Nucleic acid-

 Nucleic acids are complex macromolecules that are composed of nucleotide

monomers linked together through phosphodiester bonds.
 There are two main types of nucleic acids: deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA).
 A nucleotide has 3 components –
1. Nitrogenous base - It is a nitrogen-containing molecule with the properties
of a base.
2. Pentose sugar - It is a five-carbon sugar molecule.
3. Phosphate group

Nitrogenous Bases

Purines - Purines are double-ring structures consisting of a pyrimidine ring fused

with an imidazole ring. The main purine bases found in DNA and RNA are
adenine (A) and guanine (G).

 Adenine (A) - It has a purine ring structure consisting of a six-membered

pyrimidine ring fused with a five-membered imidazole ring. Chemically, it
is 6-aminopurine.
 Guanine (G) - It also has a purine ring structure but with an additional
oxygen atom and a double bond within the imidazole ring. Its chemical
name is 2-amino-6-oxypurine.

Pyrimidines - Pyrimidines are single-ring structures with a six-membered ring.

The main pyrimidine bases found in DNA and RNA are cytosine (C), thymine (T),
and uracil (U).

 Cytosine (C) - It has a pyrimidine ring structure with two nitrogen atoms and
a carbon atom in the ring. The chemical name is 4-amino-2-oxypyrimidine.
 Uracil (U) - It is a pyrimidine base found in RNA in place of thymine. It is
known as 2,4-dioxypyrimidine.
 Thymine (T) - It is a pyrimidine base found specifically in DNA and has a
methyl group attached to the pyrimidine ring. It is thus called 5-
Methyluracil.
Pentose Sugar

Pentose sugars are five-carbon sugars that play a critical role in the structure and
function of nucleic acids, such as DNA and RNA.

 Ribose - Ribose is a component of RNA (ribonucleic acid). Ribose has a

hydroxyl group (-OH) attached to each carbon atom, except 2' position,
which has a single hydrogen atom (-H).
 Deoxyribose - It is a component of DNA (deoxyribonucleic acid). It is
derived from ribose by the removal of one oxygen atom, resulting in the
absence of the hydroxyl group at 2' position.
Phosphate

Phosphate (PO4 3- ) consists of one phosphorus atom (P) covalently bonded to

four oxygen atoms (O). The phosphorus atom is at the center of a tetrahedral
arrangement, with three oxygen atoms forming single bonds and one oxygen atom
forming a double bond.

Phosphodiester bond

The monomeric deoxynucleotides in DNA are held together by 3’, 5’

phosphodiester bonds.
Chargaff's Rules

Chargaff's rules, proposed by biochemist Erwin Chargaff, describe the base

composition of DNA and the pairing relationships between its nucleotide bases.

The rules are as follows: Amount of Purine = Amount of Pyrimidine, Amount of

A = T and C = G. this is known as chargaff;s rule of molar equivalence between
the purines and pyrimidines. In DNA, Base Ratio of A+T /G+C is always constant
for a particular species, but may vary among different groups of organisms.

ssDNA and RNA do not obely this rule.

DNA double helix

James Watson and Francis Crick proposed that DNA must be formed like a double
helix in 1953. This is called the Watson-Crick Structure of DNA.

The important features of Watson-Crick model or double helix model of DNA

are as follows:

1. The DNA molecule consists of two polynucleotide chains or strands that spirally
twisted around each other and coiled around a common axis to form a right-handed
double-helix.

2. The two strands are antiparallel i.e. they run in opposite directions so that the 3′
end of one chain facing the 5′ end of the other.

3. The sugar-phosphate backbones remain on the outside, while the core of the
helix contains the purine and pyrimidine bases.
4. The two strands are held together by hydrogen bonds between the purine and
pyrimidine bases of the opposite strands.

5. Adenine (A) always pairs with thymine (T) by two hydrogen bonds and guanine
(G) always pairs with cytosine (C) by three hydrogen bonds. This complementarity
is known as the base pairing rule. Thus, the two stands are complementary to one
another.

6. The base sequence along a polynucleotide chain is variable and a specific

sequence of bases carry the genetic information.

7. The base compositions of DNA obey Chargaff’s rules (E.E. Chargff, 1950)
according to which A = T and G = C; as a corollary ∑ purines (A+G) = ∑
pyrimidines (C + T); also (A + C) = (G + T). It also states that ratio of (A + T) and
(G + C) is constant for a species (range 0.4 to 1.9).

8. The diameter of DNA is 20nm or 20 Å . Adjacent bases are separated 0.34 nm

or by 3.4 Å along the axis. The length of a complete turn of helix is 3.4 nm or 34 Å
i.e. there are 10bp per turn.

9. The DNA helix has a shallow groove called minor groove (˜1.2nm) and a deep
groove called major groove (~2.2nm) across.

