five nucleotide units. The phosphate groups are symbolized by , and each deoxyribose is symbolized by a vertical line, from $C- 1^{'}$ $upper C hyphen 1 prime$ at the top to $C- 5^{'}$ $upper C hyphen 5 prime$ at the bottom (but keep in mind that the sugar is always in its closed-ring β-furanose form in nucleic acids). The connecting lines between nucleotides (which pass through ) are drawn diagonally from the middle ( $C- 3^{'}$ $upper C hyphen 3 prime$ ) of the deoxyribose of one nucleotide to the bottom ( $C- 5^{'}$ $upper C hyphen 5 prime$ ) of the next.

A figure shows a schematic representation of the nucleotide sequence of an amino acid.

The 5 prime end is on the left and the 3 prime end is on the right. A circle labeled P is at the left with a short diagonal line extending downward to its right. The diagonal line meets a long vertical line that extends up to A. A diagonal line extends from just below the middle of this vertical line to P in a circle, then continues down to meet a second vertical line that extends up to C. A diagonal line extends from just below the middle of this vertical line to P in a circle, then continues down to meet a third vertical line that extends up to G. A diagonal line extends from just below the middle of this vertical line to P in a circle, then continues down to meet a third vertical line that extends up to T. A diagonal line extends from just below the middle of this vertical line to P in a circle, then continues down to meet a third vertical line that extends up to A. A diagonal line extends from just below the middle of this vertical line to end at O H at the same height where P in a circle was for the other units. This produces a horizontal line of circles labeled P with O H instead of P in the right-hand position.

Some simpler representations of this pentadeoxyribonucleotide are ${pA-C-G-T-A}_{OH}$ $pA hyphen upper C hyphen upper G hyphen upper T hyphen upper A Subscript OH$ , pApCpGpTpA, and pACGTA.

Key Convention

The sequence of a single strand of nucleic acid is always written with the $5^{'}$ $5 prime$ end at the left and the $3^{'}$ $3 prime$ end at the right — that is, in the $5^{'} \to 3^{'}$ $5 prime right-arrow 3 prime$ direction.

A short nucleic acid is referred to as an oligonucleotide. The definition of “short” is somewhat arbitrary, but polymers containing 50 or fewer nucleotides are generally called oligonucleotides. A longer nucleic acid is called a polynucleotide.

The Properties of Nucleotide Bases Affect the Three-Dimensional Structure of Nucleic Acids

Free pyrimidines and purines are weakly basic compounds and thus are called bases. The purines and pyrimidines common in DNA and RNA are aromatic molecules (Fig. 8-2), a property with important consequences for the structure, electron distribution, and light absorption of nucleic acids. Electron delocalization among atoms in the ring gives most of the bonds in the ring partial double-bond character. One result is that pyrimidines are planar molecules and purines are very nearly planar, with a slight pucker. Free pyrimidine and purine bases may exist in two or more tautomeric forms depending on the pH. Uracil, for example, occurs in several readily interconverted forms called tautomers — lactam, lactim, and double lactim forms (Fig. 8-9). The structures shown in Figure 8-2 are the tautomers that predominate at pH 7.0. All nucleotide bases absorb UV light, and nucleic acids are characterized by a strong absorption at wavelengths near 260 nm (Fig. 8-10).

A figure shows tautomeric forms of uracil. — FIGURE 8-9 Tautomeric forms of uracil. The lactam form predominates at pH 7.0; the other forms become more prominent as pH decreases. The other free pyrimidines and the free purines also have tautomeric forms, but they are more rarely encountered.

A graph shows the absorption spectra of common nucleotides. — FIGURE 8-10 Absorption spectra of the common nucleotides. The spectra are shown as the variation in molar extinction coefficient with wavelength. The molar extinction coefficients at 260 nm and pH 7.0 ( $ε_{260}$ $epsilon 260$ ) are listed in the table. The spectra of corresponding ribonucleotides and deoxyribonucleotides, as well as the nucleosides, are essentially identical. For mixtures of nucleotides, a wavelength of 260 nm (dashed vertical line) is used for absorption measurements.

FIGURE 8-10 Absorption spectra of the common nucleotides. The spectra are shown as the variation in molar extinction coefficient with wavelength. The molar extinction coefficients at 260 nm and pH 7.0 ( $ε_{260}$ $epsilon 260$ ) are listed in the table. The spectra of corresponding ribonucleotides and deoxyribonucleotides, as well as the nucleosides, are essentially identical. For mixtures of nucleotides, a wavelength of 260 nm (dashed vertical line) is used for absorption measurements.

