Biomolecules of the Cell - Nucleic Acids (Part

1)

Nucleic acids are considered to be the building blocks of all

the living organisms. The building blocks of nucleic acids are
nucleotides. DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid) are the nucleic acids. They can be
described as the polymers of nucleotides linked through
phosphodiester bonds. Don't worry, before going ahead and
learning more about nucleic acids, we will go through the
basics. Keeping in mind the basics, lets will start with
nucleotides.
Bases, Nucleosides and Nucleotides:
Nucleotide has a distinctive structure and is composed of the
following components which are bound together covalently:
a. Base (contains nitrogen) This can be either a pyrimidine
or a purine (explained below)
b. Sugar (5-carbon or pentose) This can be either ribose or
deoxyribose
c. A phosphate group
When a base and sugar is present (no phosphate), then it is
called a nucleoside as can be seen in the adjacent figure.
When all the three components (base, sugar and phosphate)
are bonded together, then this is known as nucleotide.
Nucleotides can also exist in activated forms containing
either two phosphates (diphosphate) or three phosphates
(triphosphate).
When the sugar in the nucleotide is ribose, then the
nucleotide is called ribonucleotide and when the sugar is
deoxyribose, then nucleotide becomes deoxynucleotide.

Let us have a look at the structure of a nucleotide and make

the concepts all the more clear. In this adjacent figure, the
structure of deoxyadenosine monophosphate will depict all
the three components as sugar, base (here, deoxyribose) and
phosphate. In comparison, the diagram on the right has an
extra hydroxyl group (-OH) on 2 carbon atom of ribose sugar,
making it ribonucleotide (instead of deoxyribonucleotide).
Also, in this diagram, note the 5 and 3 carbon atoms. If we
understand these 5' and 3' carbon atoms, this will aid in
understanding the polarity of the nucleic acids. The 5 carbon
atom is attached to the phosphate group while 3 carbon
atom is attached to a hydroxyl (-OH) group.
There are five bases known as Adenine (A), Guanine (G),
Cytosine (C), Uracil (U) and Thymine (T). The point to
remember is that Uracil is not present in DNA but present in
RNA while Thymine is not present in RNA, but present in DNA.
Here is the table showing all the five bases with their
structure, abbreviations and their nucleoside and nucleotide
forms.
Another way to categorize nucleotide bases is as purines
and pyrimidines. Purines include A and G (which are
double-ring members) while pyrimidines include the
remaining T, C and U (which are single-ring members). A
point to remember is that in double-stranded nucleic acids,
the pairing is always between a purine and a pyrimidine.
Polynucleotides:

The polynucleotides are polymeric compounds consisting of

15 or more nucleotide monomers covalently bonded together
in a chain. As we have seen above, the carbon atom in the
sugar is numbered 1 to 5. The hydroxyl (OH) group on the
3 carbon of one nucleotide can react with the phosphate
attached to the 5 carbon of another (adjacent) nucleotide to
from a dinucleotide held together by phosphate ester bonds.
These bonds are also called phosphodiester bonds. As the
chain contributes more and more nucleotides to itself; it
begins to grow and hence, becomes a polynucleotide.
A short segment in the adjacent figure will make it all the
more clear. Remember that DNA is read from 5 end to the 3
end. If we read this DNA segment, then the sequence goes
like this adenine (A), cytosine (C), guanine (G) and thymine
(T).

DNA and RNA are the main polynucleotides. First, we will

have a look at DNA.

DNA (Deoxyribonucleic Acid):

DNA is the molecule that encodes the blueprint of an

organism meaning the DNA contains all the information
required to build up and maintain an organism. Let me ask
you one question, by whom was DNA first discovered? You
might be thinking, Watson and Crick..!! Let me make it clear
to you, the answer here is NO. The DNA was first discovered
in 1868 by Swiss-physician Friedrich Miescher. He isolated
a compound from the nuclei of white blood cells. This
compound was neither a protein, nor a carbohydrate, nor a
lipid but a unique type of biomolecule. Miescher named it
nuclein as he had isolated it from the nuclei of the cell.
Today, this molecule is called DNA.

Erwin Chargaf was a biochemist who did an extensive

research on chemical analysis of the base composition of
DNA and stated that the base composition of DNA varied
from organism to organism but was independent of age, sex,
nutritional status or any other environmental factors. He
came up with certain relationships which were called the
'Chargafs rule' and they are as follows:
a. The amount of adenine is always equal to the amount of
thymine (A=T).
b. The amount of guanine is always equal to the amount of
cytosine (G=C).
c. The amount of A+G is 50% of the total amount of bases in
the molecule.
d. The amount of T+C is 50% of the total amount of bases in
the molecule.

