GENETIC MATERIAL

Genetic material
The genetic material of a cell or an organism refers to those materials found in
the nucleus, mitochondria and cytoplasm, which play a fundamental role in determining the structure and nature
of cell substances, and capable of self-propagating and variation.

This material gets transferred from the parental generation to the offspring.

Characteristics
It must be stable (chemically and structurally).

It must be capable of being expressed when needed.

It must be capable of accurate replication.

It must be transmitted from parent to progeny.

It must periodically mutate to generate variation.

It must be able to store and express the information.

Types of Genetic material
1. DNA – Deoxyribonucleic acid
2. RNA – Ribonucleic acid
Nucleic Acids
Chromosomes mainly consists of nucleoproteins which are mainly composed of nucleic acids and proteins.
The protein combined with DNA is commonly either histone or protamine.
Nucleic acids are polymers that are built up by repeatedly linking together smaller molecules, called monomers.
These monomers are called ‘nucleotides’.
Phosphate group
Each nucleotide is made up of 2 molecular parts - Nitrogen base
Nucleoside Ribose (RNA)
Structure of Ribose and Deoxyribose sugars – 5 carbon sugars Sugar molecule
Deoxyribose
(DNA)
 Nitrogen bases

Pyrimidines (single ring structures) Purines (two ring structures)

1. Thymine 1. Adenine
2. Cytosine DNA
2. Guanine
3. Uracil RNA

Methyl group is absent in uracil whereas present in thymine at

the C-5 position.
DNA uses thymine instead of uracil because thymine has greater
resistance to photochemical mutation, making the genetic
message more stable.
Outside of the nucleus, thymine is quickly destroyed. Uracil is
resistant to oxidation and is used in the RNA that must exist
outside of the nucleus.
Nucleosides in DNA Nucleosides in RNA
 Nucleotide structure
Nucleotide is derived from nucleoside by the addition of phosphate group.
Phosphate group + Sugar + Nitrogen base
 Polynucleotide chain
Sequence of nucleotides (monomer units) are joined together by phosphodiester bonds to form polynucleotide chain.
A phosphodiester bond exists between the phosphate (5’ carbon end) of one nucleotide and the sugar (3' carbon) of the next
nucleotide.
This forms a backbone of alternating sugar and phosphate molecules known as the sugar-phosphate backbone.
This chain will have a direction. If it starts from C3, it would end in C5 and if it starts with C5 it would end in C3

