This document provides an instruction on nucleic acid chemistry. It discusses topics including nucleosides and nucleotides, their composition and classification. It also discusses polynucleotides or nucleic acids, their classification and notations. For DNA, it describes the double helix model including its primary, secondary and tertiary structures. It also discusses how DNA is associated with proteins like histones and its general organization in the human genome. For RNA, it describes its base composition and different types including mRNA, tRNA, rRNA and their general structures and functions.

1. Instruction to Nucleic acids Chemistry
Faculty of health sciences
Department of human biology
2022

2. Topics
 Nucleosides and Nucleotides
o Composition, classification.
o Formation of phosphodiester bonds.
o Functions of nucleotides in an organism.
 Polynucleotides or nucleic acids
o Classification and notations.
 Structure and properties of DNA
o Base composition. (Primary structure)
o The double helix model of DNA. (Secondary structure)
o Biological meaning of the double helix.
o Association of DNA with proteins. Histones. (Tertiary stricture)
o General organization of DNA in human genome.
 Structure and properties of RNA
o Base composition.
o Types of RNA. General structure and functions.

3. Nucleosides and Nucleotides
• Nucleosides are formed by joining a sugar and a nitrogenous base.
• Nucleotides are molecules formed by joining phosphoric acid to a
nucleoside.
Nucleotide
Phosphoric acid
Nucleoside

4. Nucleotides > Bases

5. Nucleotides > classification
Deoxynucleotides
AND
Ribonucleotides

6. • Building blocks of Nucleic Acids.
• Donnors of phosphates groups (ATP).
• ATP is also the universal currency of free energy in Biological Systems.
• Structural components of complex biomolecules such as NADH, FADH2,
Coenzyme A, etc.
• Covalently bound, activate some precursors in biosynthesis of biomolecules
(UDP-Glucose, CDP- Choline, etc).
• Acting as an intracellular second messengers (cAMP, cGMP)
• As carriers of sugars, that are made available through the action of nucleoside
phosphorylases when suitable carbon and energy sources are not available
Nucleotides > Functions of nucleotides in the
organism

7. Nucleotides > Formation of phosphodiester bonds

8. Polynucleotides
Polynucleotides are linear
polymers of nucleotides
linked 3 to 5 by
phosphodiester
bridges.

9. Nucleoside analogues for disease control
(HIV)
Katherine L. Seley-Radtke and Mary K. Yates, 2018

10. Nucleic acids > Classification and notations
AND

11. DNA > Structure and properties
Hydrogen Bonds
Phosphate
Group
Deoxyribose
Sugar
Covalent
Bond
’ End
5
’ End
3
3’ End
’ End
5
Cytosine
Purine Pyrimidine
Antiparallel strands
Thymine
Guanine
Adenine

12. DNA > The double helix model of DNA/Biological
meaning of the double helix
• The DNA molecule twists to shrink the spaces between the hydrophobic bases on
the inside. The spiral shape discourages water from flowing between them, these
bases twist slightly in order to maximize their hydrophobic interactions with each
other, and it is this twisting of the stacked bases that gives rise to a helix
• Two factors are mainly responsible for the stability of the DNA double helix: base
pairing between complementary strands and stacking force.
• The stacking force attracts the bases above and below each other on the
same strand
• Hydrogen bonds in a DNA molecule also contribute greatly to the stability of
the double helix

13. DNA > The double helix model of DNA
GROOVES
• The surface of the double
helix contains two grooves of
unequal width.
• These two grooves are called
the major and minor groove
based on their sizes.
• Most protein–DNA contacts
are made in the major groove,
because the minor groove is
too narrow. The distance between two base pairs is 0.34 nanometers. The length of one turn of
the double-helix is 3.4 nanometers and 10 bases per turn of helix . The width of the
DNA molecule is 2 nanometers

14. DNA > Forms of double helix model

15. DNA > Association of DNA with proteins/Histones
• The DNA (~3b) inside a human cell is packed into
the nucleus to occupy only 10% of the total cellular
volume.
• For such efficient packing, DNA needs to be folded
into higher-order structures.
• The step by step packing of DNA is carried out by
specialized proteins, the most abundant of which
are called histones.
• Histones are small proteins with a high positive
charge (they contain many lysine and arginine
residues), which helps the histones bind tightly to
DNA
• Eight histone proteins form a disc or “histone core”,
around which 146 DNA base pairs wrap; this is the
fundamental packing unit and is known as the
nucleosome
DNA Double
Helix
Nucleosome
Histones
H1 Histone
Nucleosomes,
or “beads on a
string”

16. DNA > Association of DNA with proteins/Histones

17. DNA > General organization of DNA in human genome

18. Human Chromosome Map of Inherited Diseases

19. RNA >Structure and properties
 Eukaryotic RNAs are single
stranded polynucleotides, some
of them form well-defined
secondary and tertiary
structures.
 RNAs do not have thymine,
instead, they contain Uridine.
 The presence of 2’ OH makes
“most” of these molecules
unstable.

20. RNA > Types of RNA/ General structure and
functions
o mRNA - messenger RNA - is a "copy" of the
DNA base sequence of a gene. It is used to
transfer the genetic information from DNA,
which is a storage molecule and quite
inaccessible, to ribosomes
o 5’ cap added – This helps with mRNA
attachment to the ribosome and
protects from exonucleases
(degradation).
o Poly-A tail – helps it get out of nucleus
and protect RNA from degradation.

21. RNA > Types of RNA/ General structure and
functions
o tRNA – transfer RNAs bring the
necessary amino acids corresponding
to the appropriate mRNA codon.
o Molecules of tRNA are not identical
o Each carries a specific amino acid on one end
o Each has an anticodon on the other end; the
anticodon base-pairs with a complementary
codon on mRNA
o A tRNA molecule consists of a single RNA
strand that is about 80 nucleotides long
o Because of hydrogen bonds, tRNA actually
twists and folds into a three-dimensional
molecule
o tRNA contains modified bases.

22. RNA > Types of RNA/ General structure and
functions
o rRNA - Ribosomal RNA is a component of the
ribosome, the protein manufacturing machinery
of all living cells.
o Ribosomal RNA provides two functions in the
protein factory
o Decoding mRNA, a function that is carried
buy the small subunit
o Peptidyl transferase activity, carried by the
big subunit

23. o snRNA - small nuclear RNA - regulates and provides the catalytic machinery
for splicing mRNA.
o gRNA - guide RNA - directs editing of RNA to specific sites.
o miRNA - micro RNA - inhibits translation by base pairing with complementary
sequences of mRNA.
o Signal Recognition Particle - RNA/protein molecule that binds to the
"Signal Sequence" on polypeptides to be sent to the endoplasmic reticulum.
RNA > Types of RNA/ General structure and
functions