Nucleotides: Structure, Function, & Replication PDF

S E C T I O N Structure, Function, & VII Replication of Informational Macromolecules C H A...

S E C T I O N Structure, Function, & VII Replication of Informational Macromolecules C H A P T E R Nucleotides Victor W. Rodwell, PhD 32 O B J E C TI V E S Write structural ormulas to represent the amino- and oxo-tautomers o a purine and o a pyrimidine and state which tautomer predominates under After studying this chapter, physiologic conditions. you should be able to: Reproduce the structural ormulas or the principal nucleotides present in DNA and in RNA and the less common nucleotides 5-methylcytosine, 5-hydroxymethylcytosine, and pseudouridine (ψ). Represent d-ribose or 2-deoxy- d-ribose linked as either a syn or an anti conormer to a purine, name the bond between the sugar and the base, and indicate which conormer predominates under most physiologic conditions. Number the C and N atoms o a pyrimidine ribonucleoside and o a purine deoxyribonucleoside, including using a primed numeral or C atoms o the sugars. Compare the phosphoryl group transer potential o each phosphoryl group o a nucleoside triphosphate. Outline the physiologic roles o the cyclic phosphodiesters cAMP and cGMP. Appreciate that polynucleotides are directional macromolecules composed o mononucleotides linked by 3′ → 5′-phosphodiester bonds. Be amiliar with the abbreviated representations o polynucleotide structures such as pTpGpT or TGCATCA, or which the 5′-end is always shown at the let and all phosphodiester bonds are 3′ → 5′. For specic synthetic analogs o purine and pyrimidine bases and their derivatives that have served as anticancer drugs, indicate in what ways these compounds inhibit metabolism. 329 330 SECTION VII Structure, Function, & Replication o Inormational Macromolecules NH2 NH O OH BIOMEDICAL IMPORTANCE In aition to serving as precursors o nucleic acis, purine an pyrimiine nucleoties participate in metabolic unctions as iverse as energy metabolism, protein synthesis, regulation FIGURE 32–2 Tautomerism of the oxo and amino functional o enzyme activity, an signal transuction. When linke to groups of purines and pyrimidines. vitamins or vitamin erivatives, nucleoties orm a portion o many coenzymes. As the principal onors an acceptors o pyrimiines with an NH2 group are weak bases (pKa values phosphoryl groups in metabolism, nucleosie tri- an iphos- 3-4), although the proton present at low pH is associate, not phates such as AP an ADP are the principal players in the as one might expect with the exocyclic amino group, but with energy transuctions that accompany metabolic interconver- a ring nitrogen, typically N1 o aenine, N7 o guanine, an N3 sions an oxiative phosphorylation. Linke to sugars or lip- o cytosine. he planar character o purines an pyrimiines is, nucleosies constitute key biosynthetic intermeiates. he acilitates their close association, or “stacking,” that stabilizes sugar erivatives UDP-glucose an UDP-galactose participate ouble-strane DNA (see Chapter 34). he oxo an amino in sugar interconversions an in the biosynthesis o starch an groups o purines an pyrimiines exhibit keto–enol an glycogen. Similarly, nucleosie-lipi erivatives such as CDP- amine–imine tautomerism (Figure 32–2), although physi- acylglycerol are intermeiates in lipi biosynthesis. Roles that ologic conitions strongly avor the amino an oxo orms. nucleoties perorm in metabolic regulation inclue AP- epenent phosphorylation o key metabolic enzymes, allo- steric regulation o enzymes by AP, ADP, AMP, an CP, an Nucleosides Are N-Glycosides control by ADP o the rate o oxiative phosphorylation. he Nucleosides are erivatives o purines an pyrimiines that cyclic nucleoties cAMP an cGMP serve as the secon mes- have a sugar linke to a ring nitrogen o a purine or pyrimi- sengers in hormonally regulate