2. 2
NUCLEOTIDES
The basic unit of nucleic acids is nucleotides. They also act as
coenzymes, are part of energy carriers and some may function as
chemical messengers.
Nucleotide = Nitrogen base+ Pentose sugar + Phosphoric acid
The two types of pentose sugars in nucleotides are-ribose (C5H10O5) and
deoxyribose (C5H10O4)
It occur in à- furanose-state or pentagon ring with one oxygen and four
carbon atoms. The fifth carbon having-CH₂OH complement lies outside
the ring.
Carbon atom 2 contains two hydrogen in deoxyribose whereas in ribose
it has a hydroxyl (-OH) group instead of a second hydrogen.
Deoxyribose occurs only in those nucleotides which make up the
hereditary material DNA.
Ribose is found in nucleotides forming RNA and a number of other
compounds like AMP, ATP, NAD, NADP, FAD, CoA etc.
3. 3
Nitrogen Bases
Nitrogen bases are of two types, purines and pyrimidines
They are heterocyclic compound
They do not have OH group, but are still called bases as they have negatively
charged N and O which can accept positively charged atoms, i.e.. they act as
hydrogen-ion acceptors.
As per IUB nomenclature, unspecified purines are abbreviated as R and
unspecified pyrimidines as Y
Pyrimidine Bases
They are six membered rings with nitrogen at 1 and 3 positions.
Pyrimidine bases found in nucleic acids are mainly of three types:
1. Cytosine found in both DNA and RNA
2. Thymine found in DNA only.
3. Uracil found in RNA only.
The pyrimidine nucleus is as below
1. Cytosine: Cytosine is chemically 2-oxy-4-amino pyrimidine.
2. Thymine (5-methyl uracil): Chemically it is 2,4-dioxy 5-methyl pyrimidine
3. Uracil-Chemically it is 2, 4- dioxy pyrimidine.
4. 4
Purine Bases
The purine ring is more complex than pyrimidine ring
It is considered the product of fusion of a pyrimidine ring with an imidazole ring at
the 4 and 5 positions thus forming a 9 membered double ring structure.
It has a nitrogen at 1, 3, 7 and 9 positons.
The purines are of two types :
1. Adenine
2. Guanine
1. Adenine: Chemically it is 6-amino-purine.
2. Guanine: Chemically it 2-amino-6-oxy purine.
5. 5
Free pyrimidines and purines are weakly basic compounds, thus
are called bases.
Nucleic acids absorb UV light at wavelength near 260 nm.
The purines and pyrimidines are hydrophobic and relatively
insoluble in water at the near neutral pH of the cell.
6. 6
Nucleoside (Nitrogen Base Pentose Sugar)
The nitrogen base combines with the sugar molecule at its carbon atom 1' in a β-N
glycosidic linkage (C-N-C) by one of its nitrogen atoms (usually 1 in pyrimidines and
9 in purines).
Depending on the type of pentose sugar, nucleosides are differentiated into
ribonucleosides and deoxyribonucleosides.
Uracil produces nucleoside with only ribose sugars .
Thymine similarly forms nucleoside with only deoxyribose sugar.
Other nitrogen bases produce nucleosides with both ribose and deoxyribose sugars. .
The various nucleosides are-
1. Adenosine (adenine ribose),
2. Deoxyadenosine (adenine deoxyribose)
3. Guanosine (guanine ribose)
4. Deoxyguanosine (guanine deoxyribose)
5. Uridine (uracil ribose)
6. Deoxythymidine (thymine+ deoxyribose)
7. Cytidine (cytosine ribose).
8. Deoxycytidine (cytosine deoxyribose)
7. 7
Nucleotides are phosphoric acid esters of nucleosides and therefore also called
nucleoside phosphates.
Phosphate attaches to the sugar molecule at its 5 carbon atom, but rarely may link to
3 carbon atom or to 2 carbon atom also.
The bond between the phosphate and hydroxyl group of sugar is an ester bond. As
there is one such ester bond on either side, it is called phosphodiester bond.
The number of phosphoric or phosphate residues may be up to three in free
occurring nucleotides.
Nucleotides may be ribonucleotides (ribotides) or deoxyribo-nucleotides (in
deoxyribotides) depending on the pentose sugar present.
The various nucleotides are:-
1. adenylic acid (adenosine monophosphate or AMP)
2. deoxyadenylic acid (dAMP)
3. guanylic acid (guanosine monophosphate of GMP)
4. deoxyguanylic acid (dGMP)
5. uridylic acid (uridine monophosphate or UMP)
6. deoxythymidylic acid (deoxythymidine monophosphate or dTMP)
7. cytidylic acid (cytidine monophosphate or CMP)
8. deoxycytidylic acid (dCMP)
8. 8
Higher Nucleotides
Nucleotides having more than one phosphate group are called
higher nucleotides and they occur in the free state.
