Nucleic acid Metabolism

By Fadilah Nor Laili L, M.Biotech.

• Nucleic acids are the biopolymers, or
small biomolecules
• The monomer units or building blocks of nucleic acids
is Nucleotide
• They are the precursors of DNA and RNA
• Nucleic acids are digested in the small intestine by
Deoxyribonuclease / Phosphodiesterase to generate
Nucleotides
 Degradation of Nucleoproteins
Nucleoprotein

In Stomach Gastric acid and pepsin

Nucleic acid Protein

In small intestine Endonucleases: RNase and DNase

Nucleotide

Nucleotidase

Phosphate Nucleoside

Nucleosidase
Ribose can be
absorbed and
Liver Base Ribose catabolized to
generate energy
Functions of Nucleotides
• First, nucleotides are the activated precursors of nucleic acid
• Second, an adenine nucleotide, ATP, is the universal currency of
energy
• Third, formation of activated intermediates such as UDP-Glucose and
CDP-Diacylglycerol.
• Fourth, nucleotides are essential components of signal transduction
pathways, such as cyclic AMP and cyclic GMP
• Five, components of many co-enzymes (NAD, NADP, FAD, CoA)
Can Cells Biosynthesize Nucleotides?
Cells Make Nucleotides by Two Pathways
• De novo Pathway: The biosynthesis of nucleotides begins /very new with the use
of small metabolic precursors as a raw material
• A pyrimidine base is assembled first and then attached to ribose
• A purine base is synthesized piece by piece directly onto a ribose-based
structure
• Salvage Synthesis: The synthesis of nucleotide by recycle of the free
Nitrogen bases or nucleosides released from nucleic acid breakdown.
Structure of Nucleotides

N-b-glycosyl
bond

Ribose
or
2-deoxyribose
Purine Nucleotide Biosynthesis
• Predominantly In cytosol of Liver, and some extent in small intestine
and Thymus.

• The De Novo synthetic pathway can be divided into two Stages:

• Stage one : Formation of Inosine Mono Phosphate ( IMP )
• Stage two : Conversion of IMP to either AMP or GMP
De Novo Purine Nucleotide
Inosine monophosphate (IMP) is synthesized from amphibolic
intermediates
 N10Formyltetrahydrofolat
e
N10Formyltetrahydrofolat
e
Biosynthesis of AMP and GMP from IMP.
Regulatory mechanisms in the biosynthesis of adenine and guanine
nucleotides

IMP, AMP and GMP

availability to sufficient
concentration inhibits the
regulatory enzymes by feed
back mechanism.
Summary of Purine biosynthesis

dADP dATP

AMP ADP ATP

IMP
GMP GDP GTP

dGDP dGTP
Pyrimidine Nucleotide Biosynthesis
• In De novo pathway the Pyrimidine ring is assembled first and then
linked to Ribose phosphate
• The carbon and nitrogen atoms in the Pyrimidine ring are derived from:
• Bicarbonate (HCO3)
• Aspartate
• Glutamine
Pyrimidine Nucleotides Are Made from
Aspartate, PRPP, and Carbamoyl
Phosphate
Summary of pyrimidine biosynthesis

dTMP dTDP dTTP

Synthesis of dTMP from dUMP is catalyzed by Thymidylate Synthase
• This enzyme methylates dUMP at the 5-position to create dTMP

dUMP dUDP

UMP UDP UTP

CDP CTP

dCMP dCDP dCTP

Salvage Pathway
• Salvage pathway have mechanisms to retrieve Purine bases and
Purine nucleosides. They are used to synthesize Purine nucleotides.
• The significance of salvage pathway :
• Save the fuel.
• Some tissues and organs such as brain and bone marrow are only
capable of synthesizing nucleotides by salvage pathway.
 From Nitrogen Base to Nucleotides