events, an GP an GDP ine. Numerals with a prime (eg, 2′ or 3′) istinguish atoms play key roles in the cascae o events that characterize signal o the sugar rom those o the heterocycle. he sugar in ribo- transuction pathways. In aition to the central roles that nucleosides is d-ribose, an in deoxyribonucleosides is nucleoties play in metabolism, their meical applications 2-eoxy-d-ribose. Both sugars are linke to the heterocycle by inclue the use o synthetic purine an pyrimiine analogs an a-N-glycosidic bond, almost always to the N-1 o a pyrimi- that contain halogens, thiols, or aitional nitrogen atoms in ine or to N-9 o a purine (Figure 32–3). the chemotherapy o cancer an AIDS, an as suppressors o the immune response uring organ transplantation. Nucleotides Are Phosphorylated CHEMISTRY OF PURINES, Nucleosides PYRIMIDINES, NUCLEOSIDES, Mononucleotides are nucleosides with a phosphoryl group esteriie to a hyroxyl group o the sugar. he 3′- an & NUCLEOTIDES 5′-nucleoties are nucleosies with a phosphoryl group on the 3′- or 5′-hyroxyl group o the sugar, respectively. Since most Purines & Pyrimidines Are nucleoties are 5′-, the preix “5′-” usually is omitte when Heterocyclic Compounds naming them. UMP an AMP thus represent nucleoties Purines an pyrimiines are aromatic heterocycles, cyclic with a phosphoryl group on C-5 o the pentose. Aitional structures that contain, in aition to carbon, other (hetero) phosphoryl groups, ligate by acid anhydride bonds to the atoms such as nitrogen. Note that the smaller pyrimiine phosphoryl group o a mononucleotie, orm nucleoside molecule has the longer name an the larger purine mol- diphosphates an triphosphates (Figure 32–4). ecule the shorter name, an that their six-atom rings are numbere in opposite irections (Figure 32–1). Purines or Heterocylic N-Glycosides Exist as Syn and Anti Conformers H H 6 7 4 Steric hinrance by the heterocyclic ring blocks ree rotation C 5 N C 5 about the β-N-glycosiic bon o nucleosies or nucleoties. 1 3 N C 8 N CH 2 CH Both thereore exist as noninterconvertible syn or anti con- C C HC CH formers (Figure 32–5). While both syn an anti conormers H N 4 N9 2 N 6 3 H 1 occur in nature, the anti conormers preominate. Purine Pyrimidine Table 32–1 lists the major purines an pyrimiines an their nucleosie an nucleotie erivatives. Single-letter FIGURE 32–1 Purine and pyrimidine. The atoms are num- abbreviations are use to ientiy aenine (A), guanine (G), bered according to the international system. cytosine (C), thymine (), an uracil (U), whether ree or  CHAPTER 32 Nucleotides 331 NH2 NH2 O O N N N HN N HN 9 1 9 1 N O H2N N O N N N N HO HO HO HO O O O O OH OH OH OH OH OH OH OH Adenosine Cytidine Guanosine Uridine FIGURE 32–3 Ribonucleosides, drawn as the syn conformers. present in nucleosies or nucleoties. he preix “” (eoxy) Nucleotides Are Polyfunctional Acids inicates that the sugar is 2′-eoxy-d-ribose (eg, in AP) he primary an seconary phosphoryl groups o nucleosies (Figure 32–6). have pKa values o about 1.0 an 6.2, respectively. Since purines an pyrimiines are neutral at physiologic pH, nucleoties Modification of Polynucleotides bear a net negative charge. he pKa values o the seconary Can Generate Additional Structures phosphoryl groups are such that they can serve either as pro- Small quantities o aitional purines an pyrimiines occur in ton onors or as proton acceptors at pH values approximately DNA an RNAs. Examples inclue 5-methylcytosine o bacte- two or more units above or below neutrality. rial an human DNA, 5-hyroxymethylcytosine o bacterial an viral nucleic acis, an mono- an the i-N-methylate aenine Nucleotides Absorb Ultraviolet Light an guanine o mammalian messenger RNAs (Figure 32–7) that he conjugate ouble bons o purine an pyrimiine unction in oligonucleotie recognition an in regulating the erivatives absorb ultraviolet light. While their