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Chapter 13
Nucleotides
Overview
bull Nucleotides are phosphorylated nucleosides
bull A nucleoside is a combination of a nucleic acid base and a sugar
bull ATP is a nucleotide that participates in numerous energy transduction reactions
bull NTPs are the ultimate building blocks of nucleic acids
bull Nucleic acid polymerases are referred to as pols
bull In mammalian cells ribonucleotides are converted to deoxyribonucleotides at the
NDP level
bull DNA and RNA are structurally similar polymers
bull Nucleoside monophosphates are converted to their respective di- and triphosphate
derivatives via phosphoryl transfer from ATP
bull Nucleotides can be synthesized from small organic molecules and they are conserved
through salvage pathways
78
Nucleotides furnish the building blocks of
ribo- and deoxyribonucleic acid (RNA and
DNA) DNA in turn is the permanent geneticmaterial of animal and plant cells as well as
bacteria and some viruses It contains struc-
tural information for the synthesis of some
50000 proteins needed for general cellular
metabolism and differentiated function in
mammals and it confers uniqueness to each
organism Most DNA is found in the nucleus
however small amounts are also present in
mitochondria Unlike nuclear DNA which is
inherited from both parents mitochondrialDNA is inherited exclusively from the mother
In addition to forming DNA and RNA nucle-
otides perform a variety of intracellular
functions in energy transduction reactions
For example hydrolysis of the nucleo-
tide adenosine triphosphate (ATP) supplies
needed energy for many cell reactions and
in several metabolic pathways nucleotides
act as activated carriers of carbohydrates
amino acids lipids sulfate and methyl groupsThey are structural components of several
coenzymes including coenzyme-A (CoASH)
and nicotinamide adenine dinucleotide (NAD+
see Chapter 41) and flavin adenine dinucleotide
(FAD) and they are important allosteric regula-
tors of key intracellular enzymes For example
cyclic adenosine- and guanosine monophos-
phate (cAMP and cGMP respectively) are
second messengers that mediate the effects
of several ligands that bind to plasma membranereceptors
Nucleotides can be synthesized from small
organic molecules available in cells or they
can be generated through salvage pathways
that recycle their nitrogen bases (see Chapter
17) In rapidly dividing cells that are synthe-
sizing large quantities of RNA and DNA (eg
Copyright copy 2015 Elsevier Inc All rights reserved
7212019 3-s20-B978012391909050013X-main
httpslidepdfcomreaderfull3-s20-b978012391909050013x-main 25
24 Chapter 13 79
bone marrow intestinal epithelial cells and
many cells of young animals) the need for
nucleotides is generally greater than in nondi-
viding cells It is in these rapidly dividing cells
of adult animals that the salvage pathways
predominate Several chemotherapeuticagents exert their effects by interfering with
nucleotide biosynthesis (see Chapters 14-17)
Nucleotide StructureNucleotides are composed of a nitrogen base
(ie a purine or pyrimidine) a cyclic pentose
and one or more phosphate groups (Fig 13-1)
The nitrogen base plus the pentose (ribose or
deoxyribose) is known as a nucleoside with
addition of phosphate forming anucleotide
Two purines adenine and guanine and three
pyrimidines cytosine uracil and its meth-
ylated derivative thymine are found in DNA
and RNA (Fig 13-2) Uracil is found only in
RNA thymine only in DNA and the others are
present in both Carbon and nitrogen atoms in
the purine ring are usually numbered 1 through
9 (see structure of adenine) whereas those
in the pyrimidine ring are numbered 1 through
6 (see structure of uracil) Carbon atoms in
the nucleosides pentose moiety are assigned
prime numbers (1 through 5) to distinguish
them from those of the base to which they
are attached Ribose has a hydroxyl (OH)
group attached to the 2-carbon atom which
is replaced by a hydrogen (H) atom in deoxyri-
bose (Figs 13-1 13-3 and 13-4)
Generically nucleotides are referred to as
nucleoside phosphates (NPs) which are furtherdistinguished on the basis of their pentose
structure as either ribonucleoside- or 2-deox-
yribonucleoside phosphates The specific state
of their phosphorylation is defined by notation
of the number of phosphates (mono M di D or
tri T) and their position (eg 2 3 4 or 5) on
the pentose sugar The most frequently encoun-
tered nucleoside phosphates found in nature
have their respective phosphate(s) esterified
to the 5pentose carbon of the nucleoside andas summarized in Fig 13-1 they assume three
major forms--a nucleoside 5-monophosphate
