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Central Dogma of Biology
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.
Nucleic Acids
Nucleotides and Nucleic AcidsThe 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 structureThe nucleotide has three characteristic components Nitrogenous basePentose sugarPhosphate
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) (G)
(C) (T)(U)
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 -N-glycosidic linkages to 1 carbon of pentose sugar – (Nucleoside)
• Base is linked via a -N-
glycosidic 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
(9)
(1)
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
N10Formyl tetrahydrofolate
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.
93
2
1
65
4
7
8
NN1
2N
3
6
4
5 7
8N
9
Ribose-P
The order in which ring atoms are added is:
9 4 5 7 8 3 6 1 2
Glut Glycine For Glut CO2 Asp 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
Ribose5-
phosphate
Ribose phosphate pyrophosphokinase
ATP AMP
Activator Pi
InhibitorsPurines,
nucleosides
* 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
IMP dehydrogenase
Feed back inhibition
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
Two enzymes are involved Adenine phosphoribosyl
transferase (APRT)Hypoxanthine-guanine
phosphoribosyl transferase
(HGPRT)
Both enzymes utilize PRPP as the
source of ribose5-phosphate
group
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.
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 synthesisSources of carbon atoms in pyrimidine ringsPurine 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
Amide
Nitrogen of
Glutamine
CO2
De Novo Pyrimidine Synthesis
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
Degradation of pyrimidines- Purines are not cleaved in human cell
- pyrimidines rings can be opened and degraded to
highly soluble structure, such as -alanine and -
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
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
Regulation of Deoxyribonucleotides synthesis The regulation of this enzyme is complexNot only the activity is regulated but also substrate specificityThe 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
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
(A) (G)
(C)(T) (U)