NUCLEIC ACIDS-CHEMISTRY

Nucleic acids are defined as acidic substances first discovered in the nucleus of
the cell. Nucleic acids are concerned with the storage of genetic information within a cell
and the transfer of genetic information from one generation to the net generation (or from
cell to cell during cell division).
There are two different types of nucleic acids Deoxy- ribonucleic acid (DNA) and
Ribonucleic acid (RNA). DNA and RNA differ in their chemical composition and
function. Both DNA and RNA are polymers of simpler compounds called nucleotides
which are linked together by phospho-di-ester linkages. DNA is composed of deoxy-
ribonucleotides and RNA is composed of ribonucleotides.

Chemical organization of Nucleic acids

Organization of DNA Different Nitrogenous bases combine with 2-deoxy , D- Ribo furanose
to form the structure of deoxy ribonucleosides. The phosphoric acid group associates with
deoxy-ribonucleosides to form different deoxyribonucleotides. Deoxyribonucleotides undergo
polymerization to form the long DNA polymer.

Organization of RNA- Different nitrogenous bases combine with , D- Ribo furanose to form
the structure of ribonucleosides. The phosphoric acid group associates with ribonucleosides to
form different ribonucleotides. Ribonucleotides undergo polymerization to form the RNA
molecule.

Nitrogenous base Nitrogenous base

2-deoxy , D-
Ribofuranose , D- Ribo-
furanose

Deoxy ribo
nucleosides
Ribonucleosides

Phosphoric acid
Phosphoric acid

Deoxy
ribonucleotides Ribonucleotides

DNA RNA
Chemical organization of nucleotides and nucleic acids

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Chemistry of nucleotides
The structure of nucleotides consists of three different components.
1. A nitrogenous base.
2. A pentose sugar (2-deoxy beta,D- Ribofuranose in DNA and beta D- Ribofuranose in
RNA) and
3. A phosphoric acid group.

I Nitrogenous base
Nitrogenous bases are nitrogen containing basic compounds present in nucleotide
structure.They are divides in to two groups
1. Purines
2. Pyrimidines

Purines
Purines are nitrogenous bases containing a purine ring system (double ring) in its
structure. There are two types of purine nitrogenous bases Adenine and Guanine.
Adenine and Guanine are present both in DNA and RNA.

Purine ring system (General structure) Adenine (6-amino purine) Guanine (2-amino, 6-oxopurine)

Pyrimidines
Pyrimidines are nitrogenous bases containing a pyrimidine ring system (single ring)
in its structure. There are three different types of pyrimidine nitrogenous bases
Cytosine, Uracil and Thymine. Cytosine is present both in DNA and RNA, Uracil is
present only in RNA and Thymine is present only in DNA.

Pyrimidine ring system (General structure) Cytosine (2-oxo, 4-amino pyrimidine)

Uracil (2, 4- dioxopyrimidine) Thymine (2, 4-dioxo, 5- methyl pyrimidine)

II. Pentose Sugar

The sugar present in DNA is 2-deoxy ,D- Ribo furanose.

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The sugar present in RNA is , D- Ribo furanose

, D- Ribo furanose 2-deoxy & , D- Ribo furanose (Chemical Names)

III. Phosphoric acid (H3 PO4)

The molecular structure of phosphoric acid can be represented as follows.

General structure of Nucleotides

In the nucleotide structure the nitrogenous base is attached to the first carbon atom
of the pentose sugar via an N- Glycosidic linkage. The phosphoric acid group is attached
to the 5th carbon via an ester linkage.

General structure of a deoxy ribonucleotide General structure of a ribonucleotide

(ribonucleoside monophosphate) (deoxy ribo nucleoside monophosphate)

Nucleotides present in DNA (deoxy ribonucleoside monophosphate)

1. Deoxy adenosine mono phosphate /dAMP (deoxy adenylic acid)
2. Deoxy guanosine mono phosphate/dGMP (deoxy guanylic acid)
3. Deoxy cytidine monophosphate/dCMP (deoxy cytidylic aicd)
4. Deoxy thymidine monophospahate/ dTMP (deoxy thymidylic acid)
Nucleotides present in RNA (ribonucleoside monophosphate)

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 1. Adenosine mono phosphate /AMP (Adenylic acid)
2. Guanosine mono phosphate/GMP (Guanylic acid)
3. Cytidine monophosphate/CMP (Cytidylic aicd)
4. Uridine monophospahate/ UMP (Uridylic acid)

Important Nucleoside triphosphates

1. ATP High energy molecule (energy currency of the cell)
2. GTP- High energy molecule
3. CTP- High energy molecule
4. UTP- High energy molecule

Structure of ATP molecule

Important Nucleoside monophosphates
1. 3-5cyclic AMP (c AMP)-Cyclic AMP is a second messenger for certain hormones.
Examples of such hormones include glucagon, adrenaline etc. A second messenger is
a molecule that is produced intracellularly upon an extrtracellular hormonal
stimulation, and mediate the hormonal action within the cell.

