Nucleic Acids

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.
Nucleic acids are made of nitrogen-containing bases, phosphate groups, and sugar molecules.
Each type of nucleic acid has a distinctive structure and plays a different role in our cells.
Researchers who first explored molecules inside the nucleus of cells found a peculiar compound
that was not a protein or a lipid or a carbohydrate. It was new. While the acronyms DNA and
RNA are considered standard nomenclature these days, their names underwent a
long evolution, from nuclein to thymus nucleic acid to nucleic acid to
deoxyribonucleic acid and ribonucleic acid. DNA was first called thymus nucleic acid
because it was isolated from the thymus gland of cattle, while RNA was first
identified as yeast nucleic acid.
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are two major types of nucleic acids.
DNA and RNA are responsible for the inheritance and transmission of specific characteristics
from one generation to the other. There are prominently two types of nucleic acids known to us.

The Functions of Nucleic Acids

1. Nucleic acids are responsible for the transmission of inherent characters from parent to
offspring.
2. They are responsible for the synthesis of protein in our body
3. DNA fingerprinting is a method used by forensic experts to determine paternity. It is also
used for the identification of criminals. It has also played a major role in studies
regarding biological evolution and genetics.
Primary structure: the components of nucleic acids
Nucleic acids are a long chain or polymer of repeating subunits, called
nucleotides. Each nucleotide subunit is composed of three parts: a
nitrogenous base, a five-carbon sugar and a phosphate group.
Purine base:
The German chemist Emil Fischer in 1884 gave the name 'purine' (purum uricum). He
synthesized it for the first time in 1899 by uric acid which had been isolated from kidney stones
by Scheele in 1776. Beside from DNA and RNA, purines are also components in a number of
other important biomolecules, such as ATP, GTP, cyclic AMP, NADH, and coenzyme A. Purine
itself, has not been found in nature, but it can be produced by organic synthesis.A purine is a
heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole
ring.
Example:
Adenine:
Adenine is one of the two purine nucleobases (the other being guanine) used in forming
nucleotides of the nucleic acids (DNA or RNA). In DNA, adenine binds to thymine via two
hydrogen bonds to assist in stabilizing the nucleic acid structures. Adenine forms adenosine, a
nucleoside, when attached to ribose, and deoxyadenosine when attached to deoxyribose. It forms
adenosine triphosphate (ATP), a nucleotide, when three phosphate groups are added to
adenosine.
Guanine:
Guanine, along with adenine and cytosine, is present in both DNA and RNA, whereas thymine is
usually seen only in DNA, and uracil only in RNA. In DNA, guanine is paired with cytosine.
With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-
imidazole ring system with conjugated double bonds.
Pyrimidine base:

Chemical structure of thymine

Cytosine with numbered components. Methylation occurs on carbon number 5.

