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Nucleic Acid and Dna

Nucleic acids, including DNA and RNA, are essential for heredity, protein synthesis, and cellular functions. DNA serves as the genetic blueprint, while RNA plays a crucial role in translating that information into proteins. The structure and function of these molecules are defined by their components, including sugars, nitrogenous bases, and phosphoric acid, as well as their unique bonding and pairing mechanisms.

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17 views11 pages

Nucleic Acid and Dna

Nucleic acids, including DNA and RNA, are essential for heredity, protein synthesis, and cellular functions. DNA serves as the genetic blueprint, while RNA plays a crucial role in translating that information into proteins. The structure and function of these molecules are defined by their components, including sugars, nitrogenous bases, and phosphoric acid, as well as their unique bonding and pairing mechanisms.

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NUCLEIC ACIDS

There are two types of nucleic acids viz., DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid).
Functions of Nucleic acids

1. DNA is the chemical basis of heredity, organised into genes. They are the basic units
of genetic information
2. The genes control the protein synthesis through RNA, as shown below:
DNA→RNA→Protein
3. Used in the identification of species of organisms
4. All cellular functions are under the control of DNA
5. In eukaryotes, DNA is seen inside the nucleus and also seen in chloroplast and
mitochondrion.

Components of NA

Nucleic acids are composed of:

1. Pentose sugar:
➢ Two types of pentoses are found in nucleic acids.
➢ The sugar present in RNA is D-ribose, while DNA contains 2’-deoxy-D-ribose.
➢ The difference lies in the presence/absence of the hydroxyl group at position 2
of the sugar ring.
➢ The oxygen atom present at the second carbon of D-ribose is missing in 2’-
deoxy-D-ribose and hence, it is named as 2’-deoxy-D-ribose.
2. Nitrogenous bases:
➢ Nitrogenous bases are aromatic heterocyclic compounds, grouped into two
classes based on their chemical structure, viz., purines [adenine (A) and guanine
(G)] and pyrimidines [thymine (T) cytosine (C) and uracil (U)].
➢ Pyrimidines have a six member ring and they are numbered in clockwise
direction.
➢ Purines have fused five and six member rings and they are numbered in anti-
clockwise direction.
➢ DNA contains four different bases viz., A, G, C and T, while RNA contains the
same bases, except for thymine (T) which is replaced by uracil (U).
3. Phosphoric acid: Phosphoric acid (H3PO4) has three reactive (-OH) groups of which
two are involved in forming the sugar phosphate backbone of DNA.

Ribose sugar Deoxyribose sugar Phosphoric acid

Nitrogenous bases

NUCLEOSIDES (Sugar +Nitrogenous base = nucleoside)


➢ In nucleic acids, organic bases are linked with the pentose molecules by β-N-glycosidic
bonds or covalent bonds.
➢ The N9 of purine ring binds with the C1 of pentose sugar, while N1 of pyrimidine bonds
with C1 of pentose.
➢ The linkage between ribose and the different organic bases yield ribosides, while those
between deoxyribose and the organic bases yield deoxyribosides.
Base Ribonucleosides Deoxyribonucleosides
Adenine Adenosine Deoxyadenosine
Guanine Guanosine Deoxyguanosine
Cytosine Cytidine Deoxycytidine
Thymine/Uracil Uridine Deoxythymidine
NUCLEOTIDES (Nucoleoside + phosphate = nucleotide)
➢ A nucleotide is formed when a phosphate group is attached to either the 3’C or the 5’C
of the pentose molecule of a nucleoside.
➢ The hydroxyl groups of adenosine are esterified with phosphates to produce 5’ or 3’
mono phosphates. 5’ hydroxyl is the most commonly esterified, hence 5’ is usually
omitted while writing nucleotide names.
➢ The nucleotides produced by the different ribosides are together known as
ribonucleotides or ribotides.
➢ Similarly, the nucleotides formed by the four deoxyribosides are called as
deoxyribonucleotides or deoxyribotides

