《生物化学原理》（英文版）chapter 8 NUCLEOTIDES AND NUCLEIC ACIDS

298 Chapter 8 Nucleotides and Nucleic Acids DNA sequencing is readily automated by a varia- on of Sanger's sequencing method in which the Template df dideoxynucleotides used for each reaction are labeled unknown sonce with a differently colored fluorescent tag(Fig. 8-37) This technology allows DNa sequences containing thou- sands of nucleotides to be determined in a few hours Entire genomes of many organisms have now been se- quenced(see Table 1-4), and many very large DNA- sequencing projects are in progress. Perhaps the most DNA Poly murasa faIr dNTPs ambitious of these is the Human Genome Project, in Tear enTRy which researchers have sequenced all 3. 2 billion base pairs of the DNA in a human cell( Chapter 9). 8 Dideoxy Sequencing of DNA The Chemical Synthesis of DNA Has Been Automated Another technology that has paved the way for many biochemical advances is the chemical synthesis of oligonucleotides with any chosen sequence. The chem- knature ical methods for synthesizing nucleic acids were devel- oped primarily by H Gobind Khorana and his colleagues in the 1970s refinement and automation of these meth Dlyolabeled ods have made possible the rapid and accurate synth segments f DNA sis of DNA strands. The synthesis is carried out with the growing strand attached to a solid support(Fig. 8-38) template ith unknown sequnce using principles similar to those used by merrifield in peptide synthesis( see Fig 3-29). The efficiency of each ddition step is very high, allowing the routine labora tory synthesis of polymers containing 70 or 80 nu- cleotides and, in some laboratories, much longer strands. The availability of relatively inexpensive DNA polymers with predesigned sequences is having a pow Dyelablod segmnts rful impact on all areas of biochemistry( Chapter 9) gel amd sbjuctedto FIGURE 8-37 Strategy for automating DNA sequencing reactions Each dideoxynucleotide used in the Sanger method can be linked to a fluorescent molecule that gives all the fragments terminating in that nucleotide a particular color. All four labeled ddNTPs are added to a single tube. The resulting colored DNA fragments are then separated by size in a single electrophoretic gel contained in a capillary tube (a refinement of gel electrophoresis that allows for faster separations). All fragments of a given length migrate through the capillary gel in a single peak, and the color associated with each peak is detected using a laser beam. The DNA sequence is read by determining the sequence of CCICTTTGAYGCTGGTTCCGAAATCGO colors in the peaks as they pass the detector. This information is fed Compat cr ganeral od roah after directly to a computer, which determines the sequence. hands magnate past dut or

DNA sequencing is readily automated by a varia￾tion of Sanger’s sequencing method in which the dideoxynucleotides used for each reaction are labeled with a differently colored fluorescent tag (Fig. 8–37). This technology allows DNA sequences containing thou￾sands of nucleotides to be determined in a few hours. Entire genomes of many organisms have now been se￾quenced (see Table 1–4), and many very large DNA￾sequencing projects are in progress. Perhaps the most ambitious of these is the Human Genome Project, in which researchers have sequenced all 3.2 billion base pairs of the DNA in a human cell (Chapter 9). Dideoxy Sequencing of DNA The Chemical Synthesis of DNA Has Been Automated Another technology that has paved the way for many biochemical advances is the chemical synthesis of oligonucleotides with any chosen sequence. The chem￾ical methods for synthesizing nucleic acids were devel￾oped primarily by H. Gobind Khorana and his colleagues in the 1970s. Refinement and automation of these meth￾ods have made possible the rapid and accurate synthe￾sis of DNA strands. The synthesis is carried out with the growing strand attached to a solid support (Fig. 8–38), using principles similar to those used by Merrifield in peptide synthesis (see Fig. 3–29). The efficiency of each addition step is very high, allowing the routine labora￾tory synthesis of polymers containing 70 or 80 nu￾cleotides and, in some laboratories, much longer strands. The availability of relatively inexpensive DNA polymers with predesigned sequences is having a pow￾erful impact on all areas of biochemistry (Chapter 9). 