Chemical structure of uracil

Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine,
containing two nitrogen atoms at positions 1 and 3 of the six-member ring. It is isomeric with
two other forms of [Link] nucleobases found in nucleic acids, cytosine (C), thymine (T),
and uracil (U), are pyrimidine derivatives.
Cytosine:
Cytosine can be found as part of DNA, as part of RNA, or as a part of a nucleotide. As cytidine
triphosphate (CTP), it can act as a co-factor to enzymes, and can transfer a phosphate to convert
adenosine diphosphate (ADP) to adenosine triphosphate (ATP).The nucleoside of cytosine is
cytidine. In DNA and RNA, cytosine is paired with guanine. However, it is inherently unstable,
and can change into uracil (spontaneous deamination). This can lead to a point mutation if not
repaired by the DNA repair enzymes such as uracil glycosylase, which cleaves a uracil in DNA.
Thymine:
Thymine (T, Thy) is one of the four nucleobases in the nucleic acid of DNA that are represented
by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known
as 5-methyluracil, a pyrimidine nucleobase. As the name suggests, thymine may be derived by
methylation of uracil at the 5th carbon. In RNA, thymine is replaced with uracil in most cases. In
DNA, thymine(T) binds to adenine (A) via two hydrogen bonds, thus stabilizing the nucleic acid
structures.
Uracil:
Uracil found in RNA, it base-pairs with adenine and replaces thymine during DNA transcription.
Methylation of uracil produces thymine. It turns into thymine to protect the DNA and to improve
the efficiency of DNA replication. Uracil can base-pair with any of the bases, depending on how
the molecule arranges itself on the helix, but readily pairs with adenine because the methyl group
is repelled into a fixed position. Uracil pairs with adenine through hydrogen bonding. Uracil is
the hydrogen bond acceptor and can form two hydrogen bonds. Uracil can also bind with a
ribose sugar to form the ribonucleoside uridine. When a phosphate attaches to uridine, uridine 5'-
monophosphate is produced.
Base pairing Of DNA
Chargaff's rules was given by Erwin Chargaff which state that DNA from any cell of all
organisms should have a 1:1 ratio of pyrimidine and purine bases and, more specifically, that the
amount of guanine is equal to cytosine and the amount of adenine is equal to thymine. This
pattern is found in both strands of the DNA. They were discovered by Austrian chemist Erwin
Chargaff.
In molecular biology, two nucleotides on opposite complementary DNA strands that are
connected via hydrogen bonds are called a base pair (often abbreviated bp). In the canonical
Watson-Crick DNA base pairing, Adenine (A) forms a base pair with Thymine (T) and Guanine
(G) forms a base pair with Cytosine (C). In RNA, thymine is replaced by Uracil (U).
Five-carbon sugars
Nucleotide subunits of RNA contain a pentose (five-carbon) sugar called ribose.
Nucleotide subunits of DNA contain the sugar deoxyribose. The five carbon atoms in
each pentose sugar are assigned numbers 1 ′through 5′. Primes are used in the
numbering of the ring positions in the sugars to differentiate them from the ring
positions of the bases. Both sugars have an oxygen as a member of the five-
member ring; the 5-carbon is outside the ring. The sugars differ only in the
presence or absence (“deoxy”) of an oxygen in the 2position. This minor
distinction between RNA and DNA dramatically influences their function. The
remarkable versatility of RNA is critically dependent on this 2 -hydroxyl group
The phosphate functional group
The phosphate functional group (PO 4) gives DNA and RNA the property of an acid (a
substance that releases an Hion or proton in solution) at physiological pH, hence
the name “nucleic acid.” The linking bonds that are formed from phosphates are
esters that have the additional property of being stable, yet areeasily broken by
enzymatic hydrolysis. When a nucleotide is removed from a DNA or RNA chain, the
nucleotide is not destroyed in the process. Further, after the phosphodiester bond is
formed (see below), one oxygen atom of the phosphate group is still negatively
ionized. The negatively charged phosphates are extremely insoluble in lipids, which
ensures the retention of nucleic acids within the cell or nuclear membrane.
Nucleosides and nucleotides
A DNA or RNA chain is formed in a series of three steps. In the first reaction, each
base is chemically linked to one molecule of sugar at the 1 ′-carbon of the sugar,
forming a compound called a nucleoside. When a phosphate group is also attached
to the 5′carbon of the same sugar, the nucleoside becomes a nucleotide. Finally,
nucleotides are joined (polymerized) by condensation reactions to form a chain. The
hydroxyl group on the 3 ′-carbon of a sugar of one nucleotide forms an ester bond to
the phosphate of another nucleotide, eliminating a molecule of water. This chemical
bond linking the sugar components of adjacent nucleotides is called a
phosphodiester bond, or 5 ′3′phosphodiester bond, indicating the polarity of the
strand.
Significance of 5′ and 3′
The ends of a DNA or RNA chain are distinct and have different chemical properties.
The two ends are designated by the symbols 5 ′and 3′. The symbol 5′refers to the
carbon in the sugar to which a phosphate (PO 4) functional group is attached. The
symbol 3′refers to the carbon in the sugar ring to which a hydroxyl (OH) functional
group is attached. The asymmetry of the ends of a DNA strand implies that each
strand has a polarity determined by which end bears the 5 ′-phosphate and which
end bears the 3′-hydroxyl group. This 5′3′directionality of a nucleic acid strand
is an extremely important property of the molecule. Understanding this
directionality (polarity) is critical for understanding aspects of replication and
transcription, for reading a DNA sequence, and for carrying out experiments in the
lab. By convention, a DNA sequence is written with the 5 ′end to the left, and the
3′end to the right. This is also the direction of synthesis
Nomenclature of nucleotides
Nucleotides may contain one phosphate unit (monophosphate), two such units
(diphosphate), or three (triphosphate). When incorporated into a nucleic acid chain,
a nucleotide contains one each of the three components. When free in the cell pool,
nucleotides usually occur as triphosphates. The triphosphate form serves as the
precursor building block for a DNA or RNA chain during synthesis. Because the
nomenclature is rather complicated, scientists use shorthand for the names of the
nucleotides. For example, deoxycytidine triphosphate (DNA) and cytidine
triphosphate (RNA) are abbreviated to dCTP and CTP, respectively. The letters A, G,
C, T, and U stand for the bases but, in practice, they are commonly used to
represent the whole nucleotides containing these bases. Many of these terms are
not needed in this book; however, they are included because they are likely to be
encountered in further reading or by students involved in research. Knowing the
more complex names for deoxynucleoside triphosphates (dNTPs) and nucleoside
triphosphates (NTPs) is important for understanding scientific literature, and for
ordering the correct compound from a catalog when planning an experiment.
The length of RNA and DNA
Cellular RNAs range in length from less than one hundred to many thousands of
nucleotides; the number of nucleotides (nt) or “bases” is used as a measure of
length. Cellular DNA molecules can be as long as several hundred million
nucleotides. The number of base pairs (bp) is used as a measure of length of a
double stranded DNA. In practice, the unit of length used for DNA is the kilobase
pair (kb or kbp), corresponding to 1000 base pairs, or the megabase pair (Mb or
Mbp) corresponding to 1,000,000 base pairs. In the laboratory, researchers often
make use of short chains of single-stranded DNA (usually less than 50 bases) called
oligonucleotides.

