Nucleic acid biochemistry

1. CHEMISTRY OF NUCLEIC ACIDS AND
BIOLOGICAL FUNCTIONS.
© 2016 Paul Billiet ODWS

2. RNA AND DNA

3. NUCLEIC ACIDS
•
•
•
•
Nucleic acids are biological macromolecules containing
oxygen, hydrogen, carbon, nitrogen and phosphorus.
There are two types of nucleic acids:
ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).
Nucleic acids are made up of basic units called
nucleotides which bind together by covalent bonds to
form a polynucleotide or the nucleic acid.

4. NUCLEOTIDES
•
•
•
•
Nucleotides are the basic units forming the nucleic acid.
composed of three units:
A pentose sugar molecule. There are two basic types of
sugar in nucleic acids:
– Deoxyribose sugar involved in the composition of DNA.
– Ribose sugar involved in the composition of RNA.
A phosphate group. These are connected to the carbon
atom number 5 of the sugar molecule.

5. A nitrogenous base.
Nitrogenous bases are: adenine (A), guanine (G), cytosine
(C) and thymine (T) in a DNA molecule and uracil (U) in a
RNA molecule.
Uracil is found in RNA only instead of thymine in DNA.
Each base is connected to the carbon atom number 1 of
the sugar molecule.
Nucleic acids differ with respect to the difference of the
nitrogenous bases forming them.
NB: A combination of a base and a sugar is called a
nucleoside.

6. NUCLEIC ACID STRUCTURE
•
•
Nucleic acids are polynucleotides
Their building blocks are nucleotides
© 2016 Paul Billiet ODWS

7. NUCLEOTIDE STRUCTURE
PHOSPHATE SUGAR
Ribose or
Deoxyribos
e
NUCLEOTIDE
BASE
PURINES PYRIMIDINES
Adenine (A)
Guanine(G)
Cytocine (C)
Thymine (T)
Uracil (U)
© 2016 Paul Billiet ODWS

9. STRUCTURE OF NITROGENOUS BASE
PYRIMIDINES PURINES

11. The distribution of nucleic acids in the
eukaryotic cell
•
•
DNA is found in the nucleus
with small amounts in mitochondria and
chloroplasts
RNA is found throughout the cell
© 2016 Paul Billiet ODWS

12. DNA as genetic material: The
circumstantial evidence
1.
2.
3.
4.
Present in all cells and virtually restricted to the
nucleus
The amount of DNA in somatic cells (body cells) of
any given species is constant (like the number of
chromosomes)
The DNA content of gametes (sex cells) is half that of
somatic cells.
In cases of polyploidy (multiple sets of chromosomes)
the DNA content increases by a proportional factor
The mutagenic effect of UV light peaks at 253.7nm.
The peak for the absorption of UV light by DNA
© 2016 Paul Billiet ODWS

13. THE SUGAR-PHOSPHATE
BACKBONE
•
•
The nucleotides are all
orientated in the same
direction
The phosphate group joins
the 3rd Carbon of one sugar
to the 5th Carbon of the next
in line.
P
P
P
P
P
P
© 2016 Paul Billiet ODWS

14. ADDING IN THE BASES
•
•
The bases are attached to
the 1st Carbon
Their order is important
It determines the genetic
information of the molecule
P
P
P
P
P
P
G
C
C
A
T
T
© 2016 Paul Billiet ODWS

15. DNA IS MADE OF
TWO STRANDS OF
POLYNUCLEOTIDE
P
P
P
P
P
P
C
G
G
T
A
A
P
P
P
P
P
P
G
C
C
A
T
T
Hydrogen bonds
© 2016 Paul Billiet ODWS

16. DNA IS MADE OF TWO STRANDS OF
POLYNUCLEOTIDE
•
•
•
•
•
The sister strands of the DNA molecule run in
opposite directions (antiparallel)
They are joined by the bases
Each base is paired with a specific partner:
A is always paired with T
G is always paired with C
Purine with Pyrimidine
Thus the sister strands are complementary but not
identical
The bases are joined by hydrogen bonds, individually
weak but collectively strong.
© 2016 Paul Billiet ODWS

17. Purines & Pyrimidines
Adenine
Cytosine
Guanine
Thymine
© 2016 Paul Billiet ODWS

18. SINGLE STRAND OF DNA AND RNA

21. NOMENCLATURE

22. Biosynthesis of Purine Nucleotides:
•
•
•
There are two pathways by which nucleotides are made
available for the formation of nucleic acids:
(1) Denovo synthesis i.e. new synthesis
(2) Salvage process i.e. recycling of the bases.