The horizontal axis shows wavelength in n m ranging from 230 to over 280 and labeled in increments of 10. The vertical axis shows molar extinction coefficient, Greek letter epsilon, ranging from below 2,000 to above 14,000 and labeled in increments of 2,000. A dotted vertical line extends upward from 260 on the horizontal axis. A table labeled molar extinction coefficient at 260 n m, Greek letter epsilon subscript 260 (M superscript minus 1 c m superscript minus 1) has three columns showing curve color, molecule, and molar extinction coefficient as follows: Row 1: blue, A M P, 15,400; Row 2: green, G M P, 11,700; Row 3: orange, U M P, 9,900; Row 4: purple, lowercase d T M P, 9,200; Row 5: red, C M P, 7,500. On the graph, the curve labeled G M P begins at (230, 4,500), rises to a peak at (250, 13,500), decreases to (275, 9500), then bends to form a rounded curve to (280, 6,000) before dropping rapidly to end at a height of 3,000 at the far end of the horizontal axis. The curve labeled A M P runs below the G M P curve from (230, 2,300) until it intersects the G M P curve at (252, 13,500), then continues to increase to a peak at 260 on the horizontal axis and at almost the top of the vertical axis (around 14,900). It then decreases rapidly to (275, 2,200) before curving gradually to end just above the horizontal axis at the far right of the graph. The curve labeled U M P begins below the A M P curve at (230, 1,990), rises to (243, 4,000), then rises more slowly to a peak at (260, 9,500) before decreasing to end just above the A M P curve at the far right of the horizontal axis at about (310, 200). The curve labeled lowercase d T M P begins at (230, 1,900), rises to (245, 4,000), then rises more slowly to peak at (268, 9,450) before curving down to end at the far right side of the graph at (310, 2,300). The curve labeled C M P begins at (230, 8,100), drops slowly to (245, 6,000), rises to (274, 9,000), and then drops to end above all of the other curves at (310, 3,500). All data are approximate.

The purine and pyrimidine bases are hydrophobic and relatively insoluble in water at the near-neutral pH of the cell. At acidic or alkaline pH, the bases become charged and their solubility in water increases. Hydrophobic stacking interactions in which two or more bases are positioned with the planes of their rings parallel (like a stack of coins) are one of two important modes of interaction between bases in nucleic acids. The stacking also involves a combination of van der Waals and dipole-dipole interactions between the bases. Base stacking helps to minimize contact of the bases with water, and base-stacking interactions are very important in stabilizing the three-dimensional structure of nucleic acids, as described later.

The functional groups of pyrimidines and purines are ring nitrogens, carbonyl groups, and exocyclic amino groups. Hydrogen bonds involving the amino and carbonyl groups are the most important mode of complementary interaction between two (and occasionally three or four) complementary strands of nucleic acid. The most common hydrogen-bonding patterns are those defined by James D. Watson and Francis Crick in 1953, in which A bonds specifically to T (or U) and G bonds to C (Fig. 8-11). These two types of base pairs predominate in double-stranded DNA and RNA, and the tautomers shown in Figure 8-2 are responsible for these patterns. It is this specific pairing of bases that permits the duplication of genetic information.

A figure shows hydrogen-bonding in double stranded D N A next to photographs of James D. Watson and Francis Crick. — FIGURE 8-11 Hydrogen-bonding patterns in the base pairs defined by Watson and Crick. Here, as elsewhere, hydrogen bonds are represented by three blue lines.