298 Chapter 8 Nucleotides and Nucleic Acids FIGURE 8–37 Strategy for automating DNA sequencing reactions. Each dideoxynucleotide used in the Sanger method can be linked to a fluorescent molecule that gives all the fragments terminating in that nucleotide a particular color. All four labeled ddNTPs are added to a single tube. The resulting colored DNA fragments are then separated by size in a single electrophoretic gel contained in a capillary tube (a refinement of gel electrophoresis that allows for faster separations). All fragments of a given length migrate through the capillary gel in a single peak, and the color associated with each peak is detected using a laser beam. The DNA sequence is read by determining the sequence of colors in the peaks as they pass the detector. This information is fed directly to a computer, which determines the sequence

8.3 Nucleic Acid Chemistry 299 DMT -O Nucleotide DMT- at 3 pasition DMT -O nucleoside ⊙ protecting group NC-(CH2)2-0-P NC-(CH22-0 ( CH3)2CH-N*-CH(CH3)2 H MT Diisopropylamine activating group H Next nucleotide (CH3)2CH-N-CH(CH3)2 Diisopropylamine byproduct ①hmu Repeat steps toO until all residues are added NC-(CH2)2-0-P=0 Remove protecting groups from bases 间 emove cyanoethyl groups from phosphates FIGURE 8-38 Chemical synthesis of DNA. Automated DNA synthe- group and reacted with the bound nucleotide to form a 5, 3'linkage sis is conceptually similar to the synthesis of polypeptides on a solid which in step is oxidized with iodine to produce a phosphotri-. support. The oligonucleotide is built up on the solid support (silica) ter linkage. (One of the phosphate oxygens carries a cyanoethyl pro one nucleotide at a time, in a repeated series of chemical reactions tecting group)Reactions@2 through are repeated until all nu- with suitably protected nucleotide precursors. The first nucleoside cleotides are added. At each step, excess nucleotide is removed before (which will be the 3'end) is attached to the silica support at the 3 addition of the next nucleotide In steps 5 and 6 the remaining hydroxyl (through a linking group, R)and is protected at the 5 hy- protecting groups on the bases and the phosphates are removed, and droxyl with an acid-labile dimethoxytrityl group(DMm). The reactive in the oligonucleotide is separated from the solid support and pu- groups on all bases are also chemically protected. @2) The protecting rified. The chemical synthesis of RNA is somewhat more complicated DMT group is removed by washing the column with acid (the DMt because of the need to protect the 2 hydroxyl of ribose without ad- group is colored, so this reaction can be followed spectrophotome- versely affecting the reactivity of the 3 hydroxyl ically). 3 The next nucleotide is activated with a isopropylamino

Nucleoside attached to silica support 1 Repeat steps to until all residues are added 2 4 CH2 H O H H H Base1 O OH H 3
5
DMT Nucleoside protected at 5
hydroxyl R Si O H O H H H Base1 O H CH2 H DMT O CH2 H O H H Base1 O H R Si H O H O P H H Base2 O R Si CH2 H O H H H H Base1 O CH2 H O O O H NC (CH2)2 DMT O H O P H H H Base2 O R Si CH2 H O H H H H Base1 O CH2 H O O NC (CH2)2 DMT Oxidation to form triester 4 DMT Protecting group removed 2 2 H Next nucleotide added 3 N 2CH CH 2 H 2CH N CH(CH3) (CH3) H O P H H H Base2 O Nucleotide activated at 3
position CH2 H O O (CH3) (CH3) NC (CH2)2 Cyanoethyl protecting group Diisopropylamine byproduct DMT Diisopropylamino activating group Remove protecting groups from bases Remove cyanoethyl groups from phosphates 7 Cleave chain from silica support 5 6 5
3
Oligonucleotide chain 8.3 Nucleic Acid Chemistry 299 FIGURE 8–38 Chemical synthesis of DNA. Automated DNA synthe￾sis is conceptually similar to the synthesis of polypeptides on a solid support. The oligonucleotide is built up on the solid support (silica), one nucleotide at a time, in a repeated series of chemical reactions with suitably protected nucleotide precursors. 1 The first nucleoside (which will be the 3