Base Ribonucleotides Deoxyribonucleotides


Adenine Adenosine monophosphate (AMP) Deoxyadenosine monophosphate (dAMP)
Guanine Guanosine monophosphate (GMP) Deoxyguanosine monophosphate (dGMP)
Cytosine Cytidine monophosphate (CMP) Deoxycytidine monophosphate (dCMP)
Thymine/ Uridine monophosphate (UMP) Deoxythymidine monophosphate (dTMP)
Uracil

DNA is a polymer of deoxyribonucleotides, wherein the nucleotides are held together by 3’,
5’-phosphodiester bridges

Phosphodiester bond and complementary base pairing

➢ DNA is a polymer of deoxyribonucleotides, wherein the nucleotides are held together


by 3’, 5’-phosphodiester bridges
Chargaff’s rule of DNA composition

➢ Erwin Chargaff in 1940s quantitatively analysed the DNA hydrolysates from different
species. He observed that in all the species, the DNA had equal numbers of adenine
and thymine residues (A is equal to T) and equal numbers of guanine and cytosine
residues (G is equal to C).
➢ This is known as Chargaff’s rule of molar equivalence between the purine and
pyrimidines in DNA structure.

Watson and Crick model of DNA structure

Watson and Crick used chemical analyses and X-ray crystallographic studies of Wilkins and
Franklin to build the models of DNA molecule. In 1953, they proposed the double-helix model
of DNA, for which they were awarded the Nobel Prize in 1962. The main features of this
model are summarized below:
1. DNA is a right-handed double helix. It consists of 2 polydeoxyribonucleotide chains
twisted around each other on a common axis.
2. The two strands are antiparallel, i.e., one strand runs in the 5’ to 3’ direction, while the
other in 3’ to 5’ direction.
3. The diameter (or width) of this helix is 20 Å ( 2 nm)
4. Each turn (pitch) of the helix is 34 Å (3.4 nm) with 10 pairs of nucleotides, each pair
placed at a distance of about 3.4 Å.
5. Each strand of DNA has a hydrophilic deoxyribose phosphate backbone (3’-5’
phosphodiester bonds) on the outside (periphery) of the molecule, while the
hydrophobic bases are stacked inside (core).
6. The two polynucleotide chains are not identical, but complementary to each other due
to base pairing.
7. The two strands are held together by hydrogen bonds formed by complementary base
pairs. The A-T pair has 2 hydrogen bonds, while G-C pair has 3 hydrogen bonds (A=T,
G≡C). The G≡C is stronger by about 50 % than A=T.
8. The hydrogen bonds are formed only between purine and pyrimidine bases
9. The Watson and Crick model, proves the Chargaff’s rule ie., the content of adenine
equals to that of thymine and guanine equals to cytosine.
10. The genetic information resides on one of the 2 strands known as template strand. The
DNA has major grooves and minor grooves along the phosphodiester backbone.
Proteins interact with DNA at these grooves.

Watson and Crick model of DNA


Forms of DNA
➢ DNA exists in 6 different forms viz, A, B, C, D, E and Z
➢ Among these B, A and Z forms are important
➢ B form of DNA is described by Watson and Crick and it is the predominant form
➢ B form is a right-handed double helix with 10 base pairs per turn, spanning a
distance of 3.4 nm and a width of 2 nm.
➢ A form is also a right-handed helix. It contains 11 base pairs per turn. There is a
tilting of the base pairs by 20° away from the central axis.
➢ Z form is a left-handed helix and contains 12 base pairs per turn. The
polynucleotide strands of DNA move in a somewhat ‘Zig-Zag” fashion, hence the
name Z-DNA.
➢ Plasmids are small, circular, double-stranded DNA molecules that are distinct from
a cell's chromosomal DNA and present in microbes.

Size of DNA

➢ A base pair has a molecular weight of 660 daltons.