(abbreviated conventionally as NMP for the
ribose form or dNMP for the 2-deoxyribose
form) a nucleoside 5-diphosphate (ie NDP
or dNDP) and a nucleoside 5-triphosphate
(ie NTP or dNTP) The NTP has three phos-
phates tandemly esterified to the hydroxyl of
the 5 carbon of the pentose sugar while the
NDP and NMP forms each have respectively
two and one phosphate(s) esterified at thesame position Definition of the position of a
specific phosphate atom in an NDP or NTP
Figure 13-1
7212019 3-s20-B978012391909050013X-main
httpslidepdfcomreaderfull3-s20-b978012391909050013x-main 35
Figure 13-3
Nucleotides80
Figure 13-2
Figure 13-4
is based upon its distance from the pentose
carbon to which it is ultimately tethered Asshown in Fig 13-1 the phosphate nearest this
carbon is defined as the 983137-phosphate the
next is the 983138-phosphate and the third (in the
case of a triphosphate) is the 983143-phosphate
A less common but no less important NMP
form is the cyclic NMP (cNMP) in which the
phosphate is esterified not to a single pentose
carbon atom but to two carbons - usually
carbons 3 and 5 The cNMPs 35cAMP and
35cGMP exemplify such cNMPs Table 13-1 summarizes abbreviations of the
common 5-mono- di- and triphosphates of
the ribonucleosides adenosine guanosine
cytidine and uridine and the corresponding
2-deoxyribonucleosides 2-deoxyadeno-
sine (dA) 2-deoxyguanosine (dG) 2-deox-
ycytidine (dC) and 2-deoxythymidine (dT)
7212019 3-s20-B978012391909050013X-main
httpslidepdfcomreaderfull3-s20-b978012391909050013x-main 45
24 Chapter 13 81
Nucleoside monophosphates are converted
to their respective diphosphate derivatives
via phosphoryl transfer from ATP catalyzed
by nucleoside monophosphate kinase The
nucleoside diphosphates are then converted
to their triphosphate derivatives by nucleoside
diphosphate kinase at the expense of another
ATP The ATPs used in these phosphorylations
are derived primarily through mitochondrial
oxidative phosphorylation and secondarily through reactions of the Embden-Meyerhoff
pathway and the tricarboxylic acid cycle (see
Chapters 24-27 34 and 36)
Polynucleotide Structure and Synthesis The major polymeric forms of nucleotides
found in prokaryotes and eukaryotes are the
nucleic acids RNA and DNA As shown sche-
matically in Fig 13-3 RNA and DNA are similar
polymers differing in composition only in the2 substituent of their respective pentoses (ie
OH vs H) Both consist of tandem nucleoside
units strung together by phosphodiester bonds
between their 3 and 5 carbons
Nucleic acid polymerization is catalyzed by
nucleic acid polymerases (pols) - DNA poly-
merases in the case of DNA and RNA polymer-
ases in the case of RNA All known polymerases
use 5NTPs (eg riboNTPs for RNA or dNTPs
for DNA) as their nucleotide substrates and
they operate by the mechanism exemplified
by the polymerization of a dNTP into DNA as
shown schematically in Fig 13-4 Specifically
the polymerase catalyzes polymerization of the
5 983137-phosphate of an NTP unit to the free OH
of the NMP on the 3 primer end The 983138- and
983143-phosphates are eliminated as pyrophos-phate (PPi)
In summary nucleotides are the building
blocks of RNA and DNA and they also partic-
ipate in energy transduction reactions in a
variety of metabolic pathways Nucleotides
possess a nucleoside moiety consisting of a
cyclic pentose esterified to a ring nitrogen of
a heterocyclic pyrimidine or purine base and
a mono- di- or triphosphate group attached to
one or more of the pentose hydroxyl groupsNucleotides are generically referred to as
nucleoside phosphates (NPs) and are further
distinguished on the basis of their pentose
structure as either ribonucleoside- or 2-deox-
yribonucleoside phosphates They can be
synthesized from small organic molecules
available in cells or they can be generated
Nucleotide Nomenclature
Abbreviations of ribonucleoside 5-phosphates
Base Mono- Di- Tri-
Adenine AMP ADP ATP Guanine GMP GDP GTP
Cytosine CMP CDP CTP
Uracil UMP UDP UTP
Abbreviations of deoxyribonucleoside 5-phosphates
Base Mono- Di- Tri-
Adenine dAMP dADP dATP
Guanine dGMP dGDP dGTP
Cytosine dCMP dCDP dCTP
Thymine dTMP dTDP dTTP
Table 13-1
Note Nucleoside phosphates using pyrimidines as the nitrogen base are by convention referred to as ldquoidinesrdquo (eg uridinecytidine and thymidine) whereas those using purines are referred to as ldquoosinesrdquo (eg adenosine and guanosine)
7212019 3-s20-B978012391909050013X-main
httpslidepdfcomreaderfull3-s20-b978012391909050013x-main 55
through salvage pathways that recycle their
nitrogen bases The most common NPs in
nature have their respective phosphate(s)
esterified to the 5 pentose carbon of the nucle-