end) is attached to the silica support at the 3
hydroxyl (through a linking group, R) and is protected at the 5
hy￾droxyl with an acid-labile dimethoxytrityl group (DMT). The reactive groups on all bases are also chemically protected. 2 The protecting DMT group is removed by washing the column with acid (the DMT group is colored, so this reaction can be followed spectrophotomet￾rically). 3 The next nucleotide is activated with a diisopropylamino group and reacted with the bound nucleotide to form a 5
,3
linkage, which in step 4 is oxidized with iodine to produce a phosphotri￾ester linkage. (One of the phosphate oxygens carries a cyanoethyl pro￾tecting group.) Reactions 2 through 4 are repeated until all nu￾cleotides are added. At each step, excess nucleotide is removed before addition of the next nucleotide. In steps 5 and 6 the remaining protecting groups on the bases and the phosphates are removed, and in 7 the oligonucleotide is separated from the solid support and pu￾rified. The chemical synthesis of RNA is somewhat more complicated because of the need to protect the 2
hydroxyl of ribose without ad￾versely affecting the reactivity of the 3
hydroxyl.

300 Chapter 8 Nucleotides and Nucleic Acids RY 8. 3 Nucleic Acid Chemist a Native DNA undergoes reversible unwinding "O-p-0-P-0-P-0-CH Donne and separation of strands(melting) on heating or at extremes of pH DNAs rich in G=C pairs Anhydro L have higher melting points than DNAs rich in Anhy dride A=T pairs a Denatured single-stranded DNAs from two species can form a hybrid duplex, the degree of hybridization depending on the extent of H C-C-0-C-CH, H, C-C-0-CH sequence similarity. Hybridization is the basis for important techniques used to study and Aotic anhydride Methyl notate isolate specific genes and rNAs a curtay lie acid a carboxylie aid hydride a DNA is a relatively stable polymer. Spontaneous reactions such as deamination of certain bases FIGURE 8-40 The phosphate ester and phosphoanhydride bonds of hydrolysis of base-sugar N-glycosyl bonds ATP. Hydrolysis of an anhydride bond yields more energy than hy- radiation-induced formation of pyrimidine drolysis of the ester. A carboxylic acid anhydride and carboxylic acid ester are shown for comparison dimers, and oxidative damage occur at very low ates, yet are important because of cells' very low tolerance for changes in genetic material. shates are generally labeled a, B, and y. Hydrolysis of a DNA sequences can be determined and dNA nucleoside triphosphates provides the chemical energy polymers synthesized with simple, automated to drive a wide variety of cellular reactions. Adenosine protocols involving chemical and enzymatic 5-triphosphate, ATP, is by far the most widely used for this purpose, but UTP, GTP, and CTP are also used in some reactions. Nucleoside triphosphates also serve as the activated precursors of DNA and RNa synthesis, as 8. 4 other functions of nucleotides described in Chapters 25 and 26 In addition to their roles as the subunits of nucleic acids The energy released by hydrolysis of ATP and the ucleotides have a variety of other functions in every other nucleoside triphosphates is accounted for by the cell: as energy carriers, components of enzyme cofac. structure of the triphosphate group. The bond between Nucleotides Carry Chemical Energy in Cells 8-40). Hydrolysis of the ester linkage yields about 14 k/mol under standard conditions, whereas hydrolysis The phosphate group covalently linked at the 5 hy- of each anhydride bond yields about 30 kJ/mol ATP hy- droxyl of a ribonucleotide may have one or two addi- drolysis often plays an important thermodynamic role tional phosphates attached. The resulting molecules are in biosynthesis. When coupled to a reaction with a pos- referred to as nucleoside mono- di-, and triphosphates itive free-energy change, ATP hydrolysis shifts the equi- (Fig. 8-39). Starting