This document discusses nucleotide chemistry. Nucleotides are organic compounds composed of a phosphate group, nitrogenous base, and a sugar molecule. They serve as the building blocks of nucleic acids DNA and RNA. Nucleotides also function as sources of chemical energy through molecules like ATP and GTP, and participate in cellular signaling through molecules like cAMP and cGMP. The document goes on to describe the specific sugars, bases, nucleosides, and nucleotides that make up DNA and RNA. It provides details on nucleotide nomenclature and classification and discusses important adenosine-containing nucleotides and their roles, such as ATP serving as an important energy source in many cellular processes.

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