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Biomolecules
Nucleic acids
Nucleic acids
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August2010
Nucleic acids are polynucleotides joined
together to make large macromolecules.
The important nucleic acids are
deoxyribonucleic acid (DNA) and various
types of ribonucleic acids (RNA).
DNA is the genetic material found in cells and
contains instructions that help determine the
structure and function of cells
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Nucleic acids
They are polynucleotides
{ The primary structure of DNA and RNA
is a linear arrangement of nucleotides
{ Formed by the condensation of two or
more nucleotides.
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Nucleic acids
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The condensation most commonly occurs
between the 3'-hydroxyl of one nucleotide and
the OH of a 5'-phosphate of a second
nucleotide
with the elimination of H2O, forming a
phosphodiester bond
Success nucleotides of both DNA and RNA
are covalently linked to each other through a
phosphate gp
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Formation of nucleic acids
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The formation of phosphodiester bonds in
DNA and RNA exhibits directionality
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It proceeds in the 5' ----> 3' direction
The primary structure of DNA or RNA
molecules is represented with the nucleotide
sequences written from left to right
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with the 5' -----> 3' direction as shown: 5'-
GATC-3'
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Structure of DNA molecule
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DNA encodes the genetic information
It is a helix of two strands wound around each
other
The chains run in opposite direction (antiparallel).
The two strands form a "double helix"
structure, which was first discovered by James
D. Watson and Francis Crick in 1953.
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Mechanism of DNA formation
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DNA polymerase catalyzes DNA synthesis
The enzyme requires a DNA template
3'-OH of one sugar attacks the 5' phosphate of
a deoxyribonucleoside triphosphate
Each successive nucleotide residue is added to
the 3' end of the nucleic acid.
Chain growth is always in the 5' -> 3'
direction!!!
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DNA base pairing
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A DNA molecule has two strands, held
together by the hydrogen bonding between
their bases.
Purine bases of one chain form hydrogen
bonds with pyrimidines of the other chain in
the crucial phenomenon of base pairing
Adenine can form two hydrogen bonds with
thymine
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DNA base pairing
Cytosine can form three hydrogen
bonds with guanine.
{ (C:G) and (A:T) base pairs found in
natural DNA molecules are very strong
{ Other base pairs e.g (G:T) and (C:T)
may also form hydrogen bonds but are
not as strong as those in natural DNA
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Base pairing
G-C Base Pair
A-T Base Pair
Base pairings
In any given molecule of DNA, the
concentration of adenine (A) is equal to
thymine (T).
{ and the concentration of cytosine (C) is
equal to guanine (G).
{ This means that A will only base-pair
with T, and C with G.
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Base pairings
According to this pattern, known as
Watson-Crick base-pairing, the basepairs composed of G and C contain three
H-bonds, whereas those of A and T
contain two H-bonds.
{ This makes G-C base-pairs more stable
than A-T base-pairs.
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Complementarity of DNA strands
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They obey the (A:T) and (C:G) pairing rule.
Due to the specific base pairing, DNA's two
strands are complementary to each other.
Hence, the nucleotide sequence of one strand
determines the sequence of another strand.
The sequence of the two strands can be written
as 5' -ACT- 3‘ OR 3' -TGA- 5‘
Thus the chains are anti-parallel
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Base pairing
between DNA's
two strands
Phosphodiester
bonds
Orientation of the chains
The anti-parallel nature of the helix
stems from the orientation of the
individual strands.
{ From any fixed position in the helix, one
strand is oriented in the 5' ---> 3'
direction and the other in the 3' ---> 5'
direction.
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Orientation of the chains
The backbone consists of the phosphate
gp linking the deoxyribose sugars
{ The purine and pyrimidine bases face
inside the double helix where A-T & G-C
base pairs are formed
{ The double helix of DNA contains two
deep grooves between the deoxyribosephosphate chains
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Double helix structure
The normal righthanded "double
helix" structure of
DNA, also known
as the B form.
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The Double Helix-summary
1. The backbone of each strand consists
of alternating deoxyribose and
phosphate groups.
2. The two strands are "antiparallel”
3. The DNA strands are assembled in the
5′ to 3′ direction
4. Each base forms hydrogen bonds with
the one directly opposite it, forming
watson-crick pairs
Forms of DNA
In solution, the double helix of DNA has
been shown to exist in several different
forms.
{ This forms depends upon sequence
content and ionic conditions
{ Exists as B or Z-form.
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B-form of DNA
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In B-form structure, DNA prevails under
physiological conditions of low ionic strength
and a high degree of hydration.
Hence, there are about 10 pairs of nucleotides
per turn
This form make two grooves of different
widths, referred to as the major groove and the
minor groove, which may facilitate binding
with specific proteins.
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Z-form
In a Z form structure the DNA bases
seem to zigzag.
{ The DNA molecule with alternating G-C
sequences in alcohol or high salt solution
tends to have such structure.
{ One turn spans 4.6 nm, comprising 12
base pairs.
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Forms of DNA
Comparison
between B form
and Z form
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Ribonucleic acid (RNA)
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RNA is a nucleic acid polymer consisting of
ribonucleotide monomers
RNA plays several important roles in the
processes that translate genetic information
from deoxyribonucleic acid (DNA) into
protein products;
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RNA acts as a messenger between DNA and the protein
synthesis complexes known as ribosomes,
It forms vital portions of ribosomes
It acts as an essential carrier molecule for amino acids to
be used in protein synthesis
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Comparison with DNA
RNA and DNA differ in three main
ways
{ Unlike DNA which is double-stranded,
RNA is a single-stranded molecule in
most of its biological roles and has a
much shorter chain of nucleotides
{ Secondly, while DNA contains
deoxyribose, RNA contains ribose sugar
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Structures of RNA and DNA
Comparison with DNA
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These hydroxyl groups make RNA less stable
than DNA because it is more prone to
hydrolysis.