Structure of cyclic AMP

DEOXYRIBONUCLEIC ACID (DNA)

DNA is the genetic material of all eukaryotic organisms, bacteria and DNA viruses.
DNA is the store house of genetic informations. DNA contains genes. DNA is the
polymer of deoxy ribonucleotides. There are 4 different types of deoxy ribonucleotides in
DNA. They are linked together by 3-5- phospho di-ester linkages to form the polydeoxy-
ribonucleotide structure.
1. Deoxy adenosine mono phosphate /dAMP (deoxy adenylic acid)
2. Deoxy guanosine mono phosphate/dGMP (deoxy guanylic acid)
3. Deoxy cytidine monophosphate/dCMP (deoxy cytidylic aicd)
4. Deoxy thymidine monophospahate/ dTMP (deoxy thymidylic acid)
Structure of the poly deoxy ribonucleotides
The structure of the poly deoxy ribonucleotide consists of hundreds or thousands of
deoxyribonucleotides which are linked together by 3-5- phosphodiester linkages.This

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polymer has a 3 end with a free sugar OH group and a 5 end with a free phosphoric
acid group.

WATSON & CRICK DNA STRUCTURE

(DUBLE- HELLICAL MEDEL OF DNA)

The structure of DNA molecule was proposed by James Watson and Francis Crick.
The structure of DNA consist of two poly deoxy ribonucleotide strands which are
wound around each other in a right handed manner around an imaginary to form a
right handed double helix. The two strands are joined by pairing between the
nitrogenous bases of opposing strands. This double helical structure of the DNA
resembles a spiral stair case. The steps of the stair case are represented by the base pairs
and the hand rails are represented by the sugar phosphate backbones.The two strands are
running parallel to each other. The two strands are running in opposite direction, one in
5-3 direction and other in 3 to 5 direction.
Base pairing rule :The bases of the two strands are paired by strict base pairing rule.
1. A purine always pairs with a pyrimidine.
2. Adenine always pairs with Thymine.
3. Guanine always pairs with cytosine.
4. Two hydrogen bonds are formed between adenine and thymine.
5. Three hydrogen bonds are formed between guanine and cytosine.

Complimentary nature :Due to the complimentarily in base pairing, the two strands of the
DNA molecule are also complimentary to each other.
1. when there is adenine in one strand, there will be Thymine in the corresponding position in the
other strand. When there is Guanine in one strand the corresponding position of the other strand
will be occupied by cytosine.
2. There will be equal number of nucleotides in both strands.
3. The number of adenine nucleotide in one strand will be equal to the number of Thymine
nucleotide in the opposing strand and also in the entire DNA.
4. Similarly the number of Guanine nucleotide will be same as the number of Cytosine
nucleotide.

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Major forces stabilizing DNA Structure :The forces stabilizing the double helical
structure can be divided in to two categories- covalent bonds and non-covalent bonds.
I. Covalent bonds
1. 3-5Phosphodiester linkages the nucleotides present in each strand are joined
by a special type of linkage called phosphodiester linkages. It is linkage in which
the 5th carbon of one nucleotide is linked with the 3rd carbon of another nucleotide
through a phosphoric acid group, hence the name phosphor di-ester linkage. It is a
covalent linkage and it is considered as the backbone of DNA.