from the ribose, the three phos- librium of the overall process to favor product forma 0-0-0- Abbreviations of ribonucleoside Abbreviations of deoxyribonucleoside Base Mono- Di- Tri- Mono- Di- Tri- Adenine AMP ADP AtP Adenine damP dAdP dATP Guanine GMP GDP GTP Guanine dgmp dgdp dGTP OHOH Cytosine CMP CDP CTP Cytosine dcmP dCDP dCTP NMP Uracil UMP UDP UT Thymine dTmP dTdp dTTP FIGURE 8-39 Nucleoside phosphates. General structure of the nucleoside 5'-mono-, di, and triphosphates(NMPS, NDPs, and NTPs)and their standard abbreviations In the deoxyribonucleoside phosphates(dNMPs, dNDPs, and dNTPs), the pentose is 2'-deoxy-D-ribose

SUMMARY 8.3 Nucleic Acid Chemistry ■ Native DNA undergoes reversible unwinding and separation of strands (melting) on heating or at extremes of pH. DNAs rich in GqC pairs have higher melting points than DNAs rich in AUT pairs. ■ Denatured single-stranded DNAs from two species can form a hybrid duplex, the degree of hybridization depending on the extent of sequence similarity. Hybridization is the basis for important techniques used to study and isolate specific genes and RNAs. ■ DNA is a relatively stable polymer. Spontaneous reactions such as deamination of certain bases, hydrolysis of base-sugar N-glycosyl bonds, radiation-induced formation of pyrimidine dimers, and oxidative damage occur at very low rates, yet are important because of cells’ very low tolerance for changes in genetic material. ■ DNA sequences can be determined and DNA polymers synthesized with simple, automated protocols involving chemical and enzymatic methods. 8.4 Other Functions of Nucleotides In addition to their roles as the subunits of nucleic acids, nucleotides have a variety of other functions in every cell: as energy carriers, components of enzyme cofac￾tors, and chemical messengers. Nucleotides Carry Chemical Energy in Cells The phosphate group covalently linked at the 5
hy￾droxyl of a ribonucleotide may have one or two addi￾tional phosphates attached. The resulting molecules are referred to as nucleoside mono-, di-, and triphosphates (Fig. 8–39). Starting from the ribose, the three phos￾phates are generally labeled ,
, and . Hydrolysis of nucleoside triphosphates provides the chemical energy to drive a wide variety of cellular reactions. Adenosine 5
-triphosphate, ATP, is by far the most widely used for this purpose, but UTP, GTP, and CTP are also used in some reactions. Nucleoside triphosphates also serve as the activated precursors of DNA and RNA synthesis, as described in Chapters 25 and 26. The energy released by hydrolysis of ATP and the other nucleoside triphosphates is accounted for by the structure of the triphosphate group. The bond between the ribose and the phosphate is an ester linkage. The ,
and
, linkages are phosphoanhydrides (Fig. 8–40). Hydrolysis of the ester linkage yields about 14 kJ/mol under standard conditions, whereas hydrolysis of each anhydride bond yields about 30 kJ/mol. ATP hy￾drolysis often plays an important thermodynamic role in biosynthesis. When coupled to a reaction with a pos￾itive free-energy change, ATP hydrolysis shifts the equi￾librium of the overall process to favor product forma- 300 Chapter 8 Nucleotides and Nucleic Acids Abbreviations of ribonucleoside 5
-phosphates Base Mono- Di- Tri￾Adenine Guanine Cytosine Thymine AMP GMP CMP UMP ADP GDP CDP UDP ATP GTP CTP UTP Abbreviations of deoxyribonucleoside Base Mono- Di- Tri￾Adenine Guanine Cytosine Uracil dAMP dGMP dCMP dTMP dADP dGDP dCDP dTDP dATP dGTP dCTP dTTP 5
-phosphates O O CH2 H O P O O O P O P O O O O H H H H Base O OH  NMP NDP NTP FIGURE 8–39 Nucleoside phosphates. General structure of the nucleoside 5
-mono-, di-, and triphosphates (NMPs, NDPs, and NTPs) and their standard abbreviations. In the deoxyribonucleoside phosphates (dNMPs, dNDPs, and dNTPs), the pentose is 2
-deoxy-D-ribose. FIGURE 8–40 The phosphate ester and phosphoanhydride bonds of ATP. Hydrolysis of an anhydride bond yields more energy than hy￾drolysis of the ester. A carboxylic acid anhydride and carboxylic acid ester are shown for comparison.

