Each nucleotide is composed of three parts: nitrogenous base like purine and pyrimidine, a sugar and a phosphate group

1. Dr. Pawan Kumar Kanaujia
Assistant Professor
Molecular Biology
(Theory)
Molecular basis of life:
Structures and function of DNA and RNA

2. Unit 1- Molecular basis of life:
Structures and function of DNA and RNA

3. Introduction
 DNA molecule is a hereditary material which is transmitted from
generation to generation.
 It is the largest molecule in the living cell comprising of several
millions of nucleotide chain.
 It is in the sequence of nucleotides in the polymers where genetic
information carried by chromosomes is located.
 Each nucleotide is composed of three parts: nitrogenous base like
purine and pyrimidine, a sugar (deoxyribose) and a phosphate group.
 The nitrogenous base determines the identity of the nucleotide.
 RNA is a nucleic acid having almost similar structure as that of DNA
molecule except a uracil base instead of thymine.
 There are three different species of RNA. All these are essential in
the normal functioning of the cell especially in protein synthesis.
 RNA molecule is not the information carrier excepting in few viruses.
 Moreover these molecules are less stable compared to DNA
molecule.
Further explanation regarding their structure and functions are given in
the following slides.

4. Building Blocks
of
Nucleic Acids
Fig: (a) Chemical structures of the pyrimidines and purines that serve as
the nitrogenous bases in RNA and DNA. The convention for numbering
carbon and nitrogen atoms making up the two categories of bases is shown
within the structures that appear on the left. (b) Chemical ring structures of
ribose and 2-deoxyribose, which serve as the pentose sugars in RNA and
DNA, respectively.

5. Nucleic Acids

6. Fig: Structures and names of the nucleosides and nucleotides of RNA and DNA.

7. If a molecule is composed of a purine or pyrimidine base and a
ribose or deoxyribose sugar, the chemical unit is called a nucleoside.
If a phosphate group is added to the nucleoside, the molecule is now
called a nucleotide.
Nucleosides and nucleotides are named according to the specific
nitrogenous base (A, T, G, C, or U) that is part of the molecule.
The bonding between components of a nucleotide is highly specific.
The C-1 atom of the sugar is involved in the chemical linkage to the
nitrogenous base. If the base is a purine, the N-9 atom is covalently
bonded to the sugar; if the base is a pyrimidine, the N-1 atom bonds
to the sugar.
In deoxyribonucleotides, the phosphate group may be bonded to
the C-2, C-3, or C-5 atom of the sugar.

8. Deoxyribonucleic Acid (DNA):
Watson and Crick in 1953, discovered the 3-dimentional model
of DNA molecule and postulated that it consist of two helical
strands wound around the same axis forming a right handed
double helical structure.
The hydrophilic backbone of alternating deoxyribose and
phosphate groups are on the exterior of the double helix facing
the surrounding aqueous media.
The purine and pyrimidine bases of both the strands are stacked
in the interior of the double helix, with their hydrophobic bases
forming nearly planar ring structures very close together and
perpendicular to the long DNA axis.
The pairing of the two strands form major and the minor grooves
on the surface of the duplex. An individual nucleotide base of one
strand is paired with the same plane with base of the other strand.
The vertically stacked bases inside the double helix is around
3.4Å apart and 34Å constitutes a full complete turn bearing
10base pairs.

9. In1953, The discovery of the structure of DNA or
postulated a three dimensional model of DNA structure
• James Watson – American ornithologist
• Francis Crick – British Physicist
Watson and
Crick with their
DNA model

10. DNA structure:
Nucleotides
Nucleosides
Phosphate
Sugar
(2’deoxyribose)
Bases
Purines
Adenine
Guanine
Pyrimidines
Thymine
Cytosine

11. Nucleotides:
Deoxyribonucleic acid (DNA) is structurally and functionally complex
macromolecule molecule found in various organisms.
It is much more abundant in eukaryotes as compared to the
prokaryotes.
Therefore, it has to have certain property (i.e. super coiling) by which
it can suitably be accommodated in the cell.
It is made of four different types of building blocks so called
nucleotides.
Nucleotides are composed of nucleosides (bases + 2’deoxyribose)
and phosphate groups.

12. The four types of bases composing DNA are:
Purines (double ring structure):
Adenine and Guanine
Pyrimidines (single ring structure):
Thymine and Cytosine
(Source:
http://www.ch.cam.ac.uk/magnus/molecules/nucleic/bases.html.,n.d.)
The sugar is a 2′-deoxyribose and is phosphorylated at its 5’hydroxyl
group. Free nucleotides contain either one, two, or three phosphates
indicating mono, di, or triphosphate form of nucleotide.

