NUCLEIC ACIDS
DEPARTMENT OF BIOCHEMISTRY
Kyobe Ronald Kimanje
Bsc, MSc, PhD candidate

NUCLEIC ACIDS:
 Nucleic acids were discovered by Friedrich Miescher in
1869.
 Nucleic acids are polymeric macromolecules, or large
biological molecules, essential for all known forms of life.
 Nucleic acids, which include DNA (deoxyribonucleic
acid) and RNA (ribonucleic acid), are made from
monomers known as nucleotides.
 They are involved in storage, transmition and
expression of genetic information.

Occurrence and nomenclature:
 Nucleic acids were named for their initial discovery
within the nucleus, and for the presence of phosphate
groups (related to phosphoric acid).
 Nucleic acids are now known to be found in all life
forms as well as some nonliving entities, including
within bacteria, archaea, mitochondria, chloroplasts
and viruses.
 All living cells contain both DNA and RNA (except
some cells such as mature red blood cells), while
viruses contain either DNA or RNA, but usually not
both.

Types of nucleic acids:
 There are two types of nucleic acids, namely;
1. Deoxyribonucleic acid
2. Ribonucleic acid
Deoxyribonucleic acid (DNA) is a nucleic acid
containing the genetic instructions used in the
development and functioning of all known living
organisms (with the exception of RNA viruses).
 The DNA segments carrying this genetic information
are called genes.

Deoxyribonucleic acid contd...
 Other DNA sequences have structural purposes, or are
involved in regulating the use of this genetic
information.
 DNA consists of two long polymers of simple units
called nucleotides, with backbones made of sugars and
phosphate groups joined by ester bonds.
 These two strands run in opposite directions to each
other and are, therefore, anti-parallel.
 Attached to each sugar is one of four types of
molecules called nitrogenous bases.

Deoxyribonucleic acid contd...
 It is the sequence of these four nitrogenous bases
along the backbone that encodes information.
 Within cells DNA is organized into long structures
called chromosomes.
 During cell division these chromosomes are duplicated
in the process of DNA replication.
 Eukaryotic organisms store most of their DNA inside
the cell nucleus and some of their DNA in organelles,
such as mitochondria or chloroplasts.

Deoxyribonucleic acid contd...
 Within the chromosomes, proteins such as histones
compact and organize DNA.
 These compact structures guide the interactions
between DNA and other proteins
 This helps in controlling which parts of the DNA are
transcribed.

Forms of DNA and their features:

Ribonucleic acid:
 Ribonucleic acid (RNA) functions in converting
genetic information from genes into the amino acid
sequences of proteins
 RNA is formed from DNA by the process known as
transcription
 The three universal types of RNA include transfer RNA
(tRNA), messenger RNA (mRNA), and ribosomal RNA
(rRNA).
 Messenger RNA acts to carry genetic sequence
information between DNA and ribosomes, directing
protein synthesis.

Special features of mRNA
1. They contain a continuous sequence of nucleotides
encoding a specific polypeptide
2. They are found in the cytoplasm.
3. They are attached to ribosomes when they are translated.
4. Most mRNAs contain a significant noncoding segment,
that is, a portion that does not direct the assembly of
amino acids.
5. Eukaryotic mRNAs have special modifications at their 5'
and 3‘ termini that are not found on either bacterial
mRNAs or on tRNAs or rRNAs.
The 3 end of nearly all eukaryotic mRNAs has a string of 50
to 250 adenosine residues that form a poly(A) tail, whereas
the 5 end has a methylated guanosine cap

Ribonucleic acid contd….
 Ribosomal RNA is a major component of the
ribosome, and catalyzes peptide bond formation.
 Transfer RNA serves as the carrier molecule for amino
acids to be used in protein synthesis, and is
responsible for decoding the mRNA.

Structure of tRNA

Purines and pyrimidines:
 Pyrimidines are six-membered heterocyclic aromatic rings
containing two nitrogen atoms.
 The atoms are numbered in a clockwise fashion.
 The purine ring structure is represented by the
combination of a pyrimidine ring with a five-
membered imidazole ring to yield a fused ring system.
 The common naturally occurring pyrimidines are
cytosine, uracil, and thymine (5-methyluracil).
 Cytosine and thymine are the pyrimidines typically
found in DNA, whereas cytosine and uracil are
common in RNA.

Purines and pyrimidines contd...
 Adenine (6-amino purine) and guanine (2-amino-6-
oxy purine), the two common purines, are found in
both DNA and RNA.
 Other naturally occurring purine derivatives include
hypoxanthine, xanthine, and uric acid.

Purine and pyrimidine rings:

Nucleosides and nucleotides:
 Nucleosides are compounds formed when a base is
linked to a sugar via a glycosidic bond.
 Nucleosides are named by adding the ending –idine to
the root name of a pyrimidine or -osine to the root
name of a purine.
 The common nucleosides are thus cytidine, uridine,
thymidine, adenosine, and guanosine.

Nucleosides and nucleotides contd..
 A nucleotide results when phosphoric acid is
esterified to a sugar -OH group of a nucleoside.
 The nucleoside ribose ring has three -OH groups
available for esterification, at C-2', C-3', and C-5‘
 The vast majority of monomeric nucleotides in the cell
are ribonucleotides having 5'-phosphate groups.