Then, what was the contribution of Watson and Crick. So,

here lies the answer

- in 1953, James D. Watson and Francis Crick described

the molecular structure and shape of DNA.
When the counterion is Na+ and the relative humidity is 92%,
then DNA fibers assume what is known as B conformation. I
would like to jot some points/features of B form of DNA from
my HOD, Dr. Avinash Upadhyays book Molecular Biology
because they are so beautifully explained in the book that I
still remember them even after years.
Watson and Crick described the shape of DNA as double
helix and following are the features of B-DNA:

i. Double-stranded helix: DNA consists of two

polynucleotide strands coiled around each other to form a
double stranded helix.
ii. Plectonomic coil: The two strands are coiled around each
other in such a way that they cannot be separated without
unwinding the helix (plectonomic coil).
iii. Antiparallel: The two strands are antiparallel to one
another meaning they run in opposite directions. Both the
strands have one 5' phosphate terminus and one 3 hydroxyl
(-OH) terminus. Antiparallel strands mean that the 5
terminus of one strand is adjacent to 3 adjacent of another
strand and vice-versa (as can be seen in the adjacent figure).
iv. Right handed helix: The helix is a right-handed helix.
v. Diameter: The diameter of the helix is 20.
vi. Sugar phosphate backbone - Hydrophilic: The sugar-
phosphate backbones of both the strands are hydrophilic in
nature and follow the helical path and are towards the outer
edge of the molecule where they will be able to interact with
the aqueous environment.
vii. Bases - Hydrophobic: The bases are hydrophobic in
nature and they are placed at the interior of the helix.
viii. Planar base pairs: The planes of the bases are
perpendicular to helical axis. Each base is hydrogen bonded
to a base on the opposite strand to from a planar base pair.
Two types of purine-pyrimidine base pairs can occur as A..T
and C...G. There are two hydrogen bonds between A and T
and three hydrogen bonds between C and G. This is the
reason why the helix has a constant diameter of 20.
xi. Complementary base pairing: This specificity of the
base pairing is referred to as complementary base pairing.
x. Thickness: The bases have a Vander Waals thickness of
3.4.
xi. Base pairs per turn: There are 10 base pairs per turn of
the helix and hence, the helix rises by 34 per turn.
xii. Rotation per base pair: If there are 10 base pairs per
turn, then each base pair rotates by 36 (as one rotation is
360 and divided by 10 will give 36) and hence, a 36 turn
per base pair is present.
xiii. Major and minor grooves: The angle of the glycosidic
linkages lead to the formation of two external helical grooves.
One of the groove is deep and wide and is called the major
groove. Another groove is shallow and narrow. This is the
minor groove.

the A-form of DNA.

A-form of DNA:
The following are certain characteristics of A-DNA:
i. This form of DNA exists when the relative humidity is
around 75%.
ii. The A-DNA is also right-handed helix like B-DNA.
iii. A-DNA is shorter and wider than B-DNA.
iv. The diameter of A-DNA is 23 as against 20 in B-DNA.
v. There are 11 base pairs per turn (more than B-DNA which
has 10 base pairs per turn).
vi. The rise per turn is 28.
vii. Thus, if we calculate, rise per base pair (28/11base
pairs), we get 2.6.
viii. The base pairs are not perpendicular to the helical axis
instead they are tilted 20 w.r.t. helical axis.
ix. Just like B-DNA, A-DNA also has major groove and minor
groove; however, the former is very deep and latter is very
shallow as can be seen in the adjacent diagram.

Does A-DNA have any biological importance? Yes. A-DNA is

observed in some biological context as follows.
A 3 base pair segment of A-DNA is present at the active site
of DNA polymerase.
Also, gram positive bacteria undergoing sporulation contain a
high proportion (20%) of small acid soluble-spore proteins
(SASPs). Some of these SASPs induce B-DNA to assume the A-
form of DNA (atleast in vitro).
Another instance where A-form of DNA is present is during
RNA-DNA hybrids. RNA-DNA hybrids do occur in the cell at
different junctions for example, during replication (where
replication is initiated by RNA primer) and also during
transcription (where RNA is made on DNA template). These
RNA-DNA hybrids cannot take up the B-form of DNA (because
of the 2' oxygen of RNA) and hence, they resemble A-form of
DNA.