oside The phosphate nearest this carbon is
the 983137-phosphate the next is the 983138-phosphateand the third (in the case of a triphosphate)
is the 983143-phosphate Nucleoside monophos-
phates are converted to their respective di-
and triphosphate derivatives via phosphoryl
transfer from ATP
DNA and RNA are similar polymers differing
in composition only in the 2substituent of
their respective pentoses (ie H vs OH) Both
consist of tandem nucleoside units strung
together by phosphodiester bonds between their 3 and 5 carbons Nucleic acid polymeri-
zation is catalyzed by nucleic acid polymerases
(pols) which use 5-NTPs as their nucleotide
substrates
OBJECTIVES
bull Recognize several ways in which nucleotidescontribute to energy transduction reactions
bull Identify cell types in the adult organism thatcontinually synthesize large quantities of RNAand DNA
bull Outline the ways in which nucleotides can besalvaged by the organism (see Chapter 17)
bull Know the difference between a nucleoside anda nucleotide
bull Identify structural differences between andamong the purines and pyrimidines present inDNA and RNA
bull Identify the purine and pyrimidine nucleoside triphosphates involved in RNA biosynthesis
bull Contrast primary structural differences betweenRNA and DNA and between AMP and cAMP
bull Discuss how nucleoside monophosphates areconverted to their respective triphosphate deriv-atives
bull Identify and explain the steps involved in nucleicacid polymerization
QUESTIONS
1 Which one of the following is a nucleoside a ATP
b Adenosine c GDP
d AMP e Adenine
2 Select the FALSE statement below regardingnucleotides
a They are products of the reaction catalyzedby nucleic acid polymerases
b They are the building blocks of both DNAand RNA
c They are structural components of severalcoenzymes
d In several metabolic pathways they act ascarriers of carbohydrates amino acids and
lipids e They are composed of a nitrogen base a
pentose and one or more phosphate groups
3 The hydroxyl group (OH) attached to the2-carbon atom of ribose is replaced by what indeoxyribose
a A sulfhydryl group
b Oxygen c Hydrogen
d Phosphate e Ammonia
4 Which one of the following is a purine found inboth DNA and RNA
a Cytosine
b Thymine c Uracil
d Adenosine e Guanine
5 Which one of the following is NOT character-istic of a nucleic acid polymerase
a It may use dNTPs as substrates
b It may use NTPs as substrates c It catalyzes growth of the polymer from the 5 end
d It catalyzes attack of a hydroxyl group on the a-phosphate of an incoming NTP
e It catalyzes a synthetic reaction in whichPPi is released as one of the products
6 Coenzyme A possesses a nucleotide a True b False
A N S W E R S
1 b
2 a
3 c
4 e
5 c
6 a
Nucleotides82
7212019 3-s20-B978012391909050013X-main
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24 Chapter 13 79
bone marrow intestinal epithelial cells and
many cells of young animals) the need for
nucleotides is generally greater than in nondi-
viding cells It is in these rapidly dividing cells
of adult animals that the salvage pathways
predominate Several chemotherapeuticagents exert their effects by interfering with
nucleotide biosynthesis (see Chapters 14-17)
Nucleotide StructureNucleotides are composed of a nitrogen base
(ie a purine or pyrimidine) a cyclic pentose
and one or more phosphate groups (Fig 13-1)
The nitrogen base plus the pentose (ribose or
deoxyribose) is known as a nucleoside with
addition of phosphate forming anucleotide
Two purines adenine and guanine and three
pyrimidines cytosine uracil and its meth-
ylated derivative thymine are found in DNA
and RNA (Fig 13-2) Uracil is found only in
RNA thymine only in DNA and the others are
present in both Carbon and nitrogen atoms in
the purine ring are usually numbered 1 through
9 (see structure of adenine) whereas those
in the pyrimidine ring are numbered 1 through
6 (see structure of uracil) Carbon atoms in
the nucleosides pentose moiety are assigned
prime numbers (1 through 5) to distinguish
them from those of the base to which they
are attached Ribose has a hydroxyl (OH)
group attached to the 2-carbon atom which
is replaced by a hydrogen (H) atom in deoxyri-
bose (Figs 13-1 13-3 and 13-4)
Generically nucleotides are referred to as
nucleoside phosphates (NPs) which are furtherdistinguished on the basis of their pentose
structure as either ribonucleoside- or 2-deox-
yribonucleoside phosphates The specific state
of their phosphorylation is defined by notation
of the number of phosphates (mono M di D or
tri T) and their position (eg 2 3 4 or 5) on
the pentose sugar The most frequently encoun-
tered nucleoside phosphates found in nature
have their respective phosphate(s) esterified