➢ In general, the size of the DNA is referred to by its sequence length in bases (base
pairs). The sequence length of DNA varies with the species

➢ One kilobase (kb) is equal to 1000 bases


➢ One megabase (Mb) is equal to 1 million
➢ One gigabase (Gb) is equal to 1 billion bases

➢ Viruses - range from 1,682 bases to 1,290,000 bases


➢ The size of the Viruses range from 1,682 bases to 1,290,000 bases
➢ The size of the E.coli genome is ~4 Mb
➢ The size of the human genome is ~3.4 Gb

Melting Temperature (Tm)

➢ It is the temperature at which half of the helical structure of DNA is lost.


➢ Since G-C pairs are more stable (because of 3 hydrogen bonds) that A-T pairs, the Tm
is greater for DNA with higher GC content.
Renaturation

➢ Renaturation or reannealing is the process in which the separated or 2 complementary


DNA strands combine to form a double helix.

Hyperchromic effect

The absorbance of DNA is read at 260 nm because it shows maximum absorbance at this
wavelength. Loss of helical structure (double-stranded to single-stranded form) could be
measured by an increase in absorbance at 260 nm. This is called the hyperchromic effect.

Hypochromic effect

It is the decrease in absorbance at 260 nm, and it could be observed when the DNA is in
double-stranded or helical form.

DNA Functions

1. DNA is the chemical basis of heredity, organised into genes. They are the basic units
of genetic information

2. The genes control the protein synthesis through RNA, as shown:


DNA→RNA→Protein

3. Used in the identification of species of organisms

4. All cellular functions are under the control of DNA

5. In eukaryotes, DNA is seen inside the nucleus and also seen in chloroplast and
mitochondrion

STRUCTURE OF RNA

➢ RNA is a polymer of ribonucleotides, held together by 3’5’-phosphodiester bridges.


➢ RNAs are synthesised from DNA and are involved in protein synthesis. RNAs vary
in their structure.

The major difference between DNA and RNA:


Characteristic DNA RNA
Pentose Deoxyribose ribose
Base A,T,G,C. Thymine A,U,G,C. Thymine is replaced by Uracil.
present, Uracil absent
Number of Generally double Generally single stranded
strands stranded
Chargaff’s rule obeyed Not obeyed due to single stranded nature
Susceptibility to Not susceptible to Alkali hydrolyzes RNA to 2’,3’ – cyclic
alkali hydrolysis hydrolysis diesters
Orcinol colour No colour Gives green colour in orcinol reaction due to
reaction ribose
Function Genetic material only Generally involved in protein biosynthesis.
Genetic material in some viruses
Origin Replication of (i) Genetic RNA either through transcription
preexisting DNA of DNA or through replication of RNA
(mostly) (ii) Non-genetic RNA from transcription of
DNA

Functions and types of RNA


1. RNA performs several functions, especially in protein synthesis which are carried out
by three different types of RNA viz., mRNA, tRNA and rRNA
➢ Messenger RNA (mRNA) (5-10 %) : Specifies the sequence fo amino acids in the
protein synthesis.
➢ Transfer RNA (tRNA) (10-20 %) : Delivers the amino acids to ribosomes for
protein synthesis.
➢ Ribosomal RNA (rRNA) (50 – 80 %): It is found in combination with proteins
and it associated with the structure and function of ribosomes, the factories of
protein synthesis.
2. Apart from these, human cell contain small nuclear RNA (snRNA) which are involved
in RNA processing.
3. RNA as ribonucleoprotein participates in the post-translational modification of other
RNAs
4. RNA (not DNA) is the genetic material carrying hereditary information in many
viruses.
mRNA

