BIOCHEMISTR

Y
Metabolism of Nucleic
Acids
 Metabolism of Nucleic Acids
Nucleic acids and their derivatives are not
dietary essentials.
They are synthesized in vivo from amino acids
and other substances.
They influence the general pattern of
metabolism (chromosomes, viruses, and other
cells) and act as cytoplasmic regulators of
protein synthesis.
The free nucleotides & adenylic systems act as
co-enzymes influencing cetain specific reactions
 Digestion and Absorption
The protein components of
nucleoproteins undergo the same digestive
breakdown as proteins and releases the
nucleic acid.
DNA & RNA are hydrolyzed by
deoxyribonuclease and ribonuclease
(nucleodepolymerases) of the pancreatic
juice, respectively, into purine and
pyrimidine nucleotides.
 Digestion and Absorption
Non – specific phosphatases hydrolyzes
the sugar phosphate bond of the
mononucleotides (nucleotidase action)
forming nucleosides and phosphoric acid.
Hydrolysis of nucleosides in the intestines
is doubtful; they are probably absorbed as
such.
Their metabolism happens mainly in the
tissues.
 Digestion and Absorption
Extracts from the liver, spleen,
kidney, and bone marrow causes the
break in N – glucoside linkage of
nucleosides.
There are purine and pyrimidine
nucleosidases that may either be
hydrolytic or phosphorolytic.
 Digestion and Absorption
Pyrimidine nucleotides are not
completely digested to free bases.
These end products of nucleic acid
digestion are readily absorbed in the
small intestines via the portal blood
reaching the liver before entering the
systemic circulation.
 General Survey of Nucleic Acid
Metabolism
Non – nitrogenous constituents:
◦ The phosphoric acid portion is derived from
the foods and from endogenous sources.
◦ After completing its metabolic role, it is
excreted through the urine in the form of
inorganic phosphate.
◦ The ribose and deoxyribose are supplied by
glucose and its derivatives.
◦ It is believed that they are oxidized into CO2
and H2O
 General Survey of Nucleic Acid
Metabolism
Nitrogenous constituents
◦ The purines are fragmented into waste
products except a small amount of adenine
which contributes in the synthesis of nucleic
acid.
◦ Large amounts of pyrimidine nucleosides are
used for the synthesis of nucleic acids.
◦ Small fragments like ammonia, CO2, formate
and glycine are drawn upon for building up of
purine and pyrimidine components of nucleic
acids.
 General Survey of Nucleic Acid
Metabolism
Nitrogenous constituents (continuation)
◦ Preformed bases from the diet plays a more
important role in the case of pyrimidines than
those of purines.
The catabolic waste products of nucleic
acids together with the unused bases of
the diet are excreted through the urine.
The purines are degraded into uric acid
while pyrimidines are converted into urea.
 Purine Biosynthesis
Picture of the Origin of Purines

From CO2 From glycine

From C N
Aspartate N C From
C Formate
From C C
Formate N N

From amide N of glutamine

 Steps of Purine Biosynthesis
(1) 5 – phosphoribosyl – 1 –
pyrophosphate is the key
substance in the biosynthesis of
purine and pyromidine
nucleotides. This is formed from
ribose – 5 – phosphate and ATP
catalyzed by a kinase causing the
transfer of pyrophosphate.
 Steps of Purine Biosynthesis
(2) 5 – phosphoribosyl – 1 –
pyrophosphate reacts with
glutamine to form an acid labile
amino sugar, 5 – phosphorylribosyl
- a - amine
(3) Phosphoribosyl amine in the
presence of ATP, glycine, and Mg++
forms glycinamide ribonucleotide.
 Steps of Purine Biosynthesis
(4) Formylation of glicinamide by
transfer of formyl folic acid derivative,
catalyzed by transformylase forming α-N-
formylglycinamide ribonucleotide.
(5) transfer of NH2 from glutamine to α-
N-formylglycinamide ribonucleotide.
(6) 5 – aminoimidazole ribonucleotide
ring is formed in the presence of ATP and
Mg++.
