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VI Sem,B.Sc., Biochemistry Nucleic acids

NUCLEIC ACIDS

Nucleic Acids (14-marks) 05 Hours
Types, components of nucleic acids – nitrogenous bases (A, G, C, U, T – structures only), sugars present in
nucleic acids (ribose and deoxyribose) and phosphate group.
Nucleosides and nucleotides – nomenclature and stru ctures. Partial structure of polynucleotide’s, structure
of DNA (Watson and Crick model), biological importan ce of DNA, RNA – types and their biological roles
(structures not required).
Central dogma of molecular biology (basic principles on ly), genetic code and its features, replication (semi
conservative mechanism), brief mention of transcription and translation.

Introduction:
Defination: Nucleic acids are long-chain polymeric molecules, the monomer (the repeating unit) is known as the
nucleotides and hence sometimes nucleic acids are referred to as polynucleotides.
There are prominently two types of nucleic acids known to us.
Deoxyribonucleic Acid (DNA)
Chemically, DNA is composed of a pentose sugar, phosphoric acid and some cyclic bases containing nitrogen.
The sugar moiety present in DNA molecules is β-D-2-deoxyribose. The cyclic bases that have nitrogen in them
are adenine (A), guanine (G), cytosine(C) and thymine (T). These bases and their arrangement in the molecules of
DNA play an important role in the storage of information from one generation to the next one. DNA has a
double-strand helical structure in which the strands are complementary to each other.
Ribonucleic Acid (RNA)
RNA molecule is also composed of phosphoric acid, a pentose sugar and some cyclic bases containing nitrogen.
RNA has β-D-ribose in it as the sugar moiety. The heterocyclic bases present in RNA are adenine (A), guanine
(G), cytosine(C) and uracil (U). In RNA the fourth base is different from that of a DNA. The RNA generally
consists of a single strand which sometimes folds back; that results in a double helix structure.
Functions of Nucleic Acids

Nucleic Acid is responsible for synthesis of protein in our body
RNA is a vital component for protein synthesis.
Loss of DNA content is linked to many diseases.
DNA is an essential component required for transferring genes from parents to offspring.
All the information of a cell is stored in DNA.
DNA fingerprinting is a method used by forensic experts to determine paternity. It is also used for

identification of criminals.

Components of Nucleic acid:
1) Nitogenous bases : Purines and pyrimidines are both organic compounds that take part in the synthesis

of DNA and RNA, therefore they are called as the building blocks of the genetic materials.

Purines Pyrimidines
Purine is a heterocyclic aromatic organic Pyrimidine is a heterocyclic aromatic organic
compound composed of a pyrimidine ring compound that is composed of carbon and
fused with imidazole ring. hydrogen.
It comprises adenine and guanine as It comprises Cytosine, thymine, uracil as
nucleobases. nucleobases
It consists of two hydrogen-carbon rings and It consists of one hydrogen-carbon ring and
four nitrogen atoms two nitrogen atoms
The melting point of purine is 214 °C The melting point of pyrimidine is 20-22 °C

 

P avan Kumar K, Dept. Of Chemistry, GFGC Tumakuru. Page 1

 

VI Sem,B.Sc., Biochemistry Nucleic acids

Structures:
Purines Pyrimidines

Adenine Guanine Cytosine Thymine Uracil

 

 

2) Sugar: There are two types of sugars present in Nucleic acids.
The sugar moiety present in DNA molecules is β-D-2-deoxyribose where as RNA has β-D-ribose moiety.

3) Phosphoric acid residue: It is present in both DNA and RNA.

Nucleosides and Nucleotides:
Nucleosides: a compound that consists of a purine or pyrimidine base combined with deoxyribose or

ribose and is found especially in DNA or RNA. Examples: Adenosine, Guanosine.
Nucleotides: Nucleotides are the building blocks of nucleic acids; they are composed of three sub unit

molecules: a nitrogenous base (also known as nucleobase), a five-carbon sugar (ribose or deoxyribose),
and at least one phosphate group. Examples: AMP, ADT, ATP.

