NUCLEIC
ACIDS
OBJECTIVES
Identify/ recognize nucleic acid
 Components in nucleic acid – monosaccharide,
nucleobases, phosphoric acid
 Differentiate - between 2 types of nucleic acids,
DNA and RNA
- between nucleotide and
nucleoside
 Definition – nucleotide, nucleoside, DNA and
RNA

Nucleic Acids


Nucleic acid: a biopolymer containing three types of
monomer units
– a nitrogenous base (nucleobases), either purine or
pyrimidine
– a monosaccharide (aldopentose), either D-ribose or 2deoxy-D-ribose
– phosphoric acid/phospharyl group
Two types - RNA (Ribonucleic Acid)
- DNA (Deoxyribonucleic Acid)
Nucleobases
Nonpolar

Heterocylic compounds containing C, H, N, and O

Purine and pyrimidine
methyl
1 ring
structure
(C)
(T)
(U)
2 ring
structure
(A)
(G)
Monosaccharide/sugar
Polar
Only  anomer
present in nucleic
acid
2 type of aldopentoses found
- Ribose (RNA)
- 2-deoxyribose (DNA)
 Deoxyribose, derivative of ribose – lacks an oxygen
atom at C2

Nucleosides


Nucleoside: a compound that consists of D-ribose or 2-deoxyD-ribose (monosaccharide) covalently bonded to a nucleobase
by a -N-glycosidic bond
Covalent linkage forms between N9 of purines or N1 of
pyrimidines to C1 (anomeric carbon of ribose or 2-deoxyribose)
Lack phosphate group
Pyrimidine
Purine
Nucleotides


Nucleotide: a nucleoside in
which a molecule of phosphoric
acid/phosphoryl group is
esterified with an -OH of the
monosaccharide, at the 5’-OH
As constituents of cofactors,
Coenzyme A (CoA), flavin
adenine dinucleotide (FAD) &
nicotinamide adenine
dinucleotides (NAD)
Nucleobase, aldopentose
sugar and phosphoryl group
Phosphoric acid - polar
5’ = attach to
C5 of pentose
SUGAR?
NOMENCLATURE of
Nucleotide
Based on the nucleoside,
plus the phosphate group
Nucleotide Sequence
 Gene:
Sequence of nucleotides that
encodes a polypeptide, eventually
forming a functional protein
 Gene:
a discrete unit of hereditary
information consisting of a specific
nucleotide sequence in DNA (RNA in
some viruses)
 The
nucleotide sequence is depending on
the bases (nucleobases) present
Nucleic Acid:
DNA
Nucleoside
1. Bases = ATGC
2. Aldopentose =
Ribose
3. Phosphoryl group
Naming of nucleotide: if
Base adenine  Deoxyadenosine 5’
monophosphate
Biopolymer,
nucleotide
as monomer
RNA
1. Bases = AUGC
2. Aldopentose =
Deoxyribose
3. Phosphoryl group
Naming of nucleotide: if
Base adenine Adenosine
5’monophosphate
Nucleic Acid - DNA and RNA
 DNA
stands for deoxyribonucleic
acid. It is the genetic code molecule
for most organisms.
 RNA
stands for ribonucleic acid. RNA
molecules are involved in converting
the genetic information in DNA into
proteins. In retroviruses, RNA is the
genetic material.
NUCLEIC ACIDS ARE POLYMERS OF NUCLEOTIDES
Nucleic Acids



DNA or RNA
– consist of a chain of nucleotides joined together
by phosphodiester bonds
DNA = material of inheritance, carrier of genetic
information
RNA = DNA code is transcribed into RNA which in
turn is translated into the corresponding protein
transcription
DNA
translation
RNA
protein
DNA


DNA and RNA are polymers
whose monomer units are
nucleotides =
polynucleotides
Polynucleotide = DNA
and RNA
Hydrolysis – break bond
Condensation – form bond
Deoxyribonucleic acids,
DNA: a biopolymer that
consists of a backbone of
alternating units of 2deoxy-D-ribose and
phosphoryl group
–
the 3’-OH of one
nucleotide is joined to
the 5’ P of the next
nucleotide by a
phosphodiester bond
3’ 5’ -phosphodiester bond
DNA structure

Levels of structure
– 1° structure: the order of bases on the
polynucleotide sequence; the order of
bases specifies the genetic code
– 2° structure: the three-dimensional
conformation of the polynucleotide
backbone = double helix structure
– 3° structure: supercoiling
– 4° structure: interaction between DNA
and proteins
DNA - 1° Structure

