Structure & Functions

of Nucleotides

Dr Nabeela Faisal
SPECIFIC LEARNING OBJECTIVES

Describe the chemistry of purines and pyrimidines

and their linkage in nucleic acid synthesis
Explain the structure and nomenclature of
nucleotides, biomedical importance of natural and
synthetic analogues
 Biomedical importance of Nucleotides
Serve as precursors of nucleic acids.
Ribonucleoside and deoxyribonucleoside phosphates (nucleotides) are
essential for all cells. Without them, neither ribonucleic acid (RNA)
nor deoxyribonucleic acid (DNA) can be produced, and, therefore,
proteins cannot be synthesized or cells proliferate.
Purine and pyrimidine nucleotides participate in metabolic
functions as diverse as
i. energy metabolism,
ii. protein synthesis,
iii. regulation of enzyme activity and
iv. signal transduction.
 BIOMEDICAL IMPORTANCE
When linked to vitamins or vitamin derivatives,
nucleotides form a portion of many coenzymes. (such as
coenzyme A, flavin adenine dinucleotide (FADH2),
nicotinamide adenine dinucleotide (NADH), and
nicotinamide adenine dinucleotide phosphate (NADPH).
As the principal donors and acceptors of phosphoryl
groups in metabolism, nucleoside tri- and diphosphates
such as ATP and ADP are the principal players in the
energy transductions that accompany metabolic
interconversions and oxidative phosphorylation.
BIOMEDICAL IMPORTANCE
The cyclic nucleotides cAMP and cGMP serve as the second
messengers in hormonally regulated events, and GTP and
GDP play key roles in the cascade of events that characterize
signal transduction pathways.
Linked to sugars or lipids, nucleosides constitute key
biosynthetic intermediates :
i. The sugar derivatives UDP-glucose and UDP-galactose
participate in sugar interconversions and in the biosynthesis
of starch and glycogen.
ii. Similarly, nucleoside-lipid derivatives such as
CDP-acylglycerol are intermediates in lipid biosynthesis.
 BIOMEDICAL IMPORTANCE
Roles that nucleotides perform in metabolic regulation
include:
i. ATP-dependent phosphorylation of key metabolic enzymes,
ii. allosteric regulation of enzymes by ATP, ADP, AMP, and
CTP, and
iii. control by ADP of the rate of oxidative phosphorylation.
Nucleotides also serve as carriers of activated intermediates
in the synthesis of some carbohydrates, lipids, and conjugated
proteins .
(For example, uridine diphosphate (UDP)- glucose and
cytidine diphosphate (CDP)-choline).
 BIOMEDICAL IMPORTANCE
In addition to the central roles that nucleotides play in
metabolism, their medical applications include :
i. the use of synthetic purine and pyrimidine analogs
that contain halogens, thiols, or additional nitrogen
atoms in the chemotherapy of cancer and AIDS,
and
ii. as suppressors of the immune response during
organ transplantation.
 Sources
The purine and pyrimidine bases found in nucleotides can be
synthesized
1. de novo or
2. can be obtained through salvage pathways that allow the
reuse of the preformed bases resulting from normal cell
turnover.
Note: Little of the purines and pyrimidines supplied by diet are
utilized and are degraded instead.
CHEMISTRY OF PURINES, PYRIMIDINES,
NUCLEOSIDES & NUCLEOTIDES

Purines & Pyrimidines are heterocyclic compounds

Purines and pyrimidines are nitrogen-containing heterocycles,

cyclic structures that contain, in addition to carbon, other
(hetero) atoms such as nitrogen.
 Nitrogenous Bases
Note that the smaller
pyrimidine molecule has the
longer name and the larger
purine molecule the shorter
name, and that their six-atom
rings are numbered in opposite
directions
(Figure 32–1).
Adenine is 6 amino purine Guanine is 2-amino-6oxopurine
(keto form)
 Nucleosides Are N-Glycosides
Nucleosides are derivatives of purines and
pyrimidines that have a sugar linked to a ring
nitrogen of a purine or pyrimidine.
Numerals with a prime (e.g, 2′ or 3′) distinguish
atoms of the sugar from those of the heterocycle.
The sugar in ribonucleosides is D-ribose(β, D
ribofuranose, and in deoxyribonucleosides is
2-deoxy-D-ribose.
Both sugars are linked to the heterocycle by a
a-N-glycosidic bond, almost always to the N-1 of a
pyrimidine or to N-9 of a purine (Figure 32–3).
 Ribonucleosides

Both sugars are linked to the heterocycle by a a-N-glycosidic bond,

almost always to the N-1 of a pyrimidine or to N-9 of a purine
(Figure 32–3).
In a nucleoside, nitrogenous base is attached
to carbon-1' of the pentose sugar.
Nucleotides are Phosphorylated
Nucleosides
Mononucleotides are nucleosides with a phosphoryl group
esterified to a hydroxyl group of the sugar.
The 3′- and 5′-nucleotides are nucleosides with a phosphoryl
group on the 3′- or 5′-hydroxyl group of the sugar, respectively.
Since most nucleotides are 5′-, the prefix “5′-” usually is
omitted when naming them.
UMP and dAMP thus represent nucleotides with a phosphoryl
group on C-5 of the pentose.
Additional phosphoryl groups, ligated by acid anhydride
bonds to the phosphoryl group of a mononucleotide, form
nucleoside diphosphates and triphosphates
(Figure 32–4).
 ATP

