Class 11th

Sheikh Imtiyaz Sir

STRUCTURE OF DNA
class 11th
Sheikh Imtiyaz (M.sc M Phil Botany)

STRUCTURE OF DNA
Meischer coined the term nuclein, Ataman found that nuclein is acidic in
nature and he coined the term nucleic acid. Emil Fischer found that nucleic
acid is of two types viz DNA and RNA. Term RNA was coined by Emil
Fischer while as erm DNA was coined by Zacheris. Kossel found that DNA
is a polymer of deoxy ribonucleotides. Each deoxy ribonucleotide is made
up of nitrogenous base, deoxyribose sugar and phosphoric acid.
Nitrogenous bases are of two types Purines and Pyrimidines. Purines are
double ringed heterocyclic nitrogenous bases containing nitrogen at
position number 1,3,7 and 9. Examples of purine bases are Adenine and
Guanine.
Pyrimidines are single ring heterocyclic nitrogenous base containing
nitrogen at position numbers 1,3. Examples are Cytosine, Uracil and
Thymine.

In DNA adenine, Guanine, Cytosine and Thymine bases are present. Uracil
is absent while as in RNA adenine, Guanine, cytosine and uracil is present,
thymine is absent.
Deoxyribose Sugar:- Pentose sugar is present in DNA in the form of
deoxyribose sugar(aldose sugar)
Phosphoric acid:- It is a tribasic acid in which phosphorous is pentavalent.

In deoxyribonucleotide nitrogenous base binds with carbon number one of

deoxyribose sugar by a bond called Glycoside bond while as phosphoric
acid binds with carbon number 5 by a bond called Phophoester bond. Two
landmarks which helps in determining structure of DNA are, (a) Chargaff’s
rule (b) X-ray diffraction technique.

Chargaff’s Rule:- It is also called as equivalence rule and was given by

Erwin Chargaff. Main points of Chargaff’s rule are as follows

➔ Purines are always equal to pyrimidines.

➔ Adenine is always equal to thymine and Cytocine is always equal to
Guanine.
➔ Sugar and phosphoric acid are present in equimolar amounts.
 ➔ A+T/C+G is called as base ratio. It is specific for specific species. Base
ratio is mostly less than 1 in prokaryotes but in Eukaryotes base ratio
is mostly more than 1.
➔ C+T/A+G is called as Equivalence ratio and it is always equal to 1.

Q. In a double stranded DNA adenine is 18%. What is the percentage of

Thymine, cytosine and Guanine??

A = T = 18% and A+T = 18%+18%= 36%

C+G = 100 – 36 = 64%

C= G = 32%

Q. In a double stranded DNA adenine is 20%. What is the percentage of

mymine, Cytosine and Guanine?

A = T = 20%, A+T = 20+20= 40%

C + G= 100- 40= 60%. C =G = 30%.

 When C+T/ A+G is equal to one, genetic material is double stranded

DNA.
 When C+T/A+G is not equal to one, genetic material is single
stranded DNA.
 When C+U/A+G is equal to one, genetic material is double stranded
RNA.
 When C+U/A+G is not equal to one, genetic material is single
stranded RNA.

X-ray diffraction technique:- Austbury performed X-ray diffraction and

obtained a photograph of DNA and found that DNA is a polymer of
deoxyribonucleotides and the distance between the two
deoxyribonucleotides is 3.4Å. Franklin Roslind performed X-ray diffraction
crystallography and obtained a photograph which is properly called as
photograph 51. She found that DNA is double stranded and helical and
distance between the two strands is 20Å. Each helix contains 10 base pairs
and the length of helix is 34Å. Roslind failed to prove double stranded
nature of DNA.