Deoxyribonucleic acid (DNA):

Deoxyribonucleic acid or DNA, is a nucleic acid that contains the genetic instructions used in the
development and functioning of all known living organisms (with the exception of RNA viruses).
The main role of DNA molecules is the long-term storage of information. DNA is often
compared to a set of blueprints, like a recipe or a code, since it contains the instructions needed
to construct other components of cells, such as proteins and RNA molecules. The DNA segments
that carry this genetic information are called genes, but other DNA sequences have structural
purposes, or are involved in regulating the use of this genetic information.
DNA consists of two long polymers of simple units called nucleotides, with backbones made of
sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions
to each other and are therefore anti-parallel. Attached to each sugar is one of four types of
molecules called bases. It is the sequence of these four bases along the backbone that encodes
information.
Two helical strands form the DNA backbone. Another double helix may be found by tracing the
spaces, or grooves, between the strands. These voids are adjacent to the base pairs and may
provide a binding site. As the strands are not directly opposite each other, the grooves are
unequally sized. One groove, the major groove, is 22 Å wide and the other, the minor groove, is
12 Å wide. The narrowness of the minor groove means that the edges of the bases are more
accessible in the major groove. As a result, proteins like transcription factors that can bind to
specific sequences in double-stranded DNA usually make contacts to the sides of the bases
exposed in the major groove. This situation varies in unusual conformations of DNA within the
cell, but the major and minor grooves are always named to reflect the differences in size that
would be seen if the DNA is twisted back into the ordinary B form.
DNA Biological Functions

DNA is vital for all living beings – even plants. It is important for inheritance, coding for
proteins and the genetic instruction guide for life and its processes. DNA holds the instructions
for an organism's or each cell’s development and reproduction and ultimately death.

1. Synthesis of Proteins
A protein is a complex molecule found in the body that is abundant and is vital for most
living functions. There are many different types of proteins that include structural proteins,
messenger proteins, enzymes and hormones. These perform various functions from forming the
organs, skin and bones and the body to performing actions and functions via messengers,
enzymes and [Link] carries the codes for proteins. However, the actual protein differs a
lot from the codes present on the DNA. The basic steps include:
a. Transcription

The first step that occurs is a process known as transcription. Here the information on the DNA
is written down onto a different molecule called the RNA. This molecule acts as a messenger to
carry the information to other parts of the cell.
 b. Translation

The next step is called translation. In this step the cell organelles called ribosomes come into
play. These ribosomes act as translators by translating the messenger's code into the proper
protein format or a chain of amino acids that form the building blocks of the protein. Each amino
acid is formed by combining three bases on the RNA.

c. Modification and folding

The third step is modification and folding and structuring of the final protein and sending it to
the required areas in the body.

