Storage and Expression of

Genetic Information
Nucleotide Metabolism
 Objectives
• Identify and characterize the nucleotides and
nucleic acids and determine their roles in the
normal function of the human body
• Recognize the importance of nucleotides and
nucleic acid in pharmacotherapeutics
• Explain the nucleotide and nucleic acid
metabolic pathways
• Discuss the biochemical basis of genetics and
some common diseases
Nucleotide Metabolism
 Topic Outline
• Structure and Function
– Nitrogenous Bases
– Sugars found in nucleosides and nucleotides
– Nucleosides
– Nucleotides
• Metabolism of Nucleotides
– Purine Nucleotides
• De Novo Purine Biosynthesis
• Salvage Pathway for Purine Nucleotides
• Degradation of Purine Nucleotides
 Topic Outline
• Metabolism of Nucleotides
– Pyrimidine Nucleotides
• Biosynthesis of Pyrimidine Nucleotides
• Degradation of Pyrimidine Nucleotides
– Conversion of Ribonucleotides to
Deoxyribonucleotides
– Synthesis of Thymidine Monophosphate
Structure and Function
 Nitrogenous Bases:
Purines and Pyrimidines
• Properties
– Nonpolar
– Weakly basic
– Electron-rich nature (-OH & -NH substituents)
– Capacity for hydrogen bonding
– Aromatic ring system:Strong absorbance of UV
light (250-280 nm)
– Easily separated by chromatography and
electrophoresis
 Structure:
Purine and Pyrimidine Bases
O NH 2
7 6
N 5 1 N N
N NH N
8
NH 4 2 NH N NH 2
9 N NH N
3
Purine Guanine Adenine

RNA
O NH 2 O
4 3
5 N H 3C
NH N NH
6 2
N
1 NH O NH O NH O
Pyrimidine Uracil Cytosine Thymine
DNA
Pentoses of Nucleosides & Nucleotides

*Garett and Grisham Biochemistry

Nucleoside=Base + Sugar
H N
2 7 NH2
6
1 5 N 4
N 3
5 N
8 2
2 4 N9 6
N N O
3 1

5’
HO 5’
O HO
O
4’ 1’ 4’ 1’

3’ 2’ 3’ 2’
OH OH OH
adenosine 2’-deoxycytidine
 Nucleosides: Properties
• More water-soluble than free bases
• Relatively stable in alkali
• Separated chromatographically
• Purine nucleosides are easily hydrolyzed in
acidic environment
• Pyrimidine nucleosides are resistant to acid
hydrolysis
 Nucleoside Naming

Base Nucleoside Deoxynucleoside

Adenine Adenosine 2’-deoxyadenosine
Guanine Guanosine 2’-deoxyguanosine
Cytosine Cytidine 2’-deoxycytidine
Uracil Uridine -
Thymine - 2’-deoxythymidine
Nucleoside structures
Purine Nucleoside Analogues

NH2
NH2 O
N N
N N N NH
N N N N N N
OH OH
O O OH
OH O

OH
OH
Deoxyadenosine Vidarabine Didanosine
 Purine Nucleoside Analogues

O NH
O
N N
NH N N
NH
N N NH2 N
N N NH 2
N NH 2
OH OH
O OH O
O

OH
deoxyguanosine acyclovir abacavir
 Pyrimidine Nucleoside
Analogues
O O
H3C H 3C
NH NH zidovudine
thymidine
N O H N O
HO
O O
O
O
F O
H 3C
OH F N3 NH
F NH
HO N O
N O O
HO
O

OH stavudine
trifluridine
 Pyrimidine Nucleoside
Analogues
NH2 NH2
NH2

N N
N

N O N O
N O
HO HO HO
O O S

O
OH

2’ deoxycytidine zalcitabine lamivudine

Nucleotide=Base +Sugar + Phosphate

H N NH2
2 7
6 4
1 5 N 3
N 5 N
8 2
6
2 4 N9 N O
N 1
O-
3
O-
5’ 5’
O P O O P O
O O
O 4’ O 4’ 1’
1’
3’ 2’
3’ 2’
OH
Adenosine-5’-
OH OH 2’deoxycytidine-5’-
monophosphate monophosphate
Four Common Ribonucleotides
Cyclic Nucleotides
Coenzyme A

ADP
 Functions of Nucleotides
• DNA & RNA Precursors / Building Block
• Source of Energy
• Carriers of activated intermediates
• Component of coenzymes
• Regulatory signals
• High-energy intermediates
 Properties of Nucleotides
1. phosphate group acts as a strong acid
(pKa 1)
2. The amine groups of the purine and
pyrimidine bases can be protonated.
3. The bases can tautomerize;
4. Nucleotides absorb light strongly in the
near-ultraviolet region of the spectrum.
Properties of Nucleotide

Matthews, van Holde, Ahern Biochemistry 3rd ed

Metabolism of Nucleotides
De Novo Purine Nucleotide
Synthesis
CO2
GLYCINE

ASPARTIC ACID
C N
6
5C
7
N1
8
C FORMATE
FORMATE
C2 3
4
C 9
N N

GLUTAMINE AMIDE
 Synthesis of
5’-Phosphoribosyl 1’-pyrophosphate
O
- OH
O P O
O
OH

