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Central Dogma of Biology
Nucleic Acids
Nucleic Acids Are Essential For Information Transfer in Cells
 Information encoded in a DNA molecule is transcribed via
synthesis of an RNA molecule
 The sequence of the RNA molecule is "read" and is translated into
the sequence of amino acids in a protein.
 Compound contained C, N, O, and high amount of P.
 Was an acid compound found in nuclei therefore named nucleic
acid
 1944 Oswald, Avery, MacLeod and McCarty demonstrated that
DNA is the molecule that carrier genetic information.
 1953 Watson and Crick proposed the double helix model for the
structure of DNA Nucleic acids are long polymers of nucleotides.
Nucleotides and Nucleic Acids
The amino acids sequence and nucleotide sequence in RNA is specified by
a nucleotide sequence in the cell’s DNA
Gene: segment of a DNA molecule that contains the information
required for the synthesis of a functional biological product whether a
protein or RNA
The cell contains thousands of genes and DNA molecules
Nucleic Acids are polymers of
nucleotides.
Deoxyribonucleic acid - DNA - Storage of
genetic information.
Ribonucleic acid - RNA - carriers of
genetic information and catalysis.
Nucleotide Structure: Nitrogenous base
+ ribose phosphate:
Nucleotides structure
The nucleotide has three characteristic components
Nitrogenous base
Pentose sugar
Phosphate
Nitrogenous Bases
Nitrogenous base: derivatives of Purines and pyrimidines
DNA and RNA contain the same purine bases and the pyrimidine base
Cytosine But Thymine found only in DNA and Uracil found only in RNA
(A)
(C)
(G)
(U)
(T)
Pentoses of Nucleotides
• D-ribose (in RNA)
• 2-deoxy-D-ribose (in
DNA)
• The difference - 2'-OH
vs 2‘-H
• This difference affects
secondary structure and
stability
Bases are attached by b-N-glycosidic linkages to 1
carbon of pentose sugar – (Nucleoside)
• Base is linked via a b-Nglycosidic bond
• The carbon of the
glycosidic bond is anomeric
• Named by adding -idine to
the root name of a
pyrimidine or -osine to the
root name of a purine
• Sugars make nucleosides
more water-soluble than
free bases
Nucleosides
(1)
(9)
Nucleotides
• Phosphate ester of nucleosides
The plane of the base is oriented perpendicular
to the plane of the pentose group
RNA contains Ribose while DNA contains 2'deoxy-D-Ribose
Nucleoside: Nitrogenous base + ribose:
Ribonucleotides
Adenosine 5'-monophosphate, Adenylate, AMP
Guanosine 5'-monophosphate, Guanylate, GMP
Cytidine 5'-monophosphate, Cytidylate, CMP
Uridine 5'-monophosphate, Uridylate, UMP
Deoxyribonucleotides
Deoxythymidine 5' monophosphate,
Deoxythymidine, dTMP ……..
NMP=== Nucleoside mono phosphate.
Numbering of Ribose sugar is given 1’, 2’, …, 5’
Unusual nucleotides
Modified nucleotides found in some viral DNA and in Transfer RNA. These
modifications include methylation, hydroxymethylation, glycosylation,
acetylation ..
Other Functions of Nucleotides
• Nucleoside 5'-triphosphates are carriers of energy
• Bases serve as recognition units
• Cyclic nucleotides are signal molecules and regulators of
cellular metabolism and reproduction
• Structural component of some coenzymes, e.g CoA,
FAD, NADH, NADPH
• ATP is central to energy metabolism
• GTP drives protein synthesis
• CTP drives lipid synthesis
• UTP drives carbohydrate metabolism
De novo synthesis of purine nucleotides
The atoms of purine ring are contributed by a number of compounds
including amino acids (aspartic acid, glycine and glutamine) CO2, and
tetrahydrofolate. These compounds donates N and C to constructed
Ribose 5-phosphate.