2. Coding for proteins

DNA is read by the messengers that break it open into single stranded polynucleotide
chains and is copied into RNA. RNA forms opposite bases from that present on the DNA. For
example, G on the DNA forms C on the RNA strand. Each of the bases gets together in threes
and these form particular amino acids. There are 20 such amino acids. These are also known as
the building blocks of proteins. The amino acids first form a long chain called the polypeptide
chain. This polypeptide chain undergoes conformational and structural changes and folds and
refolds over itself to form the final complex structure of the protein.

3. DNA replication

Apart from coding for proteins, DNA also replicates. This helps in a variety of functions
including reproduction to maintenance and growth of cells, tissues and body systems. In this
process the DNA strands, that are tightly wound with each other, unwind and literally unzip to
leave several bases without their partners on the other strand and remain along the backbone of
the molecule. The bases are very specific about which base they will attach to and the adenine
only pairs with thymine and guanine will only pair with cytosine. Unpaired bases come and
attach to these free bases and a new strand is formed that is complementary to the original
sequence. The end result is a strand that is a perfect match to the original one prior to it
unzipping. This result in two new pairs of strands and two coiled DNA. Each of the new DNA
contains one strand from the mother pair and a new one.

4. DNA inheritance

DNA is important in terms of heredity. It packs in all the genetic information and passes
it on to the next generation. The basis for this lies in the fact that DNA makes genes and genes
make chromosomes. Humans have 23 pairs of chromosomes – a total of 46 chromosomes.
Twenty-two of these pairs, called autosomes, look the same in both males and females. The 23rd
pair is called the sex chromosomes and differs between males and females. Females have two
copies of the X chromosome or XX, while males have one X and one Y chromosome.

Both parents have reproductive cells – sperms in fathers and ovum or eggs in mothers.
These sperms and eggs contain half the number of chromosomes – 23 each. When the egg and
the sperm fertilizes, this gives rise to a cell that has the complete set. Thus a person inherits half
of his or her genes from each of the parents.

Ribonucleic acid (RNA)

RNA STRUCTURE
Ribonucleic acid (RNA) is a biopolymer macromolecule as DNA. It consists of small subunits
called nucleotides composed of:
• Purine nucleobases [Adenine− (A), Guanine−(G)]
• Pyrimidine nucleobases [Cytosine−(C), Uracil−(U)]
• D-ribose pentose sugars [C5H10O5]
• Phosphate groups [PO43-]
The backbone bonding between RNA nuclotides (i.e. the bonds between the phosphate group
and an adjacent ribose sugar) occurs through phosphodiester bonds. A phosphate group is
attached to the 3'−carbon position of one ribose and on the 5'−carbon position of the next

CHARACTERISTICS
• RNA does not self replicate in order to multiply; instead it is encoded by DNA genes
• RNA is synthesized in order for the translation of DNA to be possible
• The DNA-RNA function is highly interdependable, i.e., if there is problem with DNA,
there will be a problem with the RNA functions and vice versa (no RNA = no DNA
translation can occur, thus DNA is useless without its RNA genes)
TYPES OF RNA
RNA genes of DNA encode for 3 major types of RNA:
• Messenger RNA
• Ribosomal RNA
• Transfer RNA
1. Messenger RNA [mRNA]
mRNA genes are the genes that encode only for proteins but this encoding has an RNA
intermediate. The DNA is firstly transcribed into mRNA and subsequently translated into a
protein product. So the mRNA genes are the genes that encode for mRNA in order to synthesize
proteins. mRNA constitutes only the 5% of the total RNA. RNA polymerase II is the enzyme
responsible for the transcription of the corresponding genes into mRNA. The polymerase binds
on the TATA box which acts more or less as a promoter, located about 25 base pairs upstream
the Transcription Start Site−TSS, along with the transcription factors giving rise to the
Transcription Initiation Complex−TIC. In order for this complex to be functional a proper
sequence of events of binding the TF and the polymerase on the promoter must occur as: TFII-D,
TFII-A, TFII-B, RNA pol II, TFII-F, TFII-H TFII-E TFII-J. As soon as the TIC is formed then
transcription begins giving rise to pre−mRNA which include both exons and introns.
Transcription ends without recognition of an adenine rich area but rather by automatic
disassembling οf the Transcription Complex. The pre−mRNA is then submitted to processing
that involves splicing - removal of introns and merging of the adjacent exons- and capping -
addition of 7−methylguanosine on the 5' end of the mRNA so that mRNA cannot be cleaved by
exonucleases. It also serves as a recognition site of the mRNA prior to translation for the small
ribosomal subunit.