Z-form of DNA:

Another form of DNA is Z-DNA and is called so because of its

zigzag pattern of the phosphate backbone. The following are
some of the characteristics:
i. The main characteristic is that Z-DNA is a left-handed
double helix.
ii. The formation of Z-DNA is base sequence dependent
(composition dependent). Only alternating purine and
pyrimidine polymers can form Z-DNA. Thus, this zigzag forms
the repeating unit of Z-DNA which is a dinucleotide.
iii. The right handed DNA can be transited to left handed DNA
(Z-DNA) in solutions that include high ionic strength,
hydrophobic solvents, presence of certain trivalent cations or
covalent modification with bulky alkylating agents.
iv. It contains approximately 12 base pairs per turn of the
helix.
v. Rise per turn of the helix is 44.
vi. The helix rises by 2.7 per base pair.
vii. The base pairs are perpendicular of the helix (just like that
of B-DNA).
viii. Regarding the grooves in Z-DNA, it possesses only a
minor groove. There is no discernible major groove and the
minor groove is extremely deep and narrow.

The following table will give you an idea of major structural

differences between three major forms of DNA (B-DNA, A-DNA
and Z-DNA).

Ribonucleic Acid (RNA):

Coming to another type of nucleic acid which is RNA. As we
have seen the major difference between RNA and DNA in
previous post, here I will discuss about its types and
structure.
Types of RNA:
There are various kinds of RNAs. Here, the RNAs have been
classified into two major groups as coding RNAs and non-
coding RNAs.
Coding RNA - mRNA
a. Coding RNAs:
mRNA (messenger RNA) is coding RNA that is involved in the
process of translation in the cell. It is called messenger as it
carries information from DNA to the ribosome which is the
site of protein synthesis. The coding sequence of mRNA
determines the amino acid sequence in the protein that is
produced.
b. Non-coding RNAs:
Most of the RNAs do not code for any proteins and these
types of RNA fall under another group as non-coding RNAs
(ncRNAs). These so called non-coding RNAs can be encoded
by their own genes. The most prominent examples are rRNA
(ribosomal RNA) and tRNA (transfer RNA), both of which are
involved in the process of translation.
Some other examples of noncoding RNAs are those involved
in gene regulation and RNA processing. There are also some
non coding RNAs that are able to catalyse chemical reactions
such as cutting and ligating other RNA molecules and
catalysis of peptide bond formation in ribosome. Such
catalytic RNAs are called ribozymes.

Structure of RNA:
The structure of RNA is described as follows:

Primary Structure of RNA:

Primary structure of RNA is somewhat similar to that of DNA;
the only difference being the sugar (ribose) component which
has an additional hydroxyl group at 2' carbon and thymine is
replaced with uracil (see figure on the left).
Note: The hydroxyl group on the 2' carbon atom of ribose
make it more labile as compared to DNA and it provides a
chemically reactive group. Because of this lability, RNA is
cleaved into mononucleotides by alkaline solution and DNA is
not.
RNA is a polynucleotide chain that can be double stranded or
single stranded, linear or cicular.

Secondary Structure of RNA:

There are various types of RNA exhibiting different

conformations. The simplest secondary structures in single
stranded RNAs are formed by pairing of complementary
bases. Two major forms of secondary structures are hairpins
and stem loops.
Hairpins are formed by pairing within approximately 5-10
nucleotides of each other whereas in stem loop, there is
pairing of bases that are separated by approximately 50 to
several hundreds of nucleotides
. Tertiary Structure of RNA:

These simple folds (hairpin and stem-loops) can cooperate to

form more complicated tertiary structures, and one of such
structure is 'pseudoknot' as can be seen in the adjacent
figure.
tRNA is a well-defined example of tertiary structure of RNA.
tRNA is a type of RNA that is involved in translation process
of protein synthesis. They have a L-shaped 3D structure that
allows them to fit into the P and A-sites of the ribosome. The
figure depicted as tRNA above under non-coding RNAs is the
three-dimensional structure of tRNA.
Tertiary Structure of RNA:
These simple folds (hairpin and stem-loops) can cooperate to
form more complicated tertiary structures, and one of such
structure is 'pseudoknot' as can be seen in the adjacent
figure.
tRNA is a well-defined example of tertiary structure of RNA.
tRNA is a type of RNA that is involved in translation process
of protein synthesis. They have a L-shaped 3D structure that
allows them to fit into the P and A-sites of the ribosome. The
figure depicted as tRNA above under non-coding RNAs is the
three-dimensional structure of tRNA.

Here, we complete the nucleic acids topic. Any comments or

doubts are welcome.!

Posted by Namrata Heda at 4:42 PM

Labels: Forms of DNA, Nucleic Acid, RNA
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Biomolecules of the Cell - Nucleic Acids (Part 2)
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