to the 5pentose carbon of the nucleoside andas summarized in Fig 13-1 they assume three
major forms--a nucleoside 5-monophosphate
(abbreviated conventionally as NMP for the
ribose form or dNMP for the 2-deoxyribose
form) a nucleoside 5-diphosphate (ie NDP
or dNDP) and a nucleoside 5-triphosphate
(ie NTP or dNTP) The NTP has three phos-
phates tandemly esterified to the hydroxyl of
the 5 carbon of the pentose sugar while the
NDP and NMP forms each have respectively
two and one phosphate(s) esterified at thesame position Definition of the position of a
specific phosphate atom in an NDP or NTP
Figure 13-1
7212019 3-s20-B978012391909050013X-main
httpslidepdfcomreaderfull3-s20-b978012391909050013x-main 35
Figure 13-3
Nucleotides80
Figure 13-2
Figure 13-4
is based upon its distance from the pentose
carbon to which it is ultimately tethered Asshown in Fig 13-1 the phosphate nearest this
carbon is defined as the 983137-phosphate the
next is the 983138-phosphate and the third (in the
case of a triphosphate) is the 983143-phosphate
A less common but no less important NMP
form is the cyclic NMP (cNMP) in which the
phosphate is esterified not to a single pentose
carbon atom but to two carbons - usually
carbons 3 and 5 The cNMPs 35cAMP and
35cGMP exemplify such cNMPs Table 13-1 summarizes abbreviations of the
common 5-mono- di- and triphosphates of
the ribonucleosides adenosine guanosine
cytidine and uridine and the corresponding
2-deoxyribonucleosides 2-deoxyadeno-
sine (dA) 2-deoxyguanosine (dG) 2-deox-
ycytidine (dC) and 2-deoxythymidine (dT)
7212019 3-s20-B978012391909050013X-main
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24 Chapter 13 81
Nucleoside monophosphates are converted
to their respective diphosphate derivatives
via phosphoryl transfer from ATP catalyzed
by nucleoside monophosphate kinase The
nucleoside diphosphates are then converted
to their triphosphate derivatives by nucleoside
diphosphate kinase at the expense of another
ATP The ATPs used in these phosphorylations
are derived primarily through mitochondrial
oxidative phosphorylation and secondarily through reactions of the Embden-Meyerhoff
pathway and the tricarboxylic acid cycle (see
Chapters 24-27 34 and 36)
Polynucleotide Structure and Synthesis The major polymeric forms of nucleotides
found in prokaryotes and eukaryotes are the
nucleic acids RNA and DNA As shown sche-
matically in Fig 13-3 RNA and DNA are similar
polymers differing in composition only in the2 substituent of their respective pentoses (ie
OH vs H) Both consist of tandem nucleoside
units strung together by phosphodiester bonds
between their 3 and 5 carbons
Nucleic acid polymerization is catalyzed by
nucleic acid polymerases (pols) - DNA poly-
merases in the case of DNA and RNA polymer-
ases in the case of RNA All known polymerases
use 5NTPs (eg riboNTPs for RNA or dNTPs
for DNA) as their nucleotide substrates and
they operate by the mechanism exemplified
by the polymerization of a dNTP into DNA as
shown schematically in Fig 13-4 Specifically
the polymerase catalyzes polymerization of the
5 983137-phosphate of an NTP unit to the free OH
of the NMP on the 3 primer end The 983138- and
983143-phosphates are eliminated as pyrophos-phate (PPi)
In summary nucleotides are the building
blocks of RNA and DNA and they also partic-
ipate in energy transduction reactions in a
variety of metabolic pathways Nucleotides
possess a nucleoside moiety consisting of a
cyclic pentose esterified to a ring nitrogen of
a heterocyclic pyrimidine or purine base and
a mono- di- or triphosphate group attached to
one or more of the pentose hydroxyl groupsNucleotides are generically referred to as
nucleoside phosphates (NPs) and are further
distinguished on the basis of their pentose
structure as either ribonucleoside- or 2-deox-
yribonucleoside phosphates They can be
synthesized from small organic molecules
available in cells or they can be generated
Nucleotide Nomenclature
Abbreviations of ribonucleoside 5-phosphates
Base Mono- Di- Tri-
Adenine AMP ADP ATP Guanine GMP GDP GTP
Cytosine CMP CDP CTP
Uracil UMP UDP UTP
Abbreviations of deoxyribonucleoside 5-phosphates
Base Mono- Di- Tri-
Adenine dAMP dADP dATP
Guanine dGMP dGDP dGTP
Cytosine dCMP dCDP dCTP
Thymine dTMP dTDP dTTP
Table 13-1
Note Nucleoside phosphates using pyrimidines as the nitrogen base are by convention referred to as ldquoidinesrdquo (eg uridinecytidine and thymidine) whereas those using purines are referred to as ldquoosinesrdquo (eg adenosine and guanosine)
7212019 3-s20-B978012391909050013X-main
httpslidepdfcomreaderfull3-s20-b978012391909050013x-main 55
through salvage pathways that recycle their
