Nucleic acid metabolism
and Genetic information
transfer
DEVIPRIYA P V
M PHARM

CONTENTS
 Biosynthesis of purine and pyrimidine nucleotides
 Catabolism of purine nucleotides and
Hyperuricemia and Gout disease
 Organization of mammalian genome
 Structure of DNA and RNA and their functions
 DNA replication (semi conservative model)
 Transcription or RNA synthesis
 Genetic code
 Translation or Protein synthesis and inhibitors

Biosynthesis of purine
nucleotides
 Ribose 5-phosphate is the starting material for purine nucleotide
synthesis.
 lt reacts with ATP to form phosphoribosyl pyrophosphate
(PRPP).
 Glutamine transfers its amide nitrogen to PRPP and produce 5-
phosphoribosyl amine by the action of enzyme PRPP glutamyl
amidotransferase.
 Phosphoribosylamine reacts with glycine in the presence of ATP
to form glycinamide ribosyl 5-phosphate (GAR).
 N10-Formyl tetrahydrofolate donates the formyl group and the
product formed is formylglycinamide ribosyl 5-phosphate.
 Glutamine transfers the second amido amino group to produce
formyl glycinamidine ribosyl 5-phosphate.

 5-aminoimidazole ribosyl 5-phosphate is formed in an ATP
dependent reaction.
 Addition of CO2 occurs to yield aminoimidazole carboxylate ribosyl
5-phosphate.
 Aspartate condenses with aminoimidazole carboxylate ribosyl 5-
phosphate to form aminoimidazole 4-succinyl carboxamide ribosyl
5-phosphate.
 Adenosuccinate lyase cleaves off fumarate to form
aminoimidazole 4-carboxamide ribosyl 5-phosphate.
 N1O-Formyl tetrahydrofolate donates a one-carbon moiety to
produce formaminoimidazole 4-carboxamide ribosyl 5-phosphate.
 The final reaction catalysed by cyclohydrolase leads to ring
closure with an elimination of water molecule.
 The product obtained is inosine monophosphate( lMP), the parent
purine nucleotide from which other purine nucleotides can be
synthesized.

 The purines can be directly converted to the corresponding
nucleotides, and this process is known as salvage pathway.
 Adenine phosphoribosyl transferase catalyses the formation of
AMP from adenine.
 Hypoxanthine-guanine phosphoribosyl transferase (HGPRT)
converts guanine and hypoxanthine, respectively, to GMP and IMP.

Degradation of purine
nucleotides
 The end product of purine metabolism in humans is uric acid.
 The nucleotide monophosphates (AMP, IMP and GMP) are
converted to their respective nucleoside forms (adenosine,
inosine and guanosine) by the action of nucleotidase.
 The amino group, either from AMP or adenosine, can be removed
to produce IMP or inosine, respectively.
 Inosine and guanosine are respectively, converted to
hypoxanthine and guanine by purine nucleoside phosphorylase.
 Adenosine is not degraded by this enzyme, hence it has to be
converted to inosine.
 Guanine undergoes deamination by guanase to form xanthine.
 Xanthine oxidase converts hypoxanthine to xanthine, and
xanthine to uric acid.

Disorders of purine metabolism
Hyperuricemia and gout:
 Hyperuricemia refers to an elevation in the serum uric acid
concentration.
 This is sometimes associated with increased uric acid excretion
(uricosuria).
 Gout is a metabolic disease associated with overproduction of
uric acid.
 ln severe hyperuricemia, crystals of sodium urate get deposited
in the soft tissues, particularly in the joints.
 Such deposits are commonly known as tophi.
 This causes inflammation in the joints resulting in a painful gouty
arthritis.
 Sodium urate and/or uric acid may also precipitate in kidneys
and ureters that results in renal damage and stone formation

 Gout was found to be often associated with high living, over-eating
and alcohol consumption.
 Gout is of two types-primary and secondary.
 Primary gout is an inborn error of metabolism due to
overproduction of uric acid. This is mostly related to increased
synthesis of purine nucleotide.
 Secondary gout is due to various diseases causing increased
synthesis or decreased excretion of uric acid.
 The drug of choice for the treatment of primary gout is allopurinol.
 Besides the drug therapy, restriction in dietary intake of purines
and alcohol is advised.
 Consumption of plenty of water will also be useful.
 The anti-inflammatory drug colchicine is used for the treatment of
gouty arthritis.
 Other antiinflammatory drugs-such as phenylbutazone,
indomethacin , oxyphenbutazone, corticosteroids are also useful.

