NUCLEOTIDE CHEMISTRY By: Prachand Man Singh Rajbhandari BSc Medical Biochemistry ( Nobel College, Pokhara University, Nepal) MSc Medical Biochemistry (JN Medical College, KLE University, Belgaum)
NUCLEOTIDE CHEMISTRY
By: Prachand Man Singh RajbhandariBSc Medical Biochemistry ( Nobel College, Pokhara University, Nepal)
MSc Medical Biochemistry (JN Medical College, KLE University, Belgaum)
Contents:
1. Introduction
2. History
3. General features of nucleotides
4. Nomenclature
5. Individual properties of bases
6. Classification
7. Synthetic analogues of biomedical importance
Introduction
• Nucleotides are organic compounds made up of a PO4
group, nitrogenous base & a sugar molecule.
• These are the building blocks of nucleicacids (DNA and RNA).
• They serve as sources of chemical energy (ATP, GTP),participate in cellular signalling (cAMP, cGMP) andfunction as important cofactors of enzymatic reactions(coA, FAD, FMN, NAD+).
HISTORY
In 1869, Miescher discovered "nuclein" (DNA) in the
cells from pus & later he separated it into a protein and
an acid molecule. It came to known as nucleic acid after
1874.
1926 , Levene proposed “Tetra nucleotide theory”
which states that Nucleic acid consists of only 4 nitrides
as it gives 4 diff nucleotides on hydrolysis.
In 1950, Erwin Chargaff shows that the four
nucleotides are not present in nucleic acids in
stable proportions.
1957, Sir Alexander R.Todd of Cambridge
University gave structure of nucleotide.
General features of nucleotides
SUGARS
Two main sugars
Present in furanose form
Lacks 2’-OH group
Bases
• Purines :
– Adenine (A)
– Guanine (G)
• Pyrimidines :
– Cytosine (C)
– Uracil (U)
– Thymine (T) The bases are abbreviated by their first letters (A, G, C, T, U).
The purines (A, G) occur in both RNA & DNA.
Among the pyrimidines, C occurs in both RNA & DNA, but
T occurs in DNA, and U occurs in RNA.
DNA: A,G,C,T
RNA: A,G,C,U
Some minor bases:
Minor bases of DNA Minor bases of RNA
• 5-Methylcytidine occurs in DNA of animals and
higher plants.
• N6-methyladenosine occurs in bacterial DNA.
Nucleosides =Ribose/Deoxyribose +
Bases
The bases are covalently attached to the 1’ position of a
pentose sugar ring, to form a nucleoside
Nucleotides = nucleoside + phosphate
A nucleotide is a nucleoside with one or more phosphate groups
bound covalently to the 3rd or 5th hydroxyl group of pentose sugar. Most
of nucleoside phosphate involve in biological function are 5’- phosphates.
Since 5’- phosphates are most often seen, they are written without any
prefix.
H
H
Ribonucleotide Deoxy-ribonucleotide
Nucleoside
NOMENCLATURE:-
Nucleosides phosphorylated on the 3’ or 5’ C of
ribose are termed ; nucleoside 3’- monophoshate &
nucleoside 5’- monophoshate.
‘5’ is by convention omitted when naming
nucleotide.
Abbrevations such as AMP, GTP denotes the
phosphate is esterified to 5’ of pentose.
Additional phosphate group is attached to preexisting
phosphate of mononucleotide ,
- nucleotide diphosphate – ADP
- nucleotide triphosphate – ATP
Nucleotide nomenclature:
Nucleotide nomenclature:
Individual properties :-
PROPERTIES OF PURINE BASES:-
Sparingly soluble in water
Absorb light in UV region at 260 nm.
(detection & quantitation of nucleotides)
Capable of forming hydrogen bond
Properties of pyrimidine bases :-
Soluble at body pH
Also absorb UV light at 260 nm
Capable of forming hydrogen bond
Pyrimidine base :-
Aromatic base atoms are numbered 1 to 6 for pyrimidine
Atoms or group attached to base atoms have same
number as the ring atom to which they are bonded
Cytosine :-
Chemically is 2-oxy ,4-amino pyrimidine
Exist both lactam or lactim form
Thymine :-
Chemically is 2,4 dioxy ,5-methyl pyrimidine
Occurs only in DNA
URACIL :-
Chemically is 2,4 dioxy pyrimidine
Found only in RNA
PURINE BASES :-
Aromatic base atoms numbered 1 to 9
Purine ring is formed by fusion of pyrimidine ring
with imidazole ring
Numbering is anticlockwise
Adenine :-
Chemically it is 6-aminopurine
Guanine :-
Chemically is 2-amino,6-oxy purine
Can be present as lactam & lactim form
CLASSIFICATION:
Adenosine
nucleotides
ATP, ADP, AMP, Cyclic AMP
Guanosine
nucleotides
GTP, GDP, GMP, Cyclic GMP
Uridine
nucleotides
UTP, UDP, UMP, UDP-G
Cytosine
nucleotides
CTP, CDP, CMP and certain deoxy CDP
derivatives of glucose, choline and
ethanolamine
Miscellaneous PAPS (active sulphate), SAM (active
methionine), certain coenzymes like NAD+,
FAD, FMN, Cobamide coenzyme, CoA
ADENOSINE CONTAINING
NUCLEOTIDES
ATP (ADENOSINE TRIPHOSPHATE)
Many synthetic reactions requires energy, e.g. arginosuccinate
synthetase reaction in urea cycle.