Nucleoside and Nucleotide nomenclature

 

P avan Kumar K, Dept. Of Chemistry, GFGC Tumakuru. Page 2

 

VI Sem,B.Sc., Biochemistry Nucleic acids

Structures of Nucleosides of RNA
NH2 O NH O

2
N N N NH N NH

HO N N
O HO N N NH HO N O HO N O

O 2
O O

OH OH OH OH OH OH OH OH

Adenosine Guanosine Cytidine Thymidine

Structures of Nucleosides of DNA

NH O
2 NH2 O

N N
N NH N H3C

NH

HO N N HO N N NH
O 2 HO N O

O HO N O
O O

OH OH OH OH

deoxy Adenosine deoxy Guanosine deoxy Cytidine deoxy Thymidine

Structures of Nucleotides of DNA

 

Structures of Nucleotides of RNA

 

P avan Kumar K, Dept. Of Chemistry, GFGC Tumakuru. Page 3

 

VI Sem,B.Sc., Biochemistry Nucleic acids

Partial structure of Polynucleotide of DNA: Partial structure of Polynucleotide of RNA:
The monomeric deoxvnucleotides in DNA are held together The monomeric nucleotides in RNA are held
by 3′,5′-phosphodiester bridges. together by 3′,5′-phosphodiester bridges.

 

 

Watson – Crick Model:
In 1953, J.D. Watson (an American biologist) and F.H.C. Crick (a British Physicist) proposed the three-
dimensional model of physiological DNA. For this Watson, Crick and Wilkins got Nobel Prize in medicine in
1962. Term DNA was given by Zaccharis.
The important features of Watson – Crick Model or double helix model of DNA are as follows:

1. The DNA molecule consists of two polynucleotide chains or strands that spirally twisted around each
other and coiled around a common axis to form a right-handed double-helix.

2. The two strands are antiparallel i.e. they ran in opposite directions so that the 3′ end of one chain facing
the 5′ end of the other.

3. The sugar-phosphate backbones remain on the outside, while the core of the helix contains the purine and
pyrimidine bases.

4. The two strands are held together by hydrogen bonds between the purine and pyrimidine bases of the
opposite strands.

5. Adenine (A) always pairs with thymine (T) by two hydrogen bonds and guanine (G) always pairs with
cytosine (C) by three hydrogen bonds. This complimentarily is known as the base pairing rule. Thus, the
two stands are complementary to one another.

6. The base sequence along a polynucleotide chain is variable and a specific sequence of bases carries the
genetic information.

7. The base compositions of DNA obey Chargaff s rules. According to which A=T and G=C; as a
corollary purines (A+G) = pyrimidines (C+T); also (A+C) = (G+T). It also states that ratio of (A+T)
and (G+C) is constant for a species.

P avan Kumar K, Dept. Of Chemistry, GFGC Tumakuru. Page 4

 

VI Sem,B.Sc., Biochemistry Nucleic acids

8. The diameter of DNA is 2 nm (20 A). Adjacent bases are separated 0.34nm (3.4 A) along the axis. The
length of a complete turn of helix is 3.4nm (34 A) i.e. there are 10 base pairs per turn.

9. The DNA helix has a shallow groove called minor groove and a deep groove called major groove across.

(A) Thymine pairs with adenine by 2
hydrogen bonds

(B) Cytosine pairs with guanine by 3
hydrogen bonds.

(A) Watson-Crick model of DNA helix (B) Complementary base pairing in DNA helix. Complementary base paiing in DNA

Biological importance of DNA:
1. Hereditary material: The genetic information stored in the nucleotide sequence of DNA helps in synthesis

of specific proteins or polypeptides and transmit the information to daughter cells or offspring’s.
2. Autocatalytic role DNA:DNA undergoes replication (self-duplication) in the S-phase of cell cycle. During

the process each DNA strand of a double helix can act as template for the synthesis of daughter strand.
3. Hetero catalytic role: During transcription any one strand of DNA acts as template for the synthesis of

RNA. This is called the hetero catalytic role of RNA.
4. Variations: DNA undergoes recombination its meiosis and occasional mutation (changes in nucleotide

sequences) which creates variations in population and ultimately contributes to evolution.
5. DNA controls cellular metabolism, growth, and differentiation.
6. DNA finger printing (-DNA typing or profiling): This technique is used to identify criminals, determine

paternity, verification of immigrant etc.
7. Recombinant DNA technology (Genetic engineering): It involves the artificial cleaving and rejoining

DNA sequences from two or more organisms to create recombinant DNA. This technology is employed for
production of genetically modified organisms (GMOs), genetically modified foods (GMFs), vaccines,
hormones, enzymes, clones etc.