Primary Structure: the
sequence of bases along
the pentosephosphodiester backbone
of a DNA molecule
– base sequence is read
from the 5’ end to the
3’ end
– System of notation
single letter (A,G,C
and T) Pg 237, Campbell
and Farrel. READ!
5’ – G G C A T T G C G C - 3’
On the right
3’ 5’ -phosphodiester bond
Segment of DNA Chain
5’-end
N
O
C
C N
C N
C
H2N
N
-2
O3PO CH2
O
H
H
H
H
H
O
CH
N
C
guanine
O
C
O
N
O P O CH2
O
O
H
H
H
H
H
O
3’-5’
link
CH3
C
CH
thymine
NH2
C
N
CH
C
CH
O
N
O P O CH2
O
O
H
H
H
H
OH H
3’-end
• 5’ end –
phosphate group
is free
• 3’end – 3’ OH
in deoxyribose is
free
cytosine
DNA - 2° Structure

Secondary structure: the ordered
arrangement of nucleic acid
strands
 Double helix: a type of 2°
structure of DNA molecules in
which two antiparallel
polynucleotide strands are coiled
in a right-handed manner about
the same axis
• The chains run antiparallel and are
held together by hydrogen
bonding between complementary
base pairs: A=T, G=C.
DNA double helix
DNA structural elements
2 right-handed, helical, polynucleotide chains,
coiled around a common axis to form a double helix
 2 characteristic: Major groove and minor groove –
binding site for drug or polypeptide
 2 strands run in opposite direction
(antiparallel)-3’,5’-phosphodiester bridges run in
opposite direction
 1 base (purine) from single strand link to
1 base (pyrimidine) from other stand
(complimentary)
 Bases are perpendicular to helix axis
 Polarity and non-polarity regions
 Aqueous environment – polar, charged, covalent
backbone deoxyribose and phosphate groups
outside of the helix
 Hydrophobic purine and pyrimidine bases avoid
water by turning towards the inside of the structure

OH
P
Groovy DNA
DNA-protein interaction
T-A Base Pairing



Base pairing is complementary: A=T, GC
A major factor stabilizing the double helix is base
pairing by hydrogen bonding between T-A and
between C-G
T-A base pair comprised of 2 hydrogen bonds
Complementary base pairing
G-C Base Pair

G-C base pair comprised of 3 hydrogen bonds

G-C base pair comprised of 3 hydrogen bonds
Forms of DNA



B-DNA
– considered the physiological form
– a right-handed helix, inside diameter 11Å
– 10 base pairs per turn (34Å) of the helix
A-DNA
– a right-handed helix, but thicker than B-DNA
– 11 base pairs per turn of the helix
– has not been found in vivo
Z-DNA
• a left-handed double helix
• may play a role in gene expression
• Z-DNA occurs in nature, usually consists of
alternating purine-pyrimidine bases
• Methylated cytosine found also in Z-DNA
Structural features of A-, B-, and Z- DNA
Type
Helical senses
Diameter (Å)
Base pairs/turn
Major groove
Minor groove
Pg 294, Concepts
in Biochemistry.
3/e 2006 John
Wiley & Sons
A-DNA
right handed
~26
11
narrow/deep
wide/shallow
B-DNA
right handed
~20
10
wide/deep
narrow/deep
20 Å
Z-DNA
left handed
~18
12
Flat
narrow/deep
DNA - 3° Structure
Tertiary structure: the
three-dimensional
arrangement of all atoms
of a nucleic acid;
commonly referred to as
supercoiling
 Supercoiling- Further
coiling and twisting of
DNA helix.

DNA
DNA can forms tertiary structure by twist
into complex arrangement – supercoil
 Circular DNA: a type of double-stranded
DNA in which the 5’ and 3’ ends of each
strand (2 polynucleotide chains) are
joined by phosphodiester bonds
 Can be found in microorganisms
(bacteriophages, bacteria)
 Circular twisted into supercoiled
DNA - 3° Structure
 Supercoil - results of extra
twisting in the linear duplex form

DNA

Circular DNA: In microorganisms
(bacteriophages, bacteria)

Circular twisted into supercoiled
DNA - 3° Structure

In eukaryotes, the 3° structure
involves histone (protein)Chromatin: DNA molecules
wound around particles of
histones in a beadlike structure
PROPERTIES OF
SUPERCOIL
 Supercoiled
is less stable than the relaxed
form
 Compact hence it more easily stored in the
cell
 Play a regulatory role in DNA replication
Bacteriophage :
DNA – threadlike
structure
Super DNA Coiled Topology
Double helix can be considered to a 2-stranded,
right handed coiled rope
 Can undergo positive/negative supercoiling

Counterclockwise
clockwise
DNA - 4° Structure
Four stranded form of DNA (quadruplex DNA)
 Role in regulating and stabilizing telomeres and in
regulation of gene expression
 Small molecules such as porphyrins and
anthraquinones present, to stabilize the structure

G-quadruplex