NUCLEIC ACIDS

 Nucleic acids are biopolymers, or large biomolecules, essential to all

known forms of life.
 They are composed of nucleotides, which are the monomers made of
three components: a 5-carbon sugar, a phosphate group and
a nitrogenous base.
 The two main classes of nucleic acids are deoxyribonucleic acid (DNA)
and ribonucleic acid (RNA).
 If the sugar is ribose, the polymer is RNA.
 If the sugar is the ribose derivative of deoxyribose, the polymer is DNA.
 Nucleic acids are naturally occurring chemical compounds that serve as
the primary information-carrying molecules in cells and makeup the
genetic material.
 Nucleic acids are found in abundance in all living things, where they
create, encode, and then store information of every living cell of every
life-form on Earth.
 In turn, they function to transmit and express that information inside
and outside the cell nucleus to the interior operations of the cell and
ultimately to the next generation of each living organism.
 The encoded information is contained and conveyed via the nucleic acid
sequence, which provides the 'ladder-step' ordering of nucleotides
within the molecules of RNA and DNA.
 They play an especially important role in directing protein synthesis.
 Strings of nucleotides are bonded to form helical backbones.
 Typically , one for RNA, two for DNA—and assembled into chains of
base-pairs selected from the five primary, or canonical, nucleobases,
which are: 
adenine
cytosine
guanine 
thymine and uracil.
 Thymine occurs only in DNA and uracil only in RNA.


 Using amino acids and the process known as protein synthesis, the

specific sequencing in DNA of these nucleobase-pairs enables storing
and transmitting coded instructions as genes.
  In RNA, base-pair sequencing provides for manufacturing new proteins
that determine the frames and parts and most chemical processes of all
life forms.

TWO MAJOR TYPES OF NUCLEIC ACIDS:

Deoxyribonucleic acid:
Deoxyribonucleic acid (DNA) is a nucleic acid containing the genetic
instructions used in the development and functioning of all known living
organisms.
The DNA segments carrying this genetic information are called genes.
Likewise, other DNA sequences have structural purposes or are involved in
regulating the use of this genetic information. Along with RNA and proteins,
DNA is one of the three major macromolecules that are essential for all known
forms of life.
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 nucleobases
(informally, bases). It is the sequence of these four nucleobases along the
backbone that encodes information.
This information is read using the genetic code, which specifies the sequence
of the amino acids within proteins.
The code is read by copying stretches of DNA into the related nucleic acid RNA
in a process called transcription.
Within cells, DNA is organized into long structures called chromosomes.
During cell division these chromosomes are duplicated in the process of DNA
replication, providing each cell its own complete set of chromosomes.
Eukaryotic organisms (animals, plants, fungi, and protists) store most of their
DNA inside the cell nucleus and some of their DNA in organelles, such as
mitochondria or chloroplasts.

In contrast, prokaryotes (bacteria and archaea) store their DNA only in the
cytoplasm.
Within the chromosomes, chromatin proteins such as histones compact and
organize DNA. These compact structures guide the interactions between DNA
and other proteins, helping control which parts of the DNA are transcribed.

Ribonucleic acid:
Ribonucleic acid (RNA) functions in converting genetic information from
genes into the amino acid sequences of proteins.
The three universal types of RNA include transfer RNA (tRNA), messenger
RNA (mRNA), and ribosomal RNA (rRNA). 
Messenger RNA acts to carry genetic sequence information between DNA and
ribosomes, directing protein synthesis and carries instructions from DNA in
the nucleus to ribosome . 
Ribosomal RNA reads the DNA sequence, and catalyzes peptide bond
formation. 
Transfer RNA serves as the carrier molecule for amino acids to be used in
protein synthesis, and is responsible for decoding the mRNA.
 Ribonucleic acid (RNA)
It is a polymeric molecule essential in various biological roles
in coding, decoding, regulation and expression of genes. RNA and
deoxyribonucleic acid (DNA) are nucleic acids.
Along with lipids, proteins, and carbohydrates, nucleic acids constitute one of
the four major macromolecules essential for all known forms of life.
Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA, RNA is
found in nature as a single strand folded onto itself, rather than a paired
double strand.
Cellular organisms use messenger RNA (mRNA) to convey genetic information
(using the nitrogenous bases of guanine, uracil, adenine, and cytosine,
denoted by the letters G, U, A, and C) that directs synthesis of specific proteins.
Many viruses encode their genetic information using an RNA genome.
Some RNA molecules play an active role within cells by :
 catalyzing biological reactions
 controlling gene expression
 sensing and communicating responses to cellular signals.
One of these active processes is protein synthesis, a universal function in
which RNA molecules direct the synthesis of proteins on ribosomes.
This process uses transfer RNA ( tRNA ) molecules to deliver amino acids to
the ribosome, where ribosomal RNA (rRNA) then links amino acids together
to form coded proteins.