6
5
1
2
4
3
7
8
9
N10Formyl tetrahydrofolate
The order in which ring atoms are added is:
9
Glut
4 5 7
Glycine
8
3
6
1
For
Glut
CO2
Asp
6
1 N
2
5
2
N7
8
N
3
4
N
9
Ribose-P
For
De novo synthesis of purine nucleotides
* Synthesis of 5-phosphoribosyl-1-pyrophosphate (PRPP)
-Ribose 5-phosphate is synthesized from HMP (Hexose monophosphate
pathway)
- Ribonucleotides are first synthesized then may reduced to
deoxyribonucleotides
Inhibitors
Purines,
nucleosides
Activator
Pi
Ribose5-phosphate
Ribose phosphate
pyrophosphokinase
ATP
AMP
* Synthesis of 5-phosphoribosyl-1-pyrophosphate (PRPP)
•The amide group of the glutamine replaces pyrophosphate group
attached to PRPP, this reaction is mediated by Glutamine:phosphoribosyl
pyrophosphate amidotransferase.
•This enzyme is inhibited by
end product of this pathway
purine 5’-nucleotides AMP,
GMP and IMP.
• This reaction is the
committed step in purine
nucleotide synthesis
De novo synthesis of
purine nucleotides
* Synthesis Inosine
monophosphate (IMP)
• IMP is the parent purine nucleotide
•the synthesis of IMP requires 4 ATP
molecules
Inhibitors of Purine synthesis
•Specific inhibitors that inhibits the
growth of rapidly growing
microorganisms e.g Sulfonamides
•Structural analogues for folic acid
(methotroxate)
* Conversion of IMP into AMP and GMP
-this reaction is energy-requiring pathway
Adenylosuccinate
synthetase
Feed back
inhibition
IMP dehydrogenase
Feed back
inhibition
Conversion of IMP into AMP and GMP
* Conversion Nucleoside momophosphate (NMP) to nucleoside
diphosphate (NDP) and triphosphate (NTP)
•NDP and NTP are synthesized from the corresponding NMP by
Nucleoside monophosphate kinases
•These kinases don't discriminate between ribose or deoxyribose
in the substrate.
•ATP is the source of the transferred phosphate
examples
AMP + ATP  2 ADP  adenylate kinase (highly active in the
liver)
GMP + ATP  GDP + ADP  Guanylate kinase
Nucleoside diphosphates and triphosphates are interconverted
by nucleoside diphosphate kinase
GDP + ATP  GTP + ADP
CDP + ATP  CTP + ADP
De novo synthesis of
purine nucleotides
Salvage Pathway for Purines
Salvage Pathway: Purines that results from the normal turnover of cellular
nucleic acids or that obtained from the diet and not degraded can be
reconverted into nucleoside triphosphates and used by the body.
Two enzymes are involved
Adenine phosphoribosyl
transferase (APRT)
Hypoxanthine-guanine
phosphoribosyl transferase
(HGPRT)
Both enzymes utilize PRPP as the
source of ribose5-phosphate group
Degradation of Purine
nucleotides
Degradation of Purine nucleotides
 Purines are sequentially degraded into uric acids (in humans)
 Several steps will be involved in this catabolic pathway
Degradation of Dietary nucleic acids in the small intestine
• Ribonucleases and deoxyriboncleases secreted in the pancreatic
juice can hydrolyze RNA and DNA into oligonucleotides.
