APCH 12632
Dr. Dulith Abeykoon
Nucleic Acids
Nucleic Acids
❖ Nucleic acids are bio polymers and composed of nucleotides.
❖ Therefore, nucleic acids are also referred to as polynucleotides.
❖As the name suggests, they are located in the nucleus of an
eukaryotic cell, however in prokaryotes these nucleic acids are
found in the cytoplasm as
they do not contain any organized
nucleus.
❖ Extra-nuclear DNA also exists; in mitochondria and chloroplasts.
❖ Nucleic acids contain carbon, hydrogen, oxygen, nitrogen and
phosphorous.
Nucleic Acids
Nucleic Acids
Nucleic Acids
❖These polymers are specialized for transmission of
information (genetic information).
❖ Nucleic acids present in most living cells either in the free
state or bound to proteins as nucleoproteins.
Nucleic Acids (DNA / RNA)
Nucleic acids play a vital role
1. Pass characteristics of animals from generation to
generation
2. Store all the information needed to make us what we are
3. Mistakes in them cause genetic diseases
Deoxyribonucleic acid (DNA)
Nucleic acids
Ribonucleic acid (RNA)
Nucleoside = Sugar + N containing base
Nucleotide = Nucleoside + Phosphate
Nucleic acids = Polymers of nucleotides = polynucleotides
Components of a Nucleotide
1) Pentose sugar (5 carbon sugar)
2) N containing bases
Purines (Double rings)
Eg: Adenine, Guanine
Pyrimidines (Single
ring)
Eg: Cytosine, Thymine,
Uracil
Purines
Pyrimidines
❖Purines & pyrimidines are “Heterocycles”, ie ring structures
that contain carbon and other (hetero) atoms such as
nitrogen
❖The presence of NH2 groups makes them weak bases
❖The purines & pyrimidines are “planar” structures and this
facilitates the stacking of the bases in the double stranded
DNA structures
3) Phosphate group
Phosphate groups are important because they link the sugar on
one nucleotide onto the phosphate of the next nucleotide to
make polynucleotides
Structure of a nucleotide
Nucleosides
Nucleoside → Purine / Pyrimidine + ribose sugar/deoxyribose sugar.
The link is N- glycosidic bond.
Basic purine
ring
C 6
1
2
N
C
C
4
3 N
5
HOCH2
N9
4
1
2
OH
8
C
C
C6
N glycosidic link.
Note the N atoms linking
the ribose.
1
5
HOCH2
O
3
N
2
C
C
5
3
7
5
N
C4
Basic
pyrimidine
ring
OH
N
O
4
1
2
3
OH
OH
5
P
Adding in the bases
1
4
• The bases are attached to the
Carbon
• The order of the bases is important.
It determines the genetic information
of the molecule
1st
3
G
2
P
C
P
C
P
A
P
T
P
T
Nomenclature of nucleosides
Ribonucleosides.
Adenine + Ribose → Adenosine
Guanine + Ribose → Guanosine
Purines → ending “ osine”.
Cytosine + Ribose → Cytidine
Thymine + Ribose → Thymidine
Uracil + Ribose → Uridine
Pyrimidines → ending “dine”.
Deoxy ribonucleosides.
Adenine + Deoxy ribose →
Guanine + Deoxy ribose →
Deoxy adenosine
Deoxy guanosine
Cytosine + Deoxy ribose →
Thymine + Deoxy ribose →
Deoxy cytidine
Deoxy thymidine
Nucleotides
Nucleotides are phosphorylated nucleosides
The phosphoryl group is most often esterified to the 5’ OH of
.the ribose
−
O
I
O=P–O
I
O −
5
CH2
BASE
O
4
1
2
3
OH
OH
Nucleotide monophosphate
Nomenclature of nucleotides.
Ribonucleotides
Adenosine + Pi
Guanosine + Pi
Cytidine
+ Pi
Uridine
+ Pi
→ Adenosine monophosphate (AMP)
→ Guanosine monophosphate (GMP)
→ Cytidine monophosphate (CMP)
→ Uridine monophosphate
(UMP)
Deoxy ribonucleosides.
d Adenosine
d Guanosine
d Cytidine
d Thymidine
+ Pi → dAMP
+ Pi → dGMP
+ Pi → dCTP
+ Pi → dTMP
This nucleotide can be further phosphorylated with another phosphate
being ligated to the existing phosphoryl group by a acid anhydrate bond.
─
−
O
O
O
|
||
I
5
HO – P – O – P – O – P – O
CH2
BASE
O
||
|
||
4
1
O
O −
O
2
3
OH
OH
Nucleotide monophosphate
Nucleotide diphosphate.