COMPARISON WITH DNA :

The chemical structure of RNA is very similar to that of DNA, but differs in
three primary ways:

 Unlike double-stranded DNA, RNA is a single-stranded molecule in many of

its biological roles and consists of much shorter chains of nucleotides.
However, a single RNA molecule can, by complementary base pairing, form
intra strand double helixes, as in tRNA.
 While the sugar-phosphate "backbone" of DNA contains deoxyribose, RNA
contains ribose instead. Ribose has a hydroxyl group attached to the
pentose ring in the 2' position, whereas deoxyribose does not.

The hydroxyl groups in the ribose backbone make RNA more

chemically labile than DNA by lowering the activation energy of hydrolysis.

 The complementary base to adenine in DNA is thymine, whereas in RNA, it

is uracil, which is an unmethylated form of thymine.
Like DNA, most biologically active RNAs,
including mRNA, tRNA, rRNA, snRNAs, and other non-coding RNAs, contain
self-complementary sequences that allow parts of the RNA to fold and pair
with itself to form double helices.
Analysis of these RNAs has revealed that they are highly structured.
Unlike DNA, their structures do not consist of long double helices, but rather
collections of short helices packed together into structures akin to proteins.
In this fashion, RNAs can achieve chemical  catalysts (like enzymes).
For instance, determination of the structure of the ribosome—an RNA-protein
complex that catalyzes peptide bond formation—revealed that its active site is
composed entirely of RNA.

CHEMICAL COMPOSITION OF RNA:

Each nucleotide in RNA contains :
 a ribose sugar, with carbons numbered 1' through 5'.
 A base is attached to the 1' position, in
general, adenine (A), cytosine (C), guanine (G), or uracil (U).
 Adenine and guanine are purines
 Purines are double ringed compounds made up of carbon,hydrogen and
nitrogen.
 cytosine and uracil are pyrimidines
  Pyrimidines are single ringed compounds made up of carbon,hydrogen
and nitrogen.
 A phosphate group is attached to the 3' position of one ribose and the 5'
position of the next.
 The phosphate groups have a negative charge each, making RNA a
charged molecule (polyanion).
 The bases form hydrogen bonds between cytosine and guanine,
between adenine and uracil .
 Triple hydrogen bonds are found between cytosine and guanine.
 Double hydrogen bonds are found between adenine and uracil.

SYNTHESIS OF RNA
 Synthesis of RNA is usually catalyzed by an enzyme—RNA polymerase
—using DNA as a template, a process known as transcription. Initiation
of transcription begins with the binding of the enzyme to
a promoter sequence in the DNA (usually found "upstream" of a gene).
 The DNA double helix is unwound by the helicase activity of the enzyme.
 The enzyme then progresses along the template strand in the 3’ to 5’
direction, synthesizing a complementary RNA molecule with elongation
occurring in the 5’ to 3’ direction.
 The DNA sequence also dictates where termination of RNA synthesis
will occur.
 Primary transcript RNAs are often modified by enzymes after
transcription. For example, a poly(A) tail and a 5' cap are added to
eukaryotic pre-mRNA and introns are removed by the spliceosome.
 There are also a number of RNA-dependent RNA polymerases that use
RNA as their template for synthesis of a new strand of RNA. For
instance, a number of RNA viruses (such as poliovirus) use this type of
enzyme to replicate their genetic material. Also, RNA-dependent RNA
polymerase is part of the RNA interference pathway in many organisms.

