DNA and RNA molecules are linear polymers built from individual units called nucleotides connected by bonds called phosphodiester linkages. DNA and RNA are used to store and pass genetic information from one generation to the next.
2. Introduction to Nucleic Acids
DNA and RNA molecules are linear
polymers built from individual units
called nucleotides connected by bonds
called phosphodiester linkages.
DNA and RNA are used to store and pass
genetic information from one generation
to the next.
3. Each nucleotide
consists of:
1. A sugar
molecule
2. A phosphate
group
3. Nitrogenous
base
Introduction to Nucleic Acids
4.
5.
6. Introduction to Nucleic Acids
In both DNA and RNA, each nucleotide consists
of a linear backbone that consists of repeating
sugar-phosphate units.
However, it’s the nitrogenous bases that are
responsible for storing the genetic information.
7.
8. Introduction to Nucleic Acids
DNA exists predominantly in its double helix form.
The helix consists of two strands running in an
antiparallel fashion. They are held together by a
variety of interactions, including hydrogen bonds.
The inside of the helix consists of the non-polar
nitrogenous bases.
The exterior portion of the helix contains
negatively-charged phosphate groups.
Each strand is complementary to the other one.
9.
10. Functions of DNA
DNA molecules are used to:
Store genetic information that can be
accessed by the organism and used to
build proteins.
Pass down genetic information to
offspring.
Introduction to Nucleic Acids
11. Functions of RNA
RNA molecules are used to:
Transcribe the information stored in DNA
into a form that can be understood and
read by the cell.
Assist in the protein synthesis process.
DNA RNA Proteins
Introduction to Nucleic Acids
13. Pentose sugars
The pentose (five-carbon)
sugar
In RNA is ribose
In DNA is deoxyribose,
with no O atom on carbon
2′
has carbon atoms
numbered with primes to
distinguish them from the
atoms in the bases
14. Pentose sugars
The absence of this –OH group stabilizes the structure
of DNA making it more resistant to hydrolysis.
15. The sugars of nucleic acids are connected
to one another by 3’- to -5’
phosphodiester linkages.
The –OH group on the 3rd carbon of one
sugar is connected to the –OH group on the
5th carbon of an adjacent sugar via a
phosphate group.
Backbone and Phosphodiester Bond
16. Nucleotides are linked by a phosphodiester bond between
the phosphate group at the C-5' position and the OH
group on the C-3' position
17. This chain of repeating sugar-phosphate
units makes the backbone of the nucleic
acids.
This backbone remains constant and
unchanged.
Backbone and Phosphodiester Bond
18. The phosphate groups contain a negative
charge. This means that:
In an aqueous environment, these hydrophilic
regions interact with the polar H2O molecules
to stabilize the structure of DNA.
The phosphodiester linkages are much less
likely to be attacked by nucleophilic agents,
which means that they are less susceptible to
hydrolysis.
Backbone and Phosphodiester Bond
19. Nitrogenous Bases
The bases vary from one nucleotide to the
next.
There are two categories of bases – purines
and pyrimidines.
20. Nitrogenous Bases
PURINES
Consist of two fused ring structures.
Both DNA and RNA have two types of
purines – adenine and guanine.
21.
22. Nitrogenous Bases
PYRIMIDINES
Pyrimidines contain a single ring.
DNA contain two pyrimidines – thymine
and cytosine.
In RNA, the thymine is replaced by uracil.
25. Each base has its preferred tautomeric form
Purine and Pyrimidine
26. Nitrogenous Bases
The sequence of these bases is unique to the
nucleic acid.
Because it is the bases that vary from
nucleotide to nucleotide along the linear
polymer, it’s the sequence of these bases that
determine the genetic code.