Forms of DNA
Factors Affecting Different Forms of DNA –

1. Ionic or Hydration environment - A-DNA is favoured by low hydration, while Z-

DNA is favoured by high salt concentration.

2. Nucleotide sequence - Z-DNA is favoured by specific sequences of alternating

purinepyrimidine steps.

3. Presence of proteins - Proteins may bind to B-DNA and drive it to form A or Z-

DNA.

Organization of DNA in Eukaryotes

If the DNA from all 46 chromosomes in a human cell nucleus was laid out end to
end, it would measure approximately two meters; however, its diameter would be
only 2 nm. Considering that the size of a typical human cell is about 10 µm
(100,000 cells lined up to equal one meter), DNA must be tightly packaged to fit in
the cell’s nucleus. At the same time, it must also be readily accessible for the genes
to be expressed. During some stages of the cell cycle, the long strands of DNA are
condensed into compact chromosomes.

Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a

complex type of packing strategy to fit their DNA inside the nucleus.

At the most basic level, DNA is wrapped around proteins known as histones to
form structures called nucleosomes.

The histones are evolutionarily conserved proteins that form an octamer of eight
histone proteins attached together. DNA, which is negatively charged because of
the phosphate groups, is wrapped tightly around the histone core, which has an
overall positive charge.

This nucleosome is linked to the next one with the help of a linker DNA. This is
also known as the “beads on a string” structure. This is further compacted into a 30
nm fiber, which is the diameter of the structure.

At the metaphase stage, the chromosomes are at their most compact, are
approximately 700 nm in width, and are found in association with scaffold
proteins.
Properties of RNA

Ribonucleic acid (RNA), unlike DNA, is usually single-stranded. A nucleotide in

an RNA chain will contain ribose (the five-carbon sugar), one of the four
nitrogenous bases (A, U, G, or C), and a phosphate group. Here, we'll take a look
at four major types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA),
transfer RNA (tRNA), and regulatory RNAs.

Messenger RNA (mRNA)

Messenger RNA (mRNA) is an intermediate between a protein-coding gene and

its protein product. If a cell needs to make a particular protein, the gene encoding
the protein will be turned “on,” meaning an RNA-polymerizing enzyme will come
and make an RNA copy, or transcript, of the gene’s DNA sequence. The transcript
carries the same information as the DNA sequence of its gene. However, in the
RNA molecule, the base T is replaced with U. For instance, if a DNA coding
strand has the sequence 5’-AATTGCGC-3’, the sequence of the corresponding
RNA will be 5’-AAUUGCGC-3’.

Once an mRNA has been produced, it will associate with a ribosome, a molecular
machine that specializes in assembling proteins out of amino acids. The ribosome
uses the information in the mRNA to make a protein of a specific sequence,
“reading out” the mRNA’s nucleotides in groups of three (called codons) and
adding a particular amino acid for each codon.

Ribosomal RNA (rRNA) is a major component of ribosomes, where it helps

mRNA bind in the right spot so its sequence information can be read out. Some
rRNAs also act as enzymes, meaning that they help accelerate (catalyze) chemical
reactions – in this case, the formation of bonds that link amino acids to form a
protein. RNAs that act as enzymes are known as ribozymes.
Transfer RNAs (tRNAs) are also involved in protein synthesis, but their job is to
act as carriers – to bring amino acids to the ribosome, ensuring that the amino acid
added to the chain is the one specified by the mRNA. Transfer RNAs consist of a
single strand of RNA, but this strand has complementary segments that stick
together to make double-stranded regions. This base-pairing creates a complex 3D
structure important to the function of the molecule.

Clover leaf structure of tRNA

The secondary folded structure of tRNA has three hairpin loops, which give it an
appearance of three-leafed clover. The main constituents of tRNA are:

Acceptor arm

It is formed by the base pairing of 7-9 nucleotides of 5’ terminal and 3’ terminal.

The 5’ terminal has a phosphate group and the 3’ ends with a specific sequence of
CCA or CCA tail. The amino acid attaches to the 3’ hydroxyl group of the acceptor
arm.

The aminoacylation of tRNA or charging of tRNA is the first step of the translation
process. The enzyme aminoacyl tRNA synthetases catalyse the reaction.

DHU Loop

D arm has a stem of 3-4 base pairs and it ends in a loop called D loop as it
generally contains dihydrouridine, a modified nucleotide.

Anticodon Loop

It has a 5 base pair long stem. It has an anticodon loop, which contains the
complementary codon (3 nucleotides sequence) present on mRNA for the amino
acid it carries. These unpaired bases of anticodon loop pair with the mRNA codon.
Each codon is identified by a specific tRNA.

TΨC Loop

The T arm consists of a stem of 4-5 bp and a loop containing pseudouridine,

modified uridine.
Variable Loop

It is present between the TΨC loop and the anticodon loop. Its size varies from 3-
21 bases. It helps in the recognition of the tRNA molecule.