Ribonucleic acid:
RNA is a polymer of ribonucleotides held together by 3′,5′-phosphodiester bridges. Although RNA has certain
similarities with DNA structure, they have specific differences

1. Pentose: The sugar in RNA is ribose in contrast to deoxyribose in DNA.
2. Pyrimidine : RNA contains the pyrimidine uracil in place of thymine (in DNA).
3. Single strand: RNA is usually a single stranded polynucleotide. However, this strand may fold at certain

places to give a double stranded structure, if complementary base pairs are in close proximity.
4. Chargaff’s rule-not obeyed : Due to the single-stranded nature, there is no specific relation between

purine and pyrimidine contents. Thus the guanine content is not equal to cytosine (as is the case in DNA).

P avan Kumar K, Dept. Of Chemistry, GFGC Tumakuru. Page 5

 

VI Sem,B.Sc., Biochemistry Nucleic acids

5. Susceptibility to alkali hydrolysis: Alkali can hydrolyse RNA to 2′,3′-cyclic diesters.This is possible due
to the presence of a hydroxyl group at 2′ position. DNA cannot be subjected to alkali hydrolysis due to
lack of this group.

TYPES OF RNA:
The three major types of RNAs with respect to their cellular composition given below

1. Messenger RNA (mRNA):( 5-1O %) functions as a carrier of genetic information from the DNA in the
cell nucleus to the site of protein synthesis in the cytoplasm. mRNA has a short lifetime (usually less than
one hour); it is synthesized as it is needed, then rapidly degraded to the constituent nucleotides.

2. Ribosomal RNA (rRNA): (80-85 %) the main component of ribosomes that are the site of protein
synthesis. rRNA accounts for 80-85% of the total RNA of the cell. rRNA accounts for 65% of a
ribosome’s structure (the remaining 35% is protein).

3. Transfer RNA (tRNA) : (10-20%) delivers individual amino acids to the site of protein synthesis. tRNA
is specific to one type of amino acid; cells contain at least one specific type of tRNA for each of the 20
common amino acids. tRNA is the smallest of the nucleic acids, with 73-93 nucleotides per chain.

Central dogma of molecular biology:
The central dogma of molecular biology states that “genetic information contained in the DNA is
transferred to RNA molecules and then expressed in the structure of synthesized proteins”.

There are two steps in the flow of genetic information:

Transcription: in eukaryotes, the DNA containing the stored information is in the nucleus of the cell,
and protein synthesis occurs in the cytoplasm. The information stored in the DNA must be carried out of
the nucleus by mRNA.

Translation: mRNA serves as a template on which amino acids are assembled in the sequence necessary
to produce the correct protein. The code carried by mRNA is translated into an amino acid sequence by
tRNA.

The communicative relationship between mRNA nucleotides and amino acids in a protein is called the
genetic code.

Genetic Code:
Genetic Code refers to the relationship between the sequence of nitrogenous bases (UCAG) in mRNA and the
sequence of amino acids in a polypeptide chain. In other words, the relationship between the 4 letters language of
nucleotides and twenty letters language of amino acids is known as genetic code.
Features of Genetic Code:

1. Genetic code is triplet in nature: The sequence of three nucleotides or nitrogen bases codes for one
amino acid. Ex: AAA, UAC, AAU, etc.

P avan Kumar K, Dept. Of Chemistry, GFGC Tumakuru. Page 6

 

VI Sem,B.Sc., Biochemistry Nucleic acids

2. Genetic code is universal: A particular codon codes for the same amino acid in all organisms from
bacteria to higher plants and animals. Ex: AUG codes for Methionine, UUU codes for phenylalanine. (some
exceptions in mitochondrial and
protozoan codons)

3. Genetic code is non-overlapping:
The nitrogen bases are read
continuously in groups of three
without sharing or overlapping.