spectra are hal-lives o RNAs. Free heterocyclic bases inclue hypoxan- pH-epenent, at pH 7.0 all the common nucleoties absorb thine, xanthine, an uric aci (Figure 32–8), intermeiates light at wavelengths aroun 260 nm. he concentration o in the catabolism o aenine an guanine (see Chapter 33). nucleoties an nucleic acis thus oten is expresse in terms Methylate heterocycles o plants inclue the xanthine eriva- o “absorbance at 260 nm.” he mutagenic eect o ultraviolet tives caeine o coee, theophylline o tea, an theobromine o light is ue to its absorption by nucleoties in DNA that results cocoa (Figure 32–9). in chemical moiications (see Chapter 35). Nucleotides Serve Diverse NH2 N Physiologic Functions N In aition to their roles as precursors o nucleic acis, AP, O– O O– N N GP, UP, CP, an their erivatives each serve unique HO P O P O P O CH2 – O NH2 NH2 O O O N N N N OH OH N N N N HO HO O O Syn Anti OH OH OH OH FIGURE 32–5 The syn and anti conformers of adenosine FIGURE 32–4 ATP, its diphosphate, and its monophosphate. differ with respect to orientation about the N-glycosidic bond. 332 SECTION VII Structure, Function, & Replication o Inormational Macromolecules TABLE 32–1 Purine Bases, Ribonucleosides, and Ribonucleotides Purine or Pyrimidine X=H X = Ribose X = Ribose Phosphate NH2 Adenine Adenosine Adenosine monophosphate (AMP) N N N N X O Guanine Guanosine Guanosine monophosphate (GMP) H N N H2N N N X NH2 Cytosine Cytidine Cytidine monophosphate (CMP) N O N X O Uracil Uridine Uridine monophosphate (UMP) H N O N X O Thymine Thymidine Thymidine monophosphate (TMP) H CH3 N O N dX physiologic unctions iscusse in other chapters. Selecte is about 1 mmol/L. he intracellular concentration o the examples inclue the role o AP as the principal biologic inormation carrier cAMP (about 1 nmol/L) is six orers o transucer o ree energy, an the secon messenger cAMP magnitue below that o AP. Other examples inclue ae- (Figure 32–10). he mean intracellular concentration o nosine 3′-phosphate-5′-phosphosulate (Figure 32–11), the AP, the most abunant ree nucleotie in mammalian cells, sulate onor or sulate proteoglycans (see Chapter 50) an NH2 NH2 O O N N CH3 N N HN HN N N N N O N O N O O O O O O O O O O O O P P P P – O O– – O O– – O O– – O O– OH OH OH H OH OH OH H AMP dAMP UMP TMP FIGURE 32–6 Structures of AMP, dAMP, UMP, and TMP.  CHAPTER 32 Nucleotides 333 NH2 NH2 CH3 O CH3 CH2OH H3C N N N N O O N N O N N H H CH3 5-Methylcytosine 5-Hydroxymethylcytosine FIGURE 32–9 Caffeine, a trimethylxanthine. The dimethyl- H3C CH3 xanthines theobromine and theophylline are similar but lack the N O CH3 methyl group at N-1 and at N-7, respectively. N N N HN 7 N H2N N N N H NH2 O Dimethylaminoadenine 7-Methylguanine N N N HN FIGURE 32–7 Four uncommon naturally occurring pyrimi- dines and purines. N H2N N N N O CH2 O CH2 or sulate conjugates o rugs; an the methyl group onor O O S-aenosylmethionine (Figure 32–12). GP serves as an allo- – – O P O O P O steric regulator an as an energy source or protein synthe- sis, an cGMP (Figure 32–10) serves as a secon messenger O O in response to nitric oxie (NO) uring relaxation o smooth OH OH muscle (see Chapter 51). UDP-sugar erivatives participate in sugar epimerizations FIGURE 32–10 cAMP, 3′,5′-cyclic AMP, and cGMP, 3′, 5′-cyclic GMP. an in biosynthesis o glycogen (see Chapter 18), glucosyl isaccharies, an the oligosaccharies o glycoproteins an proteoglycans (see Chapters 46 & 50). UDP-glucuronic aci orms the urinary glucuronie conjugates o bilirubin (see Chapter 31) an o many rugs, incluing aspirin. CP par- ticipates in biosynthesis o phosphoglyceries, sphingomyelin, P an other substitute sphingosines (see Chapter 24). Finally, Adenine Ribose P O SO32– many coenzymes incorporate nucleoties as well as structures similar to purine an pyrimiine nucleoties (Table 32–2). FIGURE 32–11 Adenosine 3′-phosphate-5′-phosphosulfate. O O HN N HN N NH2 N N O N N N H H H N Hypoxanthine Xanthine N N (6-oxopurine) (2,6-dioxopurine) COO– CH3 CH2 O O H CH CH2 CH2 S HN N + O NH3+ O N N H HO OH Uric acid (2,6,8-trioxypurine) Methionine Adenosine FIGURE 32–8 Structures of hypoxanthine, xanthine, and uric acid, drawn as the oxo tautomers. FIGURE 32–12 S-Adenosylmethionine. 