A phosphodiester bond occurs when exactly two of the

hydroxyl groups in phosphoric acid react with hydroxyl
groups on other molecules to form two ester bonds.
Here we see linking of two pentose (5 carbon sugar) rings to
a phosphate group by strong, covalent ester bonds.
DNA
DNA is the information molecule. It stores instructions for making other large molecules, called proteins.
These instructions are stored inside each of our cells, distributed among 46 long structures called chromosomes.
These chromosomes are made up of thousands of shorter segments of DNA, called genes.
Each gene stores the directions for making protein fragments or whole proteins.
DNA structure
J. D. Watson and F. H. C. Crick in 1953 showed that DNA has a double helical structure with two
polynucleotide chains connected by hydrogen bonds and running in opposite directions.
Chargaff's rule (the equivalence rule)
Chargaff's rules state that DNA from any cell of any organism should have a 1:1 stoichiometric ratio (base pair
rule) of pyrimidine and purine bases (A + G = T + C)
The amount of guanine should be equal to cytosine and the amount of adenine should be equal to thymine (A = T
and G = C). They were discovered by chemist Erwin Chargaff in 1950.
DNA double helical structure
DNA polynucleotide chain has the form of regular helix.
The helix has a diameter of 20Ǻ between the two chains.
The helix makes one complete turn every 34 Ǻ along its length.
Each turn has stack of ten nucleotides and thus the inter nucleotide distance is 3.4 Ǻ.
In DNA molecule, the adjacent nucleotides are joined by phosphodiester bridges.
The DNA molecule consists of two polynucleotide chains wrapped helically around each other, with sugar –
phosphate chain on outer side and nitrogen bases (Purines + pyrimidines) on inner side of helix.
The two chains are held together by hydrogen bonds between specific pairs of nitrogen bases.
Adenine can bond only with Thymine by 2 hydrogen bonds (A=T) and Guanine can bond only to cytosine by 3
bonds (G C).
Thus the two chains are complementary to each other i.e., the sequence of nucleotides in one chain dictates the
sequence in other.
The two chains are considered antiparallel (opposite in direction).
One chain has phosphodiester linkage in 3’ 5’ direction, while the other has in just reverse order 5’ 3’.
The helix has 2 external grooves, a deep wide one called ‘major groove’ and a shallow narrow one called
‘minor groove’.
Puckered
In general terms, puckered means "wrinkled, folded or creased".
In conformational analysis this is used to refer to the non-planar geometry of a cyclic structure. Ring flipping. The
process by which a ring changes it's conformation.
Conformation
Any of the spatial arrangements which the atoms in a molecule may adopt and freely convert between, especially
by rotation about individual single bonds.
Sugar puckering
Sugar pucker correlates with phosphorus-phosphate distances along each strand.
The sugar puckers in DNA/RNA structures are predominately in either C3′-endo or C2′-endo conformation.
 Structural conformations of DNA include
1. A – DNA
2. B – DNA
3. Z – DNA
The most abundant type is B – DNA, commonly called as Watson & Crick model of DNA double helix.
A – DNA
Rare type of structural conformation in DNA.
A – DNA is double stranded helical structure almost similar to B – DNA but with more compact structural
organisation.
Discovered by Rosalind Franklin and the credit of naming A-DNA and B-DNA was also accounted to her.
Structural features of A – DNA
✔ Right handed helix.
✔ The helix diameter is 23 Ǻ.
✔ Much wider and flatter than B – DNA.
✔ The helix pitch (height of a turn) is 28.6 Ǻ.
✔ Contains on an average 11 base pairs per turn.
✔ A-DNA has a hollow central core. The base pairs are inclined to helical axis.
✔ Narrow & deep major grooves; wide and shallow minor grooves.
✔ The deoxyribose sugar pucker is of C3’ endo form.
B – DNA
Most common and predominate type of structural conformation of DNA in the cells.
Structural features of B – DNA
✔ Right handed helix.
✔ Bases occupy the core whereas the sugar phosphate backbone forms the periphery of the helix.
✔ The helical diameter is 20 Ǻ.
✔ Each turn possess an helical height of 34 Ǻ.
✔ Each turn consists of 10 base pairs.
✔ The distance between adjacent base pairs is 3.4 Ǻ.
✔ B – DNA has a solid central core.
✔ Wide & deep major groove; narrow & deep minor groove.
✔ The deoxyribose sugar pucker is of C2’ endo form.
 Z – DNA
Two strands coil in left handed helices leading to zig – zag pattern of phosphodiester backbone.
Has an alternating purine and pyrimidine sequences.
Structural features of Z – DNA
✔ Left handed helix.
✔ Helix diameter is 18 Ǻ.
✔ Total height of helix turn is 44 Ǻ.
✔ The nucleotide pairs in Z – DNA occur as dimers.
✔ Each helical turn contains 12 nucleotides (6 dimers).
✔ Flat major groove; narrow & deep minor groove.
✔ Has solid core at the centre.
✔ The sugar pucker is C2’ endo for pyrimidine and C3’ endo
for purine.
RNA
Ribose nucleic acid (RNA) is single stranded.
The RNA molecule folds up on itself either entirely or in certain regions.
In the folded regions, majority of bases are complementary and are joined by hydrogen bonds.
In the unfolded regions the bases have no complements.
Due to this RNA does not have purine – pyrimidine equality as found in DNA.
RNA differs from DNA in having ‘ribose’ sugar.
The nitrogen bases in RNA include – Adenine (A), Guanine (G), Cytosine (C) and Uracil (U).
The pyrimidine uracil substitutes thymine of DNA.
Types of RNA

1. Messenger RNA / mRNA / Template RNA

2. Ribosomal RNA / rRNA

3. Transfer RNA / tRNA / Soluble RNA

All the 3 forms of RNA are made from DNA template.

Transfer RNA (tRNA) and messenger RNA (mRNA) are synthesised from DNA templates of chromosomes
while the ribosomal RNA (rRNA) are synthesised from Nucleolar DNA.

These 3 types of RNA are synthesised during different stages of development.

rRNA and tRNA comprise almost to about 95 – 98 % of total RNA.

1. Messenger RNA / mRNA
Jacob and Monad (1961) proposed the name – messenger RNA for the RNA carrying the information from
DNA to ribosomes for protein synthesis.
It consists of only 3 – 5 % of cellular RNA.
Structure
Always single stranded.
There is certain amount of random coiling in extracted mRNA but there is no base pairing.
If base pairing occurs it destroys the ‘biological activity’ of mRNA.
mRNA is transcribed from DNA, thus the sequence of nitrogen bases is complementary to the sequence on DNA.
‘Each gene transcribes its own m RNA’. Thus the types of mRNA found in a cell will approximately be equal
to the number of functional genes present in the cell.

When one gene (cistron) codes for single mRNA strand, the mRNA is said to be ‘monocistronic’. However
monocistronic mRNA’s will code for only single protein.

When sequence of genes code for single mRNA strand the mRNA is said to be ‘polycistronic’. A polycistronic
mRNA will code for more than one protein.
 Structural features
1. Methylated cap
At the 5’ end of mRNA, the nitrogen bases (usually guanine) is methylated at the 7th position.
The rate of protein synthesis depends on the presence of the cap.
Without the cap, the mRNA molecule bind very poorly to the ribosomes.
2. Non – coding region 1 (NC 1)
The cap is followed by a region of 10 – 100 nucleotides. This region is rich in A and U residues and does not
translate protein. ( 5’ UTR – un translated regions).
3. Initiation codon
The initiating codon is AUG in both prokaryotes and eukaryotes.
4. Coding region
The coding region consists of 1500 nucleotides on an average and translates the polypeptide chains to form
proteins. (CDS – coding sequences).
5. Termination codon
Termination of translation on mRNA is brought about by termination codon. In eukaryotes, the termination
codons are UAA, UAG and UGA.
6. Non – coding region 2 (NC 2)
It consists of 50 – 150 nucleotides and does not translate into proteins. (3’ UTR – Untranslated regions).
7. Poly (A) Tail
At the 3’ end of mRNA, a polyadenylate or poly (A) tail / sequence is present which is usually 200-250
nucleotides long.
Stability of mRNA

mRNA is short lived and is degraded by ribonucleases if found in the cell for longer periods of time.