Biosynthesis of pyrimidine nucleotides

 Glutamine transfers its amido nitrogen to CO2 catalysed by
carbamoyl phosphate synthetase II to produce carbamoyl
phosphate.
 Carbamoyl phosphate condenses with aspartate to form
carbamoyl aspartate. This reaction is catalysed by aspartate
transcarbamoylase.
 Dihydroorotase catalyses the pyrimidine ring closure with a loss
of H2O.
 Orotate is formed by NAD+ dependent dehydrogenation.
 Ribose-5-phosphate is added to orotate to produce orotidine
monophosphate (OMP). This reaction is catalysed by orotate
phosphoribosyltransferase.
 OMP undergoes decarboxylation to uridine mono-phosphate
(UMP)
 By an ATP-dependent kinase reaction, UMP is converted to
UDP which serves as a precursor for the synthesis of dUMP,
dTMP, UTP and CTP..

Organization of mammalian
genome
 The total DNA (genetic information) contained in an organism
or a cell is regarded as the genome.
 The genome is the storehouse of biological information.
 lt includes the chromosomes in the nucleus and the DNA in
mitochondria, and chloroplasts.

Structure of DNA
 DNA is a polymer of deoxyribonucleotides.
 It is composed of monomeric units namely
deoxyadenylate (dAMP), deoxyguanylate
(dGMP), deoxycytidylate (dCMP) and
deoxythymidylate (dTMP).
 The monomeric deoxvnucleotides in DNA
are held together by 3',5'-phosphodiester
bridges.
 Chargaff's rule of DNA composltion:
 DNA had equal numbers of adenine and
thymine residues (A = T) and equal numbers
of guanine and cytosine residues (G = C).
 The double helical structure of DNA was
proposed by James Watson and Francis
Crick.

1. The DNA is a right handed double helix. lt consists of two
polydeoxyribo nucleotide chains twisted around each other on a
common axis.
2. The two strands are antiparallel, i.e., one strand runs in the 5' to 3'
direction while the other in 3' to 5‘ direction.
3. The width (or diameter) of a double helix is 20 A0(2 nm).
4. Each turn of the helix is 34 A0 (3.4 nm) with 10 pairs of nucleotidese,
ach pair placed at a distance of about 3.4 A0.
5. Each strand of DNA has a hydrophilic 3'-5' phosphodiester bonds on
the outside of the molecule while the hydrophobic bases are stacked
inside.
6. The two polynucleotide chains are not identical but complementary to
each other due to base pairing.
7. The two strands are held together by H-bonds formed by
complementary base pairs . ( A-T pair has 2 and G-C pair has 3
hydrogen bonds).
8. The hydrogen bonds are formed between a purine and a pyrimidine
only.
9. The complementary base pairing in DNA helix proves Chargaffs rule.
10. The genetic information resides on one of the two strands known as
template strand or sense strand. The opposite strand is antisense

Structure of RNA
 RNA is a polymer of ribonucleotides held together by 3',5'-
phosphodiester bridges.
 Pentose: The sugar in RNA is ribose (deoxyribose in DNA).
 Pyrimidine : RNA contains the pyrimidine uracil (thymine in
DNA).
 Single strand: RNA is usually a single stranded polynucleotide.
 Chargaff's rule-not obeyed.
 Susceptibility to alkali hydrolysis : Alkali can hydrolyseRNA to
2',3'-cyclic diesters (presence of a hydroxyl group at 2' position).
 Types of RNA:
1. Messenger RNA (mRNA):
2. Transfer RNA (tRNA):
3. Ribosomal RNA (rRNA: ):

 The mRNA is synthesized in the nucleus as heterogeneous
nuclear RNA (hnRNA).
 mRNA is capped at the 5'-terminal end by 7-methylguanosine
triphosphate.
 The 3'-terminal end of mRNA contains a polymer of adenylate
residues (20-250 nucleotides) which is known as poly (A) tail.
 The structure of tRNA resembles a clove leaf and contain
acceptor arm, the anticodon arm, The D arm, the TYC arm, the
variable arm.