334 SECTION VII Structure, Function, & Replication o Inormational Macromolecules TABLE 32–2 Many Coenzymes and Related Compounds Nucleoside Triphosphates Have Are Derivatives of Adenosine Monophosphate High-Group Transfer Potential NH2 Nucleotie triphosphates have two aci anhyrie bons an N N Adenine one ester bon. Relative to esters, aci anhyries have a high- group transer potential. ΔG0′ or the hyrolysis o each o the N N two terminal (β an γ) phosphoryl groups o a nucleosie tri- O phosphate is about –7 kcal/mol (–30 kJ/mol). his high-group R O P O CH2 transer potential not only permits purine an pyrimiine O – n O nucleosie triphosphates to unction as group transer reagents, most commonly o the γ-phosphoryl group, but also on occa- sion transer o a nucleotie monophosphate moiety with an R'' O OR' accompanying release o PPi. Cleavage o an aci anhyrie bon typically is couple with a highly energonic process such D-Ribose as covalent bon synthesis, or example, the polymerization o Coenzyme R R Rè n nucleosie triphosphates to orm a nucleic aci (see Chapter 34). Active Methioninea H H 0 methionine SYNTHETIC NUCLEOTIDE Amino acid adenylates Amino acid H H 1 ANALOGS ARE USED IN Active sulate SO32– H PO32– 1 CHEMOTHERAPY Synthetic analogs o purines, pyrimiines, nucleosies, an 3′,5′-Cyclic AMP H PO32– 1 nucleoties moiie in the heterocyclic ring or in the sugar NADb Nicotinamide H H 2 moiety have numerous applications in clinical meicine. heir NADPb Nicotinamide PO32– H 2 toxic eects relect either inhibition o enzymes essential or nucleic aci synthesis or their incorporation into nucleic acis FAD Ribofavin H H 2 with resulting isruption o base pairing. Oncologists employ Coenzyme A Pantothenate H PO32– 2 5-luoro- or 5-ioouracil, 3-eoxyuriine, 6-thioguanine an a 6-mercaptopurine, 5- or 6-azauriine, 5- or 6-azacytiine, an Replaces phosphoryl group. b R is a vitamin B derivative. 8-azaguanine (Figure 32–13), which are incorporate into DNA prior to cell ivision. he purine analog allopurinol, use in treatment o hyperuricemia an gout, inhibits purine O O I HN 5 HN 6 N O O N N HO HO O O F O N HN O HN 5 8 N H2N N O N N H HO H H HO OH 5-lodo-2-deoxyuridine 5-Fluorouracil 6-Azauridine 8-Azaguanine SH SH OH 6 N 6 N 6 N N N1 5 N 2 4 3 N H2N N N N N N H H H 6-Mercaptopurine 6-Thioguanine Allopurinol FIGURE 32–13 Selected synthetic pyrimidine and purine analogs.  CHAPTER 32 Nucleotides 335 NH2 o a secon nucleotie. his orms a dinucleotide in which the NO2 pentose moieties are linke by a 3′,5′-phosphoiester bon to N N orm the “backbone” o RNA an DNA. he ormation o a inucleotie may be represente as the elimination o water HO O N N S between two mononucleoties. Biologic ormation o inucle- O H 3C oties oes not, however, occur in this way because the reverse NH N reaction, hyrolysis o the phosphoiester bon, is strongly HO avore on thermoynamic grouns. However, espite an N N extremely avorable ΔG, in the absence o catalysis by phospho- OH diesterases hyrolysis o the phosphoiester bons o DNA Cytarabine Azathioprine occurs only over long perios o time. DNA thereore persists or consierable perios, an has been etecte even in os- FIGURE 32–14 Cytarabine and azathioprine. sils. RNAs are ar less stable than DNA since their 2′-hyroxyl groups (absent rom DNA) can unction as nucleophiles or the biosynthesis an xanthine oxiase activity. Cytarabine is use chemical hyrolysis o 3′,5′-phosphoiester bons. in chemotherapy o cancer, an azathioprine, which is catabo- Posttranslational