nitrogen bases The most common NPs in
nature have their respective phosphate(s)
esterified to the 5 pentose carbon of the nucle-
oside The phosphate nearest this carbon is
the 983137-phosphate the next is the 983138-phosphateand the third (in the case of a triphosphate)
is the 983143-phosphate Nucleoside monophos-
phates are converted to their respective di-
and triphosphate derivatives via phosphoryl
transfer from ATP
DNA and RNA are similar polymers differing
in composition only in the 2substituent of
their respective pentoses (ie H vs OH) Both
consist of tandem nucleoside units strung
together by phosphodiester bonds between their 3 and 5 carbons Nucleic acid polymeri-
zation is catalyzed by nucleic acid polymerases
(pols) which use 5-NTPs as their nucleotide
substrates
OBJECTIVES
bull Recognize several ways in which nucleotidescontribute to energy transduction reactions
bull Identify cell types in the adult organism thatcontinually synthesize large quantities of RNAand DNA
bull Outline the ways in which nucleotides can besalvaged by the organism (see Chapter 17)
bull Know the difference between a nucleoside anda nucleotide
bull Identify structural differences between andamong the purines and pyrimidines present inDNA and RNA
bull Identify the purine and pyrimidine nucleoside triphosphates involved in RNA biosynthesis
bull Contrast primary structural differences betweenRNA and DNA and between AMP and cAMP
bull Discuss how nucleoside monophosphates areconverted to their respective triphosphate deriv-atives
bull Identify and explain the steps involved in nucleicacid polymerization
QUESTIONS
1 Which one of the following is a nucleoside a ATP
b Adenosine c GDP
d AMP e Adenine
2 Select the FALSE statement below regardingnucleotides
a They are products of the reaction catalyzedby nucleic acid polymerases
b They are the building blocks of both DNAand RNA
c They are structural components of severalcoenzymes
d In several metabolic pathways they act ascarriers of carbohydrates amino acids and
lipids e They are composed of a nitrogen base a
pentose and one or more phosphate groups
3 The hydroxyl group (OH) attached to the2-carbon atom of ribose is replaced by what indeoxyribose
a A sulfhydryl group
b Oxygen c Hydrogen
d Phosphate e Ammonia
4 Which one of the following is a purine found inboth DNA and RNA
a Cytosine
b Thymine c Uracil
d Adenosine e Guanine
5 Which one of the following is NOT character-istic of a nucleic acid polymerase
a It may use dNTPs as substrates
b It may use NTPs as substrates c It catalyzes growth of the polymer from the 5 end
d It catalyzes attack of a hydroxyl group on the a-phosphate of an incoming NTP
e It catalyzes a synthetic reaction in whichPPi is released as one of the products
6 Coenzyme A possesses a nucleotide a True b False
A N S W E R S
1 b
2 a
3 c
4 e
5 c
6 a
Nucleotides82
7212019 3-s20-B978012391909050013X-main
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Figure 13-3
Nucleotides80
Figure 13-2
Figure 13-4
is based upon its distance from the pentose
carbon to which it is ultimately tethered Asshown in Fig 13-1 the phosphate nearest this
carbon is defined as the 983137-phosphate the
next is the 983138-phosphate and the third (in the
case of a triphosphate) is the 983143-phosphate
A less common but no less important NMP
form is the cyclic NMP (cNMP) in which the
phosphate is esterified not to a single pentose
carbon atom but to two carbons - usually
carbons 3 and 5 The cNMPs 35cAMP and
35cGMP exemplify such cNMPs Table 13-1 summarizes abbreviations of the
common 5-mono- di- and triphosphates of
the ribonucleosides adenosine guanosine
cytidine and uridine and the corresponding
2-deoxyribonucleosides 2-deoxyadeno-
sine (dA) 2-deoxyguanosine (dG) 2-deox-
ycytidine (dC) and 2-deoxythymidine (dT)
7212019 3-s20-B978012391909050013X-main
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24 Chapter 13 81
Nucleoside monophosphates are converted
to their respective diphosphate derivatives
via phosphoryl transfer from ATP catalyzed
by nucleoside monophosphate kinase The
nucleoside diphosphates are then converted
to their triphosphate derivatives by nucleoside
diphosphate kinase at the expense of another
ATP The ATPs used in these phosphorylations
are derived primarily through mitochondrial
oxidative phosphorylation and secondarily through reactions of the Embden-Meyerhoff
pathway and the tricarboxylic acid cycle (see
Chapters 24-27 34 and 36)
Polynucleotide Structure and Synthesis The major polymeric forms of nucleotides
found in prokaryotes and eukaryotes are the
nucleic acids RNA and DNA As shown sche-
matically in Fig 13-3 RNA and DNA are similar