27. DNA RNA
o
H
H
H
H
H
CH2
Deoxyribose sugar
(O on C2 is missed)
o
OH
H
H
H
H
CH2
Ribose sugar
(no missed O)
Ribo-Nucleic-AcidDeoxiribo-Nucleic-Acid
Single stranded nucleic acidDouble stranded nucleic acid
Bases: A, G, C, T Bases: A, G, C, U
28. Repeated Sugar - Phosphate
Sugar–Phosphate-Base
Polynucleotide
DNA backbone
One nucleotide
DNA Molecule
DNA Double stranded
RNA single stranded
T C G A T A G
A G TC T A C
UUmRNA
DNA
30. Nucleoside
A nucleoside
has a base linked by
a glycosidic bond to
C1′ of a sugar (ribose
or deoxyribose)
is named by changing
the end of the base
name to osine for
purines and idine for
pyrimidines
31. Formation of a Nucleoside
A nucleoside forms when a sugar combines with a base.
32. The bases are
covalently attached
to the 1’ position of
a pentose sugar
ring and a N of the
base to form a
nucleoside
33. Nucleotides
Defined as a nucleoside attached to one or
more phosphate groups.
In most biological nucleotides, the phosphate
is attached to the 5th carbon of the sugar.
A molecule having a phosphoryl group
attached to the C5′ —OH group of a
nucleoside
34. A nucleotide is a nucleoside with one or more phosphate groups bound
covalently to the 3’-, 5’, or ( in ribonucleotides only) the 2’-position. In the
case of 5’-position, up to three phosphates may be attached.
Deoxyribonucleotides
(containing deoxyribose)
Ribonucleotides
(containing ribose)
Phosphate ester bonds
Nucleic Acid Structure
Nucleotides
35. Nucleotides
When naming nucleotides, we begin with
the nucleoside component, then label the type
of linkage and then label the # of phosphate
groups.
Nucleoside 5’ -Phosphate
Sugar base Linkage # of phosphates
40. Nucleotides
Nucleic acids have polarity – the 5’ end has a
phosphate group and the 3’ end has a –OH
group.
By convention, we always write the nucleotide
sequence beginning at the 5’ end and towards
the 3’ end.
50. Primary Structure of Nucleic Acids
In the primary structure of nucleic acids:
Nucleotides are joined by phosphodiester
bonds.
51. The 3’-OH group of the sugar in one nucleotide forms an ester bond to the phosphate
group on the 5’-carbon of the sugar of the next nucleotide.
52. Structure of Nucleic Acids
A nucleic acid polymer:
Has a free 5’-phosphate
group at one end and a free
3’-OH group at the other
end.
Is read from the free 5’-end
using the letters of the
bases.
This example reads
5’—A—C—G—T—3’.
53. In RNA, A, C, G, and U are linked by 3’-5’ ester bonds between ribose and
phosphate.
54. In DNA, A, C, G, and T are linked by 3’-5’ ester bonds between deoxyribose and
phosphate.
56. Watson-Crick Model of DNA
Maurice Wilkins and
Rosalind Franklin were
able to obtain x-ray
diffraction
photographs of a DNA
fiber.
These diffraction patterns
indicated that DNA had a
helical structure.
57. Watson-Crick Model of DNA
Deduced by James
Watson and Francis Crick
in 1953.
DNA is the genetic
material of all organisms
except for some viruses.
Essential for replicating
DNA and transcribing RNA
The foundation of the
molecular biology
58. Watson-Crick
Model of DNA
James Watson and
Francis Crick deduced
the features of the
structure of DNA.
1. A single DNA molecule
consists of two
individual nucleic acid
chains that wind
about a common
axis. These two
polynucleotide chains
run in opposite
directions.
59. The two strands of the double helix are held together by base
pairing in an anti-parallel orientation
A:T & G:C base
pairs
60. Watson-Crick
Model of DNA
2. The backbone of the
nucleic acids is found
on the exterior of the
DNA while the
nitrogenous bases
are found on the
inside.
61.
62. Watson-Crick
Model of DNA
3. The nitrogenous bases lie
perpendicular to the common
axis. These bases are stacked on
top of one another by a distance
of 3.4 A° (0.34 nm).
