Nucleic Acids

Discovery
Nucleic acids were first isolated in 1869 by Friedrich Miescher from the nuclei of
pus cells. Due to their isolation from nuclei nature, they were named nucleic acids.
It was also separated from the sperm cells of fish.

The amino acid sequence of a polypeptide is programmed by a discrete unit of

inheritance known as a gene. Genes consist of DNA (deoxyribonucleic acid), called
nucleic acids. The name nucleic comes from DNA’s location in the nuclei of cells.
The other type of nucleic acid is RNA (ribonucleic acid).

Nitrogen Bases
There are two kinds of nitrogen-containing bases - purines and
pyrimidines. Purines consist of a six-membered and a five-membered nitrogen-
containing ring, fused together. Pyrimidines have only a six-membered nitrogen-
containing ring. There are 4 purines and 4 pyrimidines that are of concern to us.

Purines
 Adenine
 Guanine
Adenine and guanine are found in both DNA and RNA. Hypoxanthine and
xanthine are not incorporated into the nucleic acids as they are being synthesized
but are important intermediates in the synthesis and degradation of the purine
nucleotides.

Pyrimidines
 Uracil
 Thymine
 Cytosine

Cytosine is found in both DNA and RNA. Uracil is found only in RNA. Thymine
is normally found in DNA. Sometimes tRNA will contain some thymine as well as
uracil.
 Difference

Nucleosides
If a sugar, either ribose or 2-deoxyribose, is added to a nitrogen base, the resulting
compound is called a nucleoside. Carbon 1 of the sugar is attached to nitrogen 9 of
a purine base or to nitrogen 1 of a pyrimidine base. The names of purine nucleosides
end in -osine and the names of pyrimidine nucleosides end in -idine. The
convention is to number the ring atoms of the base normally and to use l', etc. to
distinguish the ring atoms of the sugar. Unless otherwise specificed, the sugar is
assumed to be ribose. To indicate that the sugar is 2'-deoxyribose, a d- is placed
before the name.
  Adenosine
 Guanosine
 Thymidine
 Cytidine

Structure

Nucleotides
Adding one or more phosphates to the sugar portion of a nucleoside results in
a nucleotide. Generally, the phosphate is in ester linkage to carbon 5' of the suger.If
the phosphate is in the position, however, the position must be designated. For
example, 3'-5' cAMP indicates that a phosphate is in ester linkage to both the 3' and
5' hydroxyl groups of an adenosine molecule and forms a cyclic structure. Some
representative names are:

 AMP = adenosine monophosphate = adenylic acid

 CDP = cytidine diphosphate
 dTTP = deoxy thymidine triphosphate (more commonly designated TTP)
Structure

Polynucleotides

Nucleotides are joined together by 3'-5' phosphodiester bonds to form

polynucleotides. Polymerization of ribonucleotides will produce an RNA while
polymerization of deoxyribonucleotides leads to DNA.
 Structure and Properties of DNA &RNA
S.N. DNA RNA
1. DNA stands for Deoxyribonucleic Acid. RNA stands for Ribonucleic Acid. The
The sugar portion of DNA is 2- sugar portion of RNA is Ribose.
Deoxyribose.
2. DNA is a double-stranded molecule RNA usually is a single-strand helix
consisting of a long chain of nucleotides. consisting of shorter chains of nucleotides.
3. The bases present in DNA are adenine, The bases present in RNA are adenine,
guanine, cytosine and thymine. guanine, cytosine and uracil.
4. DNA is self-replicating. RNA is synthesized from DNA on an as-
needed basis.
5. Base Pairing :AT (adenine- Base Pairing :AU (adenine-uracil)GC
thymine)GC (guanine-cytosine). (guanine-cytosine).
6. Purine and Pyrimidine bases are equal in There is no proportionality in between the
number. number of Purine and Pyrimidine bases.
7. DNA is susceptible to UV damage. Compared with DNA, RNA is relatively
resistant to UV damage.
8. Hydrogen bonds are formed between Base pairing through hydrogen bonds,
complementary nitrogen bases of the occurs in the coiled parts.
opposite strands (A-T, C-G).
9. DNA is found in the nucleus of a cell and Depending on the type of RNA, this
in mitochondria. molecule is found in a cell’s nucleus, its
cytoplasm, and its ribosome.
10. DNA can’t leave the nucleus. RNA leaves the nucleus (mRNA).
11. The C-H bonds in DNA make it fairly The O-H bond in the ribose of RNA makes
stable, plus the body destroys enzymes the molecule more reactive, compared with
that would attack DNA. The small DNA. RNA is not stable under alkaline
grooves in the helix also serve as conditions, plus the large grooves in the
protection, providing minimal space for molecule make it susceptible to enzyme
enzymes to attach. attack.
12. DNA is only two types: intra nuclear and Three different types of RNA: m-RNA, t-
extra nuclear. RNA and r-RNA.
13. Its quantity is fixed for cell. The quantity of RNA of a cell is variable.
14. It is long lived. Some RNAs are very short lived while
others have somewhat longer life.
15 . Functions:Long-term storage of genetic Functions:Used to transfer the genetic code
information; transmission of genetic from the nucleus to the ribosomes to make
information to make other cells and new proteins. RNA is used to transmit genetic
organisms. information in some organisms and may
have been the molecule used to store
genetic blueprints in primitive organisms .
 Diagram of DNA &RNA Structure:

TYPES AND FUNCTIONS OF RNA:

Like DNA, RNA is a polymer of ribonucleotides. The RNA molecules occur as
single strand, which may be folded back on itself, to give double helical
characteristics. The nitrogenous bases that are present in RNA are cytosine(C) with
guanine(G) and uracil(U) with adenine(A). RNA is synthesized by DNA in a process
known as transcription.
Types of RNA:
There are 3 main types of RNAs:
i- Messenger RNA (mRNA)
ii- Transfer RNA (tRNA)
iii- Ribosomal RNA (rRNA)
All these three types are synthesized from DNA in the nucleus and then are moved
out in the cytoplasm to perform their specific functions.

Function of RNA:
Following are the functions of different types of RNA:

 Messenger RNA (mRNA):

As the name indicates it takes the genetic message from the nucleus to the
ribosomes in the cytoplasm to form particular proteins. Messenger RNA carries the
genetic information from the DNA to ribosomes, where amino acids are arranged
according to the information in the mRNA to form specific protein molecule. This
type of RNA consist of a single strand of variable length. Its length depends upon
the size of the gene as well as the protein for which it is taking the message. For
example, for a protein molecule of 1,000 amino acids, mRNA will have the length
of 3,000 nucleotides. mRNA is about 3 to 4% of the total RNA in the cell.

 Transfer RNA (tRNA):

It comprises about 10 to 20% of the cellular RNA. Transfer RNA molecules are
small, each with a chain length of 75 to 90 nucleotides. It transfers amino acid
molecules to the site where peptide chains are being synthesized. There is one
specific tRNA for each amino acid. So the cell will have at least 20 kinds of tRNA
molecules. Transfer RNA picks up amino acids and transfers them to ribosomes,
where they are linked to each other to form proteins.

 Ribosomal RNA (rRNA):

It is the major portion of RNA in the cell, and may be up to 80% of the RNA. It is
strongly associated with the ribosomal protein where 40 to 50% of it is present. It
acts as machinery for the synthesis of proteins. On the surface of the ribosomes the
mRNA and tRNA molecules interact to translate the information from genes into a
specific protein.

DNA Sequencing
Definition:
“ Sequencing DNA means determining the order of the four chemical building
blocks- called bases- that make up the DNA molecule.”
It is the technique used to determine the nucleotide sequence of DNA. It is the
blueprint that contains the instructions for building an organism, and no
understanding of genetic function or evolution could be complete without obtaining
this information.
Method of DNA Sequencing:
The general method of DNA sequencing is as follows;

1) First the piece of chromosome is taken that contains 50 million or 250 million
nucleotide bases. These bases are then converted into smaller pieces.

2) The pieces are used as templates for further processing. These templates
produce set of fragments of different lengths.

3) The technique of Agarose DNA gel electrophoresis is used to separate the

fragments and keep them in order.

4) Fluorescent dyes are used to separate the set of fragments on the agarose gel and
keep them in sequence.

5) The final bases at the end of each strand fragment are identified which when
combined together make the short strand which was generated in the first step.

6) When the automated sequencers are used for the analysis of resulting
electropherograms, they show four-color chromatogram in which peaks are
showing. These peaks represent the four DNA bases.

7) After the visualization of the bases, now computers are use and all the four
fragments are combined together to make a long stretch. This long fragment is
analyzed for gene coding regions, errors and for many other characteristics.
Applications of DNA sequencing:

Forensics:
DNA sequencing has been applied in forensics science to identify particular
individual because every individual has unique sequence of his/her DNA. It is
particularly used to identify the criminals by finding some proof from the crime
scene in the form of hair, nail, skin or blood samples. DNA sequencing is also used
to determine the paternity of the child. Similarly, it also identifies the endangered
and protected species.

Medicine:
In medical research, DNA sequencing can be used to detect the genes which are
associated with some heredity or acquired diseases. Scientists use different
techniques of genetic engineering like gene therapy to identify the defected genes
and replace them with the healthy ones. . Scientists are now able to identify the
genes which are responsible for causing genetic diseases like Alzheimer's disease,
Cystic fibrosis, myotonic dystrophy and many other diseases caused by the
disability of genes to function properly.

Agriculture:
DNA sequencing has played vital role in the field of agriculture. The mapping and
sequencing of the whole genome of microorganisms has allowed the agriculturists
to make them useful for the crops and food plants. For example, specific genes of
bacteria have been used in some food plants to increase their resistance against
insects and pests and as a result the productivity and nutritional value of the plants
also increases. These plants can also fulfill the need of food in poor countries.
Similarly, it has been useful in the production of livestock with improved quality
of meat and milk.