Glycosidic
bond

Ester bond
 Nucleoside producing nucleotide
The addition of one or more phosphate groups to a nucleoside produces a
nucleotide. The first phosphate group is attached by an ester linkage to the 5 -OH
of the pentose, forming a nucleoside 5 -phosphate or a 5 -nucleotide.
The type of pentose is denoted by the prefix in the names “5 -ribonucleotide”
and “5 -deoxyribonucleotide.”
If one phosphate group is attached to the 5 -carbon of the pentose, the structure
is a nucleoside monophosphate, like adenosine monophosphate AMP also called
(adenylate).
If a second or third phosphate is added to the nucleoside, a nucleoside
diphosphate (for example, adenosine diphosphate ADP or triphosphate (for
example, adenosine triphosphate ATP) results .The second and third phosphates
are each connected to the nucleotide by a “high-energy” bond.
Note: The phosphate groups are responsible for the negative charges
associated with nucleotides and cause DNA and RNA to be referred to as
“nucleic acids.”
Difference of nucleotides and nucleosides
Structures of AMP, dAMP, UMP, TMP
 Tautomers
Tautomers are structural isomers of chemical
compounds that readily interconvert.
The chemical reaction interconverting the two is called
tautomerization.
This conversion commonly results from the relocation
of a hydrogen atom within the compound.
 Tautomerism
The oxo and amino groups
of purines and pyrimidines
exhibit ketoenol and
amine-imine tautomerism
(Figure 32–2), although
physiologic conditions
strongly favor the amino
and oxo forms.
 Tautomerism
Purines or pyrimidines with an ---NH2 group are weak bases
(pKa values 3-4), although the proton present at low pH is
associated, not as one might expect with the exocyclic amino
group, but with a ring nitrogen, typically N1 of adenine, N7 of
guanine, and N3 of cytosine.

The planar character of purines and pyrimidines facilitates

their close association, or “stacking, "that stabilizes
double-stranded DNA .
 Heterocylic N-Glycosides Exist
as Syn and Anti Conformers
Steric hindrance by the
heterocycle dictates that there
is no freedom of rotation about
the β-N-glycosidic bond of
nucleosides or nucleotides.
Both therefore exist as non
interconvertible syn or anti
conformers (Figure 32–5).
While both syn and anti
conformers occur in nature, the
anti conformers predominate.
Modification of Polynucleotides can
Generate Additional Structures
Small quantities of additional purines and pyrimidines
occur in DNA and RNAs.
Examples include
❖ 5-methylcytosine of bacterial and human DNA,
❖ 5-hydroxymethylcytosine of bacterial and viral nucleic
acids, and
❖ mono- and the di-N-methylated adenine and guanine of
mammalian messenger RNAs (Figure 32–7)
that function in oligonucleotide recognition and in
regulating the half-lives of RNAs.
Oligonucleotides, or oligos, are short single strands of
synthetic DNA or RNA that serve as the starting point for
many molecular biology and synthetic biology
applications
 Unusual (modified) bases
Unusual (modified) bases are occasionally found in some
species of DNA and RNA (for example, in some viral DNA)
and in transfer RNA (tRNA).
Base modifications include
i. methylation,
ii. glycosylation,
iii. acetylation, and
iv. reduction.
Some examples of unusual bases are shown in Figure 32.7.
Note: The presence of an unusual base in a nucleotide
sequence :
i. may aid in its recognition by specific enzymes or
ii. protect it from being degraded by nucleases.
Unusual Bases
Hypoxanthine (6-oxopurine)

Xanthine (2,6-Dioxopurine)

Uric Acid (2,6,8-trioxypurine)

Intermediates in the catabolism

of adenine and guanine
 Xanthine Derivatives
Methylated heterocycles of
plants include the xanthine
derivatives :
caffeine of coffee,
theophylline of tea, and
theobromine of cocoa
(Figure 32–9).
 Xanthine Derivatives
Caffeine of coffee :
1,3,7 trimethyl xanthine