Several types of RNA (tRNA, rRNA) contain
a great deal of secondary structure, which help
promote stability.
Thirdly, the base-pair of adenine is not
thymine, as it is in DNA, but rather uracil,
which is a unmethylated form of thymine.
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Messenger RNA (mRNA)
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Messenger RNA is RNA that carries
information from DNA to the ribosome sites
of protein synthesis in the cell.
In eukaryotic cells, once mRNA has been
transcribed from DNA, it is exported from the
nucleus into the cytoplasm, where it is bound
to ribosomes and translated into its
corresponding protein
In prokaryotic cells, mRNA can bind to
ribosomes while it is being transcribed from
DNA.
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Genetic Code
Transfer RNA (tRNA)
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Transfer RNA is a small RNA chain of about
74-95 nucleotides that transfers a specific
amino acid to a growing polypeptide chain at
the ribosomal site of protein synthesis during
translation.
It has sites for amino-acid attachment and an
anticodon region for codon recognition that
binds to a specific sequence on the messenger
RNA chain through hydrogen bonding.
It is a type of non-coding RNA
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Structure of tRNA: Modified bases
such as dihydrouridine (D),
pseudouridine (ψ), inosine (I) and
methylguanine are present.
Ribosomal RNA (rRNA)
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Ribosomal RNA is the catalytic component of the
ribosomes, the protein synthetic factories in the cell.
Eukaryotic ribosomes contain different rRNA molecules
from prokaryotic ribosomes
rRNA molecules are extremely abundant and make up at
least 80% of the RNA molecules found in a typical
eukaryotic cell.
In the cytoplasm, ribosomal RNA and protein combine to
form a nucleoprotein called a ribosome.
The ribosome binds mRNA and carries out protein
synthesis.
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Catalytic RNA
Certain RNAs are able to catalyse chemical
reactions.
{ These include cutting and ligating other RNA
molecules and also the catalysis of peptide
bond formation in the ribosome
Double-stranded RNA
{ Double-stranded RNA (or dsRNA) is RNA
with two complementary strands, similar to
DNA
{ dsRNA forms the genetic material of some
viruses
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Chemical Stability of Nucleic Acids
Hydrolysis by acids and alkali
{ DNA is generally quite stable. It will resist
attack in acid and alkali solutions.
{ However, in mild acid solutions - at pH4 - the
β-glycosidic bonds to the purine bases are
hydrolyzed
{ Protonation of purine bases (N7 of guanine,
N3 of adenine) occurs at this pH
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Chemical Stability of Nucleic Acids
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Protonated purines are good leaving groups
hence the hydrolysis
In contrast to DNA, RNA is very unstable in
alkali solutions due to hydrolysis of the
phophodiester backbone.
The 2'OH group in ribonucleotides renders
RNA molecules susceptible to strand cleavage
in alkali solutions
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Hydrolysis by enzymes
Enzymatic hydrolysis of DNA
{ DNA is hydrolyzed by deoxyribonucleases.
{ These enzymes hydrolyze the phosphodiester
linkages
{ These enzymes may digest a DNA strand from
the end(s) - exonucleases - or internally endonucleases.
Enzymatic hydrolysis of RNA
{ Ribonucleases are enzymes that cleave RNA
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Thermal properties of DNA
DNA can be copied (replicated).
{ Each daughter cell acquires the same
amount of genetic material as the mother
cell.
{ The two strands of the helix must first be
separated, in a process termed
denaturation.
{
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Denaturation of DNA
This process can also be carried out in
vitro by extreme pH and Temperature
(80-90ºC).
{ If a solution of DNA is subjected to high
temperature, the H-bonds between bases
become unstable and the strands of the
helix separate.
{ The process is referred to as thermal
denaturation.
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Melting temperatures
During thermal denaturation, a point is
reached at which 50% of the DNA
molecule exists as single strands.
{ This point is the melting temperature
(TM), and is characteristic of the base
composition of that DNA molecule
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Annealing
When thermally melted DNA is cooled,
the complementary strands will again reform the correct base pairs, in a process
is termed annealing or hybridization
{ The rate of annealing is dependent upon
the nucleotide sequence of the two
strands of DNA.
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Base compositions
The base composition of DNA varies
widely from molecule to molecule and
even within different regions of the same
molecule.
{ Regions of the duplex that have
predominantly A-T base-pairs will be
less thermally stable than those rich in
G-C base-pairs.
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Spontaneous causes of Base
alterations
Tautomerization
{ The bases of DNA are subject to spontaneous
structural alterations called tautomerization
{ These bases are capable of existing in two forms
between which they interconvert.
{ The various tautomer forms of the bases have
different pairing properties
{ For example, guanine and Thymine can exist in
keto or enol forms
{ The keto form of guanine is favored
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Tautomerization
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If G is in the enol form, it base pair with T instead of the
normal C . The result is a G:C to G:T transition
Spontaneous Base alterations
Deamination
{ Another mutagenic process occurring in cells is
spontaneous base degradation.
{ The deamination of cytosine to uracil happens at
a significant rate in cells.
{ Deamination can be repaired by a specific repair
process which detects uracil, not normally
present in DNA
{ otherwise the U will cause A to be inserted
opposite it and cause a C:G to T:A transition
when the DNA is replicated.
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Spontaneous base alterations
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Deamination of methylcytosine to thymine also
occurs.
Methylcytosine occurs in the human genome
If the meC is deaminated to T, there is no repair
system which can recognize and remove it
(because T is a normal base in DNA).
This means that wherever CpG occurs in genes it
is a "hot spot" for change.
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