moiication o preorme polynucleo- lize to 6-mercaptopurine, is employe uring organ trans- tides can generate aitional structures such as pseudouri- plantation to suppress immunologic rejection (Figure 32–14). dine, a nucleosie in which d-ribose is linke to C-5 o uracil by a carbon-to-carbon bond rather than by the usual β-N- Non-Hydrolyzable Nucleoside glycosiic bon. he nucleotie pseuouriylic aci (ψ) arises by rearrangement o a UMP o a preorme tRNA. Similarly, Triphosphate Analogs Serve as methylation by S-aenosylmethionine o a UMP o preorme Research Tools tRNA orms MP (thymiine monophosphate), which con- Synthetic, non-hyrolyzable analogs o nucleosie triphos- tains ribose rather than eoxyribose. phates (Figure 32–15) allow investigators to istinguish the eects o nucleoties ue to phosphoryl transer rom eects Polynucleotides Are Directional meiate by occupancy o allosteric nucleotie-bining sites on regulate enzymes (see Chapter 9). Macromolecules Directional 3′ → 5′ phosphoiester bons link the monomers o polynucleoties. Since each en o a polynucleotie thus DNA & RNA ARE is istinct, we reer to the “5′-en” or the “3′-en” o a poly- POLYNUCLEOTIDES nucleotie. Since the phosphoiester bons all are 3′ → 5′, the representation pGpGpAppCpA inicates that the termi- he 5′-phosphoryl group o a mononucleotie can esteriy a nal 5′-hyroxyl is phosphorylate. More concisely, the rep- secon hyroxyl group, orming a phosphodiester. Most com- resentation GGAC, which shows only the base sequence, is monly, this secon hyroxyl group is the 3′-OH o the pentose by convention written with the 5′-base (G) at the left an the 3′-base (C) at the right. O O O Pu/Pyy R O P O P O P O– SUMMARY – – – O O O Uner physiologic conitions, the amino an oxo tautomers o Parent nucleoside triphosphate purines, pyrimiines, an their erivatives preominate. O O O Nucleic acis contain, in aition to A, G, C, , an U, traces Pu/Py R O P O P CH2 P O– o 5-methylcytosine, 5-hyroxymethylcytosine, pseuouriine (ψ), an N-methylate heterocycles. O– O– O– Most nucleosies contain d-ribose or 2-eoxy-d-ribose linke O O O to N-1 o a pyrimiine or to N-9 o a purine by a β-glycosiic H bon whose syn conormers preominate. Pu/Py R O P O P N P O– A prime numeral inicates the hyroxyl to which the O– O– O– phosphoryl group o the sugars o mononucleoties (eg, 3′-GMP, 5′-CMP) is attache. Aitional phosphoryl groups linke to the rst by aci anhyrie bons orm nucleosie FIGURE 32–15 Synthetic derivatives of nucleoside triphos- iphosphates an triphosphates. phates incapable of undergoing hydrolytic release of the termi- nal phosphoryl group. (Pu/Py, a purine or pyrimidine base; R, ribose Nucleosie triphosphates have high group transer potential or deoxyribose.) Shown are the parent (hydrolyzable) nucleoside an participate in covalent bon syntheses. Te cyclic triphosphate (top) and the unhydrolyzable β-methylene (center) and phosphoiesters cAMP an cGMP unction as intracellular γ-imino derivatives (bottom). secon messengers. 336 SECTION VII Structure, Function, & Replication o Inormational Macromolecules Mononucleoties linke by 3′ → 5′-phosphoiester bons orm polynucleoties, irectional macromolecules with REFERENCES istinct 3′- an 5′-ens. When represente as ppGp or Aams RLP, Knowler J, Leaer DP: Te Biochemistry of the Nucleic GCACA, the 5′-en is at the le, an all phosphoiester Acids, 11th e. Chapman & Hall, 1992. bons are 3′ → 5′. Blackburn GM, Gait MJ, Loaks D, et al: Nucleic Acids in Chemistry and Biology, 3r e., RSC Publishing, 2006. Synthetic analogs o purine an pyrimiine bases an their Pacher P, Nivorozhkin A, Szabo C: Terapeutic efects o xanthine erivatives serve as anticancer rugs either by inhibiting an oxiase inhibitors: renaissance hal a century aer the iscovery enzyme o nucleotie biosynthesis or by being incorporate o allopurinol. Pharmacol Rev 2006;58:87. into DNA or RNA.