Theophylline of tea :
1,3 dimethyl xanthine

Theobromine of cocoa :
3,7 dimethyl xanthine
 Caffeine
Caffeine increases intracellular concentrations of cyclic
adenosine monophosphate (cAMP) by inhibiting
phosphodiesterase enzymes in skeletal muscle and
adipose tissues.
People most commonly use caffeine for mental
alertness, headache, migraine, athletic performance,
memory, and obesity. It is also used for asthma,
gallbladder disease, low blood pressure, depression,
and many other conditions.
Nucleotides are Polyfunctional Acids
The primary and secondary phosphoryl groups of
nucleosides have pK values of about 1.0 and 6.2,
a

respectively.
Nucleotides therefore bear significant negative
charge at physiologic pH.
The pK values of the secondary phosphoryl groups
a

are such that they can serve either as proton donors or

as proton acceptors at pH values approximately two
or more units above or below neutrality.
Nucleotides absorb Ultraviolet Light
The conjugated double bonds of purine and
pyrimidine derivatives absorb ultraviolet light at pH
7.0 at a wavelength close to 260 nm.
The concentration of nucleotides and nucleic acids
thus often is expressed in terms of “absorbance at 260
nm.”
The mutagenic effect of ultraviolet light is due to its
absorption by nucleotides in DNA that results in
chemical modifications.
Nucleotides Serve Diverse Physiologic Functions

Role as precursors of nucleic

acids.
ATP, GTP, UTP, CTP, and
their derivatives each serve
unique physiologic functions.
Selected examples include the
role of ATP as the principal
biologic transducer of
free energy, and the second
messenger cAMP
The mean intracellular concentration of ATP, the most
abundant free nucleotide in mammalian cells, is about 1
mmol/L.

Since little cAMP is required, the intracellular cAMP

concentration (about 1 nmol/L) is six orders of magnitude
below that of ATP.
cAMP structure
Nucleotides; Physiologic Functions
Other examples include adenosine 3′-phosphate-5′-
phosphosulfate (Figure 32–11), the sulfate donor for sulfated
proteoglycans and for sulfate conjugates of drugs; and the
methyl group donor S-adenosylmethionine (Figure 32–12).
GTP serves as an allosteric regulator and as an energy source
for protein synthesis.
cGMP (Figure 32–10) serves as a second messenger in
response to nitric oxide (NO) during relaxation of smooth
muscle.
Nucleotides; Physiologic Functions
UDP-sugar derivatives participate in sugar epimerizations
and in biosynthesis of glycogen , glucosyl disaccharides,
and the oligosaccharides of glycoproteins and
proteoglycans .
UDP-glucuronic acid forms the urinary glucuronide
conjugates of bilirubin and of many drugs, including
aspirin.
CTP participates in biosynthesis of phosphoglycerides,
sphingomyelin, and other substituted sphingosines .
Finally, many coenzymes incorporate nucleotides as well
as structures similar to purine and pyrimidine nucleotides
Major Precursors for the biosynthesis of a variety of
important compounds

Biopterin

Histidine
Nucleoside Triphosphates Have
High Group Transfer Potential
Nucleotide triphosphates have two acid anhydride bonds and
one ester bond. Unlike esters, acid anhydrides have a high group
transfer potential.

ΔG ′ for the hydrolysis of each of the two terminal (β and γ) phosphoryl

0

groups of a nucleoside triphosphate is about −7 kcal/mol (−30 kJ/mol).

This high group transfer potential not only permits purine and pyrimidine
nucleoside triphosphates to function as group transfer reagents, most
commonly of the γ-phosphoryl group, but also on occasion transfer of a
nucleotide monophosphate moiety with an accompanying release of PP . i

Cleavage of an acid anhydride bond typically is coupled with a highly

endergonic process such as covalent bond synthesis, for example, the
polymerization of nucleoside triphosphates to form a nucleic acid.
SYNTHETIC NUCLEOTIDE ANALOGS ARE
USED IN CHEMOTHERAPY
Synthetic analogs of purines, pyrimidines,
nucleosides, and nucleotides modified in the
heterocyclic ring or in the sugar moiety have
numerous applications in clinical medicine.
Their toxic effects reflect:
i. either inhibition of enzymes essential for nucleic acid
synthesis or
ii. their incorporation into nucleic acids with resulting
disruption of base pairing.
SYNTHETIC NUCLEOTIDE ANALOGS ARE USED
IN CHEMOTHERAPY
Oncologists employ 5-fluoro- or 5-iodouracil,
3-deoxyuridine, 6-thioguanine and 6-mercaptopurine,
5- or 6-azauridine,5- or 6-azacytidine, and
8-azaguanine
(Figure 32–13), which are incorporated into DNA prior
to cell division.
The purine analog allopurinol, used in treatment of
hyperuricemia and gout, inhibits purine biosynthesis
and xanthine oxidase activity.
Allopurinol is a structural analog of the natural purine
base, hypoxanthine.
Synthetic purine & pyrimidine Analogs
 Examples
Cytarabine is used in
chemotherapy of cancer.
Azathioprine, which is
catabolized to
6-mercaptopurine,is
employed during organ
transplantation to suppress
immunologic rejection
Dietarily non essential -Nucleotides
• Nonessential in Diet : Ingested nucleic acids and
nucleotides are not essential in diet .Normal human tissues
can synthesize purines and pyrimidines from amphibolic
intermediates in quantities and at times appropriate to meet
variable physiologic demand.
• Following their degradation in the intestinal tract, the
resulting mononucleotides may be absorbed or converted
to purine and pyrimidine bases.
• The purine bases are then oxidized to uric acid, which may
be absorbed and excreted in the urine.
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