Intended learning outcomes
At the end of this lecture you should be able to:
 Recognize the structural components of a DNA and a RNA
molecule. (LO 5.1)
 Recognize and apply the conventions used to represent these
components and the conventions used to represent DNA or RNA
base sequences. (LO 5.2)
 Explain polarity of a DNA or RNA chain. (LO 5.3)
 Explain the importance of hydrogen-bonding and base-pairing in
defining nucleic acid secondary structure. (LO 5.4)
 Describe the key features of the DNA double helix. (LO 5.5)
Nucleic Acids: DNA and RNA
Nucleic
acids:
are
linear
polymers
of
nucleotides
‘polynucleotides’ that required for the storage and
expression of genetic information.
There are two chemically distinct types of nucleic acids:

Deoxyribonucleic acid (DNA)

Ribonucleic acid (RNA)
Nucleic Acids: DNA and RNA
DNA: is polymer of deoxyribonucleotides covalently linked
by 3‫→׳‬5‫ ׳‬phosphodiester bond carrying the genetic
information in all cellular forms of life and some viruses.
RNA: is polymer of ribonucleotides covalently linked by
3‫→׳‬5‫׳‬
phosphodiester
bond
that
function
as
an
intermediary in the transfer of genetic information from
DNA to protein
Nucleotides: Building blocks of nucleic acids
Nucleotides: are basic building block of DNA and RNA
Each nucleotide consists of three components:
a nitrogenous base, a pentose sugar and a phosphate
molecule
Nucleoside composed of only :
a nitrogenous base and a pentose sugar
Nucleotides components
1-Nitrogenous base: There are two types
Purine: have a two-ring structure (Adenine (A) and Guanine (G))
Pyrimidine: have a one-ring structure (Thymine (T) Cytosine (C) and Uracil (U)
DNA has A,G,T,C and RNA has A,G,U,C
Adenine
Guanine
Cytosine
Uracil (in RNA)
Thymine (in DNA)
Nucleotides components
 Note the similarity between the 6-membered rings
 Also that these structures are ‘planar’ (it can be
represented on a flat surface) because of the double
bonds, and unsaturated
Nucleotides components
2-Pentose sugar: There are two types
Ribose in RNA
2-Deoxyribose in DNA
5
5
HO
HO
1
4
3
2
1
4
3
2
3-A phosphate group: The phosphate groups are strongly acidic
and are the reason DNA and RNA are called acids.
Nucleotides structure
Nucleotides are formed by covalent bonding of the phosphate, base,
and sugar.
N-glycocdic bond
Phosphate ester
bond
Nucleotides Nomenclature
Deoxyribonucleotide
Deoxyadenosine (Nucleoside)
Deoxyadenosine monophosphate (dAMP)
Deoxyadenosine diphosphate (dADP)
Deoxyadenosine triphosphate (dATP)
Nucleotides Nomenclature
Base
Nucleoside
Nucleotide
In RNA:
Adenine (A)
Adenosine
Adenosine monophosphate (AMP)
Guanine (G)
Guanosine
Guanosine monophosphate (GMP)
Uracil (U)
Uridine
Uridine monophosphate
Cytosine (C)
Cytidine
Cytidine monophosphate (GMP)
(UMP)
In DNA:
Adenine (A)
Deoxyadenosine
Deoxyadenosine monophosphate (dAMP)
Guanine (G)
Deoxyguanosine
Deoxyguanosine monophosphate
(dGMP)
Thymine (T)
Deoxythymidine
Deoxythymidine monophosphate
(dTMP)
Cytosine (C)
Deoxycytidine
Deoxycytidine monophosphated (CMP)
Polynucleotides
 Nucleotides
are
covalently
linked via 3'→5' phosphodiester
bonds to form polynucleotides
chains.
 The resulting chain has polarity,
with both a 5'-end (the end with
free phosphate) and a 3'-end (
the end with free hydroxyl
group) that are not linked to
other nucleotides, resulting in
chain with 5'→3' direction
 The bases written in the
conventional 5'→3' direction:
5'-AGCT-3‘
 DNA has two polynucleotides
chains and RNA has only one
 Each single-strand nucleic acid chain has a polarity
The Watson-Crick Model of DNA Structure
According to Watson and Crick model
(1953)
 DNA is composed of two polynucleotide
chains running in opposite directions
(antiparallel),
5'→3'direction,
3'→5'direction.
one
chain
the
run
other
in
in
The Watson-Crick Model of DNA Structure
 The two chains are twisted (coiled)
around each other in a right-handed
to form a double helix.
 the
hydrophilic
deoxyribose-
phosphate backbone of each chain is
on the outside the molecule, whereas
the hydrophobic bases are stacked
inside where they are paired by
hydrogen
bonds.
structure
resembles
ladder.
The
overall
the
twisted
The Watson-Crick Model of DNA Structure
 Base pairing is highly specific: A in one
chain pairs with T in the opposite chain
by two hydrogen bonds , and C pairs
with G by three bonds.
 The base pairing of the model makes
the two polynucleotide chains of DNA
complementary in base composition. If
one strand has the sequence 5′ACGTC-3′, the opposite strand must be
3′-TGCAG-5′, and the double-stranded
structure would be written as
5′-ACGTC-3′
3′-TGCAG-5′
 Chargaff Rule (base ratio):
A=T , G = C,
Total purines=Total pyrimidines
The Watson-Crick Model of DNA Structure
 One complete turn is 10 base pairs
and space between base pairs is
0.34nm
 The spatial relationship between the
two strands in the helix creates a
major (wide) groove and a minor
(narrow) groove. The bases in these
grooves exposed and therefore
interact with proteins or other
molecules.
 The third -OH group on the
phosphate is free and dissociates a
hydrogen ion at physiologic pH.
Therefore, each DNA helix has
negative charges coating its surface
that facilitate the binding of specific
proteins.
Base pairing and Hydrogen bonds formation
Cytosine
Guanine
Important of Watson-Crick Model
 Genetic information is stored in the sequence of bases in the DNA,
which have a high coding capacity .
 The model offers a molecular explanation for mutation. Because
genetic information is stored as a linear sequence of bases in DNA,
any change in the order or number of bases in a gene can result in
a mutation that produces an altered phenotype.
 The complementary nature of the two polynucleotide DNA
strands helps explain how DNA is copied; each strand can be used
as a template to reconstruct the base sequence in the opposite
strand, and also the mechanisms of transcription and translation
(allows a strand of DNA to serve as a template for the synthesis of
a complementary strand of RNA that used to direct the process of
protein synthesis).
DNA Denaturation and Renaturation
DNA Denaturation & Renaturation : the double strands can
separate into single strands by disruption the hydrogen bonds
between the paired bases using acidic or alkaline pH or heating.
(phosphodiester bond are not broken by such treatment).
complementary DNA strands can reform the double helix under
appropriate conditions.
DNA degradation: Phosphodiester bonds (in DNA & RNA) can be
cleaved hydrolytically by chemicals, or hydrolyzed enzymatically
by nucleases (deoxyribonucleases), only RNA can be cleaved by
alkali
RNA stem-loop structure
 RNA is Single strand.
 Single strand loops back on itself, thus one side will run
antiparallel
and
hydrogen
complimentary bases
bonds
will
form
between