TYPES OF RNA :
There are three different kinds of RNA:
 Messenger RNA
 Transfer RNA
 Ribosomal RNA
 They all are single-stranded but they differ from each other in the
number of nucleotides and configuration .

Messenger RNA:
 The name mRNA was coined by Jacob and Monod.
 It forms between 3 % to 5% of the total RNA content of a cell.
 A molecule of mRNA is a single strand made up of up to several
thousand nucleotides.
 It is made in the nucleus from where it passes through nuclear pore to
the ribosome where triplets of bases in the mRNA act as codons in the
synthesis of proteins .
 The molecular weight of an average size mRNA in a molecule is about
5,00,000 daltons.
 It is heterogeneous because the size of its molecule varies greatly and
its sedimentation coefficient is 8S.
 In its structure mRNA has a cap at its 5’ end which bears methylated
guanosine ; the 3’ end is protected by a polyadenylate poly-A sequence
of 200 to 250 nucleotides.
 It transcribes the genetic information coded in the structure of DNA
molecule and translates into protein.
 The average lifespan of a mRNA in the E-coli is about two minutes
after which the molecules are broken down by ribonuclease enzyme.
 However it may survive for many hours and even days in eukaryotes .
 It is synthesized by DNA dependent RNA polymerase enzyme.
 If mRNA carries the codes for the synthesis of a single protein molecule
it is called monocistronic type as in eukaryotes and if it codes for more
than one kind of proteins ,it is known as polycistronic type as in
prokaryotes.
 A single strand of DNA is the blueprint for the mRNA which is
transcribed from that DNA strand.
 The sequence of base pairs is transcribed from DNA by
an enzyme called RNA polymerase. Then the mRNA moves from
the nucleus to the ribosomes in the cytoplasm to form proteins.
 The mRNA translates the sequence of base pairs into a sequence
of amino acids to form proteins. This process is called translation.
 DNA does not leave the nucleus for various reasons.
 DNA is a very long molecule, and is bound in with proteins,
called histones, in the chromosomes.
 mRNA, on the other hand is able to move and to react with various cell
enzymes.
 Once transcribed, the mRNA leaves the nucleus and moves to the
ribosomes.
 Two kinds of non-coding RNAs help in the process of building proteins
in the cell.
 They are transfer RNA (tRNA) and ribosomal RNA (rRNA).

Transfer RNA:
 Soluble RNA: It is about 10% to 15% of the total RNA of the cell.
 It is single-stranded and make the smallest ones 4S with 70-90
nucleotides.
 It functions as adaptors for carrying amino acid molecules to the site of
protein synthesis.
 There are about 100 different types of tRNA found in bacterial, plants
and animal cells.
 It is synthesized in the nucleus.
 However it is presumed that it might be synthesized in the nucleolus.
 tRNA is more stable in prokaryotes than in eukaryotes.
 Its structure proposed by Holly et. al. in 1965 was known as the Clover
leaf model.
 According to this model the single strand of tRNA is folded upon itself
to form five arms.
 Each arm consists of a stem and ends in a loop .
These arms are:
 Acceptor arm :
This arm bears a constant CCA sequence at 3’ end where as the 5’ end
bears guanine or cytosine.
The amino acid molecule binds to the 3’ end of the CCA sequence hence
it is known as amino acid binding site.
 D –Arm:
It is made up of 15 to 18 nucleotides.
It bears a loop at its end called as loop-I or dihydrouridine loop(D-loop)
or DHU loop.
 Anti -codon arm:
It bears loop-ii or anticodon loop which contains 7 nucleotides .
It recognises the complementary codon on m-RNA.
 Variable arm :
It is a very small arm which may have 5 base pairs.
 TѰC Arm: (Ribothymine pseudouridine cytosine ):
It contains pseudouridine (Ѱ).
This arm and the loop on it are involved in binding tRNA to ribosomes.

In a cell at least 20 different types of tRNA’s are found. They bind

specific amino acids and transfer them to the site of protein synthesis.
The different RNA’s differ in sequence of base triplets making up the
anticodons by which tRNA binds to the codons of mRNA during protein
synthesis.