They have high-energy bonds between the 2 and 3 phosphates and
so these function as energy carriers
Classification
1. Adenosine nucleotides. ATP, ADP, AMP and Cyclic AMP
2. Guanosine nucleotides. GTP, GDP, GMP and Cyclic GMP
3. Uridine nucleotides. UTP, UDP, UMP, UDP-G
4. Cytidine nucleotides. CTP, CDP, CMP and certain deoxy CDP
derivatives of glucose, choline,
ethanolamine.
9. 9
Functions of Nucleotides
1. They are building blocks of nucleic acids, ribonucleotides for RNAs
while deoxyribonucleotide produce DNA
2. Cyclic AMP cAMP) is the mediator of hormone action by acting as a
second messenger
3. Cyclic GMP (cGMP) is functional in Ca2+ or Calmodulin mediated
chemical reaction
4. Higher nucleotides behave as energy carriers, ATP is known an energy
currency of the cell.
5. Nucleotides produced by nicotinamide and riboflavin function as
coenzymes (NAD+, NADP+, FMN and FAD) of dehydrogenases and
oxidases.
6. CoA from pantothenic acid functions as Acyl group carrier.
7. UDP and ADP are involved in synthesis of polysaccharides while CDP
and CTP are required in phospholipid synthesis.
10. 10
Discovery of DNA
History
Nucleic acids first isolated by Friedrich Miescher from pus cells. He named it as Nuclein.
Name Nucleic acid was given by Altmann.
Presence of purine and pyrimidine bases in nucleic acids was discovered by Fisher Levene
found that deoxyribose nucleic acid contains phosphoric acid and deoxyribose sugar. He
characterized four types of nucleotides.
Chargaft-Found that purines = pyrimidine in DNA and also adenine= thymine; Guanine =
Cytosine.
Astbury-Found by x-ray diffraction that DNA has many nucleotides which are arranged
perpendicular to the long axis of the molecule and separated from each other by 0.34 nm.
In 1953,Wilkins and Franklin got very fine X-ray photographs of DNA. The photographs
showed that DNA is a helix with a width of 2 nm. One tum of helix was 3.4 nm with 10
layers of bases stacked in it.
Watson and Crick, received Nobel Prize of Medicine and Physiology (1962) for building a
double helix model of DNA.
Watson and Crick based their model on the X-ray diffraction data produced by Maurice
Wilkins and Rosalind Franklin. They published their data in the American Journal "The
Nature on the basis of their work on E. coli.
In vitro synthesis of DNA-Korenberg (1959)
11. 11
Important features of Watson and Crick double helical model of DNA
1. The double helix comprises of two polynucleotide chains
2. The two strands (polynucleotide chains) of double helix are antiparallel
(5՛ 3՛ while opposite one from 3՛ 5՛)
3. Each polynucleotide chain has a sugar-phosphate backbone with
nitrogenous bases directed inside the helix and the sugar phosphate on the
outside. These bases are stacked in a pile on top of each other.
4. The nitrogenous bases of two antiparallel polynucleotide strands are
linked through hydrogen bonds. There are two hydrogen bonds between A
and T. and three between G and C. The hydrogen bonds are the attractive
forces between the two polynucleotides of double helix and serve in
holding structure together. The plane of one base pair stacks over the other
in double helix. This, in addition to H-bonds, confers stability to the
helical structure.
12. 6. The two polynucleotides in a double helix are complementary.
The sequence of nitrogenous bases in one determines the
sequence of the nitrogenous bases in the other Complimentary
base pairing is of fundamental importance in molecular genetics.
7. Ten base pair occur per turn of helix (34A0). The spacing between
adjacent base pairs is 3.4A0. The helix is 20A0 in diameter.
8. The double helix has two different grooves: a major groove (2.2
nm) and a minor groove (1.2 nm) wide. Minor groove-site of
attachment of histone proteins and Major groove-site of
attachtmennt of non-histone proteins.
9. DNA is negatively charged and dextrorotatory.
10. Molecular configuration of DNA is 3D
11. DNA is acidic. For is compaction, it requires basic proteins.
12
13. Linear and Circular DNA.
DNA closed covalently at its two ends is called circular DNA
It occurs in nucleoid of bacteria and randomly in viruses, mitochondria and plastids. In
linear DNA the two ends are free. It is seen in eukaryotic cells, some prokaryotes and cell
organelles.
The DNA in coiled and super-coiled to get accommodated in small space .
In prokaryotes DNA occurs in nucleoid and plasmids and is circular
In eukaryotes, it occurs mainly in the chromatin of nucleus (linear) and small quantities
are found in mitochondria and plastids (circular or linear).
13
14. 14
Types of DNA
The model proposed by Watson and Crick in the DNA duplex model.