4. Genetic code is degenerate: Most
of the amino acids are coded by more
than one codon, such codons are
called degenerate or synonymous
Codons and the phenomenon is called
degeneracy. Ex: Alanine is coded by
GCA, GCC, GCU and GCG.

5. Genetic code is comma less: The

codons are read continuously from
one end to other without any break or punctuation marks between the codons.

6. Genetic code is non-ambiguous or specific: A particular codon always codes for the same amino acid
without any mistake this characteristic is called nonambiguity.

7. Genetic code has an initiator codon: The protein synthesis starts or initiates by a particular codon
called initiator codon. Ex: AUG present near the 5′ end of the m-RNA act as initiator codon in most of
the organisms which codes for methionine. Therefore methionine is the first amino acid in most of the
proteins. Rarely GUG act as initiator codon in some bacteria which codes for formyl-methionine.

8. Genetic code has non-sense or terminator codons: The codons which do not code for any amino acid
and signal the termination of protein synthesis are called non-sense codons. Ex: UAA, UAG and UGA.

9. Principle of co linearity: The linear order of the nitrogen bases in DNA determines the linear order of
m-RNA codons. This in turn determines the linear order of amino acids in a polypeptide. This principle is
called co linearity.

Semi conservative replication of DNA:
The replication occurs during S-phase of Inter phase during
cell cycle. The process of replication is proved qualitatively by
J.Herbert Tayler and quantitatively by Meselson and Stahl.
Mechanism: The process of replication involves the following
steps.

Activation of nucleotides: The nucleotides of DNA
such as d-AMP, d-TMP, d-GMP and d-CMP are
activated and phosphorylated by ATP in to d-ATP, d-
TTP, d-GTP and d-CTP respectively.

Unwinding of DNA helix: The initiation of
replication or uncoiling of the DNA helix starts at a
specific point called origin of replication.The unwinding of DNA strands is catalyzed by Helicases. DNA
Gyrases (Topoisomerases) remove the coils that accumulate in front of the replication fork. The
separation of DNA strands during the initiation of replication forms a Y-shaped structure called
replication fork. The separated DNA strands act as master strands or template strands for the formation
of new strands.

P avan Kumar K, Dept. Of Chemistry, GFGC Tumakuru. Page 7

 

VI Sem,B.Sc., Biochemistry Nucleic acids

Formation of RNA-primer: The synthesis of new strand always proceeds in 5′”3′ direction. During the
initiation of replication a short segment of RNA is synthesized with the help of an enzyme RNA primase
called RNA primer.

Initiation and elongation of DNA strand: The DNA nucleotides are now added to exposed bases of
parental DNA strand from the end of RNA primer. This process is catalyzed by DNA Polymerase III and
Mg+2. The addition of nucleotides of DNA proceeds only in 5′”3′ direction. The two new strands of DNA
produced in opposite or antiparallel direction called bidirectional replication. In one strand the synthesis
of new DNA strand goes on continuously in 5′”3′ direction and this new strand is called leading strand. In
the opposite strand (3′”5′) the addition of nucleotides proceeds as short segments away from the
replication fork called lagging strand. The short single stranded fragments of DNA of the lagging strand
are called Okazaki fragments. The lagging strand has many RNA primers. Later the RNA primers are
removed and replaced by DNA nucleotides by an enzyme DNA polymerase I. The Okazaki fragments are
joined by DNA Ligase enzyme.

Termination of replication: The termination of replication is signaled by specific sequence of DNA
nucleotides. After replication the DNA polymerase II takes an editing role to remove abnormal nitrogen
bases and incorporate the normal bases (proof reading). This process is called genetic repair
mechanism.

Transcription:
The process of copying genetic information from one strand of the DNA into RNA is called transcription. (The
biosynthesis of RNA from DNA is called transcription.)