FUNCTIONS OF DNA FUNCTIONS OF RNA
 DNA is the chemical basis of
heredity and regarded as the
reserve bank of genetic
information
 DNA is exclusively
responsible for maintaining
the identity of different species
of organisms.
 Every aspects of cellular
information is under the
control of DNA.
 The DNA is organized into
genes, the fundamental units
of genetic information.
 The genes control the protein
synthesis through the
mediation of RNA.
 mRNA transfers genetic
information from genes to
ribosomes to synthesize
proteins.
 rRNA provides structural
framework for ribosomes.
 tRNA transfers amino acid to
mRNA for protein synthesis.
 hnRNA serves as precursor
for mRNA and other RNAs.

DNA replication (semi conservative model)
 Replication is a process in which DNA copies itself to
produce identical daughter molecules of DNA.
 Replication is semi conservative.
 The parent DNA has two strands complementary to each
other.
 Both the strands undergo simultaneous replication to
produce two daughter molecules.
 Each one of the newly synthesized DNA has one-half of
the parental DNA (one strand from original) and one-half
of new DNA.
 This type of replication is known as semiconservative
since half of the original DNA is conserved in the daughter
DNA
 Each strand serves as a template, over which a new
complementary strand is synthesized

 A specific protein called dna A binds at the origin for replication
causes the double-stranded DNA to separate.
 The two complementary strands of DNA separate at the site of
replication to form a bubble.
 For the synthesis of new DNA, a short fragment of RNA is
required as a primer.
 The replication of DNA occurs in 5' to 3‘ direction, simultaneously
, on both the strands of DNA.
 DNA synthesis is continuous in the leading strand and
discontinuous in the lagging strand.
 The separation of the two strands of parent DNA results in the
formation of a replication fork and the active synthesis of DNA
occurs in this region.
 DNA helicases bind to both the DNA strands at the replication
fork and separate the strands.
 Single-stranded DNA binding (SSB) proteins / DNA helix-
destabilizing proteins provide the template for new DNA
synthesis

 The synthesis of a new DNA
strand in 5‘ to 3' is catalyzed
by DNA polymerase III.
 The DNA strand (leading
strand) with its 3'-end (3'-OH)
oriented towards the fork can
be elongated by sequential
addition of new nucleotide.
 Okazaki pieces are the small
fragments of the
discontinuously synthesized
DNA.
 These are produced on the
lagging strand of the parent
DNA.
 Okazaki pieces are joined to
form a continuous strand of
DNA with the help of DNA
polymerase I and DNA
ligase.

Transcription or RNA
synthesis
 Transcription is a process in which RNA is synthesized
from DNA.
 one of the two strands of DNA serves as a template(
non-coding strand or sense strand) and produces
working copies of RNA molecules.
 The other DNA strand which does not participate in
transcription is known as coding strand or antisense
strand.
 The product formed in transcription is referred to as
primary transcript (inactive).
 They undergo certain post-transcriptional modifications
to produce functionally active RNA molecules
 Transcription involves three different stages- initiation,

Initiation:
 Sigma factor of RNA polymerase bind to the promoter region in
DNA
 There are two base sequences on the coding DNA strand which
the sigma factor of RNA polymerase can recognize for initiation
of transcription.
 There are two base sequences o n the coding DNA strand
1. Pribnowbox (TATA box) consists of 6 nucleotide bases(
TATAAT) located on the left side about 10 bases away from the
starting point of transcription.
2. The '-35' sequence contains a base sequence TTCACA, which
is located about 35 bases away on the left side from the site of
transcription start.
Elongation:
 The sigma factor is released and transcription proceeds.
 RNA is synthesized from 5' end to 3' end antiparallel to the DNA
template.
 RNA polymerase utilizes ribonucleotidte triphosphates (ATP,
CTP, CTP and UTP) for the formation of RNA

Termination :
 The process of transcription stops by termination
signals.
 Two types of termination are identified.
Rho( ρ) dependent termination:
 A specific protein (ρ factor) binds to the growing RNA
or weakly to DNA, and in the bound state it acts as
ATPase and terminates tanscription and release RNA.
Rho( ρ) independent termination:
 Termination occurs due to the formation of hairpins of
newly synthesized RNA.
 This occurs due to the presence of palindromes

Genetic code
 The 3 nucleotide (triplet) base sequences in mRNA that act
as code words for amino acids in protein constitute the
genetic code or simply codons.
 The codons are composed of the four nucleotide bases,
namely the purines-adenine (A) and guanine (C), and the
pyrimidines-cytosine (C) and uracil (U).
 These 4 bases produce 64 different combinations of 3 base
codons.
 The nucleotide sequence of the codon on mRNA is written
from the 5'-end to 3' end.
 61 codons code for the 20 amino acids found in protein.
 The 3 codons UAA, UAG and UCA do not code for amino
acids. They act as stop signals in protein synthesis. These 3
codons are known as termination codons or non-sensec
odons