13. Nucleoside Diphosphates and Triphosphates
Nucleotides are also described by the term nucleoside monophosphate
(NMP). The addition of one or two phosphate groups results in
nucleoside diphosphates (NDPs) and triphosphates (NTPs), respectively.
The triphosphate form is significant because it serves as the precursor
molecule during nucleic acid synthesis within the cell. In addition,
adenosine triphosphate (ATP) and guanosine triphosphate (GTP) are
important in cell bioenergetics because of the large amount of energy
involved in adding or removing the terminal phosphate group. The
hydrolysis of ATP or GTP to ADP or GDP and inorganic phosphate (Pi) is
accompanied by the release of a large amount of energy in the cell.
Fig: Structures of nucleoside diphosphates and triphosphates. Deoxythymidine
diphosphate and adenosine triphosphate are diagrammed here.

14. Polynucleotide chain showing specific base pairing:
Guanine pairs with Cytosine by 3-hydrogen bonds (G=C) and Adenine
pairs with Thymine by 2-hydrogen bonds (A=T).
Thus the m.p. of the G=C base pair is higher as compared to the A=T
base pair.
The DNA strands are antiparallel, running two strands in the opposite
directions.
The bases in the two antiparallel strands are complementary to each
other.
That is wherever Adenine occurs in one chain, Thymine is found in
the other chain. Similarly. Wherever Guanine occurs in one chain,
Cytosine is found in the other chain.
This complementarity of the two strands could efficiently replicate
by: separating the two strands and synthesizing a complementary
strand for each in which each per existing strand acts as a template to
the synthesizing the new strands.

15. Polynucleotides
Fig: (a) Linkage of two nucleotides by the formation of a C-3′-C-5′ (3′-5′)
phosphodiester bond, producing a dinucleotide. (b) Shorthand notation
for a polynucleotide chain.

16. Bonding in DNA
3
5 3
5
covalent
phosphodiester
bonds
hydrogen
bonds

17. The linkage between two mononucleotides consists of a phosphate
group linked to two sugars. It is called a phosphodiester bond because
phosphoric acid has been joined to two alcohols (the hydroxyl groups
on the two sugars) by an ester linkage on both sides. Figure shows the
phosphodiester bond in DNA. The same bond is found in RNA. Each
structure has a C-5′ end and a C-3′ end. Two joined nucleotides form a
dinucleotide; three nucleotides, a trinucleotide; and so forth. Short
chains consisting of up to approximately 30 nucleotides linked together
are called oligonucleotides; longer chains are called polynucleotides.

19. Special properties of DNA brought about by the virtue of its structure
Since two strands of DNA run in opposite direction there is
complementary base pairing. It is capable of transmitting the genetic
information to the next generation.
DNA structure being double stranded form the hydrophobic bases are
protected from the outside aqueous environment and hydrophilic ones
facing outside. The replication is also efficiently carried out.
Two complementary strands unwind and each preexisting strand act as
template for new developing strand. Having large number of hydrogen
bonding between the bases make them extremely stable.
Moreover each base stacking, one above the in a planar manner gives
large hydrophobic interactions which gives additional stability to the DNA.
Pyrimidine base in DNA is thymine instead of Uracil.
The thymine large additional non reactive methyl group which shields
from other chemical or biological attacks. This gives extra stability to DNA
unlike RNA molecule.
Thus RNA is less stable than the DNA molecule. By the virtue of all those
properties DNA is extremely suited to be the genetic material in the living
organisms.

21. Ribonucleic Acids (RNAs):
RNA is one of the two nucleic acids found in organisms like animals,
plants, viruses, and bacteria. They are non-genetic material and they
simply translate messages that are encoded in the DNA into protein
synthesis. RNAs occur in cytoplasm and in the nucleus as well.
And are usually common in single stranded form besides some
unusual double stranded form as in Retroviruses. Here they do act as a
carrier of genetic information.
Also in some exceptional cases like TMV, viroids, and virusoids they
function as a genetic material for they do not have DNA molecules for
instructing the cells during protein synthesis.
The usual non- genetic RNAs are transcribed on the DNA template
forming 3 main types of RNAs (tRNA, mRNA, and rRNA).

22. RNA structure:
RNA is much similar to DNA molecules in which it is made of 4-
different building blocks- ribonucleotides.
The RNAs’ pyrimidine base is modified where it lacks a methyl group
and is replaced by Uracil.
The ribose has maximum number of hydroxyl group. These are the
two main differences between DNA and RNA molecules
Nucleotides
Nucleosides
Phosphate
Sugar (ribose)
Bases
Purines
Adenine
Guanine
Pyrimidines
Uracil
Cytosine

23. The four main bases in RNA are:
Purines: Adenine and Guanine
Pyrimidines: Uracil and Cytosine
(Source: http://www.ch.cam.ac.uk/magnus/molecules/nucleic/bases.html.,n.d.)