 Steps of Purine Biosynthesis
(7) Carboxylation of 5 – aminoimidazole
ribonucleotide to 5 – amino – 4 –
carboxylic nucleotide.
(8) Formation of 5 – aminoimidazole – 4
– succinocarboxyamide ribonucleotide in
the presence of ATP, aspartic acid, and
Mg++.
 Steps of Purine Biosynthesis
(9) Non – hydrolytic cleavage through the
catalyzing action of adenylosuccinase
forming 5 – aminoimidazole – 4 -
carboxyamide ribonucleotide
(10) formation of 5 –
formamidoimidazole – 4 - carboxyamide
ribonucleotide
(11) closure of the ring by inosinicase
produces inosinic acid (hypoxanthine
ribonucleotide)
 Steps of Purine Biosynthesis
(12) Formation of adenylic acid from
inosinic acid through the initial formation
of adenylosuccinic acid in the presence of
aspartic acid and guanosine triphosphate.
Subsequent non – hydrolytic cleavage of
adenylosuccinic acid to form adenylic and
fumaric acid. This is catalyzed by
adenylosuccinase.
 Steps of Purine Biosynthesis
Guanylic acid is synthesized from
inosinic acid.
Inosinic acid is first oxidized to
xanthylic acid in the presence of K+
ions.
Xanthylic acid in the presence of
glutamine and ATP forms guanylic
acid.
 Regulation of Biosynthesis of Purine
Nucleotide
Feedback mechanisms regulate the rate of
the novo synthesis of purine nucleotides
and the relative formation of the end
products, adenylic acid and guanylic acid.
The 1st control is exerted in the rxn that is
unique of purine synthesis leading to the
transfer of amino group to 5 –
phosphoribosyl – 1 – pyrophosphate
(PRPP) to form 5 – phosphoribosylamine.
 Regulation of Biosynthesis of Purine
Nucleotide
This reaction is catalyzed by a
regulatory (allosteric) enzyme which
is inhibited by the end products AMP
and GMP.
When AMP or GMP is in excess, this
step 5 – phosphoribosyl – 1 –
pyrophosphate (PRPP) is inhibited.
 Regulation of Biosynthesis of Purine
Nucleotide
The 2nd control mechanism is in the latter
stage.
Excess of GMP gives rise to allosteric
inhibition in its formation from inosinic
acid without affecting the formation of
AMP.
On the other hand, excess of AMP results
in inhibition or its formation without
affecting the synthesis of GMP.
Other Pathways of Purine Synthesis
Purine nucleotides can also be
formed from free purines or purine
derivatives derived from the
breakdown of nucleic acids or
nucleotides (salvage pathways).
Free purines react with 5 –
phosphoribosyl – 1 – pyrophosphate
(PRPP) to yield 5’ – nucleotides.
Other Pathways of Purine Synthesis
The rxns are reversible and catalyzed by
two distinct enzymes of the liver: adenine
phosphoribosyl transferase (APRT) &
hypoxanthine – guanine phosphoribosyl
transferase (HGPRT).
◦ Adenine + PRPP Adenylic acid + PPi
◦ Guanine + PRPP Guanylic acid + Ppi
◦ Hypoxanthine + PRPP Inosinic acid + PPi
 The Catabolic Fate of Purine
Degradation of purines leads to uric acid
in men and in apes.
Guanosine is acted upon by nucleoside
phosphorylase liberating guanine.
Adenosine may undergo similar
phosphorylysis, but it 1st undergoes
hydrolytic deamination to inosine which
is converted to hypoxanthine.
Hypoxanthine is oxidized into xanthine.
 The Catabolic Fate of Purine
Guanine also forms xanthine in hydrolytic
deamination.
Xanthine is then further oxidized by
xanthine oxidase forming uric acid which
is the end product in man and apes.
In other mammals, where another enzyme
uricase, a copper protein, is present, the
uric acid is subsequently converted into
allantoin by aerobic oxidation.