WATSON AND CRICK MODEL:- Watson and crick did not perform any
experiment, they collected data from previous workers regarding physical
and chemical aspects of DNA and develop a model for its structure in
1953. They were awarded Nobel prize along with Wilkins for this work.
According to Watson and Crick DNA is a double stranded, helical and anti-
parallel in nature and two strands of DNA are not coiled upon each other.
They coil around a central axis. Thus distance between the two strands
remain same at every point (plectonemic nature). Each strand is a polymer
of deoxyribonucleotide which are connected with each other through
phosphodicster bond. Each deoxyribonucleotide is made up of H3PO4,
deoxyribose sugar and nitrogenous base. Phosphoric acid is connected
with carbon sugar number 5 of deoxyribose sugar by a bond called
phosphoester bond and the nitrogenous base is connected with carbon
number 1 of deoxyribose sugar by Glycosidic bond. In case of Purine
glycosidic linkage is C₁, N₉ and in case of pyrimidine glycosidic linkage is
C₁N₁. The two strands of DNA are anti-parallel which is important for
bringing adjacent nitrogenous bases close to each other so that hydrogen
bonds are formed between them. Base pairing is complementary i.e.,
Adenine form 2 hydrogen bonds with thymine and cytosine form 3
hydrogen bonds with Guanine. One of the strand has polarity 5’---3’ and
the other strand has polarity of 3’---5’, distance between two strands is
20Å, angle of helix is 36 degree, one helix contains 10 base pairs and the
length of helix is 34Å.
Fig. Structure of DNA given by Watson and Crick

PROPERTIES OF DNA

1. DNA is acidic in nature, because of presence of phosphoric acid.

2. DNA is plectonemic in nature i.e., distance between two strands
remains same at every point.
3. DNA is double stranded, helical and the 2 strands are anti parallel.
4. DNA is dextrorotatory i.e., bonds plane polarized towards right side.
5. DNA shows hyper chromatic shift i.e., its absorption spectrum
increases in UV region when it is converted into single stranded
form.
 6. Out of 2 strands of DNA, genetic information is present only in one
strand and it is called as antisense or template strand while as other
strand does not contain genetic information and is called as sense
strand. Sense strand is important for providing stability. Strand with
3’-5’ polarity is antisense strand and strand with 5’-3’ polarity is
sense strand. M-RNA is formed from an antisense strand.
7. DNA shows denaturation at a temperature of 80-90⁰C. At that time,
DNA gets converted into single stranded due to breaking of hydrogen
bonds. But when temp is decreases and reaches up to 65⁰C, DNA
shows renaturation i.e., it again gets converted into double stranded
form.

Semi Conservative Replication:- It is that type of replication in which one

strand of the daughter duplex is derived from the parent strand and the
other strand is new. Semi conservative replication of DNA was first proved
by Mathew Messelson and Franklin Stahl in 1958 in E.coli (prokaryote).
They grew E.coli in a culture medium containing ammonium chloride
(NH₄Cl) in which heavy isotope of nitrogen (Nⁱ⁵). samples were taken after
every 20 mins because DNA of E coli completes its replication during this
time. DNA was tested for the heavy isotope of nitrogen through density
gradient centrifugation using CsCl₂ (cesium chloride). When DNA is mixed
with CsCl₂ it will settle down at a particular height in centrifugation,
heavier towards the base and lighter towards the supernatural. A
fluorochrome dye called Ethidium bromide was used to enhance the
contrast as the dye is specific for DNA.

They found that DNA of the first generation was hybrid or intermediate
(Nⁱ⁵ Nⁱ⁴) and it settled in CsCl₂ solution above the level of heavy DNA Nⁱ⁵
Nⁱ⁵. in 2nd generation 50% intermediate and 50% light DNA was found
during density gradient centrifugation. In 3rd generation 25% intermediate
and 75% light DNA was obtained in the ratio of 1:3. This observation is
possible only if two strands of DNA duplicate separate at the time of
replication and acts as a template for the synthesis of new complementary
strands and during duplex formation, parent strand forms double stranded
DNA with its daughter strand.

In Eukaryotes semi -conservative replication was discovered by Taylor and

Woods in Vicia faba (broad beans) by using isotope of hydrogen Hᶟ in
thymidine nucleotide.