II. Non-covalent bonds.

1 H- Bonds formed between the nitrogenous bases of opposing strands.
2 Van der Waals forces formed between uncharged atoms of both strands.
3 Hydrophobic interaction forces The nitrogenous bases are uncharged and
hydrophobic, whereas phosphate groups of each strand are negatively charged
and hydrophilic. Therefore the bases become stacked inside the double helical
structure and the phosphate group tends to be in the periphery.
All these forces together give the DNA molecule a most energetically stable and
comfortable conformation i.e. the double helical structure.
Helix parameters of the double helical structure are
1. The DNA molecule is having a width of 2.0 nm.
2. The height of one turn (pitch of the helix) is 3.4 nm.
3. There are 10.4 base pairs in each turn (n=10.4).
4. The distance contributed by one base pair is 3.4/10.4=0.34nm
There are two grooves that run along the length of the DNA molecule .They are:-
1. Major groove-Major groove is the space between two adjacent turns in the
DNA molecule. It is having a width of 1.2nm.
2. Minor grove Minor groove is the space between the two strands of the helix.
It is having a width of 0.6nm.

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 Structure of DNA (Watson Crick Model)

RIBONUCLEIC ACID (RNA)

RNA is the polymer of ribonucleotides i.e. polyribonucleotide. There are four different
types of ribonucleotides. They are:-
1. Adenosine mono phosphate /AMP (adenylic acid)
2. Guanosine mono phosphate/GMP (guanylic acid)
3. Cytidine monophosphate/CMP (cytidylic aicd)
4. Thymidine monophospahate/ UMP (thymidylic acid)
Apart from these usual nucleotides, some of the RNA molecules may contain unusual
nucleotides like
1. 7-methyl guanosine triphosphate.- mRNA.
2. Dihydro uridine monophosphate tRNA.
3. Peudouridine monophosphate tRNA.
4. Ribothymidine monophosphate-tRNA.
The ribonucleotides are linked together by 3-5 phosphodiester linkages.RNA
molecules are synthesized in the nucleus by a process called transcription using DNA as a
template. It is the first stage in gene expression process. RNA molecules perform
different functions in the cell in connection with the process of protein synthesis. RNA
molecules are transported in to the cytoplasm soon after its synthesis.

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Comparison of poly ribonucleotide and polydeoxyribonucleotide strands
Classification of RNA molecules
Based on their specific functions RNA molecules are classified in to the following type.
1. messenger RNA (mRNA)
2. transfer RNA (t RNA)
3. ribosomal RNA (r RNA)
1. messenger RNA
Messenger RNA molecules are involved in the transport of genetic information from
gene (DNA) to the site of protein synthesis in the cytoplasm. m RNA molecule acts as the
template for protein biosynthesis. mRNA constitutes only 0.6to 1% of the total cellular
RNAs.mRNA molecules are of varying sizes and its molecular weight ranges from
30,000 to 50,000 Daltons. M RNA molecule is single stranded. In the mRNA molecule 3

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adjacent bases are called a codon which code for amino acids during protein synthesis.
Each codon specifies one amino acid.

The 5end of the mRNA molecule contains a modified base called 7- methyl guanosine
triphosphate which protects the mRNA from damage. This is called 5 cap. The 3 end
has a sequence of 20-200 adenine nucleotides which from the polyadenyl tail or poly A
tail. It protects the mRNA from nuclease attack.
There is a coding region in the centre which carries codons specifying the amino acids to
be incorporated in the protein structure.mRNA that codes for only one protein(
polypeptide) is called monocistronic mRNA.(eukaryotic mRNA) .mRNA that codes for
more than one protein(Polypeptide) is called poly cistronic mRNA.(prokaryotic mRNA).
A cistron is defined as a region of mRNA that carry information for the synthesis of
one polypeptide chain.

2. Transfer RNA (r RNA) or soluble RNA ( sRNA)

Transfer RNA is also called as soluble RNA because they are small molecules
containing only 75 nucleotides. The molecular weight is about 25000 Daltons. It
constitutes 10-20 % of the total cellular RNAs. Transfer RNA molecules are involved in
the transfer (transport) of amino acids to the site of protein synthesis. They functions as
an adapter molecule that translate the genetic information present as nucleotide sequence
in the mRNA molecule to the amino acid sequence in the polypeptide synthesized. There
are different types of tRNA molecule corresponding to each amino acid.
The primary structure of the tRNA molecule undergoes extensive folding to form a
clover leaf shaped secondary structure. This is achieved by the base pairing between self
complimentary regions in the molecule. The characteristics of the clover leaf secondary
structure are the following:-
There are four arms or loops in the secondary structure. They are:-
a)Dihydrouridylic arm or DHU arm -containing an unusual base called dihydrouracil
b)Ribothymidine arm or pseudouridine arm -containing a modified bases
pseudouridine and ribothymidine.
c) Anti-codon arm containing the anti-codon. Anti-codon refers to three adjacent
bases in the tRNA that form complimentary base pairing with the codon on the
mRNAduring translation.
d) Variable arm- It is a short loop that contains sequence that vary among different
tRNA molecules. It is present between the pseudo-uridine arm and anti-codon arm.
All the tRNA molecules have a common CCA sequence at the 3 end. The 3 end is
called amino acyl attachment site. The amino acid binds to the OH group present in
the 3 end by an ester linkage (between the OH group of tRNA and the COOH group
of the amino acid) to form the amino acyl tRNA (activated amino acid). Prokaryotic
tRNAs are more stable compared to eukaryotic tRNA.