8.4 Other Functions of Nucleotides 301 tion(recall the relationship between equilibrium con- CoA, the coenzyme a derivative of acetoacetate, re- stant and free-energy change described by Eqn 6-3 on duces its reactivity as a substrate for B-ketoacyl-Col transferase(an enzyme of lipid metabolism) by a factor of 106. Although this requirement for adenosine has not enine Nucleotides Are Components of Many been investigated in detail, it must involve the binding Enzyme Cofactors energy between enzyme and substrate(or cofactor)that is used both in catalysis and in stabilizing the initial ariety of enzyme cofactors serving a wide range of enzyme-substrate complex( Chapter 6). In the e case chemical functions include adenosine as part of thei B-ketoacyl-CoA transferase, the nucleotide moiety of structure(Fig. 8-41). They are unrelated structurally coenzyme a appears to be a binding " handle that helps except for the presence of adenosine In none of these to pull the substrate(acetoacetyl-CoA)into the active cofactors does the adenosine portion participate directly site. Similar roles may be found for the nucleoside por- in the primary function, but removal of adenosine gen- tion of other nucleotide cofactors erally results in a drastic reduction of cofactor activi- Why is adenosine, rather than some other large mol ties. For example, removal of the adenine nucleotide ecule, used in these structures? The answer here may (3.phosphoadenosine diphosphate)from acetoacetyl- involve a form of evolutionary economy. Adenosine is HS--CH2-CH2-N-C-CH2-CH2-N-C-C-C-CH2-0-P-0--P-0--CH2 o N O OUCH B-Mercaptoethylamine Pantothenic acid O=P-0- FIGURE 8-41 Some coenzymes containing adenosine. The adenosine portion is shaded in light red. Coenzyme A(CoA functions in acyl group transfer reactions: the acyl group (such as 3-Phasphoadenosine diphosphate the acetyl or acetoacetyl group) is attached to the CoA through a (3-P-ADP thioester linkage to the B-mercaptoethylamine moiety NADfunc. tions in hydride transfers, and FAD, the active form of vitamin B2 riboflavin), in electron transfers. Another coenzyme incorporating adenosine is 5-deoxyadenosylcobalamin, the active form of vita- min B12(see Box 17-2), which participates in intramolecular group transfers between adjacent carbons C-NH, CHOH Nicotinamide OH OH O=P-0 0→P=0 OH OH Nicotinamide adenine dinucleotide (NAD+) Flavin adenine dinucleotide(FAD)

tion (recall the relationship between equilibrium con￾stant and free-energy change described by Eqn 6–3 on p. 195). Adenine Nucleotides Are Components of Many Enzyme Cofactors A variety of enzyme cofactors serving a wide range of chemical functions include adenosine as part of their structure (Fig. 8–41). They are unrelated structurally except for the presence of adenosine. In none of these cofactors does the adenosine portion participate directly in the primary function, but removal of adenosine gen￾erally results in a drastic reduction of cofactor activi￾ties. For example, removal of the adenine nucleotide (3
-phosphoadenosine diphosphate) from acetoacetyl￾CoA, the coenzyme A derivative of acetoacetate, re￾duces its reactivity as a substrate for
-ketoacyl-CoA transferase (an enzyme of lipid metabolism) by a factor of 106 . Although this requirement for adenosine has not been investigated in detail, it must involve the binding energy between enzyme and substrate (or cofactor) that is used both in catalysis and in stabilizing the initial enzyme-substrate complex (Chapter 6). In the case of
