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Phanchana Sanguansermsri
Nucleic acids
• Nucleic acids are linear polymers of
nucleotides
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
Nucleotides
• Nucleotides are phosphate esters of a
pentose (ribose or deoxyribose) in which a
purine or pyrimidine base is linked to C1’ o
f the sugar
Function of nucleotides
• Monomeric unit of nucleic acid
• Energy currency: ATP
• Component of some of the cofactor of
metabolism: FAD, NAD+, coenzyme A
Nucleotide metabolism
• Synthesis of purine ribonucleotides
• Synthesis of pyrimidine ribonucleotides
• Formation of deoxyribonucleotides
• Nucleotide degradation
Synthesis of purine
ribonucleotides
Isotonic experiment
• 1948, Buchanan
– feed a variety of isotopically labeled
compounds to pigeons
– determine the positions of the labeled atoms in
their excreted uric acid (a purine)
Overview of de novo synthesis of
purine ribonucleotides
• Purines are initially formed as
ribonucleotides rather than as free bases
1. The initial synthesized purine derivative is
inosine monophosphate (IMP)
2. IMP is the precursor of both AMP and
GMP
Synthesis of inosine
monophosphate (IMP)
• IMP is synthesized in a pathway composed
of 11 reactions
• Starting material is α-D-ribose-5-
phosphate, a product of the pentose phospha
te pathway
(1) activation of ribose-5-phosphate
(2) acquisition of N9
(3) acquisition of C4, C5, and N7
(4) acquisition of C8
(5) acquisition of N3
(6) formation of imidazole ring
(7) acquisition of C6
(8) acquisition of N1
(9) elimination of fumarate
(AICAR)
(10) acquisition of C2
(AICAR)
(11) cyclization to form IMP
• In bacteria, the enzymes of IMP
biosynthesis occur as independent proteins.
• In animals, single polypeptides catalyze
– Reaction 3, 4, and 6
– Reaction 7, 8
– Reaction 10, 11
– The intermediate products of these
multifunctional enzymes are not readily release
d to the medium but are channeled to the succee
ding enzymatic activities of the pahtway.
Synthesis of guanine and adenine
ribonucleotides
• Inosine monophosphate (IMP) does not
accumulate in the cell but rapidly converted
to adenosine monophosphate (AMP) and gu
anosine monophosphate (GMP) in different
two-reaction pathways
1st reaction to convert IMP to AMP
2nd reaction to convert IMP to AMP
1st reaction to convert IMP to GMP
2nd reaction to convert IMP to GMP
• Nucleoside diphosphates and triphosphates
are synthesized by the phosphorylation of
nucleoside monophosphates.
• Nucleoside diphosphates are synthesized
from the corresponding monophosphates by
base-specific nucleoside monophosphate ki
nases.
• The enzymes do not discriminate between
ribose and deoxyribose.
Adenylate kinase
AMP + ATP ADP
---> feedforward
activation
Salvage of purines
• In most cells, the turnover of nucleic acids
releases adenine, guanine, and hypoxanthin
e. These free purines are reconverted to thei
r corresponding nucleotides through salvage
pathways.
• Salvage pathways are diverse in character
and distribution. In mammals, purines are
mostly salvage by the different enzymes.
• Adenine phosphoribosyltransferase (APRT)
mediates AMP formation using PRPP.
---> feedforward
activation
Formation of
deoxyribonucleotides
Ribonucleotide &
deoxyribonucleotide
• DNA differs from RNA in two respects:
1. Its nucleotides contain 2’-deoxyribose
residue rather than ribose residues, and
2. It contains the base thymine (5-
methyluracil) rather than uracil.
Production of deoxyribose
residues
• Deoxyribonucleotides are synthesized from
their corresponding ribonucleotides by the r
eduction of their C2’ position using the enz
yme ribonucleotide reductase rather than by
their de novo synthesis from deoxyribose-co
ntaining precursors.
• The final step in the production of all
dNTPs is the phosphorylation of the corresp
onding dNDPs.