polymers differing in composition only in the2 substituent of their respective pentoses (ie
OH vs H) Both consist of tandem nucleoside
units strung together by phosphodiester bonds
between their 3 and 5 carbons
Nucleic acid polymerization is catalyzed by
nucleic acid polymerases (pols) - DNA poly-
merases in the case of DNA and RNA polymer-
ases in the case of RNA All known polymerases
use 5NTPs (eg riboNTPs for RNA or dNTPs
for DNA) as their nucleotide substrates and
they operate by the mechanism exemplified
by the polymerization of a dNTP into DNA as
shown schematically in Fig 13-4 Specifically
the polymerase catalyzes polymerization of the
5 983137-phosphate of an NTP unit to the free OH
of the NMP on the 3 primer end The 983138- and
983143-phosphates are eliminated as pyrophos-phate (PPi)
In summary nucleotides are the building
blocks of RNA and DNA and they also partic-
ipate in energy transduction reactions in a
variety of metabolic pathways Nucleotides
possess a nucleoside moiety consisting of a
cyclic pentose esterified to a ring nitrogen of
a heterocyclic pyrimidine or purine base and
a mono- di- or triphosphate group attached to
one or more of the pentose hydroxyl groupsNucleotides are generically referred to as
nucleoside phosphates (NPs) and are further
distinguished on the basis of their pentose
structure as either ribonucleoside- or 2-deox-
yribonucleoside phosphates They can be
synthesized from small organic molecules
available in cells or they can be generated
Nucleotide Nomenclature
Abbreviations of ribonucleoside 5-phosphates
Base Mono- Di- Tri-
Adenine AMP ADP ATP Guanine GMP GDP GTP
Cytosine CMP CDP CTP
Uracil UMP UDP UTP
Abbreviations of deoxyribonucleoside 5-phosphates
Base Mono- Di- Tri-
Adenine dAMP dADP dATP
Guanine dGMP dGDP dGTP
Cytosine dCMP dCDP dCTP
Thymine dTMP dTDP dTTP
Table 13-1
Note Nucleoside phosphates using pyrimidines as the nitrogen base are by convention referred to as ldquoidinesrdquo (eg uridinecytidine and thymidine) whereas those using purines are referred to as ldquoosinesrdquo (eg adenosine and guanosine)
7212019 3-s20-B978012391909050013X-main
httpslidepdfcomreaderfull3-s20-b978012391909050013x-main 55
through salvage pathways that recycle their
nitrogen bases The most common NPs in
nature have their respective phosphate(s)
esterified to the 5 pentose carbon of the nucle-
oside The phosphate nearest this carbon is
the 983137-phosphate the next is the 983138-phosphateand the third (in the case of a triphosphate)
is the 983143-phosphate Nucleoside monophos-
phates are converted to their respective di-
and triphosphate derivatives via phosphoryl
transfer from ATP
DNA and RNA are similar polymers differing
in composition only in the 2substituent of
their respective pentoses (ie H vs OH) Both
consist of tandem nucleoside units strung
together by phosphodiester bonds between their 3 and 5 carbons Nucleic acid polymeri-
zation is catalyzed by nucleic acid polymerases
(pols) which use 5-NTPs as their nucleotide
substrates
OBJECTIVES
bull Recognize several ways in which nucleotidescontribute to energy transduction reactions
bull Identify cell types in the adult organism thatcontinually synthesize large quantities of RNAand DNA
bull Outline the ways in which nucleotides can besalvaged by the organism (see Chapter 17)
bull Know the difference between a nucleoside anda nucleotide
bull Identify structural differences between andamong the purines and pyrimidines present inDNA and RNA
bull Identify the purine and pyrimidine nucleoside triphosphates involved in RNA biosynthesis
bull Contrast primary structural differences betweenRNA and DNA and between AMP and cAMP
bull Discuss how nucleoside monophosphates areconverted to their respective triphosphate deriv-atives
bull Identify and explain the steps involved in nucleicacid polymerization
QUESTIONS
1 Which one of the following is a nucleoside a ATP
b Adenosine c GDP
d AMP e Adenine
2 Select the FALSE statement below regardingnucleotides
a They are products of the reaction catalyzedby nucleic acid polymerases
b They are the building blocks of both DNAand RNA
c They are structural components of severalcoenzymes
d In several metabolic pathways they act ascarriers of carbohydrates amino acids and
lipids e They are composed of a nitrogen base a
pentose and one or more phosphate groups
3 The hydroxyl group (OH) attached to the2-carbon atom of ribose is replaced by what indeoxyribose
a A sulfhydryl group
b Oxygen c Hydrogen
d Phosphate e Ammonia
4 Which one of the following is a purine found inboth DNA and RNA
a Cytosine
b Thymine c Uracil
d Adenosine e Guanine