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3.Ribosomal RNA (r RNA)

Ribosomal RNAs form 80% of the total cellular RNAs. These are present in the structure
of ribosomes in association with certain proteins to form the ribonucleoproteins. rRNAs
are classified into different types based on their sedimentation coefficient(S) .

r RNA( General structure) Complete Ribosome

They are:-
1. 5 S r RNA present in the 60 S large ribosomal subunit.
2. 5.8 S r RNA - present in the 60 S large ribosomal subunit.
3. 28S r RNA- present in the 60 S large ribosomal subunit.
&
4. 18 S r RNA present in the small 40 S ribosomal subunit.
Functions of r RNA
1. It is a structural component of ribosome together with proteins.
2. It interacts with tRNA during translation.
3. It provides peptidyl transferase enzymatic activity (ribozymes).

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 CHAPTER-10: MOLECULAR BIOLOGY
CENTRAL DOGMA OF MOLECULAR GENETICS
(THE PROCESS OF GENE EXPRESSION)

The genetic information is stored in the DNA molecule as definite sequence of

nucleotides i.e. in the form of the 4-letter language of n-bases (A, T, C& G). A portion of
the DNA molecule that determines a character or a property is called a gene. Human
DNA contains lakhs of such genes. A gene expresses a character by the synthesis of a
protein. These proteins will carryout the expression of that character.
The process of gene expression involves three different processes which are
collectively called as the central dogma of molecular genetics.

The processes are:-

1. Replication:-synthesis of DNA from DNA
2. Transcription: synthesis of RNA using DNA as a template and
3. Translation: synthesis of polypeptide (or protein) using RNA as a template.
Replication
The process of synthesis of a new DNA molecule using a parent DNA molecule as
a template is called DNA replication. During replication a new strand is synthesized on
each of the parental strand so that the daughter DNA molecules formed will have one
parental strand and one newly synthesized strand. It takes place in the nucleus of the cell.
DNA replication is a highly complex process that takes place just before cell
division i.e. simultaneous with the process of chromosome duplication. Replication is
carried out by the combined action of a number of enzymes. They are:-

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1.DNA polymerase: - It is the chief enzyme involved in DNA replication. It is involved in the
polymerization of ribonucleotides leading to the synthesis of a new strand. Deoxyribonucleoside
triphosphates (dNTPs) are the substrate for this enzyme. In mammals there are 5 different types of
DNA polymerases designated as alpha, beta, and gamma and so on.
2.RNA polymerase or RNA primase : - It is involved in the synthesis of an RNA primer ( a short RNA
fragment) during the initial stage.
3.DNA topoisomerase:-It is involved in the uncoiling of DNA molecule during replication.
4.DNA hellicase:-It is involved in the separation of the two parental DNA strand during replication. It
utilizes the energy of ATP hydrolysis to break the H- bonds between bases.
5.DNA ligases:-It is involved in the joining of short DNA fragments to form a long continuous strand.
Other factors involved:-
Single strand binding proteins (SSBPs): a group of proteins that bind to the separated single stand and
prevents its association again. All the above enzymes and single strand binding protein associate with the
DNA molecule to form a complex called replication fork /replisome/ DNA replicase system.The
replication fork moves along the complete length of the DNA molecule during replication.
The process of DNA replication can be summarized under the following headings.
1.Initiation 2. Elongation and 3. Termination
1.Initiation
1. DNA topoisomerase recognizes certain specific sequences on the DNA called
autonomous replicating sequences (ARS) and starts the uncoiling of DNA.
2. DNA hellicase separates the two strands of the uncoiled DNA.
3. SSBP binds to the single strands and stabilizes them.
4. DNA polymerase binds to the DNA.
5. RNA polymerase (RNA primase) synthesizes a short fragment of RNA at the 3 end of
the 3to 5 strand.