A vertical piece of double-stranded D N A is shown on the left with two base pairs expanded in the center of the image, and two photos are shown on the right. The left strand of D N A runs from 5 prime at the top to 3 prime at the bottom. It begins with a circle connected to a five-membered ring that is connected to another circle and so on, with a total of 9 nucleotide units. Each five-membered ring is connected by its right side vertex to a single hexagonal ring representing a pyrimidine or to a five-membered ring that is joined with six-membered ring representing a purine. From top to bottom, the sequence of purines and pyrimidines is C, A, A, T, C, G, T, C, and A. The right-hand strand has its 3 prime end on top and its 5 prime end on the bottom. It has a similar structure to the first strand butmirrored left to right. From top to bottom, the sequence of purines and pyrimidines is G, T, T, A, G, C, A, G, and T. Sets of three blue vertical lines are shown connecting the purines and pyrimidines between the two strands. Each C has three sets of vertical lines connecting it with a G, and each A has two sets of vertical lines connecting it with a T. A closeup of the bonds between adenine and thymine is shown to the right. Adenine has a five-membered ring on the left and a six-membered ring on the right. The six-membered ring has N in position 1 at the top right vertex connected by three vertical lines with H bonded to N at the bottom left vertex (position 1) of thymine. The six-membered ring has C 2 bonded to H, double bonds between C 2 and C 3 and C 6 and the N at position 1. It also has a double bond between C 3 and C 4 that is shared with the five-membered ring. The five-membered ring has N at position 7 double bonded to C H at position 8 and N at position 9 that is bonded to C 1 prime. C 6 of the six-membered ring is bonded to N H 2 ,and there are three vertical lines connecting one of the H atoms to O that is double bonded to C 6 of thymine. The distance between N bonded to C 6 of adenine and O bonded to C 6 of thymine is 2.8 Angstroms. The distance from N in position 1 of adenine to h bonded to N in position 1 of thymine is 3.0 Angstroms. Thymine has N 1 bonded to H that is connected by three vertical lines to N 1 of adenine, C 2 double bonded to O at the lower left, N in position 3 bonded to C 1 prime, C 4 bonded to H, C 5 bonded to C H 3, and C 6 double bonded to O that is connected to H of the N H 2 bonded to C 6 in adenine. The distance between the C 1 prime bonded to N in position 9 of adenine and the C 1 prime bonded to N in position 3 of thymine is 11.1 Angstroms. Below this closeup, a similar illustration shows three hydrogen bonds, represented as sets of three vertical lines, connecting cytosine and guanine. Guanine has a six-membered ring on the right joined with a five-membered ring on the left. The six-membered ring has N in position 1 bonded to H that is connected by three vertical lines to N in position 1 of cytosine with a distance of 3.0 Angstroms between the N atoms. The six-membered ring of guanine has C in position 2 that is bonded to N H 2 of which one H is connected by three vertical lines to O that is double bonded to C at position 2 of cytosine with a distance of 2.9 Angstroms between N and O. There is a double bond between C 2 and N in position 3. There is a double bond between C 4 and C 5 that is shared with the five-membered ring, and C 6 double bonded to O that is connected by three vertical lines to an H of N H 2 bonded to C 6 of cytosine with a distance of 2.9 Angstroms between the O and the N. The five-membered ring has N at position 7, a double bond between position 7 and position 8, C bonded to H at position 8, and N at position 9 that is further bonded to C 1 prime. Cytosine has N in position 1 connected by three vertical lines to H bonded to N in position 1 of guanine, C 2 double bonded to O that is connected by three vertical lines to H of N H 2 bonded to C 2 of guanine, N in position 3 that is bonded to C 1 prime that is a distance of 10.8 Angstroms from C 1 prime bonded to guanine, C 4 bonded to H, a double bond between C 4 and C 5, C 5 bonded to H, and C 6 bonded to N H 2 of which one H is connected by three vertical lines to O that is double bonded to C 6 of guanine. The photo of James D. Watson shows a man with short hair in a suit and tie smiling. The photo of Francis Crick, 1916 to 2004, shows a balding man in a suit and tie smiling at the camera.

SUMMARY 8.1 Some Basic Definitions and Conventions

A nucleotide consists of a nitrogenous base (purine or pyrimidine), a pentose sugar, and one or more phosphate groups. If no phosphate is present, the combination of the pentose sugar and the nitrogenous base is a nucleoside.
Nucleic acids are polymers of nucleotides, joined together by phosphodiester linkages between the $5^{'}$ $5 prime$ -hydroxyl group of one pentose and the $3^{'}$ $3 prime$ -hydroxyl group of the next.
There are two types of nucleic acid: RNA and DNA. The nucleotides in RNA contain ribose, and the common pyrimidine bases are uracil and cytosine. In DNA, the nucleotides contain $2^{'}$ $2 prime$ -deoxyribose, and the common pyrimidine bases are thymine and cytosine. The primary purines are adenine and guanine in both RNA and DNA. The nitrogenous bases have a hydrophobic character and interact via base-stacking interactions.