-ketoacyl-CoA transferase, the nucleotide moiety of coenzyme A appears to be a binding “handle” that helps to pull the substrate (acetoacetyl-CoA) into the active site. Similar roles may be found for the nucleoside por￾tion of other nucleotide cofactors. Why is adenosine, rather than some other large mol￾ecule, used in these structures? The answer here may involve a form of evolutionary economy. Adenosine is 8.4 Other Functions of Nucleotides 301 O H O P O O O O P H H H O OH CH2 O CH3 O C N CH2 NH2 N N N N C C C N CH2 C CH2 CH2 N H H H H H3C HS O O O H CH3 5
P O O O O 3
-Phosphoadenosine diphosphate (3
-P-ADP) b-Mercaptoethylamine Pantothenic acid Coenzyme A CH2 CHOH CHOH CHOH CH2 O O P O O O P O CH2 H O H H N NH2 N N N H O H 2
4
1
3
CH2 O H N O O N N H3C NH2 Riboflavin Nicotinamide adenine dinucleotide (NAD) H O H H N N N N H O H H CH2 O NH2 Flavin adenine dinucleotide (FAD) H O H H N H O H H CH2 O Nicotinamide O P O O O O P O O O FIGURE 8–41 Some coenzymes containing adenosine. The adenosine portion is shaded in light red. Coenzyme A (CoA) functions in acyl group transfer reactions; the acyl group (such as the acetyl or acetoacetyl group) is attached to the CoA through a thioester linkage to the
-mercaptoethylamine moiety. NAD func￾tions in hydride transfers, and FAD, the active form of vitamin B2 (riboflavin), in electron transfers. Another coenzyme incorporating adenosine is 5
-deoxyadenosylcobalamin, the active form of vita￾min B12 (see Box 17-2), which participates in intramolecular group transfers between adjacent carbons.

302 Chapter 8 Nucleotides and Nucle eic Acids 0-0=p0-CH Adandsnu 3, s yeli men oghesphate Gauncsine8'M celie men eghuephate Cunene 5.diph wph at, 3 diph osphate (cche AAP aAMP cehic CMP ctMP) (mesne triphosphate) puppy FIGURE 8-42 Three regulatory nucleotides certainly not unique in the amount of potential binding (cyclic AMP, or cAMP), formed from AtP in a reac energy it can contribute. The importance of adenosine tion catalyzed by adenylyl cyclase, an enzyme associ probably lies not so much in some special chemical char- ated with the inner face of the plasma membrane. Cyclic acteristic as in the evolutionary advantage of using one AMP serves regulatory functions in virtually every cell compound for multiple roles. Once ATP became the uni- outside the plant kingdom. Guanosine 3, 5 -cyclic mono- versal source of chemical energy, systems developed to phosphate (cGMP) occurs in many cells and also has synthesize ATP in greater abundance than the other nu- regulatory functions cleotides; because it is abundant, it becomes the logical Another regulatory nucleotide, ppGpp(Fig. 8-42) choice for incorporation into a wide variety of struc- is produced in bacteria in response to a slowdown in tures. The economy extends to protein structure. A sin- protein synthesis during amino acid starvation. This nu gle protein domain that binds adenosine can be used in cleotide inhibits the synthesis of the rRNa and trna a wide variety of enzymes. Such a domain, called a molecules(see Fig. 28-24)needed for protein synthe- nucleotide-binding fold, is found in many enzymes sis, preventing the unnecessary production of nucleic that bind atp and nucleotide cofactors acids Some Nucleotides Are Regulatory Molecules SUMMARy 8. 4 Other Functions of Nucleotides Cells respond to their environment by taking cues from hormones or other external chemical signals. The in- a ATP is the central carrier of chemical energy in teraction of these extracellular chemical signals (first ells. The presence of an adenosine moiety in messengers") with receptors on the cell surface often variety of enzyme cofactors may be related to leads to the production of second messengers inside binding the cell, which in turn leads to adaptive changes in a Cyclic AMP, formed from ATP in a reaction the cell interior(Chapter 