23. De Novo Synthesis:
•
•
De novo (all over again) synthesis of purine nucleotides is
synthesis of purines.The purine ring is synthesized along
with the nucleotide i.e. attached to the ribose sugar
provided from HMP pathway.
This pathway supplies ribose sugar for the formation of
the nucleotide. Activated form of D-ribose-5-phosphate
serves as the starting material on which purine ring is
build up step by step.

24. Precursors of the members of purine ring are:
•
•
•
•
•
•
i. N-1 is contributed by nitrogen of aspartate
ii. N-3 and N-9 arise from amide nitrogen of glutamine.
iii. C-2 and C-8 originate from the formate.
iv. C-6 is embedded from respiratory carbon dioxide.
v. C-4, C-5 and N-7 are taken up from glycine.

26. BIOSYNTHESIS OF PURINES

27. BIOSYNTHESIS OF PURINES

29. Purine Nucleotides

30. • Regulation of purine nucleotide biosynthesis:
Purine biosynthesis is regulated by feedback inhibition.
This inhibition is in the 1st step. It is the committed step
which is generally irreversible. Once the committed step is
passed over, the product has to be formed.

31. Salvage Pathway
•
•
•
•
The de-novo synthesis does not occur in all the cells.
Brain cells and leukocytes lack this mechanism.
In these cells purine synthesis occurs by salvage pathway.
Salvage pathway involves synthesis of purine nucleotides
from free purine bases, which are salvaged from dietary
sources and tissue breakdown.
This pathway is promoted by the action of two enzymes
which convert free purines into purine nucleotides for
reuse.

33. Genetic disorder of purine biosynthesis
•
•
•
•
•
•
Lesch-Nyhan syndrome:
This is a genetic disorder caused due to the deficiency of the
enzyme ‘Hypoxanthine Guanine Phospho Ribosyl Transferase
(HGPRT)’. When this enzyme is deficient, guanine, xanthine
and hypoxanthine are not salvaged and hence degraded to
uric acid.
This is especially seen in male children.
In female children the gene is recessive and is a carrier.
It is a male dominant gene.
Such males show (1) mental retardation and (2) tendency for
self-destruction.

34. Biosynthesis of Pyrimidine Nucleotides:
•
•
•
•
•
Pyrimidine nucleotide biosynthesis takes place in a
different manner from that of purine nucleotides.
The six membered pyrimidine ring is made first and then
attached to ribose phosphate.
The synthesis begins with carbon dioxide and ammonia
combining to form carbamoyl phosphate catalysed by the
cytosolic enzyme carbamoyl phosphate synthetase-II.
Carbamoyl phosphate combined with aspartate to form
carbamoyl asarptate aided by the enzyme aspartate
transcarbamoylase.

35. •
•
•
Dihydroorotate is formed from carbamoyl aspartate by
removal of water and closure of the ring under the
influence of the enzyme dihydroorotase.
Dihydroorotase is oxidized to orotic acid by
dehydrogenase which uses NAD+ as the electron acceptor.
Orotic acid is attached to ribose to yield orotidylic acid.
Orotidylate is then decaroxylated to form uridylate.
Uridylate is then converted to all the other pyrimidine
nucleotides viz., CMP
, UMP & TMP
.

36. Pathways of pyrimidine nucleotides
synthesis

37. Regulation of Pyrimidine Biosynthesis:
•
•
•
Regulation of pyrimidine biosynthesis is by feed back
inhibition at the committed step
The reaction catalysed by the enzyme aspartate
transcarbamoylase is inhibited by the end product i.e. CTP
.
The second site is at carbamoyl phosphate synthase- II
which is feedback inhibited by UMP
.

38. Metabolic disorder of pyrimidine
•
•
•
•
Orotic Aciduria:
It is a metabolic disorder of pyrimidine biosynthesis
characterized by accumulation of orotic acid in blood and
its increased excretion in urine.
It is caused due to the deficiency of enzyme orotidylic
acid phosphorylase and orotidylic acid decarboxylase or
orotic phosphoribosyl transferase.
This leads to non-conversion of orotic acid to UMP
. This
may even affect the synthesis of other nucleotides

39. •
•
It is generally found in children who show retarded mental
development and growth as there is no proper synthesis
of DNA.
They show megaloblastic anemia. This can be overcome
by injection of CTP and UTP
.