5 Which one of the following is NOT character-istic of a nucleic acid polymerase
a It may use dNTPs as substrates
b It may use NTPs as substrates c It catalyzes growth of the polymer from the 5 end
d It catalyzes attack of a hydroxyl group on the a-phosphate of an incoming NTP
e It catalyzes a synthetic reaction in whichPPi is released as one of the products
6 Coenzyme A possesses a nucleotide a True b False
A N S W E R S
1 b
2 a
3 c
4 e
5 c
6 a
Nucleotides82
7212019 3-s20-B978012391909050013X-main
httpslidepdfcomreaderfull3-s20-b978012391909050013x-main 45
24 Chapter 13 81
Nucleoside monophosphates are converted
to their respective diphosphate derivatives
via phosphoryl transfer from ATP catalyzed
by nucleoside monophosphate kinase The
nucleoside diphosphates are then converted
to their triphosphate derivatives by nucleoside
diphosphate kinase at the expense of another
ATP The ATPs used in these phosphorylations
are derived primarily through mitochondrial
oxidative phosphorylation and secondarily through reactions of the Embden-Meyerhoff
pathway and the tricarboxylic acid cycle (see
Chapters 24-27 34 and 36)
Polynucleotide Structure and Synthesis The major polymeric forms of nucleotides
found in prokaryotes and eukaryotes are the
nucleic acids RNA and DNA As shown sche-
matically in Fig 13-3 RNA and DNA are similar
polymers differing in composition only in the2 substituent of their respective pentoses (ie
OH vs H) Both consist of tandem nucleoside
units strung together by phosphodiester bonds
between their 3 and 5 carbons
Nucleic acid polymerization is catalyzed by
nucleic acid polymerases (pols) - DNA poly-
merases in the case of DNA and RNA polymer-
ases in the case of RNA All known polymerases
use 5NTPs (eg riboNTPs for RNA or dNTPs
for DNA) as their nucleotide substrates and
they operate by the mechanism exemplified
by the polymerization of a dNTP into DNA as
shown schematically in Fig 13-4 Specifically
the polymerase catalyzes polymerization of the
5 983137-phosphate of an NTP unit to the free OH
of the NMP on the 3 primer end The 983138- and
983143-phosphates are eliminated as pyrophos-phate (PPi)
In summary nucleotides are the building
blocks of RNA and DNA and they also partic-
ipate in energy transduction reactions in a
variety of metabolic pathways Nucleotides
possess a nucleoside moiety consisting of a
cyclic pentose esterified to a ring nitrogen of
a heterocyclic pyrimidine or purine base and
a mono- di- or triphosphate group attached to
one or more of the pentose hydroxyl groupsNucleotides are generically referred to as
nucleoside phosphates (NPs) and are further
distinguished on the basis of their pentose
structure as either ribonucleoside- or 2-deox-
yribonucleoside phosphates They can be
synthesized from small organic molecules
available in cells or they can be generated
Nucleotide Nomenclature
Abbreviations of ribonucleoside 5-phosphates
Base Mono- Di- Tri-
Adenine AMP ADP ATP Guanine GMP GDP GTP
Cytosine CMP CDP CTP
Uracil UMP UDP UTP
Abbreviations of deoxyribonucleoside 5-phosphates
Base Mono- Di- Tri-
Adenine dAMP dADP dATP
Guanine dGMP dGDP dGTP
Cytosine dCMP dCDP dCTP
Thymine dTMP dTDP dTTP
Table 13-1
Note Nucleoside phosphates using pyrimidines as the nitrogen base are by convention referred to as ldquoidinesrdquo (eg uridinecytidine and thymidine) whereas those using purines are referred to as ldquoosinesrdquo (eg adenosine and guanosine)
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through salvage pathways that recycle their
nitrogen bases The most common NPs in
nature have their respective phosphate(s)
esterified to the 5 pentose carbon of the nucle-
oside The phosphate nearest this carbon is
the 983137-phosphate the next is the 983138-phosphateand the third (in the case of a triphosphate)
is the 983143-phosphate Nucleoside monophos-
phates are converted to their respective di-
and triphosphate derivatives via phosphoryl
transfer from ATP
DNA and RNA are similar polymers differing
in composition only in the 2substituent of
their respective pentoses (ie H vs OH) Both
consist of tandem nucleoside units strung
together by phosphodiester bonds between their 3 and 5 carbons Nucleic acid polymeri-
zation is catalyzed by nucleic acid polymerases
(pols) which use 5-NTPs as their nucleotide
substrates
OBJECTIVES
bull Recognize several ways in which nucleotidescontribute to energy transduction reactions
bull Identify cell types in the adult organism thatcontinually synthesize large quantities of RNAand DNA
bull Outline the ways in which nucleotides can besalvaged by the organism (see Chapter 17)
bull Know the difference between a nucleoside anda nucleotide