Ribosomal RNA
 It makes up about 80% of the total RNA in a cell.
 Many thousand nucleotides which make up a molecule of r-RNA are
found in a complex structure partly consisting of single and partly of
double helics.
 Its molecular weight ranges between 0.55 X106 and 1.1X106 .
 Ribosomal RNA is manufactured in the nucleus under the control of
nucleolus.
 It enters the cytoplasm and binds with protein molecules to form
ribosomes.
 Over half the mass of a ribosome consists of r-RNA’s.

Heterogeneous nuclear RNA

 Abbreviated as Hn-rna.
 In mammalian cells including human being a precursor RNA is first
synthesized in the nucleoplasm.
 It is done with the help of DNA dependent RNA polymerase .
 This precursor is then degraded by the nuclease to m-RNA.
 It is then translocated to the cytoplasm where it becomes associated to
ribosomal system.
 This precursor RNA constitutes the fourth class of RNA and is called
hn-RNA.
 It can take up the form of the other RNA as well.
 Therefore it is also called the Cinderella among the nucleic acids.

Small nuclear RNA

 It is the RNA which is formed in the nucleus and take up various forms
of RNA’s to some extent.
  It forms spliceosomes which play an important role in RNA splicing.

Some other types of RNA’s:

Regulatory RNAs:
There are a number of RNAs which regulate genes, that is, they regulate the
rate at which genes are transcribed or translated.

mi-RNA
Micro RNAs (mi-RNA) act by joining an enzyme and blocking mRNA, or
speeding its breakdown. This is called RNA interference.

Si-RNA
Small interfering RNAs (sometimes called silencing RNAs) interfere with the
expression of a specific gene.
They are quite small (20/25 nucleotides) double-stranded molecules.
Their discovery has caused a surge in biomedical research and drug
development.

KEY TERMS:
SPLICING:
RNA splicing, in molecular biology, is a form of RNA processing in which a
newly made precursor messenger RNA is transformed into a mature
messenger RNA. During splicing, introns are removed and exons are joined
together.
GENETIC RNA:
RNA of certain plant viruses which forms the hereditary material is called
genetic RNA.
NON GENETIC RNA:
Other RNA involved in protein synthesis is called non-genetic RNA.
INTRONS:
non-coding ends of DNA sequence that are initially transcribed into mRNA
but later spliced out before translation. These are also called as non-sense
genes. EXONS:
coding ends of DNA sequence that are able to express themselves. These are
also called as sense genes.TRANSLATION:
In biology, the process by which a cell makes proteins using the genetic
information carried in messenger RNA (mRNA).

Functions of RNA:
 The main function of RNA is to carry information of amino
acid sequence from the genes to where proteins are assembled
on ribosomes in the cytoplasm.

 Where DNA is absent, RNA acts as the genetic material.

 The DNA usually synthesizes RNA but where DNA is absent RNA
synthesizes it.

 In combinations with protein molecules, the RNA forms ribosomes.

 Different kinds of RNA actively participate in protein synthesis.Uses

of RNA for human aid and in research :
  DNA(deoxyribonucleic acid) is considered the “blueprint” of the cell; it
carries all of the genetic information required for the cell to grow, to
take in nutrients, and to propagate. RNA–in this role–is the “DNA
photocopy” of the cell. When the cell needs to produce a certain protein,
it activates the protein’s gene–the portion of DNA that codes for that
protein–and produces multiple copies of that piece of DNA in the form
of messenger RNA, or mRNA. The multiple copies of mRNA are then
used to translate the genetic code into protein through the action of the
cell’s protein manufacturing machinery, the ribosomes. Thus, RNA
expands the quantity of a given protein that can be made at one time
from one given gene, and it provides an important control point for
regulating when and how much protein gets made.