• The reaction is catalyzed by nucleoside
diphosphate kinase (as in phosphorylation o
f NDPs).
dADP + ATP dATP + ADP
phosphoribomutase
Ribose-1-P Ribose-5-P
• Deamination of AMP to IMP, when
combined with the synthesis of AMP from I
MP (purine nucleotide cycle), has the net ef
fect of deaminating aspartate to yeild fumar
ate.
Purine nucleotide cycle
• Muscle replenishes its citric acid cycle
intermediates with fumarate generated in th
e purine nucleotide cycle.
Gout (excess of uric acid)
• Caused by deposition of crystals of sodium
urate.
• Painful arthritis, joint inflammation of
sudden onset, most often in big toe.
• May precipitate in the kidneys and ureters
as stones, resulting in renal damage and
urinary tract obstruction.
• The most prevalent cause of gout is
impaired uric acid excretion.
• Gout may also result from a number of
metabolic insufficiencies (eg. HGPRT defic
iency)
• Gout can be treated by the xanthine oxidase
inhibitor, allopurinol. The product,
alloxanthine, remain tightly bound to the re
duce form of the enzyme.
Fate of uric acid
• In human and other primates, the final
product of purine degradation is uric acid, w
hich is excreted in the urine.
• The same is true for birds, terrestrial
reptiles, and many insects.
– These organism also catabolize their excess
amino acid nitrogen to uric acid via purine bios
ynthesis.
• In all other organisms, uric acid is further
processed before excretion
Catabolism of pyrimidines
• Animal cells degrade pyrimidine
nucleotides to their component bases.
• These reactions, like those in purine
nucleotides, occur through dephosphorylati
on, deamination, and glycosidic bond cleav
ages.
• The resulting uracil and thymine are then
broken down in the liver through reduction
rather than by oxidation as occurs in purine
catabolism.
• The end products of pyrimidine catabolism,
beta-alanine and beta-aminoisobutyrate, are
amino acids and are metabolized as such.
• They are converted, through transamination
and activation reactions, to malonyl-CoA
and methylmalonyl-CoA
• Malonyl-CoA is a precursor of fatty acid
synthesis, and methylmalonyl-CoA is conve
rted to the citric acid cycle intermediate suc
cinyl-CoA.
• Catabolism of pyrimidine nucleotides
contributes to the energy metabolism of the
cell.
Summary
Synthesis of purine
ribonucleotides
• The purine nucleotide IMP is synthesized in
11 steps from ribose-5-phosphate, aspartate,
fumarate, glutamine, glycine, and HCO3-.
• IMP synthesis is regulated at its first and
second steps.
• IMP is the precursor of AMP and GMP,
which are phosphorylated to produce the co
rresponding di- and triphosphates.
Synthesis of pyrimidine
ribonucleotides
• Pyrimidine nucleotide UMP is synthesized from
5-phosphoribosyl pyrophosphate, aspartate,
glutamine, and HCO3- in six reactions.
• UMP is converted to UTP and CTP by
phosphorylation and amination.
• Biosynthesis is regulated in bacteria at the
ATCase step and in animals at the step
catalyzed by carbamoyl phosphate synthetase II
Formation of
deoxyribonucleotides
• Deoxyribonucleoside diphosphates are
synthesized from corresponding NDP by th
e action of ribonucleotide reductase.
• dTMP is synthesized from dUMP by
thymidine synthase.
Nucleotide degradation
• Purine nucleotides are degraded by
nucleosidases and purine nucleoside phosph
orylase (PNP).
• Adenine nucleotides are deaminated by
adenosine deaminase and AMP deaminase.
• The synthesis and degradation of AMP in
the purine nucleotide cycle yield the citric a
cid cycle intermediate fumarate in muscles.
• Xanthine oxidase catalyzes the oxidation of
hypoxantine to xanthine and of xanthine to
uric acid.
• In humans, the ultimate product of purine
degradation is uric acid, which is excreted.
Other organisms degrade urate further.
• Pyrimidines are broken down to
intermediates of fatty acid metabolism.
Thank you for your attention