Nucleotide chemistry

1. NUCLEOTIDE CHEMISTRY
Dr. Aamir Ali Khan
PhD Biochemistry
Principal Ghazali Institute of Medical Sciences Peshawar

2. Introduction
Nucleotides are organic compounds made up of a PO4
group, nitrogenous base & a sugar molecule.
These are the building blocks of nucleic
acids (DNA and RNA).
They serve as sources of chemical energy (ATP, GTP),
participate in cellular signalling (cAMP, cGMP) and
function as important cofactors of enzymatic reactions
(CoA, FAD, FMN, NAD+).

3. SUGARS
Two main sugars
Present in furanose form
Lacks 2’-OH group

4. 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

6. Nucleosides =Ribose/ Deoxyribose +
Bases
The bases are covalently attached to the 1’ position of a pentose sugar ring, to
form a nucleoside

7. 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.

8. H
H
Ribonucleotide Deoxy-ribonucleotide
Nucleoside

9. 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.
Abbreviations 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

10. Nucleotide nomenclature:

11. Nucleotide nomenclature:

12. Individual properties
PROPERTIES OF PURINE BASES:-
Sparingly soluble in water
Absorb light in UV region at 260 nm. (detection &
quantization of nucleotides)
Capable of forming hydrogen bond

13. Properties of pyrimidine bases
Soluble at body pH
Also absorb UV light at 260 nm
Capable of forming hydrogen bond

14. 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

15. Cytosine :-
Chemically is 2-oxy ,4-amino pyrimidine
Exist both lactam or lactim form

16. Thymine :-
Chemically is 2,4 dioxy ,5-methyl pyrimidine
Occurs only in DNA

17. URACIL :-
Chemically is 2,4 dioxy Pyrimidine
Found only in RNA

18. PURINE BASES
Aromatic base atoms numbered 1 to 9
Purine ring is formed by fusion of Pyrimidine ring with
Imidazole ring
Numbering is anticlockwise

19. ADENINE
Chemically it is 6-aminopurine

20. Guanine :-
Chemically is 2-amino,6-oxy purine
Can be present as lactam & lactim form

21. 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

22. ADENOSINE CONTAINING
NUCLEOTIDES

23. 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.

24. 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

25. 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.

26. AMP ROLE IN REGULATION

27. 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