Replication fork/DNA replicase system/replisome

2.Elongation
DNA polymerase catalyzes the sequential addition of deoxyribonucleotides to the RNA
primer leading to its extension. This takes place in the 3 to 5 parental strand and is
called leading strand.
On the other parental strand (5to 3 stand) the synthesis of new strand takes place by the
formation of short fragments called Okasaki fragments (It is discovered by a scientist
named Okasaki). The RNA primer present at the 5 end of the leading strand and the
Okasaki fragments are removed by the exonuclease activity of the DNA polymerase and

12
the spaces are filled by the addition of deoxy ribonucleotides. All the fragments are
joined by DNA ligases to form two continuous strands one on each of the parental strand.
3. Termination
The process is terminated when the complete parental DNA is replicated and two
daughter DNA molecules are formed, each of which are exact copy of the parental DNA
molecule. In each of the daughter DNA one strand is parental and one is newly
synthesized. The proof reading activity of DNA polymerase increases the fidelity of
replication.
The characteristic features of DNA replication
1. DNA replication is semi-conservative:-During replication one of the parental DNA
strand is conserved in the daughter DNA molecule, therefore it is said to be semi-
conservative.
2. The synthesis of the new strand takes place only in the 5 to 3 direction.

3. In the 3-5 parental strand replication takes place continuously.

4. In the 5-3 strand replication take place discontinuously by the formation of Okasaki
fragments.

Transcription
Transcription refers to the synthesis of RNA molecules using DNA as a template- DNA
based RNA synthesis. RNA synthesis takes place by the polymerization of
ribonucleotides by an enzyme called RNA polymerase. It takes place in the nucleus.
Characteristics of transcription
During transcription only one strand of the DNA molecule acts as a template. This strand
is called template strand whose sequence will be complimentary to the RNA (also called
sense strand/non-coding strand). The opposing strand is called anti- template strand
also called coding strand because its sequence exactly matches with that of the RNA
transcribed (also called as anti-sense strand). The synthesis of RNA molecule will takes
place only in the 5 to 3 direction. So the template strand must be in the 3 to 5
direction.
During DNA replication the entire DNA molecule makes its own copy, but in
transcription only a small portion of the DNA (gene) is copied.
The RNA molecule will have sequence complimentary to the template strand of the
DNA, but will have the exact sequence of the anti template strand of the DNA (except
that there will be uracil in place of thymine).
The enzyme responsible for transcription in mammalian system is called RNA
polymerase. There are three different types of RNA polymerases.
1. RNA polymerase I- r RNA synthesis.
2. RNA polymerase II- mRNA synthesis.
&
3. RNA polymerase III - t RNA synthesis.
The process of transcription can be described under the following headings.

1. Initiation 2. Elongation and 3. Termination

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1.Initiation
The RNA polymerase identifies a specific sequence called promoter site in the gene eg.
Hogness box (TATAA box) and CAT box (CAATA).The DNA molecule partially
unwinds with the help of so many protein factors called initiation factors (IFs). RNA
polymerase catalyzes the addition of the first nucleotide to its beta subunit according to
the complimentarily of the DNA. The enzyme gradually moves one nucleotide ahead and
catalyzes the addition of the second nucleotide.

2.Elongation
As the RNA polymerase moves along the DNA molecule (together with the movement of
the transcription bubble), more and more ribonucleotides become incorporated in to the
RNA according to the base sequence in the sense strand. As the RNA polymerase moves
ahead, the DNA molecule will unwind the downstream and wind the upstream so that we
feel the movement of the transcription bubble in the direction of the movement of the
RNA polymerase.
3.Termination
Termination takes place when the RNA polymerase recognizes certain sequences called
termination signals. When the termination signal is reached certain proteins called rho
will bind to the RNA molecule. Once the Rho is bound RNA polymerase cannot precede
further. The enzyme become dissociates from the DNA and the nascent RNA molecule is
released.
Post transcriptional modification or processing
The newly synthesized RNA molecule is called nascent RNA. It undergoes a number of
modifications to become the mature and functional RNA molecule. All these
modifications are together called post transcriptional modifications. This modification
depends on the type of RNA. Some of such changes in the case of mRNA are:-
a) Endonuclease cleavage b) Poly A tailing c) 5 capping d) Intron splicing

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Translation
The term translation refers to the process of protein biosynthesis. It takes place in the
cytoplasm with the help of tRNA, mRNA, so many enzymes and protein factors.
During translation the genetic information present in the mRNA molecule in the form of
definite sequence of nucleotides is translated in to the amino acid sequence in the
polypeptide (protein). In other words genetic information written with 4-letter language
of nucleotides in the mRNA molecule is translated in to the 20 letter language (20 amino
acids) of proteins.
The mRNA contains triplet of nucleotides (three adjacent nucleotides) called codons that
specify an amino acids. An mRNA containing 3000 nucleotides in the coding region can
code for a polypeptide containing 1000 amino acids.

