Nucleic acids

(A)Deoxyribonucleic acid (DNA

The DNA is in essence a blueprint of the
organism as it encodes information needed to
synthesize proteins.
Deoxyribonucleic acid (DNA)is a nucleic acid
that contains the genetic instructions used in the
development and functioning of all known living
organisms (with the exception of RNA viruses).
The main role of DNA molecules is the long-term
storage of information.
DNA structure

Maurice Wilkins
DNA is a polymer made of repeating subunits
called nucleotides.
Nucleotides have three parts:-a simple sugar, a
phosphate group, and a nitrogenous base.
Base + Sugar =Nucleosides.
Sugar
Purines and Pyrimidines
Primary Structure of DNA
According to the Watson-Crick model, DNA
forms a double helix that is held together by
hydrogen bonds between specific pairs of bases
(thymine to adenine and cytosine to guanine).
Each strand in the double helix is
complementary to its partner strand in terms of
its base sequence.
Thymine and guanine are connected in the 3
5 direction and the O atom of deoxyribose points
down.
Adenine and cytosine are linked in a 5 3
direction, and the O atom of the pentose points
up.
DNA molecules are the largest biologically
active molecules known, having molecular
weights greater than 1 108 dalton.
In the adjacent diagram, only five nucleotide
pairs of the ladder like DNA molecule are shown.
Uprights of the ladder consist of alternating
phosphate (P) and deoxyribose sugar (S) groups.
The cross rungs consist of purine-pyrimidine
base pairs that are held together by hydrogen
bonds (represented here by dashed lines).
A, T, G, and C represent adenine, thymine,
guanine, and cytosine, respectively.
Note that the AT pairs are held together less
In reality, the ladder is twisted into a right-
handed double helix, and each nucleotide pair is
rotated 36 with respect to its neighbor.
A DNA molecule of molecular weight 2.5 107
daltons would be made up of approximately
40,000 nucleotide pairs.
Grooves in the DNA double helix
The sugar-phosphate backbones spiral around
the outer surface of DNA.
Between these backbones are two different
sized grooves, designated the major and minor
grooves.
The major groove is approximately 50% wider
21
 Storage of DNA
In eukaryotic cells (animals, plants, fungi) DNA
is stored in the nucleus, which is separated from
the rest of the cell by a semi-permeable
membrane.
The DNA is only organized into chromosomes
during cell replication.
Between replications, the DNA is stored in a
compact ball called chromatin, and is wrapped
around proteins called histones to form
nucleosomes.
 DNA Conformation
(I)ADNA
ADNA Righthanded double stranded helix
stabilized by WatsonCrick base pairs.
One of the several types of secondary
structures that DNA
can adopt, depending on environmental
conditions.
(II)BDNA
The A form is favored in solutions that are
BDNA form is the main biologically relevant
relatively devoid of water.
secondary
structure of DNA.
Most stable doublehelix structure for random
sequence DNA molecules under physiological
Major and minor grooves are nearly equal in
size.