• Oligonucleotides are further hydrolyzed by pancreatic
phophodiesterases producing a mixture of 3’-and 5’
mononucleotides
• A family of nucleotidases remove the phosphate group releasing
nucleosides that may absorbed from GIT
• Dietary nucleotides are not used to large extent in cells because
they are converted into uric acid in the small intestine and also
used by the normal flora
Degradation
of Purine
nucleotides
Pyrimidine nucleotides synthesis
Sources of carbon atoms in pyrimidine rings
Purine ring is synthesized on an existing ribose 5-phosphate
Pyrimidine ring is synthesized then attached to ribose 5-phosphate donated
by PRPP
the sources of carbon atoms in pyrimidine rings are Glutamine, CO2, and
aspartic acid
Aspartic Acid
CO2
Pyrimidine nucleotides synthesis
- *Synthesis of carbamoyl phosphate
-The committed step of this pathway in mammalian cell is the synthesis
of carbamoyl phosphate from Glutamine and CO2
2 ATP + CO2 + Glutamine  Carbamoyl phosphate + 2ADP + Glutamate
- This reaction is mediated by Carbamoyl Phosphate Synthetase II (CPS
II)
- CPS II is inhibited by UTP and activated by ATP and PRPP
- Carbamoyl phosphate is the precursor of Urea; the pyrimidine
synthesis occurs in the cytosol while the urea production occurs in the
mitochondria by Carbamoyl Phosphate Synthetase I (CPS I)
- CPS I uses ammonia as source of nitrogen
- CPS II uses the amide group of glutamine
- Glutamine is required in the synthesis
of both Purines and Pyrimidine
Synthesis of carbamoyl phosphate
De Novo Pyrimidine Synthesis
De Novo Pyrimidine
Synthesis
Degradation of pyrimidines
- Purines are not cleaved in human cell
- pyrimidines rings can be opened and degraded to highly
soluble structure, such as b-alanine and b-aminoisobutyrate
that can serve as precursors of acetyl CoA and succinyl CoA
- Pyrimidine can be salvaged and converted into nucleotides
by the enzyme Pyrimidine phosphoribosyltransferase and it
utilizes the PRPP
Conversion of Ribonucleotides to Deoxyribonucleotides
 2’-deoxyribonucleotides are synthesized from ribonucleoside
diphosphatase
 Ribonucleotide reductase is multi subunit enzyme (2B1 and 2B2
subunits) catalyzes the reduction of NDP (ADP, GDP, CDP, UDP) into
dNDP (dADP, dGDP, dCDP, dUDP)
 The immediate donors of hydrogen atoms needed for the reduction
are two–SH groups of the enzyme itself
 The reduced form of the enzyme should be regenerated The
reducing agent is a peptide coenzyme of ribonucleotide reductase called
Thioredoxin
 The thioredoxin contain two cysteine residues that can be oxidized to
reduce the ribonucleotide reductase enzyme.
 The oxidized thioredoxin is reduced back by NADPH, this reaction is
mediated by Thioredoxine reductase
Regulation of Deoxyribonucleotides synthesis
The regulation of this enzyme is complex
Not only the activity is regulated but also substrate specificity
The binding of dATP to an allosteric site called activity site inhibits the enzyme
while the binding of ATP to this site activate the enzyme.
The binding of NTP to an allosteric site called substrate specificity will increase
the conversion of different NTP to their corresponding dNTP according to the
need of the cell
When ATP or dATP are bound to this
site  reduction of UDP, and CDP is
favored
When dTTP,or dGTP is bound  the
reduction of GDP, ADP is stimulated
Synthesis of Thymidine
monophosphate from dUMP
-dUMP is converted into dTMP by
thymidylate synthetase which utilizes
N5 N10 –methylene tetrahydrofolate
as the source of methyl group and 2
hydrogen  oxidation into
dihydrofolate.
- inhibitors of thymidylate
synthetase (5-flouro uracil) act as
anti-tumor
- DHF can be reduced into THF by
DHF reductase, which can be
inhibited by Methotrexate  inhibits
purine synthesis and decrease the
supply of THF so prevents
methylation of dUMP to dTMP
The End
Anti- conformation predominates in nucleic
acid polymers
•Conformation can be syn or anti
Nitrogenous base: derivatives of Purines and pyrimidines
DNA and RNA contain the same purine bases and the pyrimidine
base Cytosine But Thymine found only in DNA and Uracil found only
in RNA
(G)
(A)
(T)
(C)
(U)