The process of translation can be described under the following headings.

1. Activation of amino acids 2. Initiation
3. Elongation and 4. Termination
1. Activation of amino acids
Activation of amino acid refers to the synthesis of amino acyl t RNA. All the 20 different
amino acids are activated to corresponding amino acyl tRNA (eg.Methionyl t RNA,
Glycinyl tRNA etc. ). This reaction is catalyzed by an enzyme called aminoacyl tRNA
synthetases ( eg.methionyl t RNA synthetase,Glycinyl tRNA synthetase etc).

Structure of Alanine t RNA

2.Initiation
The m RNA binds to the 40S ribosomal subunit with its 5 end. This is followed by the
binding of the methionyl t RNA to the initiation codon (AUG). This is followed by the
binding of the 60S large subunit to form the initiation complex. The complex has three
different sites Peptidyl site or P -site, Acceptor site or A- site and Exit site or E-site.
The P-site contains the AUG codon of the m RNA and the first methionyl t RNA attached
to it by codon anticodon base pairing.

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 3. Elongation
The second amino acyl t RNA become attached to the A site. A peptide bond is formed
between the two amino acid to form a dipeptide which remains attached to the A Site.
This reaction is catalyzed by an enzyme called peptidyl transferase. This is followed by
the movement of the ribosome downstream by a distance of one codon. This movement is
called translocation. Now the dipeptidyl t RNA become shifted to the P site and the A
site becomes empty. The new amino acyl t RNA complimentary to the next codon (3rd)
will come and occupy the A-site and the whole process is repeated.

The elongation process continues until certain codons called stop codons (UAA, UAG
and UGA) will come and occupy the A-site. The stop codons will not have any tRNA to
bind with it.

4.Termination
When the amino acyl site becomes occupied by the stop codons the elongation process
will be stopped. This is because there is no amino acyl tRNA corresponding to stop
codons. Certain protein factors called termination factors will bind to the A Site.

This is followed by the dissociation of the ribosomal assembly and the liberation of the
polypeptide chain.
Poly ribosome or polysome Sometimes several ribosomes may carryout
the translation process in the same m RNA simultaneously. Such an m RNA
containing large numbers of ribosomes attached to it is called polyribosome or
polysome.

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Post translational modification This refers to all the chemical and structural
modifications on the polypeptide chain to convert it in to a biologically active protein.

a) Proteolytic cleavage
b) Chemical modification of amino acids such as hydroxylation ,
phosphorylation etc
c) Glycosylation
d) metal ion incorporation,
e) protein folding etc.

GENETIC CODE
The genetic code is a dictionary that identifies the correspondence between the
nucleotide sequence in the m RNA and the sequence of amino acid in the polypeptide
chain. Each amino acid in the structure of the polypeptide chain is specified by a set of
three adjacent nucleotides in the m RNA called codons. The m RNA may contain
varying number of codons. There are 64 different types of codons based on the types
of bases in the triplet. O f which 3 are stop codons and will not code for any amino
acids.
Genetic code is the term used to represent all the different codons which
together determine the amino acid sequence in the structure of polypeptide
chain/ protein.
Characteristics of the genetic code
1.Specificity- means that a particular codon always code for a specific amino
acid.For example UUU code for Phenyl alanine , and AUG code for Methionine.
2.Universality-The codes are universal that means it is the same in all the diverse
group of organism, bacteria, viruses, plants ,animals etc.

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3. Redundancy (degeneracy) - Even though one codon specifies a particular amino
acid, that particular amino acid can be coded by a number of codons. (remember,

there are 61 active codons ,but only 21 standard amino acids). For example Arginine is
coded by six different codons.