1. mRNA is synthesized in the nucleus of eukaryotes as heterogenous nuclear RNA or


hnRNA.
2. They are synthesised from DNA as a template by the enzyme RNA polymerase
3. hnRNA on processing (Splicing) liberates the functional mRNA which enter the
cytoplasm to participate in protein synthesis.
4. mRNA is single stranded, it has high molecular weight with short half life.
5. Prokaryotic mRNA is polycistronic in nature ie., same mRNA codes for more than
one polypeptide
6. Eukaryotic mRNA is monocistronic in nature ie., one mRNA codes for one
polypeptide
7. Eukaryotic mRNA is capped at the 5’ terminal end by 7-methylguanosine
triphosphate. This cap helps to prevent the hydrolysis of mRNA by 5’-exonucleases.
The cap helps in the binding and recognition of mRNA for protein synthesis (for
initiation of translation).
8. 3’ terminal end of mRNA contains a polymer of adenylate residues (25-250
nucleotides) which is known as poly (A) tail. The enzyme polyadenylate polymerase
adds “A” residues to the 3’ end of mRNA. This provides stability to mRNA, besides
preventing it from the attack of 3’ exonucleases.
9. Splicing: The hnRNA is lengthy than mRNA, because of the intervening sequence or
introns. Introns are the non coding region of a gene. They are much longer than the
exons, which are the coding region of the gene.
10. These introns are excised from the RNA by splicing process with the help of a small
nuclear RNA (snRNA), in order to produce the functional mRNA.

tRNA

➢ tRNA molecule contains 71-80 nucleotides (mostly 75) with a molecular weight of
about 25000.
➢ there are at least 20 species of tRNAs corresponding to 20 amino acids present in
protein structure
➢ the structure of tRNA was first elucidate by Holley (for alalnine)
➢ the structure of tRNA resembles a clover leaf
➢ it mainly contains 4 arms, each arm contains a base paired stem
➢ (i) Acceptor arm: this arm is capped with a sequence CCA (5’ – 3’). The amino acid
is attached to the acceptor arm
➢ (ii) Anticodon arm: This arm with the three specific nucleotide bases (anticodon), is
responsible for the recognition of triplet codon of mRNA. The codon and anticodon
are complementary to each other
➢ (iii) D arm: it is named due to the presence of dihydrouridine
➢ (iv) TψC arm: this arm contains a sequence of T, pseudouridine (represented by psi,
ψ) and C.,
➢ (v) Variable arm: This arm is the most variable in tRNA. Based on this variability,
tRNAs are classified into 2 categories: Class I tRNAs – most predominant (about
75%) form with 3-5 base pairs length. Class II tRNAs – they contain 13-20 base pair
long.
➢ Base pairs in tRNA: The structure of tRNA is maintained due to the complementary
base pairing in the arms. The four arms with their respective base pairs are given
below:
➢ Acceptor arm – 7 bp
➢ TψC arm – 5 bp
➢ Anticodon arm – 5 bp
➢ D arm – 4 bp

Structure of tRNA

Ribosomal RNA (rRNA)

➢ Ribosomes are the factories of protein synthesis


➢ They are composed of two major nucleoprotein complexes – 60S subunit and 40S
subunit
➢ The 60S subunit contains 28S rRNA and 5S rRNA and 5.8S rRNA
➢ 40 S subunit contains 18 S rRNA
➢ The function of rRNAs: It is believed to play a significant role in the binding of
mRNA to ribosomes and protein synthesis.

THE CENTRAL DOGMA

➢ DNA ultimately controls every aspect of cellular function, primarily through


protein synthesis.
➢ In 1958, Crick proposed that the central dogma of molecular biology which
states that the information present in DNA (in the form of base sequence) is
transferred to RNA by transcription and then from RNA, it is transferred to
protein by translation (in the form of amino acid sequence).
➢ This information does not flow in the reverse direction i.e. from protein to RNA
to DNA.
➢ DNA molecules provide the information for their own replication.
➢ The process of reverse transcription (RNA to DNA) has been discovered in
RNA tumor virus and certain RNA viruses replicate purely through the RNA
form.

Central Dogma of life

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