Nucleoside and nucleotide forms of DNA
and RNA bases:

Biological functions of nucleotides:
 Nucleotides are the monomeric units or building
blocks of nucleic acids.
 They form a part of many coenzymes and serve as
donors of phosphoryl groups (eg, ATP or GTP), of
sugars (eg,UDP- or GDP-sugars), or of lipid (eg, CDP-
acylglycerol).
 They serve as intermediates in various metabolic
pathways e.g UDP-Glucose, UDP-Galactose
 They serve as a source of energy in energy requiring
reactions e.g ATP
 They play a key role in energy metabolism by
accepting and donating electrons e.g. NAD and FAD

Biological functions of nucleotides contd....
 Regulatory nucleotides include the second messengers
cAMP and cGMP. ADP serves to control the process of
oxidative phosphorylation.
 They serve as allosteric regulators of enzyme activity
e. g ATP, AMP, and CTP.
 Synthetic purine and pyrimidine analogs that contain
halogens, thiols, or additional nitrogen are employed
for chemotherapy of cancer (e.g 5-azacytidine and 5-
aza-2′-deoxycytidine) and AIDS e.g the nucleoside
reverse transcriptase inhibitors (NRTIs) including
Zidovudine (AZT) and Stavudine (d4T)
They can also serve as suppressors of the immune
response during organ transplantation

Take home question
Describe the use of the DNMT inhibitors 5-azacytidine
and 5-aza-2′-deoxycytidine in treatment of cancer.

Polymerization of nucleotides:
 Nucleic acids are linear polymers of nucleotides linked 3' to 5'
by phosphodiester bonds.
 They are formed as 5'-nucleoside monophosphates are
successively added to the 3'-OH group of the preceding
nucleotide.
 Polymerization is an energy requiring process.
 Each successive nucleotide enters as a high energy nucleoside
triphosphate.
 Two phosphate groups are then removed by cleavage of their
phosphoanhydride bonds.
 The energy released is used in forming the phosphodiester
bond between the successive nucleotides.

The DNA double helix:
 The DNA double helix model was postulated by James
Watson and Francis Crick in 1953.
 According to this model, two strands of deoxyribonucleic
acid are held together by hydrogen bonds formed between
unique base pairs
 Base pairs always consist of a purine in one strand and a
pyrimidine in the other strand.
 Base pairing is very specific: if the purine is adenine,
the pyrimidine must be thymine.
 Similarly, guanine pairs only with cytosine.

The DNA double helix contd....
 A major groove and a minor groove winds along the
molecule parallel to the phosphodiester backbones.
 In these grooves, proteins can interact specifically with
exposed atoms of the nucleotides (usually by H bonding)
 This occurs without disrupting the base pairing of the
double-helical DNA molecule.
 Regulatory proteins control the expression of specific
genes via such interactions.
 Elucidation of the double helical structure of DNA
marked the beginning of molecular biology.

Denaturation of the DNA double helix:
 The double-stranded structure of DNA can be separated
(melted) into two component strands in solution by
increasing the temperature.
 Concomitant with this denaturation of the DNA molecule
is an increase in the optical absorbance of the purine and
pyrimidine bases
 This phenomenon is referred to as hyperchromicity of
denaturation.
 Due to stacking of the bases and the hydrogen bonding
between the stacks, the double-stranded DNA molecule
exhibits properties of a rigid rod.
 In solution the DNA is a viscous material that loses its
viscosity upon denaturation.

Denaturation of the DNA double helix contd....
 The strands of a given molecule of DNA separate over a
temperature range.
 The midpoint is called the melting temperature, or
Tm.
 The Tm is influenced by the base composition of the
DNA and by the salt concentration of the solution.
 DNA rich in G–C pairs, which have three hydrogen
bonds, melts at a higher temperature than DNA rich in
A–T pairs, which have two hydrogen bonds.

Renaturation of the DNA double helix:
 This can occur when appropriate physiologic temperature
and salt conditions are achieved.
 The rate of re-association depends upon the concentration
of the complementary strands.
 Re-association of the two complementary DNA strands of
a chromosome after DNA replication is a physiologic
example of renaturation.

Packaging of DNA in the nucleus:
 Histones are highly alkaline proteins found in
eukaryotic cell nuclei that package and help to
organise the DNA into structural units called
nucleosomes.
 They are the chief protein components of chromatin.
They act as spools around which DNA winds, and play
a role in gene regulation.
 Without histones, the unwound DNA in chromosomes
would be very long (a length to width ratio of more
than 10 million to 1 in human DNA).

Packaging of DNA in the nucleus contd...
 For example, each human cell has about 1.8 meters of
DNA.
 When this DNA is wound on the histones it has about
90 micrometers (0.09 mm) of chromatin.
 When the chromatin is duplicated and condensed
during mitosis, it result in about 120 micrometers of
chromosomes.

Packaging of DNA in the nucleus contd...
 Five major families of histones exist: H1/H5, H2A, H2B, H3
and H4.
 Histones H2A, H2B, H3 and H4 are known as the core
histones, while histones H1 and H5 are known as the linker
histones.
 Two of each of the core histones assemble to form one
octameric nucleosome core, approximately 63 Angstroms
in diameter (a solenoid (DNA)-like particle).
 147 base pairs of DNA wrap around this core particle 1.65
times in a left-handed super-helical turn to give a particle
of around 100 Angstroms across.

Packaging of DNA in the nucleus contd...
 The linker histone H1 binds the nucleosome at the
entry and exit sites of the DNA
 This locks the DNA into placeand allowing the
formation of higher order structure.
 The most basic such formation is the 10 nm fiber or
beads on a string conformation.
 This involves the wrapping of DNA around
nucleosomes with approximately 50 base pairs of
DNA(linker DNA) separating each pair of
nucleosomes.

Packaging of DNA in the nucleus contd...
 Higher-order structures include the 30 nm fiber and
100 nm fiber, these being the structures found in
normal cells.
 During mitosis and meiosis, the condensed
chromosomes are assembled through interactions
between nucleosomes and other regulatory proteins.