The reason for degeneracy is explained by Wobble pairing hypothesis. According to

this hypothesis ,during the codon anticodon base pairing ,only the first two bases of a
codon is actually forming strong H- bond with the last two bases of the t RNA anti-
codon. The last base of codon and first base of the anti-codon forms only transient H-
bonding. The traditional complimentary base pairing rule is applicable only for two
bases and not for the other. Therefore
A) Adenine present in the first position of t RNA anti-codon can pair with U, G, and I at
the third position of mRNA codon.

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B) Guanine can pair with C as well as U.
C) Uracil can pair with A, G and I.
D) Cytosine can pair with G and I.
4. Non- overlapping and commales- The genetic code is read in the 5 to 3
direction as shown below without any punctuation or comma between adjacent
codons.
5 AUG/GUG/CUC/AAA 3
If one nucleotide (A) is deleted from the 5 end then the reading frame will be
changed and codons will have a different structure.
5 UGG/UGC/UCA/AA 3
If one more nucleotide (C) is added at the 5 end then also the reading frame will
change.
5 CAU/GGU/GCU/CAA/A 3

MUTATIONS
Any change in the structure or sequence of nucleotide in the DNA (gene) is called
mutations. (Alterations in the original structure of the gene are termed mutations).
When the nucleotide sequence of the gene changes, the nucleotide sequence in the
corresponding m RNA also undergo changes and will be finally reflected as a change in
amino acid sequence of the protein to be synthesized. The defective protein may not
function well, and the character manifested by it will be altered.
Mutations are classified in to two major classes
1.Point mutations- refers to minute changes in the gene structure, particularly with
respect to a single nucleotide.
2.Chromosomal aberrations- refers to comparatively larger changes involving a stretch
of nucleotides or a region of the gene.
Point mutations are of different types .They are discussed below.
A. Silent mutations-If the original nucleotide is replaced by a different nucleotide
there will be a corresponding change in the codon structure. Often the change in
codon structure will not make any change in the amino acid coded by that codon.
For example, the original sequence is UCA that codes for Serine. If the A present at
the 3rd position is substituted by U, the codon will be changed to UCU that also will
code for Serine. This means that during silent mutation there is a single nucleotide
substitution, but that will not be reflected in the protein structure.
UCA- SERINE

UCU- SERINE

B. Missense mutation- There is the substitution of one nucleotide and a

corresponding change in the codon structure. As a result the new codon will code for a
different amino acid leading to a change in the amino acid sequence of the protein
synthesized.

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 For example, If the first nucleotide U substituted by C as a result of mutation ,the
amino acid coded will be different bringing about a change in the amino acid
sequence.
UCA- Serine

CCU- Proline

C. Nonsense-mutation- There is the substitution of one nucleotide and a

corresponding change in the codon structure. The modified codon is any one of the
stop codons ( UAA, UAG or UGA) ,so that premature termination of the translation
occurs. This lead to the production of an incomplete or defective or aberrant protein
having an altered function.
For example, If the first nucleotide U substituted by C as a result of mutation ,the
amino acid coded will be different bringing about a change in the amino acid
sequence.
Original codon :UAC- Tyrosine
Mutated (C substituted by A) :UAA - (Stop
codon)
Mutated (C substituted by G) :UAG-(Stop codon)

D. Frame shift mutation- addition or deletion of a single nucleotide will shift the
reading frame of the m RNA by a distance of one codon. This results in a change in the
structure of all the codons in the coding region of the m RNA leading to a change in
the amino acid sequence of the polypeptide chain.

D. Trinucleotide repeat expansion:- A sequence of 3 nucleotides are repeated in many

numbers ( tandem repeats) leading to the incorporation of many extra copies of the
amino acid in to the protein structure and protein become defective or non
functional.
E- Splice site mutation:- Mutations at the splice site of the heterogeneous m RNA can
cause changes in the original structure of the mature m RNA, leading to the synthesis
of abnormal protein.
Chromosomal aberrations are of different types -:
1) those involving only one chromosome( single chromosomal aberrations) and
2) those involving two chromosomes(reciprocal chromosomal aberrations).

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Single chromosomal aberrations are
1) deletion- a fragment of a chromosome / gene / DNA is deleted away.
2) Duplication a portion of a chromosome / gene / DNA is repeated in tandem
3) Inversion -a fragment of a chromosome / gene / DNA is first removed and then
joined back but in the reverse manner.

Reciprocal chromosomal aberrations are

1) Insertion- a fragment of one chromosome get deleted and inserted in to
another chromosome.
2) Translocation- end fragments are exchanged between two chromosomes.

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