STEPS OF DNA REPLICATION

Following steps occur during the replication of DNA;

1. Origin of Replication:- is a particular region of DNA which has a

particular nucleotide sequence called Automatic Replication
Sequence (ARS). It is also called as ORI site. In prokaryotes there is
only one ORI site but in Eukaryotes there are multiple ORI sites e.g. in
 human beings DNA contain 6000 ORI sites and in drosophila there
are 3500 ORI sites.
2. Activation of deoxyribonucleotides :- in this step deoxyribo-
nucleotides are activated with the help of ATP in presence of an
enzyme phosphorylase. Activation of deoxyribonucleotide is
important for formation of phosphodiester bonds between
deoxyribonucleotides of daughter strand. Reactions involved for
activation of deoxyribonucleotides are as follows

dAMP + ATP ------------→ dATP + AMP

dCMP + ATP -----------→ dCTP + AMP

dGMP + ATP ----------→ dGTP + AMP

dTMP + ATP -----------→ dTTP + AMP

3. Initiation or Unwinding of DNA duplex :- During initiation,

unwinding of DNA duplex takes place. This unwinding occurs with
the help of enzymes. In Eukaryotes enzyme helicase unwinds or
unzips DNA duplex by breaking of hydrogen bonds between the 2
strands. Unwinding creates tension which results in super coiling or
super twisting of DNA. Torsional forces are released by
Topoisomerase, therefore it is called as Reverse nuclease. In
prokaryotes helicase and topoisomerase enzymes are absent, their
activity is performed by DNA gyrase. After unzipping DNA appears Y
shaped and this is known as Replication fork.
 Fig. Replication Fork.

4. Priming :- During priming primers are formed at ORI sites. It is

essential for formation of DNA daughter strand. It contain RNA bases
therefore it is also called as RNA primes. RNA primers are formed in
presence of DNA dependent RNA polymerase enzyme. In
prokaryotes primers are formed by primase enzyme while as in
Eukaryotes primers are formed by DNA polymerase(alpha). Primers
are always formed in 5’-3’ direction.
5. Base Pairing :- During base pairing deoxyribonucleoside tri
phosphate come to lie opposite to the bases of two parental strands
or template strands i.e., dTTP opposite to Adenine, dATP opposite to
thymine, dCTP opposite to Guanine and dGTP opposite to cytosine.
Enzyme pyrophosphatase converts deoxyribonucleosite triphosphate
into deoxyribonucleosite monophosphate releasing 2 molecules of
inorganic phosphate (Pi) and energy is released which is used for
formation of hydrogen bonds between nitrogenous bases of parental
strand and daughter strand
2Pi + H₂O → Pi + Pi + Energy

6. Chain Elongation:- During chain elongation addition and

polymerization of deoxyribonucleotides occur on daughter strand. In
prokaryotes chain elongation occurs in the presence of an enzyme
DNA polymerase and it is of 3 types, a) DNA polymerase I. b) DNA
polymerase II, c) DNA polymerase III. DNA polymerase III is the main
enzyme which helps in addition and polymerization of
deoxyribonucleotides in daughter strands. It adds new bases only in
5’-3’direction. Due to specificity of DNA polymerase III in 5’-3’
direction is discontinuous i.e., it is formed in fragment which are
called as Okazaki fragment and this daughter strand is called as
lagging strand.

DNA polymerase I is the major repair enzyme because it removes

primers and also fills the gaps between Okazaki fragments which are
connected with each other by DNA ligase. DNA polymerase II is a
minor repair enzyme. Proof reading is done by DNA polymerase III.

In Eukaryotes chain elongation occurs in presence of DNA

polymerase which is of 5 types viz. DNA polymerase α, β, γ, δ, ε. DNA
polymerase α helps in formation of primer, DNA polymerase β
removes primers and fills gaps between Okazaki fragments , DNA
polymerase γ helps in proof reading and in mitochondrial replication,
DNA polymerase δ forms leading strand while as DNA polymerase ε
forms lagging strand.

Central Dogma :- The term central dogma was given by crick.

According to central dogma DNA does not directly form protein, it
first forms RNA by a process called Transcription and later on RNA
form proteins over ribosomes by a process called Translation.
Central dogma is as follows:

DNA → RNA -→ proteins.

Termin and Baltimore found that in retro viruses RNA forms DNA by
a process called Reverse Transcription in presence of an enzyme
Reverse Transcriptase. They challenge the universality of central
dogma and converts it into central Dogma Reverse or Temenism. It is
as follows

DNA ↔RNA → proteins

TRANSCRIPTION

It is the formation of RNA from DNA. The RNA formed contains

information similar to that of sense strand except that thymine is
replaced by Uracil. The DNA strand which acts as a template is
known as template strand or anti-sense strand or informative strand.
The transcription occurs at a particular region known as transcription
unit which has generally three regions i.e. promoter region,
structural region and terminator region.