APRTase
Adenine + PRPP--------------------------------AMP + ppi

HGPRTase
Hypoxanthine + PRPP-------------------------------- IMP + ppi

HGPRTase
Guanine + PRPP--------------------------------GMP + ppi
Pyrimidine Phosphoribosyl Transferase
Uracil + PRPP- --------------------------------- UMP + ppi
Catabolism of purine
nucleotides
Catabolism of a pyrimidine.
NH2 O O
H2O NH3 CH3
N HN HN
O N O N O
H H N thymine
uracil H
cytosine

HOOC HOOC
NH2 CH2 NH2 CH CH3
¦Â-ureidopropionate
CH2 CH2 ¦Â-ureido-
O N O N
H H isobutyrate
H2O H2O

H2N CH2 CH2 COOH H2N CH2 CH COOH

CO2 + NH3
CH3
¦Â-alanine ¦Â-aminoisobutyrate
 Purines Pyrimidines
Character De Novo Synthesis De Novo Synthesis
Number Of Steps Involved 11 Steps 6 Steps
Precursors Of Ring Amino acids :Asp Gly and Gln Amino acids :Asp and Gln
N10FormylTHF, CO2 CO2
Major Portion Glycine Aspartate
Of Ring provided by
Acquisition of Ribose-Phosphate In Starting Steps In End Steps
Formation of N-Glycosidic bond In 1st step of their biosynthesis a heterocyclic ring is formed first,
(PRPP is the 1st Substrate) then it reacts with PRPP
products of degradation Uric acid CO2, NH3, b-Amino Isobutyrate and
(poor solubility in H2O) b Ala (soluble in H2O)
Number Of ATPs Involved 6 ATPs 2ATPs
Nucleotide Produced in End IMP UMP
Ring Closure At 6 and 11 steps 3rd Step
Chromosomal Elements
• Cellular DNA contains genes and
intergenic regions, both of which may
serve functions vital to the cell.

Watson-Crick
models
DNA
• DNA consists of two strands
• Each strand is a polymer of nucleotides
• Strand has orientation due to nucleotide structure: 5’ and 3’ ends
• The two strands are antiparallel
• DNA function is information storage
• DNA passed on to descendant cells
• Accurate copying
• Repair of any damage to avoid changes
• Accurate subdivision
DNA Replication
• Replication complex binds
to replication “origin”
• Double-stranded DNA is
“melted”
• Each strand is used as a
template for DNA
synthesis
 DNA Replication
The Meselson-Stahl experiment
Enzymes are the tools of replication
• DNA Polymerase - Matches the correct nucleotides then joins adjacent
nucleotides to each other
• Primase - Provides an primer to start polymerization
• Ligase - Joins adjacent DNA strands together (fixes “nicks”)
• Helicase - Unwinds the DNA and melts it
• Single Strand Binding Proteins - Keep the DNA single stranded after it has
been melted by helicase
• Gyrase - A topisomerase that Relieves torsional strain in the DNA molecule
• Telomerase - Finishes off the ends of DNA strands
• Deoxyribonucleotides (dATP, dTTP, dCTP, dGTP)
Replication DNA Mechanism
1. Denaturation
2. Initiation
3. Elongation
4. Ligation DNA fragments
5. Termination
DNA Synthesis Proceeds in a 5’ 3’ Direction
and Is Semidiscontinuous

DNA Is Synthesized by DNA Polymerases

Mismatch Repair
Mismatch Repair
Base-Excision Repair
DNA repair by the base-excision repair pathway.
1 A DNA glycosylase recognizes a damaged base and
cleaves between the base and deoxyribose in the
backbone.
2 An AP endonuclease cleaves the phosphodiester
backbone near the AP site.
3 DNA polymerase I initiates repair synthesis from the free
3 hydroxyl at the nick, removing (with its 5n3 exonuclease
activity) a portion of the damaged strand and replacing it
with undamaged DNA.
4 The nick remaining after DNA polymerase I has
dissociated is
sealed by DNA ligase.