 For many years RNA was believed to have only three major roles in the
cell–as a DNA photocopy (mRNA), as a coupler between the genetic code
and the protein building blocks (tRNA), and as a structural component
of ribosomes (rRNA). In recent years, however, we have begun to realize
that the roles adopted by RNA are much broader and much more
interesting. We now know that RNA can also act as enzymes
(called ribozymes) to speed chemical reactions.
 In a number of clinically important viruses RNA, rather than DNA,
carries the viral genetic information.
 RNA also plays an important role in regulating cellular processes–from
cell division, differentiation and growth to cell aging and death.
 Defects in certain RNAs or the regulation of RNAs have been implicated
in a number of important human diseases, including heart disease, some
cancers, stroke and many others.
 Some scientists and doctors are researching over the use of  messenger
RNA in vaccines to treat cancer and prevent people from becoming sick.
 RNA technology is used to suppress the expression of fruit-ripening
genes so that fruits can remain on the vine longer, extending their
season and availability for marketing.
 Numerous key discoveries in biology have emerged from studies
of RNA (ribonucleic acid), including seminal work in the fields of :

-Biochemistry:

Biochemistry is the branch of science that explores the chemical

processes within and related to living organisms. It is a laboratory
based science that brings together biology and chemistry. 

-Genetics :
Genetics is a branch of biology concerned with the study of genes,
genetic variation, and heredity in organisms.

-Microbiology:
Microbiology is the study of microscopic organisms, such as bacteria,
viruses, archaea, fungi and protozoa.

This discipline includes fundamental research on the biochemistry,

physiology, cell biology, ecology, evolution and clinical aspects of
microorganisms, including the host response to these agents. -
Molecular biology :
Molecular Biology is the field of biology that studies the composition,
structure and interactions of cellular molecules – such as nucleic
acids and proteins – that carry out the biological processes essential for
the cell's functions and maintenance.
-Molecular evolution :
Molecular evolution is the process of change in the sequence
composition of cellular molecules such as DNA, RNA, and proteins
across generations.

-Structural biology:
 Structural biology is the study of the molecular structure and
dynamics of biological macromolecules, particularly proteins and
nucleic acids, and how alterations in their structures affect their
function. Structural biology incorporates the principles of molecular
biology, biochemistry and biophysics.

 Small RNAs play a role in gene silencing and post-

transcriptional regulation of gene expression. Small RNAs
have been demonstrated to be involved in biological processes,
including development, cell proliferation and differentiation, and
apoptosis.

In addition to this basic function, RNA-sequence can be used for differential

gene expression, variants detection and allele-specific expression, small RNA
profiling, characterization of alternative splicing patterns, system biology,
and single-cell RNA-seq.
Here are some important facts about RNA:
 RNA is capable of folding and forming a complex structure that serves
as a catalyst for chemical reactions or molecule binding in the body.
 Decoding of DNA is not possible directly. Hence the RNA transcribes
into mRNA following which each of the molecules encode information
for a single protein. Each of these protein sequences contains 3
nitrogen bases and the incorporation of a particular amino acid within
the protein is carried out by the mRNA.
 Proteins contribute to the genetic characteristics of human body such
as characteristics of hair, eye colour, skin colour height etc. Therefore
ultimate controllers of cellular function.
 Important functions such as coding and decoding, transcription,
regulation and expression of genes, protein binding etc. are carried out
by RNA.
 An average human cell comprises of only 1% DNA while 5% of the
total weight of the cell constitutes RNA.
 The cells of some organisms do not contain DNA. In such cases, the
genetic material is primarily composed of RNA. For example, many
kinds of viruses only contain RNA.
 Cellular processes such as cell division, ageing and death of cells are all
carried out under the regulation of Ribonucleic acid.
 Any defects in RNA can be the cause for severe human diseases such as
cancer, stroke, and other heart diseases.
 RNA is vulnerable to damage by hydrolysis hence DNA stores genetic
information as it is less susceptible to damage.