Eukaryotic mRNA’s are metabolically more stable than prokaryotic mRNA’s.

Eukaryotic mRNA’s differ from prokaryotic mRNA’s in being monocistronic, synthesis happens in the nucleus
and is transported to the cytoplasm for protein synthesis.
2. Ribosomal RNA (rRNA)

As the name suggests, it is found in the ribosomes.

Comprises of about 80% of the total cellular RNA.

In prokaryotes, the rRNA molecule is formed on a part of DNA strand called ‘ribosomal DNA’.

In eukaryotes, ribosomes are formed in the nucleolus.

The Nucleolar organiser contains the ‘ribosomal DNA’ which transcribes the RNA.

The formations of nucleoli takes place around the NOR region. The secondary constriction also contains the
genes for rRNA synthesis

rRNA consists of a single strand twisted upon itself in some regions. It has helical regions having complementary
base pairs connected by hydrogen bonds.

In the unfolded regions, the base pairs have no complements. Hence there is no purine to pyrimidine equality.
The ribosome consists of proteins and RNA.
Functions of rRNA
It makes complex with proteins and form ribosomal sub units which provide space for protein synthesis.
rRNA of smaller sub unit helps in correct orientation of mRNA to ribosome and its translation.
3. Transfer RNA
It is the second most abundantly found RNA in a cell. Also called as ‘soluble RNA’ because it is too small to be
precipitated by ultra centrifugation.
It constitutes about 10 – 20 % of the total cellular RNA.
Made up of 73 – 93 nucleotides.
It is synthesised in the nucleus on a DNA template.
tRNA is relatively small RNA having a molecular weight of 25000 – 30000 D and the sedimentation coefficient
being 3.8S.
Structure
The primary structure of tRNA was first given by ‘Holley et al (1965) which explained the nucleotide sequence
(linear sequence).
The secondary structure of tRNA – ‘Clover leaf model’ of Holley is most widely accepted model.
According to clover leaf model, the single polynucleotide chain of tRNA is folded up on itself to form ‘5 arms’.
As a result of folding the 3’ and 5’ ends of the chain come close to each other.
An ‘arm’ consists of a ‘stem and a loop’. The stem follows base pairing (A – U and G – C) and the loops do not
have base pairing.
 One arm has a stem but does not have a loop. It is called the ‘acceptor arm or acceptor stem’.
The other arms include –
Binding of a.a at the acceptor arm
✔ DHU arm / D arm.
✔ Anticodon arm
✔ The variable arm
✔ T ψ C arm

1. Acceptor arm / acceptor stem

Consists of 7 base pairs and 4 unpaired nucleotide units.
It has constant 3’ terminal called as ‘ – CCA sequence’. The fourth nucleotide that is unpaired is a variable purine
(A or G).

Amino acid attaches to the 3’ terminal of the –CCA sequence which is known as the ‘amino acid binding site’.
The 5’ end is either guanine or cytosine.
2. DHU arm / D arm
It has 15 – 18 nucleotides with 3 – 4 base pairs in the stem and 7 – 11 unpaired nucleotides in the loop.
The loop of D arm is called ‘Loop I or DHU loop (dihydrouridine loop) or D – loop’.
It acts as recognition site for the enzyme (amino acyl tRNA synthetase) that adds the amino acid to the acceptor
arm.
3. Anticodon arm
It consists of stem of 5 base pairs and a loop called ‘Loop II or anticodon loop’.
The loop consists of 7 unpaired nucleotides of which the middle 3 form the anticodon. This anticodon recognises
the 3 complementary bases which form the codon on mRNA.

4. Variable arm
This is called the ‘lump, the mini loop or Loop III’.
They are of 2 types –
a. Type I – there is a loop but stem is absent.
b. Type II – There is an arm consisting of both stem and loop.
Helps in stability of tRNA.
5. T ψ C arm
This arm has a stem of 5 base pairs and a loop of 7 nucleotides.
This T ψ C loop has ‘ribosome recognition site’.
Tertiary structure
It is L- shaped 3 – D structure.
Here the cloverleaf folds further into a L – shape.
At one end of the L lies the anticodon; at the other is the acceptor stem.
Functions of tRNA
1. To carry amino acids to mRNA during protein synthesis.
2. Each amino acid is carried by a specific tRNA. They act as temporary carriers.
3. They act as ‘intermediary’ between nucleotide sequence and the amino acid sequence.
4. They help in decoding the mRNA sequence to form the proteins.