Transcription occurs with the help of enzyme RNA polymerase. For

transcription in prokaryotes only single RNA polymerase is involved.
However in case of eukaryotes three RNA polymerases are involved
i.e. I, II, and III among which polymerase II is more important. The
promoter region contains two sites i.e. recognition site and
polymerase binding site. The polymerase enzyme consists of four
components in prokaryotes i.e. two α, β, β’. It is an apo enzyme
which requires cofactor in the form of σ (sigma) for activation. Once
the sigma factor gets attached with RNA polymerase it becomes
functional and is known as holo enzyme. The σ factor of RNA
polymerase binds with recognition site. In prokaryotes there is
special sequence of nucleotides for recognition i.e. TTGACA and
TATAAT box or Pribnoy box for polymerase binding. Once the sigma
factor gets attached with recognition site it binds the rest of RNA
polymerase with polymerase binding site. In case of Eukaryotes there
is CAAT or GC sequence for recognition and TATA box or Hogness box
for polymerase binding. In prokaryotes the RNA polymerase binds
with transcriptional unit, it breaks the hydrogen bonds and bring
activated nucleotides for synthesis of RNA. For elongation another
factor known as Nus-A factor is required in prokaryotes and for
termination another factor known as rho (ρ) factor is required. In
eukaryotes elongation occurs with the help of EF II and termination
occurs with the help of TF II. The activated ribonucleotides release
pyrophosphate which on hydrolysis releases energy and is involved
in formation of phosphodiester bond between ribonucleotides. In
prokaryotes mRNA is formed while as in eukaryotes hn RNA is
formed. The hn RNA contains both coding and non-coding
sequences. The non-coding sequences are removed by means of
Snurps.

Post Transcriptional Modifications

Post Transcriptional Modifications are those in which RNA formed

from transcript unit undergoes modifications to become stable. Four
types of modifications occur which are as follows:

1. Clevage :- it occurs in mRNA in presence of Sn-RNA III(small

nuclear RNA). In prokaryotes 30s r-RNA is directly formed which
undergoes Clevage in presence of Sn-RNA III and gets converted
into 23S, 16S and 5S. in eukaryotes 45S r-RNA is directly for NOR.
45S RNA undergoes change in presence of Sn-RNA III and gets
converted into 28S, 18S,5.8S and 5S.
2. Splicing :- In Eukaryotes cistron does not contain continuous
genetic information. Part of cistron which does not contain
genetic information is called an intron. During transcription in
Eukaryotes hn-RNA (heterogenous nuclear RNA) is synthesized.
Hn-RNA goes splicing in presence of snurphs and intronic
sequences are removed through GU-AG rule and the resulting
structure is called as m-RNA. Thus in Eukaryotes both intronic as
 well as exonic sequences are transcribed but only exonic
sequences are translated. In prokaryotes splicing does not occur.
3. Terminal additions :- occurs in m-RNA. In this type of modification
cap in form of 7-methylated guanine is added at 5’ end while as
tail i.e. poly A-tail made up of 200-250 adenine are added at 3’
end. Cap and tail prevents m-RNA from exonuclease activity in
cytoplasm.
4. Nucleotide Transformation:- it occurs in t-RNA. In this type of
modification normal bases are converted into unusual
bases(pseudo bases) e.g., deamination of adenine results in
formation of inosine. Pseudo bases are important for folding of t-
RNA which results in formation of various sites that help in
binding of amino acid and recognition of ribosomes and codons.
TYPES OF RNA
1. mRNA (messenger RNA): it means messenger RNA. It carries
instruction from DNA through a sequence of amino acids to
form protein. It constitutes only 25% of total RNA. However it is
short lived and dies after few translations. e.g. in prokaryotes it
survives only for two minutes and in case of eukaryotes it
survives for 1-4 hours, mRNA in case of eukaryotes is mainly
divided into five components.
a. Head :- it is the 7 methylated guanine region which is present
at 5 end of mRNA for disintegration.
b. Non coding region:- it is the region which does not contain any
genetic information. It contains 90-100 nucleotides. It lies
adjacent to the coding region. In Prokaryotes, there occurs
“shine dal garno” sequence adjacent to coding region.
(AGGGGAAAU) this sequence binds mRNA with ribosome.
However in Eukaryotes, 7-methylated cap or Kozak sequence
binds mRNA with ribosome.
c. Coding region :- it is the region which contains genetic
information for synthesis of protein or polynucleotide chain.
The coding region generally contains genetic information in the
 form of base triplet known as Codon. The first codon in
majority of cases is AUG while as in 10% of mRNA the first
codon is GUG. AUG codes for methionine while as GUG codes
for valine but when it acts as imitation codon it codes for
methionine. The 3 codons which act as terminator codons are
UAG, UAA and UGA. UGA was the first codon to be discovered
followed by UAA and UGA. They are also named as amber
(yellowish brown) ochre (yellowish red) and opal (milky white)
respectively.
d. Non coding region II :- This region contains 50-150 nucleotides.
It resembles with non-coding region I as it does not contain any
genetic information.
e. Tail :- It is the 5th region of mRNA and contains 50-250 adenine
bases. Through this end which is present at 3 side, mRNA
comes out from nucleus.
2. Ribosomal RNA rRNA:- It constitutes 80%of total RNA and
remain associated with ribosomes. It is formed from NOR in
eukaryotes (except SS). However in prokaryotes 3.2%of main
genome forms rRNA. There are 6 types of ribosomal RNA i.e.
28S, 23S, 18S, 16S, 5.8S and 5S. in Prokaryotes, the larger sub
unit contains 23S and 5S while as smaller subunit contains 16S.
in case of Eukaryotes, the larger ribosomal subunit contains
28S, 5.8S and 5S while as smaller component contains 18 S. so
in both prokaryotes and eukaryotes, 5 S rRNA is involved.