KEY DISCOVERIES IN RNA BIOLOGY:

  Research on RNA has led to many important biological discoveries and
numerous Nobel Prizes. 
 Nucleic acids were discovered in 1868 by Friedrich Miescher, who
called the material 'nuclein' since it was found in the nucleus. It was
later discovered that prokaryotic cells, which do not have a nucleus, also
contain nucleic acids. The role of RNA in protein synthesis was
suspected already in 1939.
 Severo Ochoa won the 1959 Nobel Prize in Medicine (shared
with Arthur Kornberg) after he discovered an enzyme that can
synthesize RNA in the laboratory. However, the enzyme discovered by
Ochoa (polynucleotide phosphorylase) was later shown to be
responsible for RNA degradation, not RNA synthesis.
 In 1956 Alex Rich and David Davies hybridized two separate strands of
RNA to form the first crystal of RNA whose structure could be
determined by X-ray crystallography.
 The sequence of the 77 nucleotides of a yeast tRNA was found
by Robert W. Holley in 1965, winning Holley the 1968 Nobel Prize in
Medicine (shared with Har Gobind Khorana and Marshall Nirenberg).
In the early 1970s, retroviruses and reverse transcriptase were discovered,
showing for the first time that enzymes could copy RNA into DNA (the
opposite of the usual route for transmission of genetic information).
For this work, David Baltimore, Renato Dulbecco and Howard Temin were
awarded a Nobel Prize in 1975.
 In 1976, Walter Fiers and his team determined the first complete
nucleotide sequence of an RNA virus genome, that of bacteriophage
MS2.
In 1977, introns and RNA splicing were discovered in both mammalian
viruses and in cellular genes, resulting in a 1993 Nobel to Philip
Sharp and Richard Roberts.
Catalytic RNA molecules (ribozymes) were discovered in the early 1980s,
leading to a 1989 Nobel award to Thomas Cech and Sidney Altman. In 1990, it
was found in Petunia that introduced genes can silence similar genes of the
plant's own, now known to be a result of RNA interference.
 TRANSCIPTION:
Transcription:
It is the process of formation of mRNA from DNA. In prokaryotes it is
completed in 3 steps initiation , elongation and termination .
Initiation: Transcription requires a specific enzyme RNA polymerase.
This enzyme was first isolated by Chamberlain and Berg from E.coli.
The RNA polymerase in prokaryotes comprises a core enzyme and Sigma
factor together to form holoenzyme. The core enzyme comprises 5
polypeptides namely two α,β,β’ and omega.
The Sigma factor initiates the process of transcription in prokaryotes.
Transcription starts with the binding of RNA polymerases to a small region of
DNA helix called promoter.
In E.coli, the sequence is located about 25 nucleotides upstream from the
position at which transcription start.
Therefore it is called -25 box. Mostly it is read as 5’-TATAAT – 3’ .
Therefore it is also called Tata box or Pribnow box.
In eukaryotes this sequence is called Goldberg hogness box.
The Sigma subunit recognises and attaches to the promoter sequence and the
other subunits co operate in catalyzing RNA synthesis. Once transcription has
started, the Sigma subunit dissociates from the core enzyme after
polymerizing about 8 ribonucleotides.
Now the coenzyme continuous the process of elongation.
Elongation :
RNA polymerase synthesizes the RNA on the DNA template in the direction 5’-
3’ and anti parallel to the DNA template.
The 3’-5’ strand of DNA which acts as template for the RNA is called
antisense strand as it has all the bases complementary to that of the RNA
synthesized.
While the other complementary strand of DNA 5’-3’ is called sense stand as it
has all the bases similar to that of the RNA synthesized except thymine and
uracil.
RNA polymerase does not need any primer to begin the work.
It also lacks endonuclease and exonuclease activity therefore it also lacks
proofreading activity and repair of mismatches.

The RNA polymerases now joins ribonucleotides like ATP ,GTP,CTP,UTP

which are derived from the NTP’s by the activity of pyrophosphate enzymes.

Termination:
In prokaryotes ,termination of transcription occurs with the help of a specific
protein called rho factor which binds to the growing RNA and acts as a ATPase
to terminate the formation of RNA .
Sometimes it is also due to the formation of hairpin loops of the newly
synthesized RNA due to the presence of palindromic sequence present in the
DNA strand.
The former mechanism of termination is called Rho dependent termination
while the latter is called Rho independent termination.

In the beginning hnRNA is formed of then there is formation of mRNA after

post transcriptional modifications. The mRNA thus formed has all the codes
of DNA copied on it in continuation irrespective of the fact that the DNA has
introns and exons.