OH OH
ribose 5-phosphate
Purine nucleosides ATP
Ribose phosphate
Mg2+
pyrophosphokinase
Inorganic phosphate
O AMP
- - -
O P O O O
O -
OH O P O P O
O O
OH OH
5'-phosphoribosyl 1’-pyrophosphate (PRPP)
 Synthesis of
5’- phosphoribosylamine
• Committed
step
 Synthesis of
Inosine monophosphate
O
• IMP
- N H2
O P O
O
“parent” OH

purine OH OH
nucleotide 5’-phosphoribosylamine

9 steps

Inosine 5’-monophosphate
 O

Conversion of N
NH

IMP to GMP & AMP

N N
O
-
O P O
O
OH
GTP + Asp
H 2O + NAD + OH OH -
GDP + Pi O
Inosine 5'-monophosphate
-
NADH + H +
IMP dehydrogenase adenylosuccinate O
synthetase O
O
NH O
N
NH
N
NH
N N O
O N N
H
- O
O P O -
O O P O
OH O
OH

OH OH
xanthosine OH OH
monophosphate (XMP) adenylosuccinate
Gln + ATP
GMP adenylosuccinase
fumarate
Glu + AMP synthetase
+ PPi NH 2
O

N N
NH NH

N NH2 N N
N O
O
- -
O P O O P O
O O
OH OH

OH OH OH OH

guanosine 5'-monophosphate adenosine 5'-monophosphate

 Conversion of
NMPs to NDPs & NTPs
Adenylate monophosphate
kinase
AMP + ATP 2ADP

GMP + ATP Guanylate kinase

monophosphate
2GDP + ADP

Nucleoside diphosphate
2ADP kinase
AMP + ATP
Nucleoside diphosphate
kinase

GDP + ATP Nucleoside diphosphate

GTP + ADP
kinase

CDP + ATP CTP + ADP

Regulation of Purine Nucleotide Synthesis
Ribose-5-phosphate

PRPP

5-
Phosphoribosylamine

IMP

Adenylosuccinate XMP

AMP GMP

ADP GDP

ATP GTP
 Purine Nucleotide Cycle

H2O AMP NH4+

deaminase

AMP IMP Aspartate + GTP

Fumarate
Adenylosuccinate
Adenylosuccinate
synthetase
lyase

Adenylosuccinate GDP + Pi
 Salvage Pathway for Purines
O
N NH

N N
O PRPP PPi O
-
N NH O P O
O
hypoxanthine-guanine OH
NH N phosphoribosyltransferase
OH OH
hypoxanthine Inosine 5'-monophosphate
Lesch-Nyhan syndrome O
N NH
O N
PRPP PPi N NH2
N O
NH -
O P O
O
NH N NH2 hypoxanthine-guanine OH
phosphoribosyltransferase
guanine OH OH
guanosine 5'-monophosphate
NH2
N NH
NH2 PRPP PPi N N
N O
NH -
O P O
O
NH adenine OH
N
phosphoribosyltransferase
adenine
OH OH
adenosine 5'-monophosphate
 Degradation of Purine Nucleotides

Adenosine Deaminase (ADA)

Deficiency
Allopurinol
Purine nucleoside phosphorylase (PNP)
deficiency
Purine Structural Analogue

O O

NH N
NH
N
NH N NH N
Allopurinol hypoxanthine
Degradation
of Dietary
Nucleic Acid

URINE
 Pyrimidine Synthesis

Amide N of Glutamine
C
N C
ASPARTIC ACID
C C
N
CO2
Pyrimidine Synthesis
 Degradation of
Pyrimidine Nucleotides
 Salvage Pathway for
Pyrimidine Nucleotides
NH2

NH2 N O
PRPP PPi O
N -
O P O
O
NH O pyrimidine OH
phosphoribosyltransferase
cytosine OH OH
cytosine
5'-monophosphate

NH

O N O
PRPP PPi O
-
NH O P O
O
pyrimidine OH
NH O
phosphoribosyltransferase
OH OH
uracil uridine
5'-monophosphate
 Conversion of Ribonucleotides to
Deoxyribonucleotides
O O 8-hydroxyquinoline O O
BASE BASE
-O Hydroxyurea -
P O P O O P O P O
O dATP O
O O O O

OH OH OH
ribonucleoside diphosphate deoxyribonucleoside diphosphate

ribonucleotide reductase

H2 O
thioredoxin (2 SH) thioredoxin (S-S)
(reduced) (oxidized)
thioredoxin reductase

+
NADP + NADPH + H
Ribonucleotide Reductase
Synthesis of dTMP from dUMP
Folic acid Analogues
 Uracil Analogues

O O O

F F
NH NH NH
O
NH O NH O N O
HO P O
O
OH

OH

Uracil 5'-fluorouracil FdUMP

End of Lecture