NOTE:- Prokaryotic rRNA are polycistronic i.e. they code for more than one
pattern while as eukaryotic is monocistronic i.e., they code for only one
protein or polypeptide chain.

3. tRNA:- It is also known as soluble RNA supernatant RNA or

adapter RNA. tRNA is difficult to separate through ultra-
centrifugation or it is soluble in 1 molar solution of NaCl. It is
known as supernatant RNA as it remains on the surface during
ultracentrifugation because of low sedimentation coefficient
i.e., 3.8S. The base ratio is 0.7 i.e., it contains more of cytosine
and guanine as compared to Adenine and Uracil. Initially tRNA
is single stranded but for stabilization it becomes double
stranded. The most accepted model in tRNA is Clover-leaf
model given by Holley, Khorana and Nirenberg for which they
were given Nobel prize. However 3 dimensional structure
which is in L form was given by Klug. The tRNA consists of four
major arms in which each arm contains a stem and a loop
except acceptor arm. The stem is formed due to base pairing of
complementary nucleotides which as the loop is present at
terminus or terminal point and contains unpaired bases. The
four major arms are as under:
a. Acceptor arm: It is the term which contains both 3’ and 5’
end. At acceptor arm(3’side) there is always presence of
sequence named as CCA-OH. The acceptor arm accepts the
amino acids but this arm is not specific to (particular amino
acid) which amino acid gets attached to this arm.
b. Tᵠ C arm:- this arm is named for the bases present in the
nucleotides of this loop. The bases are thymine, pseudo-
uracil and cytosine. The role of this arm in the molecule is
that it binds it with ribosome. Hence it is known as ribosomal
loop.
c. Anticodon arm:- this arm is present at the bottom of tRNA
and contains 3 free nucleotides at its extreme known as
anticodon. This anticodon binds with codon of mRNA in
order to link the amino acids in correct order. So it is the
anticodon site which specifies amino acid.
d. DHU arm :- This arm contains dihydrouridine, hence the
name. it is also known as amino acyl synthetase loop as this
loop binds with enzyme aminoacyl synthetase. Besides these
4 major arms, some tRNA contain a short variable arm
whose function is unknown.
4. Small Cytoplasmic RNA:- these are small RNA molecules
present in the cytoplasm. Some such small RNA molecules have
sedimentation coefficient of 6S which bind with 6 protein
molecules to form signal recognition protein (SRP). This SRP
helps in binding the ribosomes with endoplasmic reticulum.
5. Catalytic RNA’s:- these small RNA’s actually act as enzymes and
are known as ribozymes. They were first of all discovered by
Thomas Cech while working on RNA splicing in tetrahymena
(ciliated protozoa). The ribosomes act on RNA molecules and
RNA to mature mRNA, pre-ribosomal RNA to mature ribosomal
RNA. Similarly ribonuclease changes pre tRNA into mature
tRNA.
 GENETIC CODE
The cells are able to synthesize specific proteins by information flowing
from DNA which exists in the form of nucleotide sequence or nitrogen
bases known as genetic code. OR, It is defined as a sequence of
nucleotides or nitrogen bases in a DNA or mRNA which determines the
sequence of amino acids in polypeptide chain.