2. Ribosomal RNA [rRNA]

Ribosomes are non membranous organelles that participate in the translation of mRNA into a
protein product. The ribosome structure is composed of 2 subunits. A small and a large subunit
each of which primarily consists of rRNA of various sizes and a small quantity of proteins.
rRNA constitutes about the 80% of the whole RNA present in an eukaryotic cell. The large
subunit consists of rRNA of 5S, 5.8S and 28S sizes whereas the small subunit consists of rRNA
of 18S size. (where the S is the unit for rRNA size). These rRNAs are synthesized by
transcription of the rRNA genes. However, the rRNA genes encode for all rRNAs apart from the
5S rRNA which is synthesized by the tRNA genes along with all nuclear tRNAs. RNA
polymerase type I is responsible for the transcription of rRNA genes by binding on the core
element−CE, which overlaps the Transcription Start Site−TSS, along with the Transcription
Factors inducing the so called Transcription Initiation Complex designated as TIC. The rate of
the transcription is controlled by an Upstream Control Sequence−UCS located 100 base pairs
upstream to the TSS. The transcription process begins and the genes are transcribed into
pre−rRNA in the following order as situated on the gene: -18S - 5.8S - 28S-. The transcription
comes to an end when the Transcription Complex reaches an area rich in Adenines found at
about 600 base pairs downstream of the gene, indicating its end. The pre−rRNA formed includes
all rRNAs on a single strand so that cleavage has to be performed so that different size rRNAs
are separated. This task is under taken by RNases that cleave the rRNA giving rise to the
differential size rRNAs.

3. Transfer RNA [tRNA]

Transfer RNA is encoded by genes that also encode for the 5S size rRNA. RNA polymerase III
is responsible for the transcription of these genes by binding on the promoter, situated about 100
base pairs downstream the Transcription Start Site -TSS, along with the Transcription Factors
giving rise to the Transcription Initiation Complex. As soon as this complex is formed
transcription process can begin and when the Transcription Complex faces an Adenine rich
region transcription comes to an end as this area is an indication for the gene end. tRNA
constitutes 15% of the total RNA and is directly involved in the translation of the mRNA. More
specifically tRNA binds onto a specific amino acid and brings it along the translation site so that
it is bound on the newly synthesized peptide.
 • tRNA binds to its specific amino acid recognized by its side R chain in presence of the
aminoacyl tRNA synthetase enzyme. The synthetase binds the 5'-CCA-OH-3' acceptor
arm with the —COOH group of the amino acid.
• When the small ribosomal subunit faces an AUG codon on the mRNA it indicates the
commencing of the peptide formation. As soon as the AUG codon is recognized then the
first tRNA binds on the small ribosomal subunit and on the mRNA through its anticodon
arm, giving rise to the Translation Initiation Complex designated as tRNA imet. Eventually
the large ribosomal subunit binds on the complex indicating the initiation of the
translation process. Translation always begins with the methionine amino acid on the
newly synthesized peptide.
• After translocation of the Translation complex the tRNA imet enter the Peptidyl site of the
complex leaving the Aminoacyl site vacant for the next tRNA to enter, bringing together
the two adjacent amino acids so that a peptide bond can be formed in presence of the
peptidyl transferase enzyme. As soon as the peptide bond is formed, the tRNA is released
from its amino acid in presence of the tRNAdeacylase.

OTHER TYPES OF RNA

• Small interfering RNA [siRNA]: Known as short interfering RNA, a class of double
stranded RNA molecules involved in the RNA interference (RNA i) pathway. There, it
interferes with the expression of specific genes controlling the stability of the mRNA. In
this way the mRNA disintegrates (when necessary), avoiding its overexpression with a
consequent overproduction of proteins.
• Small nuclear RNA [snRNA]: They are RNA molecules transcribed by either RNA
polymerase II along with mRNA or by RNA polymerase III along with all nuclear tRNAs
and the 5S rRNA. They are primarily involved in mRNA processing such as splicing by
removal of introns from pre−mRNA and also in maintenance of the telomeres. They are
always associated with proteins giving rise to complexes are referred to as small nuclear
ribonucleoproteins−snRNP directly associated with the splicing process.
• Heterogeneous nuclear RNA [hnRNA] :hnRNA is an immature single strand of mRNA.
The terms hnRNA and pre−mRNA are almost identical.