(III)ZDNA
ZDNA form is lefthanded form of the double
helix.
ZDNA can form under physiological salt
conditions.
In ZDNA, there is a single narrow groove that
corresponds to the minor groove of BDNA, and
there is no major groove.
The backbone follows a zigzag path, giving rise
 (B)Ribonucleic acid (RNA)
Ribonucleic acid(RNA) is a ubiquitous family of
large biological molecules that perform multiple
vital roles in thecoding,decoding,regulation ,
andexpression of genes.
Together withDNA , RNA comprises thenucleic
acids, which, along withproteins, constitute the
three majormacromolecules essential for all
known forms of Structure
life.
Like DNA, RNA is assembled as a chain of
nucleotides, but is usually single-stranded.
Eachnucleotidein RNA contains aribosesugar,
with carbons numbered 1' through 5'.
A base is attached to the 1' position, in general ,
adenine (A) ,cytosine(C),guanine(G),
oruracil(U).
A phosphate group is attached to the 3' position
of one ribose and the 5' position of the next.
The phosphate groups have a negative charge
each at physiological pH, making RNA a charged
molecule (polyanion).
The bases may formhydrogen bonds between
cytosine and guanine, between adenine and
uracil and between guanine and uracil.
RNA is very similar to DNA, but differs in a few
important structural details:-(1)RNA is single
stranded, while DNA is double stranded.
(2)RNA nucleotides contain ribose sugars while
DNA contains deoxyribose.
(3)RNA uses predominantly uracil instead of
thymine present in DNA.
RNA structure is divided into three fundamental
levels of organization:- (1)Primary structure.
(2)Secondary structure.
(3)Tertiary structure.
 (1)Primary structure
Primary structure refers to the nucleotide
sequence of and RNA, which can be obtained to a
first approximation from the DNA sequence of the
gene encoding the RNA.
 (2)Secondary structure
The secondary structure of RNA is presented as
a two dimensional representation of its Watson
-Crick base pairs and intervening unpaired
regions.
Commonly described secondary structural
elements are: duplexes, single stranded regions,
hairpins, bulges, internal loops, and junctions.
 (3)Tertiary structure
A three dimensional folding.
The involvement of the oxygen of a ribose
phosphodiester bond in one hydrogen-bonding
arrangement , and a ribose2-hydroxyl group in
another.
 RNA Folding
bonds form between canonical base
pairs (GC, AU, GU and their mirrors)

G C A G C U A A G U G U U C A A

these bonds fold the sequence back on

itself to form secondary structure (helices)
U A
G C A G C
A
A A C U U G
U G
 Types of RNA
Various types of RNA:-(1)Messenger
RNA(mRNA).
(2)Transfer RNA(tRNA).
(3)Ribosomal RNA(rRNA).
(4)Small nuclear RNA(snRNA).
(5)Small nucleolar(snoRNA).
(6)Small cajal body-specific RNA (scaRNA).
(7)Micro RNA (miRNA).
(8)Small interfering RNA (siRNA).
(9)Guide RNA (g RNA).
(10)Efference RNA (eRNA).
(11)Transfer-messenger RNA (tmRNA).
 Messenger RNA(mRNA)
Single, uncoiled strand which brings instructions
from DNA in the nucleus to the site of protein
synthesis (Ribosome).
The mRNA also contains regions that are not
translated: in eukaryotes this includes the 5'
untranslated region, 3' untranslated region, 5'
capand poly-A tail
 Ribosomal RNA (rRNA)
Globular form, makes up the ribosome the
construction site of proteins (site of protein
synthesis); binds to the mRNA and uses the
instructions to assemble the amino acids in the
correct order.
80% of total RNA in the cells are rRNA.
 Transfer RNA(tRNA)
Single, folded strand that delivers the proper
amino acid to the site at the right time.
Has a specific anticodon that is complementary
to the sequence on the mRNA.
During translation , transfer RNA functions in
the transfer of amino acids to mRNA.
All tRNAs share a common secondary structure
represented by a cover leaf.
They have four-paired stems defining three
stem loops (the D loop, anticodon loop, and T
loop) and the acceptor stem to which amino acids
are added in the charging step.
RNA molecules that carry amino acids to the
growing polypeptide.
Transfer RNA (tRNA) represents 15% of total
RNA in the cell.
 Genetic code
The genetic code is the way in which the
nucleotide sequence in mRNA ( or DNA ) specifies
the amino acid sequence in protein.
A, G, U and C are organized into triple-
nucleotides called codons.
There are 64 ( 4x4x4 ) codons.
The collection of the 64 codons makes up the
genetic code.
The genetic code was deciphered in 1966 by
Nirenberg et al.
In the genetic code 61 codons specify 20 amino
acids.
They are stop codons (termination codons ,
nonsense codons).

Five feature of the genetic code

(1)Universal.
(2)Directional.
(3)Commaless.
(4)Degeneracy.
(5)Wobble.