It is a right handed spiral and is called B-DNA.
In this model the base pairs lie at nearly right angles to the axis
DNA may also exist in other alternative forms.
The important features and differences among en are summarized below:
15. Differences between Prokaryotic DNA & Eukaryotic DNA
Prokaryotic DNA
DNA content is small, less than 0.1
pg.
DNA does not occur in any organelle
It lies freely inside the cytoplasm
It consists of a single molecule.
It is naked.
It is generally circular.
Introns are absent.
Small DNA segments or plasmids
may occur.
Eukaryotic DNA
DNA content is comparatively high, more
than 1 pg.
It occurs only inside nucleus and
semiautonomous cell organelles.
Eukaryotic DNA has no direct contact with
cytoplasm
Eukaryotic DNA has several different
molecules.
Nuclear DNA is associated with histones
while organelle DNA is naked.
Nuclear DNA is linear. Organelle DNA can
be circular or linear.
Eukaryotic DNA contains superfluous
regions or introns
Plasmids are generally absent.
15
16. 16
Role of DNA
DNA is the genetic material which carries all the hereditary information. The
genetic information is coded in the arrangement of its nitrogen bases.
DNA has a unique property of replication or production of carbon copies. This
is essential for transfer of genetic information from one cell to its daughter and
from one generation to the next. Replication is semiconservative, that is, in
each new duplex one strand is derived from the parent duplex while the second
strand is formed anew.
DNA occurs inside chromosomes. During meiosis, crossing over gives rise to
new combination of genes called recombinations.
Changes in sequence of nitrogen bases due to addition, deletion or wrong
replication give rise to mutations. Mutations are the fountain head of all
variations and evolution.
DNA gives rise to RNAs through the process of transcription.
It controls the metabolic reactions of the cell through the help of specific
RNAs, synthesis of specific proteins, enzymes and hormones.
Due to differential functioning of some specific regions of DNA or genes,
different parts of the organisms get differentiated in shape, size and functions.
17. Ribonucleic Acid (RNA)
RNA is a single strand or chain which is formed by end to end polymerisation of
a number of ribonucleotides or ribotides.
The polynucleotide is characterized by the presence of ribose sugar and uracil
instead of thymine.
It is formed over sense strand DNA template through the process of transcription.
It is followed by processing to produce different types of RNAs.
A strand of RNA contains 70 -12000 ribonucleotides.
Four types of ribonucleotides occur in RNA. They are adenosine monophosphate,
guanosine monophosphate, uridine monophosphate and cytidine monophosphate.
A ribonucleotide is formed of ribose sugar, phosphoric acid and a nitrogen base.
The four nitrogen bases present in RNA are adenine, guanine (purines), cytosine
and uracil (pyrimidines).
The union of nitrogen base is with carbon 1 of ribose sugar by glycosidic bond
through 3'N or 9'N region.
Phosphate combines with carbon 5' of its sugar and carbon 3 of next sugar
(phosphodiester bond) similar to one found in DNA strand.
17
18. Nitrogen bases can be arranged in any sequence so that there is a high degree of
specificity as found in DNA.
Purine and pyrimidine ratio is not unity in RNA.
Sequence of nitrogen bases found on RNA strand is complementary to their
sequence on DNA template. For example, a sequence of ATACTG of DNA
template shall appear as UAUGAC over RNA.
There are six types of RNAs- ribosomal, transfer, messenger, genomic, small
nuclear and small cytoplasmic RNAS.
1. Ribosomal RNA (rRNA)
Ribosomal RNA constitutes 70-80% of the total RNA content of the cell.
It is a single stranded poly-ribonucleotide which is constituent of ribosomes.
It lies coiled in between and over the protein molecules.
Depending upon the sedimentation coefficient, rRNA of eukaryotic ribosomes is
of four types-28S, 18S, 5.8S and 5S.
rRNA is transcribed in the form of a longer chain of 45S unit in eukaryotes and
30S unit in prokaryotes.
It is then broken into 2-3 parts. 5S unit is often transcribed separately.
rRNAs help tRNA and mRNA in the synthesis of proteins over the ribosomes.
18
19. 2. Transfer RNA (RNA)
It is also called soluble or sRNA.
There are over 100 types of tRNA.
Transfer RNA constitutes about 15% of the total RNA.
tRNA is the smallest RNA with 70-85 nucleotides and sedimentation coefficient
of 4S.
The nitrogen bases of some nucleotides get modified. This causes coiling of
otherwise single-stranded tRNA to form L-shaped or clover leaf configuration.
tRNA has an anti codon made up of three nitrogen bases for recognizing and
attaching to the codon of mRNA.
There is a site for binding amino acid.
It lies at the 3' end opposite the anticodon and has CCa-OH group.
Amino acid or AA-binding site and anti codon are the two recognition sites of
tRNA.