ATP is required for the synthesis of Phospho creatine from
creatine, synthesis of FA from acetyl CoA, formation of
glucose from pyruvic acid, etc.
ATP is an important source of energy for muscle contraction,
transmission of nerve impulses, transport of nutrients
across cell membrane, motility of spermatozoa.
ATP is required for the formation of active methionine, which
is required for methylation reaction
ATP donates phosphate for a variety of phosphotransferase
reactions e.g., hexokinase reaction.
ATP IN UREA CYCLE:
ATP IN FA SYNTHESIS:
ATP IN PHOSPHORYLATION REACTIONS:
ATP IN SYNTHESIS OF SAM:
ADENOSINE DI PHOSPHATE (ADP)
ADP plays an important role as a primary PO4
acceptor in oxidative phosphorylation and muscle
contraction, etc
ADP is also important as an activator of the enzyme
glutamate dehydrogenase
ACTVATION OF GLUTAMATE
DEHYDROGENASE
ADENOSINE MONO PHOSPHATE
(AMP)
In the glycolytic pathway, the enzyme
phosphofructokinase is inhibited by ATP but the
inhibition is reversed by AMP.
AMP can also act as an inhibitor of certain enzymes
like fructose-1-6- bisphosphatase and
adenylosuccinate synthetase.
In resting muscles, AMP is formed from ADP, by
adenylate kinase, the AMP produced activates the
phosphorylase b enzyme of muscle and increase
breakdown of glycogen.
AMP ROLE IN REGULATION
URIDINE NUCLEOTIDES
UTP also has the role of a source of energy or an activator of
substrates in metabolic reactions, like that of ATP, but more
specific.
When UTP activates a substrate, UDP-substrate is usually
formed and inorganic phosphate is released. UDP-
glucose enters the synthesis of glycogen.
UTP is used in the metabolism of galactose, where the
activated form UDP-galactose is converted to UDP-glucose
UDP-glucuronate is used to conjugate bilirubin to a more
water-soluble bilirubin diglucuronide
UDP ROLE IN GLYCOGEN SYNTHESIS
CONJUGATION OF BILIRUBIN
UDP ROLE IN GALACTOSE METABOLISM
CYTIDINE NUCLEOTIDES
Miscellaneous :-
PAPS - Phospho Adenosine Phospho Sulphate
(active sulphate) formed in liver
Sulfates enzymes which catalyze introduction
of SO4 group
In biosynthesis of chondroitin sulfate
Formation of sulpholipids
SAM:- S- Adenosyl Methionine
Active methionine
TRANSMETHYLATION REACTIONS
PHOSPHO ADENOSINE PHOSPHO SULPHATE
SYNTHESIS OF GAG’S FROM PAPS
C AMP
Contd.
Cyclic AMP mediated activation cascade
C GMP
FUNCTIONS
c-GMP is second messenger in photo transduction
in the eyes.
It has been claimed that c-GMP as second
messengers regulate the closing and opening of Na+
channels. In the dark there are high levels of c-GMP
which bind to Na+ channels causing them to open.
Reverse occur in light.
INOSINE MONOPHOPHATE
Hypoxanthine ribonulcleotide, usually called IMP
is a precursor of all purine nucleotide synthesized
de-novo
Inosinate can also be formed by de amination of
AMP, a reaction which occurs particularly in
muscles as a part of purine nucleotide cycle
SYNTHETIC ANALOGUES OF
BIOMEDICAL IMPORTANCE
Synthetic analogues of nucleobases, nucleosides
and nucleotides are recently of wide use in medical
sciences and clinical medicine.
The heterocyclic ring structure or the sugar moiety
is altered in such a way as to induce toxic effects
when the analogues get incorporated into cellular
constituents of the body.
Theophylline
Azathiopurine
Azapurine
SOME IMPORTANT SYNTHETIC DERIVATIVES
Allopurinol is a purine analogue. This drug is an inhibitor of the enzyme
xanthine oxidase, which inhibit uric acid formation. The drug is widely used
for the treatment of gout
AZT-(azydothymidine):- thymidine analogue treatment of AIDS
(terminates DNA synthesis catalysed by reverse transcriptase of retrovirus
such as HIV)
Uses of some Synthetic analogues of
nucleotides:-
NUCLEOSIDE ANALOGUES AS
DRUGS
ANALOGUES DRUGS USES
Deoxyadenosineanalogues
Didanosine, Vidarabine
HIVChemotherapy
Deoxycytidine analogues Cytarabine,EmtricitabineLamivudineZalcitabine
ChemothrapyHIVHepatitis BHIV
Deoxyguanosineanalogues
AbacavirEntecavir
HIVHepatitis B
Deoxy-thymidine analogues
StavudineTelbivudineZidovudine
HIVHepatitis BHIV
Deoxyuridine analogues IdoxuridineTrifluridine
HIVHIV
NUCLEOTIDE ANALOGUES AS
DRUGS
Tenofovir, also called 'prodrug‘. It is approved in
the USA for the treatment of both HIV and hepatitis
B.
Adefovir, has trade names Preveon and Hepsera. It
was not approved by the FDA for treatment of HIV
due to toxicity issues, but a lower dose is approved
for the treatment of hepatitis B.
Thank you..