1. The transcription unit of DNA consists of three regions as a promoter, structural gene and a

terminator.
2. The transcription begins by the uncoiling of DNA strands due to the breakage of hydrogen bonds.
3. After the unwinding DNA dependent RNA polymerase is only capable of catalyzing the process of

elongation in association with initiation – factor (σ). It binds to promoter and initiate transcription.
4. One of the strand of DNA (3′”5′ strand) act as a template to produce RNA by complementary base

arrangement is called antisense strand
5. The strand of DNA which bears the same sequence as the RNA and not used as template during

transcription is called sense strand or coding strand.
6. The nucleotides of RNA are attracted and assembled complementary to template in the presence of DNA

dependent RNA-polymerase and Mg+. Only a short stretch of RNA remains bound to the enzyme.
7. The termination of RNA chain is brought about by certain terminator sequences on DNA & termination

factor (ρ).
8. Finally the new RNA formed and RNA-polymerase gets detached from the DNA. Again the two strands

of DNA rewind by the hydrogen bonds.

Translation:
P avan Kumar K, Dept. Of Chemistry, GFGC Tumakuru. Page 8

 

VI Sem,B.Sc., Biochemistry Nucleic acids

Translation refers to the process of polymerization of amino acids to form a polypeptide. The order and sequence
of amino acids are defined by the sequence of bases in the mRNA.

1. The amino acids are joined by a bond which is known as a peptide bond. Formation of a peptide bond
requires energy.

2. Therefore, in the first phase itself amino acids are activated in the presence of ATP and linked to their
cognate tRNA–a process commonly called as charging of tRNA or aminoacylation of tRNA to be more
specific. If two such charged tRNAs are brought close enough, the formation of peptide bond.

3. The presence of a catalyst would enhance the rate of peptide bond formation. The cellular factory
responsible for synthesizing proteins is the ribosome. The ribosome consists of structural RNAs and
about 80 different proteins.

4. Ribosome exists as two subunits; a large subunit and a small subunit. Total number of triplet codons =64
Number of sense codons =61 Number of non-sense codons =03(UAA, UAG & UGA)

5. When the small subunit encounters an mRNA, the process of translation of the mRNA to protein begins.
For initiation, the ribosome binds to the mRNA at the start codon (AUG) that is recognized only by the
initiator tRNA.

6. There are two sites in the large subunit, for
subsequent amino acids to bind to and thus,
be close enough to each other for the
formation of a peptide bond. Themribosome
also acts as a catalyst (23S rRNA in bacteria
is the enzyme- ribozyme) for the formation
of peptide bond. The ribosome moves from
codon to codon along the mRNA. Amino
acids are added one by one.

7. At the end, a release factor binds to the stop
codon, terminating translation and releasing
the complete polypeptide from the
ribosome.

8. An mRNA also has some additional sequences that are not translated and are referred as untranslated
regions (UTR). The UTRs are present at both 5′ –end (before start codon) and at 3′-end (after stop
codon). They are required for efficient translation process.

Previous year questions:
1. Write the partial structure of polyribonucleotide. [3M;2019]
2. What are nucleosides and nucleotides? Write the structure of AMP and CMP. [4M;2015,2016,2019]
3. Explain central dogma of molecular biology. [3M;2015]
4. Discuss smemiconservative method of DNA replication. [3M;2019]
5. Write the structure of heterocycle presnt only in DNA. [2M; 2015,2016]
6. Two strands of DNA are complimentary. Justify. [3M;2015]
7. Explain Watson and Crick model of DNA. [3M; 2014]
8. What are polynucleotides? Give their classification. [3M;2015]
9. What is chargaff’s rule of base equivalence? [3M;2014,2016,2018]
10. Write any two types of RNA and their functions? [3M;2016,2018]
11. Write the structures of polynucleotides? [4M;2018]
12. What is meant by transcription? [2M;2018]
13. Explain the terms leading strand and lagging strands in DNA replication. [3M;2016,2018]
14. ‘Genetic code is said to be degenerate and universal” justify. [3M;2016]
15. What are Okazaki fragments? [2M;2016]

P avan Kumar K, Dept. Of Chemistry, GFGC Tumakuru. Page 9

 

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