12). Often, the second mes- catalyzed by adenylyl cyclase, is a common senger is a nucleotide(Fig. 8-42). One of the most second messenger produced in common is adenosine 3, 5 -cyclic monophosphate hormones and other chemical signals Key terms ne273 5′end277 hairpin messenger RNA (mRNA)273 oligonucleotide 278 transfer RNA(tRNA) 273 polynucleotide 278 G tetraplex 287 nucleoside 273 major groove 282 monocistronic mRNA 287 pyrim minor purine 273 B-form DNA 284 deoxyribonucleotides 274 A-form DNA 284 second messenger 302 ribonucleotide 274 Z-form DNa 284 adenosine 3, 5 -cyclic monophos phosphodiester linkage 277 palindrome 285 hate(cyclic AMP, cAMP)302

certainly not unique in the amount of potential binding energy it can contribute. The importance of adenosine probably lies not so much in some special chemical char￾acteristic as in the evolutionary advantage of using one compound for multiple roles. Once ATP became the uni￾versal source of chemical energy, systems developed to synthesize ATP in greater abundance than the other nu￾cleotides; because it is abundant, it becomes the logical choice for incorporation into a wide variety of struc￾tures. The economy extends to protein structure. A sin￾gle protein domain that binds adenosine can be used in a wide variety of enzymes. Such a domain, called a nucleotide-binding fold, is found in many enzymes that bind ATP and nucleotide cofactors. Some Nucleotides Are Regulatory Molecules Cells respond to their environment by taking cues from hormones or other external chemical signals. The in￾teraction of these extracellular chemical signals (“first messengers”) with receptors on the cell surface often leads to the production of second messengers inside the cell, which in turn leads to adaptive changes in the cell interior (Chapter 12). Often, the second mes￾senger is a nucleotide (Fig. 8–42). One of the most common is adenosine 3
,5
-cyclic monophosphate (cyclic AMP, or cAMP), formed from ATP in a reac￾tion catalyzed by adenylyl cyclase, an enzyme associ￾ated with the inner face of the plasma membrane. Cyclic AMP serves regulatory functions in virtually every cell outside the plant kingdom. Guanosine 3
,5
-cyclic mono￾phosphate (cGMP) occurs in many cells and also has regulatory functions. Another regulatory nucleotide, ppGpp (Fig. 8–42), is produced in bacteria in response to a slowdown in protein synthesis during amino acid starvation. This nu￾cleotide inhibits the synthesis of the rRNA and tRNA molecules (see Fig. 28–24) needed for protein synthe￾sis, preventing the unnecessary production of nucleic acids. SUMMARY 8.4 Other Functions of Nucleotides ■ ATP is the central carrier of chemical energy in cells. The presence of an adenosine moiety in a variety of enzyme cofactors may be related to binding-energy requirements. ■ Cyclic AMP, formed from ATP in a reaction catalyzed by adenylyl cyclase, is a common second messenger produced in response to hormones and other chemical signals. 302 Chapter 8 Nucleotides and Nucleic Acids FIGURE 8–42 Three regulatory nucleotides. Key Terms gene 273 ribosomal RNA (rRNA) 273 messenger RNA (mRNA) 273 transfer RNA (tRNA) 273 nucleotide 273 nucleoside 273 pyrimidine 273 purine 273 deoxyribonucleotides 274 ribonucleotide 274 phosphodiester linkage 277 Terms in bold are defined in the glossary. 5
end 277 3
end 277 oligonucleotide 278 polynucleotide 278 base pair 279 major groove 282 minor groove 282 B-form DNA 284 A-form DNA 284 Z-form DNA 284 palindrome 285 hairpin 285 cruciform 285 triplex DNA 286 G tetraplex 287 H-DNA 287 monocistronic mRNA 287 polycistronic mRNA 288 mutation 293 second messenger 302 adenosine 3
,5
-cyclic monophos￾phate (cyclic AMP, cAMP) 302