24. Fig: The RNA chain elongation reaction catalyzed by RNA polymerase

26. Three main types of RNAs are described below:
Transfer RNA (tRNA):
This species of RNA are usually single stranded is the smallest polymer
in the RNAs making (10-15) % of the total RNA. The tRNA acts as an
adaptor molecule which reads the code and carries the particular
amino acid to be incorporated into the growing polypeptide chain.
Transfer RNA contains approximately 75 nucleotides, including three
anticodons and one amino acid. These anticodons are used to read
codons on the mRNA. Each codon is read by various tRNAs until the
appropriate match of the anticodon with the codon is done.
It is also known as soluble RNA (sRNA).
Every amino acid has its own tRNA- i.e. 20 tRNAs for 20 amino acids. 5′
terminus of tRNA is always phosphrylated.

27. tRNAs Share a Common Secondary Structure That Resembles a Cloverleaf
tRNA molecules show a characteristic and highly conserved pattern of
single-stranded and double stranded regions (secondary structure) that can
be illustrated as a cloverleaf (Fig. 15-4).
 The principal features of the tRNA
cloverleaf are an acceptor stem, three stem-
loops (referred to as the ψU loop, the D loop,
and the anticodon loop), and a fourth
variable loop. Descriptions of each of these
features follows.
Fig 15-4 Cloverleaf representation of the
secondary structure of tRNA. In this
representation of a tRNA, the base pairings
between different parts of the tRNA are
indicated by the dotted red lines.

28. Codon-anticodon interaction:
Here, the codon is made in such a way that always a row of three
bases (triplet) code for a specific amino acid. Hence a sequence of
triplets in the DNA is transcribed into a sequence of triplets in the
mRNA strands.
Each amino acid is covalently linked to the tRNA through the
specificity of the amino acyl tRNA synthase. There are as many tRNA
species as codons being used for translation.
Transfer RNAs also code for two or more codons, the phenomenon
so called “degeneracy”, occurs.
Roles played by tRNA:
It carries an activated amino acid to the protein synthesizing site, i.e.
on mRNA molecule.

29. tRNAs Have an L-Shaped Three-Dimensional Structure
The cloverleaf reveals regions of self-complementarity within tRNAs.
X-ray crystallography reveals an L-shaped tertiary structure in which the
terminus of the acceptor stem is at one end of the molecule and the
anticodon loop is ~70A˚ away at the other end (Fig. 15-5c).
To understand the relationship of this L-shaped structure to the cloverleaf,
consider the following: the acceptor stem and the stem of the ψU loop form
an extended helix in the final tRNA structure (Fig. 15-5b). Similarly, the
anticodon stem and the stem of the D loop form a second extended helix.
These two extended helices align at a right angle to each other, with the D
loop and the ψU loop coming together.
Three kinds of interactions stabilize this L-shaped structure.
First, the formation of the two extended regions of base pairing results in
base-stacking interactions similar to those seen in double-stranded DNA.
Second, hydrogen bonds are formed between bases in different helical
regions that are brought near each other in 3Dspace by the tertiary
structure.
Finally, there are interactions between the bases and the sugar–phosphate
backbone.

30. Fig 15-5 Conversion between the cloverleaf and the actual 3D structure
of a tRNA.
(a) Cloverleaf representation.
(b) L-shaped representation showing the location of the base-paired
regions of the final folded tRNA.
(c) Ribbon representation of the actual folded structure of a tRNA. Note that
although this diagram illustrates how the actual tRNA structure is related to
the cloverleaf representation, a tRNA does not attain its final structure by
first base pairing and then folding into an L shape.

31. Messenger RNA (mRNA):
This RNA is always single stranded constituting (5-10) % of the total
RNA molecule. It is less stable and acts as an intermediate between
DNA and protein (Lehninger, 1995).
It possesses mostly the bases – adenine, guanine, cytosine, and
uracil. Messenger RNA is transcribed on the DNA and its base
sequence is also complementary to that of the DNA segment on which
it is transcribed. Every gene (DNA) is responsible for transcription of its
own mRNA. Thus, there are as many species of mRNA as there are
genes in the cell.
Different mRNAs differ in their sequence of bases and in their length.
One gene coding for only one mRNA is known as monocistronic and
when several genes code for several mRNA strands, it is called
polycistronic.
Usually eukaryotic cells show monocistrony and polycistrony is
exclusively in the prokaryotic cells.