 The Catabolic Fate of Purine
Adenosine Guanosine
Adenosine Nucleoside
deaminase phosphorylase
Inosine Guanine
Nucleoside Guanase
phosphorylase
Xanthine oxidase
Hypoxanthine Xanthine
Xanthine oxidase
Uric acid
Uricase
Allantoin
 The Catabolic Fate of Purine
Xanthine oxidase, a flavin enzyme,
catalyzes the oxidation ofboth
hypoxanthine and xanthine.
This enzyme has an unusual dual
specificity of being able to catalyze the
oxidation of a variety of aldehydes.
Uric acid formation in mammals occurs in
the liver.
 The Catabolic Fate of Purine
On a diet rich in nucleoproteins (meat,
liver, etc) the uric acid content of the urine
is higher.
78% of uric acid is excreted unchanged in
the urine
Of the remaining 22%, a large portion is
degraded into urea, a small amount into
ammonia, and the rest excreted in the
feces.
 The Catabolic Fate of Purine
Of the uric acid miscible pool, 1/6 is in
the plasma while 5/6 is in the
extravascular fluid.
The pool is uniformly elevated in gout to
around 15 – 25 times.
Uric acid concentration in normal plasma
◦ 3.5 mg/ml = male
◦ 4.5 mg/ml = female
◦ 6 – 8 mg/ml = in gout
 The Catabolic Fate of Purine
Overproduction causes
◦ Exogenous = increased ingestion of purine
foods
◦ Endogenous = excessive breakdown of cells
◦ Increased de novo formation of purine bases
 Failure of the feedback mechanism as a result of the
alteration of enzyme protein structure
 Excessive supply of substrates
 A shunt pathway, where purine bases are degraded
into uric acid as they are formed without entering
into the formation of nucleic acid.
 The Catabolic Fate of Purine
In hereditary gout associated, there is a
failure to convert guanine and
hypoxanthihne to the nucleotides leading
to excessive production of uric acid.
The excretion of uric acid in the urine is
regulated by endocrine secretions.
Administration of 11-hydroxysteroids of
the adrenal cortex or ACTH increase the
excretion of uric acid.
 Pyrimidine Biosynthesis
Hammarsten and collaborators
found orotic acid as the precursor
of nucleic acid pyrimidines.
The key substance in the
synthesis of pyrimidine
nucleotides is carbamyl
phosphate.
Steps in Pyrimidine Biosynthesis
(1) Formation of carbamylaspartic acid
catalyzed by separate transcarbamylase.
(2) Ring closure is catalyzed by
dihydroorotase with formation of 1 –
dihydroorotic acid.
(3) dihydroorotic acid is oxidized to
orotic acid by dihydroorotic acid
dehydrogenase in which NAD+ is the
electron acceptor.
Steps in Pyrimidine Biosynthesis
(4) Coupling of orotic acid with 5 –
phosphoribosyl – 1 – pyrophosphate
with formation of pyrimidine
nucleotide, catalyzed by orotidine 5’-
phosphate pyrophosphate.
(5) Orotidine 5’-phosphate is
decarboxylated to yield uridilic acid.
Steps in Pyrimidine Biosynthesis
The pathway w/c results in the formation
of UTP involves consecutive transfers of
phosphate from ATP to uridine 5’-
phosphate with intermediate formation of
UDP.
Uridine 5’-PO4 + ATP UDP + ADP
UDP + ATP UTP + ADP
Steps in Pyrimidine Biosynthesis
Formation of cytidine nucleotide
involves the amination of uridine
triphosphate to yield cytidine
triphosphate.
There is a hereditary disorder of
pyrimidine metabolism in man, orotic
aciduria (excess orotic acid in urine).
Similarities & Differences of Purine and
Pyrimidine Biosynthesis
In purine synthesis, all intermediates
are derivatives of ribose – 5 – PO4
while in pyrimidine nucleotide, the
pyrimidine ring formed prior to the
coupling with ribose phosphate.
The initial nucleotides formed in
both cases, inosinic and orotidylic
acids are not constituents of nucleic
acids.
Similarities & Differences of Purine and
Pyrimidine Biosynthesis
Although purines contain a
pyrimidine ring fused to imidazole,
the precursors of the two rings are
different.
In both types of nucleotides, 5 –
phosphoribosyl – 1 – pyrophosphate
plays an important role in the
formation.