Nucleotide triphosphate
Nucleotides link together by phosphodiester links
‒
O
I
O=P–O
I
O
5
CH2
BASE
O
4
1
‒
3
2
OH
Phospho- diester link
(3’ → 5’)
O
I
O=P–O
I
O‒
5
CH2
BASE
O
4
1
2
3
OH
OH
The polynucleotide has
• a 3’ end and a 5’ end
• sugar – phosphate backbone
• bases stacked above each other
DNA strands have a ‘sense of direction’
written in 5’
3’ direction
A polynucleotide chain can
be represented like
DNA
❖DNA is made of two strands of polynucleotide
❖The two strands of the DNA molecule run in opposite
directions (antiparallel) and 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
❖This sister strands are complementary but not identical
❖The bases are joined by hydrogen bonds, individually weak
but collectively strong
The formation of H bonds between
complementary bases
• This ensures High Fidelity (Hi Fi)
• Because “A” can only join with
“T” & “G” can only join with “C”
Pyrimidines
Purines
Rosalind Franklin
(1952): X-ray crystallography
Franklin’s X –ray photograph shows DNA’s B form
The X-pattern in the middle is
characteristic of a helical
molecule with regular repeats
The Double Helix (1953)
Putting the evidence together: Watson and Crick Proposed the Double Helix
The double-helical structure of DNA
The 3-dimensional double helix structure of DNA, correctly
elucidated by James Watson and Francis Crick.
Complementary bases are held together as a pair by hydrogen
bonds.
Major features of Watson and Crick model
•DNA is a double-stranded helix, with the two strands connected
by hydrogen bonds
•A bases are always paired with Ts, and Cs are always paired with
Gs, which is consistent with and accounts for Chargaff's rule
(Complementary base pairing in DNA)
What is Chargaff's rule?
All DNA follows Chargaff's Rule, which states that the total
number of purines in a DNA molecule is equal to the total number
of pyrimidines.
Complementary Base pairing in DNA
Most
DNA
double
helices
are
right-handed;
that is, if you were to hold your right hand out, with your
thumb pointed up and your fingers curled around your thumb,
your thumb would represent the axis of the helix and your
fingers would represent the sugar-phosphate backbone
• The 2 antiparallel polynucleotide
chains and are held together by
pairing of complementary bases
to form double stranded DNA
structure
• The double stranded DNA is long
• Twisted into a double helix (imagine
a ladder twisted around an axis)
• Bases are in the middle
• One strand is running 5′ to 3′ top to
bottom, whereas the other strand is
running 3′ to 5′ top to bottom
•The DNA double helix is anti-parallel, which means that the 5'
end of one strand is paired with the 3' end of its complementary
strand (and vice versa).
• Nucleotides are linked to each other by their phosphate
groups, which bind the 3' end of one sugar to the 5' end of the
next sugar.
•Not only are the DNA base pairs connected via hydrogen
bonding, but the outer edges of the nitrogen-containing bases
are exposed and available for potential hydrogen bonding as
well.
•These hydrogen bonds provide easy access to the DNA for
other molecules, including the proteins that play vital roles in
the replication and expression of DNA.
Different forms of DNA
.
.
.
Different forms of DNA
B DNA
•Commonly occurring DNA form in normal physiological
conditions, this form of DNA is a right-handed double helix
•The two strands of this DNA run in two different
directions-antiparallel
•They show an asymmetrical structure, with the alternate
.
presence
of major and minor grooves.
•Between
the adjacent deoxyribonucleotides, there is a
.
distance of 0.34 nm and each turn comprises 10.5 base
pairs of length 3.4 nm
•The helical width of B-DNA is 2 nm and its backbone
comprises
sugar phosphates associated continuously
.
through phosphodiester bonds. The core comprises
nitrogenous bases
Different forms of DNA
.
.
.
Z DNA
Different forms of DNA
• Structurally differing, this form of DNA is a left-handed
double helix
• The helical width of Z-DNA is 1.8 nm, making it the
narrowest compared to the other DNA conformations
• .Its distinguishing factor is its backbone appearing as
though a zigzag
•. Each turns comprises 12 base pairs, 4.56 nm long
• Two adjacent deoxyribonucleotides are 0.37 nm apart
with the presence of hydrogen bonds between two
strands
.
• The DNA molecule with alternating G-C sequences in
alcohol or high salt solution tends to have such structure.
Different forms of DNA
.
.
.
Denaturation of DNA
❖ Breaking of H bonds between the bases under certain
conditions, separation of DNA strands and the consequent loss
of the helical structure is “denaturation”
❖ Heat can separate the DNA strands
❖ DNA with a lot of “GC” base pairs is more resistant to heat
denaturation because there are 3 H bonds between them
.
❖ The temp. at which 50% of DNA is denaturated → “melting
temperature” (Tm) of that DNA
.
❖ If the separated DNA strands are left alone → strands come
together by complimentary base pairing. This is “renaturation”
❖ Denaturation and Renaturation is the characteristic of DNA
molecules
.
❖ Strands can be separated by altering the pH of the medium to
ionize the nucleotide bases