bull Identify structural differences between andamong the purines and pyrimidines present inDNA and RNA
bull Identify the purine and pyrimidine nucleoside triphosphates involved in RNA biosynthesis
bull Contrast primary structural differences betweenRNA and DNA and between AMP and cAMP
bull Discuss how nucleoside monophosphates areconverted to their respective triphosphate deriv-atives
bull Identify and explain the steps involved in nucleicacid polymerization
QUESTIONS
1 Which one of the following is a nucleoside a ATP
b Adenosine c GDP
d AMP e Adenine
2 Select the FALSE statement below regardingnucleotides
a They are products of the reaction catalyzedby nucleic acid polymerases
b They are the building blocks of both DNAand RNA
c They are structural components of severalcoenzymes
d In several metabolic pathways they act ascarriers of carbohydrates amino acids and
lipids e They are composed of a nitrogen base a
pentose and one or more phosphate groups
3 The hydroxyl group (OH) attached to the2-carbon atom of ribose is replaced by what indeoxyribose
a A sulfhydryl group
b Oxygen c Hydrogen
d Phosphate e Ammonia
4 Which one of the following is a purine found inboth DNA and RNA
a Cytosine
b Thymine c Uracil
d Adenosine e Guanine
5 Which one of the following is NOT character-istic of a nucleic acid polymerase
a It may use dNTPs as substrates
b It may use NTPs as substrates c It catalyzes growth of the polymer from the 5 end
d It catalyzes attack of a hydroxyl group on the a-phosphate of an incoming NTP
e It catalyzes a synthetic reaction in whichPPi is released as one of the products
6 Coenzyme A possesses a nucleotide a True b False
A N S W E R S
1 b
2 a
3 c
4 e
5 c
6 a
Nucleotides82
7212019 3-s20-B978012391909050013X-main
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through salvage pathways that recycle their
nitrogen bases The most common NPs in
nature have their respective phosphate(s)
esterified to the 5 pentose carbon of the nucle-
oside The phosphate nearest this carbon is
the 983137-phosphate the next is the 983138-phosphateand the third (in the case of a triphosphate)
is the 983143-phosphate Nucleoside monophos-
phates are converted to their respective di-
and triphosphate derivatives via phosphoryl
transfer from ATP
DNA and RNA are similar polymers differing
in composition only in the 2substituent of
their respective pentoses (ie H vs OH) Both
consist of tandem nucleoside units strung
together by phosphodiester bonds between their 3 and 5 carbons Nucleic acid polymeri-
zation is catalyzed by nucleic acid polymerases
(pols) which use 5-NTPs as their nucleotide
substrates
OBJECTIVES
bull Recognize several ways in which nucleotidescontribute to energy transduction reactions
bull Identify cell types in the adult organism thatcontinually synthesize large quantities of RNAand DNA
bull Outline the ways in which nucleotides can besalvaged by the organism (see Chapter 17)
bull Know the difference between a nucleoside anda nucleotide
bull Identify structural differences between andamong the purines and pyrimidines present inDNA and RNA
bull Identify the purine and pyrimidine nucleoside triphosphates involved in RNA biosynthesis
bull Contrast primary structural differences betweenRNA and DNA and between AMP and cAMP
bull Discuss how nucleoside monophosphates areconverted to their respective triphosphate deriv-atives
bull Identify and explain the steps involved in nucleicacid polymerization
QUESTIONS
1 Which one of the following is a nucleoside a ATP
b Adenosine c GDP
d AMP e Adenine
2 Select the FALSE statement below regardingnucleotides
a They are products of the reaction catalyzedby nucleic acid polymerases
b They are the building blocks of both DNAand RNA
c They are structural components of severalcoenzymes
d In several metabolic pathways they act ascarriers of carbohydrates amino acids and
lipids e They are composed of a nitrogen base a
pentose and one or more phosphate groups
3 The hydroxyl group (OH) attached to the2-carbon atom of ribose is replaced by what indeoxyribose
a A sulfhydryl group
b Oxygen c Hydrogen
d Phosphate e Ammonia
4 Which one of the following is a purine found inboth DNA and RNA
a Cytosine
b Thymine c Uracil
d Adenosine e Guanine
5 Which one of the following is NOT character-istic of a nucleic acid polymerase
a It may use dNTPs as substrates
b It may use NTPs as substrates c It catalyzes growth of the polymer from the 5 end
d It catalyzes attack of a hydroxyl group on the a-phosphate of an incoming NTP
e It catalyzes a synthetic reaction in whichPPi is released as one of the products
6 Coenzyme A possesses a nucleotide a True b False
A N S W E R S
1 b
2 a
3 c
4 e
5 c
6 a
Nucleotides82