 Regulation of Pyrimidine Nucleotide
Biosynthesis
The rate of pyrimidine nucleotide
synthesis is regulated by feedback
mechanism through the enzyme
aspartate – transcarbamylase, which
catabolyze the 1st rxn in the sequence.
The regulatory enzyme is inhibited
by citidine triphosphate, the end
product of the reaction.
 Regulation of Pyrimidine Nucleotide
Biosynthesis
When citidine triphosphate
accumulate in excess, the enzyme
aspartate – transcarbamylase is
inhibited preventing the reaction to
proceed, depressing the formation of
citidine triphosphate.
This inhibition is prevented by ATP.
The Catabolic Fate of Pyrimidine
Cytosine and 5 – methyl cytosine is
believed to be converted into uracil and
thymine respectively.
These are probably reduced to
dihydroderivatives and after losing N and
C, for b-alanine and b-amino isobutyric
acid.
The b-alanine is deaminated and the
ammonia liberated is synthesized to urea.
Biosynthesis of Nucleotide Coenzymes
Flavin and pyrimidine
nucleotides and CoA are
derivatives of adenylic acid.
Their enzymatic synthesis are
similar to the synthesis of
mononucleotides of the nucleic
acids.
Biosynthesis of Nucleotide Coenzymes
Flavin mononucleotide (FMN) is a
riboflavin phosphate synthesized from
riboflavin and ATP through the catalyzing
action of flavokinase.
◦ Riboflavin + ATP  riboflavin 5’-PO4 + ADP
Through the action of phosphorylase,
FMN is converted to FAD.
◦ Riboflavin 5’-PO4 + ATP  FAD + ATP
Biosynthesis of Nucleotide Coenzymes
NAD is synthesized from nicotinic acid
(not nicotinamide)
◦ Nicotinic acid + PRPP Nicotinic acid
nucleotide
+ PPi
◦ Nicotinic acid nucleotide + ATP desamido-
NAD + PPi
The amide group is incorporated after
desamido-NAD is formed.
◦ Desamido – NAD + glutamine + ATP NAD+ +
glutamic acid + ADP + Pi
Biosynthesis of Nucleotide Coenzymes
Byaddition of another phosphate,
NADP is formed.
◦ NAD+ + ATP NADP + ADP
The synthesis of CoA starts with the
phosphorylation of pantothenic acid.
◦ Pantothenic acid + ATP 
4’-phosphopantothenic acid + ADP
Synthesis of Nucleotide Coenzymes
Addition of cysteine and another
phosphate forms 4’-phosphopantothenyl
cysteine.
◦ 4’-phosphopantothenic acid + ATP + cysteine
 4’phosphopantothenyl cysteine + ADP + Pi
Decarboxylation of 4’-
phosphopantothenyl cysteine forms 4’-
phosphopantotheine which is
phosphorylated to CoA
Synthesis of Nucleotide Coenzymes
◦ 4’-phosphopantothenyl cysteine – CO2  4’-
phosphopantotheine
Mg++
◦ 4’-phosphopantotheine + ATP  dephospho
CoA + Ppi
Mg++
◦ dephospho CoA + ATP  Coenzyme A + ADP
 Interrelations of Nucleic Acid
Metabolism with other Foodstuff
The metabolic pathways of proteins
provide most of the raw materials for the
synthesis of the purines and pyrimidines.
Examples are glycine, formate,
glutamine, aspartate, and ammonia.
Carbohydrates provide the keto acid
precursor of the dicarboxylic amino acids
and is also the source of the pentose.
Lipid has no direct link except the non –
specific contribution of CO2.
 Interrelations of Nucleic Acid
Metabolism with other Foodstuff
The free nucleotides exert a marked
influence on the metabolism of all
foodstuffs.
They serve as important agents in
collecting, storing, and transferring
high – energy phosphates and as co –
factors for biological oxidation.
 Interrelations of Nucleic Acid
Metabolism with other Foodstuff
The biosynthesis of purines and
pyrimidines depend on the
interrelationships with other metabolic
processes (carbohydrates & proteins)