There are also two loops, one for attaching to ribosome (Tѱ C, pseudouridine
loop) and the second for binding to an enzyme (DHU or dihydrouridine loop).
tRNA is meant for transferring amino acids to ribosomes for synthesis of
polypeptides. 19
20. 3. Messenger RNA (mRNA, Brennier and Jacob, 1960)
It is a long RNA that hardly forms 5% of the total RNA
mRNA brings instructions from the DNA for the formation of a particular type of
polypeptide. The instructions are present in the base sequence of its nucleotides.
It is called genetic code. Three adjacent nitrogen bases specify a particular amino
acid.
Formation of polypeptide occurs over the ribosome.
mRNA gets attached to ribosome, tRNAs are induced to bring amino acids in a
particular sequence according to the sequence of codons present over mRNA
mRNA has methylated region at the 5՛ terminus.
It functions as a cap for attachment with ribosome, Cap is followed by an
initiation codon (AUG or GUG) either immediately or after a small noncoding
region. Then there is coding region followed by termination codon (UAA, UAG,
or UGA).
A small noncoding region and poly A area occur at the 3' terminus
A mRNA may specify only a single polypeptide or a number of them. The former
is called monocistronic while the latter is known as polycistronic.
20
21. 4. Genomic or Genetic RNA
It is found in some viruses called riboviruses.
Genetic RNA may be single stranded (eg. Tobacco Mosaic Virus or
TMV) or double stranded (eg. Rheovirus).
Genomic RNA acts as a hereditary material. It may not replicate
directly, but first forms DNA for producing RNA of its own types.
5. Small Nuclear RNA (snRNA)
It remains inside the nucleus.
After getting complexed with a few protein molecules, snRNA
takes part in splicing and processing other RNAS.
6. Small Cytoplasmic RNA (scRNA)
It comes out in the cytoplasm, forms association with a few protein
molecules and produce signal recognition particles involved in
forming secretory proteins.
21
22. Role of RNA
RNAs are involved in expression of genetic code of DNA by
forming specific proteins.
RNA is genomic material in some viruses (eg.. TMV).
RNA is essential for folding of bacterial DNA to form nucleoid
Some RNA have enzyme activity, e.g. Ribozyme, Ribonuclease-P.
RNA primer is essential for DNA replication.
Ribosomes are built up of RNA called ribosomal RNA.
22
23. Differences between DNA & RNA
DNA
• It usually occurs inside nucleus
and some cell organelles
• DNA is the genetic material.
• It is double stranded with the
exception of some viruses (eg,
x174)
• DNA shows regular helical
coiling .
• It is Fuelgen positive.
• DNA forms chromosomes or
similar structures.
RNA
• Very little RNA occurs inside nucleus.
Most of it is found in the cytoplasm.
• RNA is not the genetic material except
in certain viruses, e.g.. Reovirus hall
• RNA is single stranded with the
exception of some viruses (eg. double
stranded in Reovirus).
• There is no regular coiling except in
parts of tRNA
• RNA is Fuelgen negative.
• rRNA forms ribosomes.
23
24. • DNA contains over a million
nucleotides.
• DNA is of only two types, nuclear and
extra nuclear.
• It contains deoxyribose sugar
• Nitrogen base thymine occurs in DNA
along with three others-adenine,
cytosine and guanine.
• Unusual bases are very few or absent.
• Renaturation after melting is slow.
• Hydrogen bonds are formed between
complementary nitrogen bases of the
opposite strands of DNA (A-T,C-G)
• Depending upon the type, RNA
contains 70-12000 nucleotides.
• There are at least three types of RNA-
mRNA, rRNA and tRNA.
• It contains ribose sugar.
• Thymine is replaced by uracil in
RNA. The other three are adenine,
cytosine and guanine.
• Many unusual or modified bases are
often present.
• It is quite fast.
• Base pairing through hydrogen bonds
occurs only in the coiled parts.
DNA RNA
Differences between DNA & RNA
24
25. • It replicates to form new DNA molecules.
• DNA transcribes genetic information to
RNA.
• DNA controls heredity, evolution,
metabolism, structure and differentiation
• Its quantity is fixed for cell
• DNA controls metabolism and genetics
including variations
• Purine and pyrimidine bases are in equal
number
• It can be hydrolysed by enzyme DNAase
• 3H precursor is 3H-thymidine
• It cannot replicate itself except in
RNA-RNA viruses.
• RNA translates the transcribed
message for forming polypeptides.
• RNA controls only protein synthesis.
• The quantity of RNA of a cell is
variable.
• It only controls metabolism under
instructions from DNA
• There is no proportionality between
purine and pyrimidine bases.
• RNA is hydrolysed by RNAase
• 3H precursor is 3H-uridine.
25
DNA RNA
Differences between DNA & RNA