 The codons AUG and GUG are the chain initiating codons.
 Universality : The same codons are used to code for the same
amino acids in all the living organisms.
 Specificity : A particular codon always codes for the same amino
acid, hence the genetic code is highly specific or unambiguous.
 Eg: UGG is the codon for tryptophan.
 It is non-overlapping, commaless and without any punctuations
 The codes are consecutive and are read one after another in a
continuous manner, e.g. AUG, CAU, GAU, GCA, etc.
 Degenerate: The codon is degenerate or redundant, since there
are 6l codons available to code for only 20 amino acids (ie, one
amino acid has more than one codon.)
 Eg: glycine has four codons.
 Wobble hypothesis explains the degeneracy of the genetic code,
i.e. existence of multiple codons for a single amino acid.

Translation or protein synthesis
 The biosynthesis of a protein or a polypeptide in a
living cell.
 The protein synthesis occurs on the ribosomes .
 The mRNA is read in the 5‘ to 3' direction and the
protein synthesis proceeds from N-terminal end to C-
terminal end.
 Steps involved in translation:
1. Activation of amino acid
2. Initiation
3. Elongation
4. Termination
5. Post-translational processing.

Activation of amino acid:
 The enzymes aminoacyl tRNA synthetase activate
the amino acids.
 The amino acid is first attached to the enzyme
utilizing ATP to form enzyme-AMP-amino acid
complex.
 The amino acid is then transferred to the 3' end of
the tRNA to form aminoacyl tRNA

Initiation of translation :
 It involves use of initiation factors (eIF)
 The process of translation initiation can be
divided into 4 steps
1. Ribosomal dissociation.
2. Formation of 43S preinitiation complex.
3. Formation of 48S initiation complex.
4. Formation of 80S initiation complex.
 The 80S ribosome dissociates to form 40S
and 60 S subunits
 A ternary complex containing met-tRNA and
elF-2 bound to GTP attaches to 40S
ribosomal subunit to form 43S preinitiation
complex.
 The binding of mRNA to 43S preinitiation
complex results in the formation of 48S
initiation complex through the intermediate
43S initiation complex.
 48S initiation complex binds to 60 S
ribosomal subunit to form 80S initiation
complex.
 As the 80S complex is formed, the initiation
factors bound to 48S initiation complex are

Elongation of translation:
 Ribosomes elongate the polypeptide chain by sequential addition
of amino acids.
 Elongation process involves use of certain elongation factors
(EF).
Steps:
(1)Binding of aminoacyl tRNA to A-site.
 The 80 S initiation complex contains met tRNA in the P-site, and
the A-site is free. Another aminoacyl-tRNA is placed in the A-site.
(2)Peptide bond formation.
 The enzyme peptidyltransferase catalyses the formation of
peptide bond
(3)Translocation.
 As the peptide bond formation occurs, the ribosome moves to the
next codon of the mRNA (towards 3'-end).
 Translocation involves the movement of growing peptide chain
from A-site to P-site.
 Translocation requires EF-2 and GTP.

Termination of translation:
 After successive addition of
amino acids, ribosome
reaches the termination
codon sequence (UAA,
UAG or UGA) on the
mRNA.
 As the termination codon
occupies the ribosomal A-
site, the release factor eRF
recognizes the stop signal.
 The 80S ribosome
dissociates to form 40S
and 605 subunits which are
recycled.
 The mRNA is also
released.

Post-translational processing:
 The proteins synthesized in translation are, as such, not
functional. so some changes are needed
 These modifications include protein folding , trimming by
proteolytic degradation, intein splicing and covalent changes
which are collectively known as Post-translational
modification.

Inhibitors of protein synthesis
 Majority of the antibiotics interfere with the bacterial protein
synthesis.
 Streptomycin inhibit initiation of protein synthesis. It causes
misreading of mRNA and interferes with the normal pairing
between codons and anticodons.
 Tetracycline inhibits the binding of aminoacyl tRNA to the
ribosomal complex.
 Puromycin enters into the growing peptide chain and causes its
release
 Chloramphenicol acts as a competitive inhibitor of
peptidyltransferase and thus interferes with elongation of peptide
chain.
 Erythromycin inhibits translocation by binding with 50S subunit of
bacterial ribosome.
 Diphtheria toxin prevents translocation in protein synthesis by
inactivating elongation factor