32. MESSENGER RNA
Polypeptide Chains Are Specified by Open Reading Frames
The translation machinery decodes only a portion of each mRNA, the
information for protein synthesis is in the form of three-nucleotide codons,
which each specifies one amino acid. The protein-coding region(s) of each
mRNA is composed of a contiguous, non-overlapping string of codons
called an open reading frame (ORF).
Each ORF specifies a single protein and starts (5’ end ) and ends (3’ end)
at internal sites within the mRNA. The first and last codons of an ORF are
known as the start and stop codons.
The start codon is usually 5’-AUG-3’ (but in bacteria 5’-GUG-3’ and
5’-UUG-3’ are also used)

33. The start codon is usually 5’-AUG-3’ (but in bacteria 5’-GUG-3’ and
5’-UUG-3’ are also used)
The start codon has two important functions.
First, it specifies the first amino acid to be incorporated into the growing
polypeptide chain.
Second, it defines the reading frame for all subsequent codons.
Because each codon is immediately adjacent to (but not overlapping with)
the next codon (codons are three nucleotides long) (Fig. 15-1).
F ig . Start codons are shaded in green, and stop codons are shaded in red.
Stop codons, of which there are three (5’-UAG-3’, 5’-UGA-3’, and
5’-UAA-3’), define the end of the ORF and signal termination of polypeptide
synthesis.
mRNAs containing multiple ORFs are known as polycistronic mRNAs
(prokaryotic mRNAs frequently contain two or more),and those encoding a
single ORF are known as monocistronic mRNAs (Eukaryotic mRNAs).

34. The structural features of mRNA are described below:
Cap: found in the 5′ end of the most eukaryotic mRNA. This is
blocked a methylated structure. In the absence of cap the mRNA binds
poorly to the ribosome eventually less protein synthesis in the cell.
Noncoding region 1: Immediately, the cap is followed by noncoding
region composed of 10-100 nucleotides. The region is rich in Adenine
and Uracil residues. This does not translate protein.
The initiation codon: In both prokaryotes and eukaryotes, it is AUG.
The coding region: This can translate protein and it is made of
approximately 1500 nucleotides.
Roles played by mRNA: Principally mRNA carries genetic information
from DNA into the ribosome, which is required for protein synthesis
during translation.

35. F ig. Structure of messenger RNA. (a) A polycistronic prokaryotic message
with three ORFs. Each ribosome binding site is indicated by a purple box
labeled RBS. (b) A monocistronic eukaryotic message. The 5’ cap is indicated
by a “ball” at the end of the mRNA.
The structures of typical prokaryotic and eukaryotic mRNAs are shown in
Figure 15-2.

36. Ribosomal RNA (rRNA):
It is also single a stranded form and the most stable kind of RNAs
constituting 80% of the total RNA in the cell. This RNA is largely
associated the cells that are rich in protein synthesis as in pancreas,
liver, etc.
The ribosomal RNA and protein bind to form a nucleoprotein called a
“ribosome”, on the cytoplasm. This ribosome provides a site on which
protein synthesis occur and carries enzymes for its functions.
The ribosome attaches to mRNA and gives stabilizing structure which
holds materials in position during protein synthesis.
The base sequence of the rRNA is complementary to that of the DNA
sequence on which it is transcribed.
Fig. structure of ribosomal RNA.
(Source:http://www.google.com/search?hl=en&q=structure+of+rRNA,n.d.)
Roles played by rRNA:
It constitutes a major part of ribosome. The since ribosome is bound
to the 5’end of the mRNA, it can check the suitable codon of mRNA
and also stimulates the assembly of amino acids in the polypeptide
chain.

37. The Ribosome Is Composed of a Large and a Small Subunit
Fig: Composition of the prokaryotic and eukaryotic ribosomes.
The rRNA and protein composition of the different subunits are indicated.
The length of the rRNA and the number of ribosomal proteins are indicated
for each subunit.

38. Basic attributes or functions brought about by RNAs on the
basis of their structures:
RNA molecule has Uracil (not stable) as one of its bases unlike DNA
molecule which has Thymine base.
Thus, RNA can easily go folding resulting in the formation of
secondary structures. When it folds, Uracil gets bound to the Adenine
whereby secondary structure is stabilized.
Ribose sugar in RNA has maximum number of OH-groups on its
carbon atoms compared to DNA molecule.
This maximum number of OH-groups in RNA helps in carrying out
other cellular processes.
The core task of RNA molecule is to manufacture protein by a process
so called translation, with the help of information from DNA.
This process involves all the three RNAs performing all different
functions to achieve the ultimate common product, protein.

39. Conclusions
DNA and RNA are found to be very important constituents in the
living cell. DNA is the usual genetic material of the most organisms
while RNA is the genetic material of some viruses.
Most of the DNA is found in the chromosomes. They are also found
in the cytoplasm as in mitochondria and chloroplast. Whereas the RNA
is formed in the chromosomes and occur in nucleolus and cytoplasm.
Basically they differ in their chemical structure. The DNA has thymine
shielded by methyl group which gives extra stability whereas RNA has
uracil without any protecting group. Thus DNA is most suited as a
hereditary material than RNA molecule.

40. Thank you! 