There are 10 bases per one
DNA turn, which means each
turn is 34° (3.4 nm) in length.
4. The length of the diameter of the
double helix is 20 A° (2 nm).
64. Double Helix
The bases on the two
separate nucleic acids form
specific base pairs.
Guanine bonds with
cytosine while adenine
bonds with thymine.
70. The DNA of most bacteria is contained in a single circular molecule, called the bacterial chromosome. The
chromosome, forms an irregularly shaped structure called the nucleoid.
In addition to the chromosome, bacteria often contain plasmids – small circular DNA molecules. Bacteria can
pick up new plasmids from other bacterial cells (during conjugation) or from the environment.
73. Stability of Nucleic Acids
Hydrogen bonding
Contributes to specific structures of nucleic
acids or protein.
For example, a-helix, b-sheet, DNA double
helix, RNA secondary structures.
74. Stability of Nucleic Acids
Stacking interaction/hydrophobic interaction
Between aromatic base pairs.
Stacking is maximized in double-stranded
DNA
It is energetically favorable to exclude water
altogether from pairs of such surfaces by
stacking them together.
75. Effect of Acid
In strong acid and at elevated
temperatures: are hydrolyzed completely to
bases, ribose or deoxyribose, and phosphate
(e.g., perchloric acid (HClO4) at > 100°C)
In more dilute mineral acid (e.g., pH 3–4), the
most easily hydrolyzed bonds are selectively
broken. E.g., glycosydic bonds attaching
purine bases to the ribose ring are broken by
formic acid.
76. Effect of Alkali-DNA
keto form enolate form keto form enolate form
3. This affects the specific hydrogen bonding between the base pairs, with
the result that the double-stranded structure of the DNA breaks down;
that is the DNA becomes denatured .
1. Increasing pH (> 7-8) has more subtle effects on DNA structure
2. The effect of alkali is to change the tautomeric state of the bases
77. Chemical Denaturation
A number of chemical agents can cause the denaturation of
DNA or RNA at neutral pH, e.g. Urea (H2NCONH2) is used in
denaturing PAGE; Formamide (HCONH2) is used Southern
and Northern blotting.
Disrupting the hydrogen bonding of the bulk water
solution
Hydrophobic effect (stacking interaction) is reduced
Denaturation of the strands
Mechanism
79. Nucleic acids absorb UV light due to the conjugated
aromatic nature of the bases
The wavelength of maximum absorption of light by
both DNA and RNA is 260 nm (lmax = 260 nm)
Applications: can be used for detection, quantitation
and assessment of purity (A260/A280)
UV Absorption
80. Thermal denaturation/melting
Heating also leads to the destruction of double-stranded
hydrogen-bonded regions of DNA and RNA.
RNA: the absorbance increases gradually and irregularly
DNA: the absorbance increases cooperatively.
melting temperature (Tm): the temperature at the mid-point of the
smooth transition, which has a 20% increase in absorbance. 80-100 °C for
long DNA molecules
Hinweis der Redaktion
Molecules that store information for cellular growth and reproduction
Large molecules consisting of long chains of monomers called nucleotides
Phosphodiester means we have the phosphate group in between these 2 ester bonds.
The bases are attached to the carbon 1 our the sugar molecule.
Changes in bases allow the DNA to store genetic information.
NH2 (Adenine) – C=O (Guanine); NH2 (Guanine)
*Play an important role in determining the types and number of interactions that are formed between the different bases in the DNA molecule.
• The bond holding the sugar to the base is a β-glycosidic bond.
Notice that the base group lies above the plane of the sugar molecule.
Adding phosphate groups to AMP forms the diphosphate ADP and the triphosphate ATP.
The 3’-OH group of the sugar in one nucleotide forms an ester bond to the phosphate group on the 5’-carbon of the sugar of the next nucleotide.
Example of RNA
Example of DNA
The DNA double helix as proposed by Watson and Crick
Even in single-stranded DNA, the bases have a tendency to stack on top of each other.