40. FUNCTIONS OF NUCLEOTIDES
1. ATP, GTP, CTP, UTP, are important
ribonucleotides which act as coenzymes.
2. Deoxyribonucleotides are required for DNA
replication and repair. Ribonucleotides are required
for RNA.
3. They are used in biosynthetic reactions like
UDP-glucose, in glycogen
synthesis and UDP- galactose in lactose synthesis.
4 Nucleotides control rates of many enzyme-
catalyzed reactions by feedback and allosteric
regulation.

41. 5 ATP acts as currency of free energy for
all cellular activities like muscle contraction,
biosynthesis of molecules and transfer
reactions.
6 Some nucleotides act as intracellular
messenger’s .eg, c AMP, c GMP are involved in
peptide hormone action
7 GTP is used in protein synthesis.
8. S-adenosyl methionine participates in
transmethylation reactions

42. TEST MCQ
•
•
Identify the purine base of nucleic acids in the following
a) Cytosine
b) Thymine
c) Uracil
d) Adenine
2. Which of the following are not the components of RNA?
a) Thymine
b) Adenine
c) Guanine
d) Cytosine

43. •
•
3. Which of the following statements is true?
a) Sugar component of a nucleotide is ribose
b) Sugar component of a nucleotide is deoxyribose
c) The bases in nucleotides are attached to a pentose
sugar moiety by a glycosidic linkage
d) The sugar molecule of the nucleotide is in L-
configuration
4. What is the composition of nucleoside?
a) a sugar + a phosphate
b) a base + a sugar
c) a base + a phosphate
d) a base + a sugar + phosphate

44. •
•
5. What is the composition of nucleotide?
a) a sugar + a phosphate
b) a base + a sugar
c) a base + a phosphate
d) a base + a sugar + phosphate
6. Group of adjacent nucleotides are joined by
a) Phosphodiester bond
b) Peptide bond
c) Ionic bond
d) Covalent bond
View Answer

45. • 7. The sugar molecule in a nucleotide is
a) Pentose
b) Hexose
c) Tetrose
d) Triose
8. Which of the following is true about phosphodiester linkage?
a) 5’-phosphate group of one nucleotide unit is joined to the
3’-hydroxyl group of the next nucleotide
b) 3’-phosphate group of one nucleotide unit is joined to the
5’-hydroxyl group of the next nucleotide
c) 5’-phosphate group of one nucleotide unit is joined to the
5’-hydroxyl group of the next nucleotide
d) 3’-phosphate group of one nucleotide unit is joined to the
3’-hydroxyl group of the next nucleotide

46. •
•
9. Which of the following is not a component of the
nucleic acid backbone?
a) Pentose sugar
b) Phosphate group
c) Nucleotide
d) Phosphodiesterase bond
10. Building blocks of nucleic acids are
a) Nucleotides
b) Nucleosides
c) Amino acids
d) Histones
View Answer

47. 11.Which of the following nucleotides is not present in RNA?
a) AMP
b) GMP
c) CMP
d) TMP
12. Which of the following nucleotides is not present in
DNA?
a) AMP
b) GMP
c) CMP
d) UMP

48. •
•
•
•
13 Which of the following involves in carrying genetic
information from DNA for protein synthesis?
a) m-RNA
b) t-RNA
c) r-RNA
d) sn-RNA
14. which of the following statement is true?
a. UDP inhibit the enzyme carbamoyl phosphate synthesis.
b. CTP inhibit the enzyme aspartate transcarbamoylase
c. orotic aciduria is a disease disorder of purine
d. Lesh-Nyhan is a diease disorder of pyrimidine.

49. •
•
•
•
•
•
•
•
•
•
15. Enzymes found in the salvage pathway of purines.
a. Adenine phosphoribosyl transferase
b. Hypoxanthine Guanine pyrophosphate transferase.
c. carbamoyl synthetase
d. aspartate transcarbamoylase.
16. Which of the following is not a precursors of denovo
purines biosynthesis
a. glutamine
b. Formate
c.glycine
d. carbonmonoxide

50. 17. With respect to nucleosides which of the following is
paired correctly?
a) Purine – Adenosine, Thymidine
b) Purine – Guanosine, Thymidine
c) Pyrimidine – Uridine, Cytidine
d) Pyrimidine – Uridine, Adenosine
18. Which one of the following is not a function of a
nucleotide?
a) Nucleic acid monomer
b) Ribozyme
c) Energy carrier molecules
d) Receptors

51. •
•
•
•
•
•
•
•
•
•
19. The monomeric deoxyribonucleotides units of DNA
include all except.
a.deoxyadenylate
b.deoxyguanylate
c. deoxycytidylate
d.deoxyuridylate
20. Which pyrimidine base contains an amino group at carbon
4?
a. Cytosine
b. Thymine
c. Uracil
d. Adenine