Genetic code contains a nitrogen base. Each set of bases in DNA can
arrange in 64 (4*4*4) possible ways. Because the number of carbon is
greater, therefore all the amino acids with the exception of methionine
(AUG) and ‘tryptophan’ UGG are coded by more than one codon. The
codons which code for same amino acids are known as synonyms e.g.,
ACU, ACC, ACG and ACA code for same amino acid i.e., “threonine”. The
genetic code was first of all hypothesized by Gammov and later on
discovered by Nirenberg and Mather (1968).

Characters Of Genetic Code

1. Triplet Organization:- Genetic code is triplet in nature i.e. it contains

3 nucleotides or 3 nitrogen bases. It was experimentally proved that
genetic code has triplet nature. It is neither singlet nor doublet. As
singlet the four bases can form four codons and hence can code only
4 amino acids. As doublet or duplet nitrogen bases can be arranged
in 16 possible ways i.e., only 16 codons will be formed which is still
insufficient for coding 20 amino acids. As triplet, 64 possible ways are
formed which are sufficient for coding 20 amino acids.
2. Non overlapping:- genetic coding is non overlapping i.e. each code is
present in the form of continuously arranged independent triplets.
No single base can be a part of 2 adjacent codons i.e., if we have to
code 2 amino acids, we require 6 nitrogen bases. However
overlapping of genetic code has been found in bacteriophage (sanger
in 1977).
3. Commaless :- Genetic code is Commaless i.e. it is without any gap or
break or in other words when first amino acid is coded, the second
one is automatically coded.
4. Start signal/initiation signal:- out of 64 codons, 2 codons are
initiation codons which are AUG and GUG in 10%. AUUG codes for in
90% methionine. While as GUG methionine in mitochondria of
mammals AUU, AUA, AUG and GUG code for methionine i.e. all the 4
act as initiation codon.
5. Termination codon:- Out of 64 codons, 3 codons are termination
codons or non-sense codons which are UAG, UGA and UAA. In
ciliated protozoa (mycoplasma UGA and UAA code for “glutamic
acid”). In mitochondria of mammals UGA codes for Tryptophan
6. Degeneracy (Redundancy):-Genetic code is degenerate. It means
single amino acid can be coded by more than one codon e.g. phenyl
alanine by 2 codons i.e. UUU and UUC isoleucine by 3 codons i.e.,
AUA, AUC and AUU, valine by 4 codons i.e. GUG, GUA, GUC and GUU,
serine by 6 codons i.e. UCU, UCA, UCG, UCC, AGC and AGU.
Wobble hypothesis
Crick proposed a hypothesis known as wobble hypothesis in 1966.
According to this hypothesis 2 bases of triplet codon show
specificity with 2 bases of tRNA anticodon while as the 3rd base of
the codon lacks specificity and is known as wobble base. That is
why a single molecule can bind more than on tRNA.

7. Genetic code is non-ambiguous:- It is non-ambiguous which means

that amino acid is coded by single codon and not by any other codon.
However exception is in the form of GUG as it codes for methionine
and valine.
8. Genetic code is Universal:-Genetic code is universally applicable i.e.
amino acid is coded by some codon in virus, tree, human being etc.
however there are some exceptions to this character like AUA codes
for isoleucine but in mitochondria of mammals it codes for
methionine. AGA codes for arginine but in mitochondria of
drosophila, it codes for serine.
9. Polarity :- Genetic code shows polarity. i.e. it is read in 5’→3’
direction. If read in 3’→5’ direction, it may change its information
e.g. CCA in 5’→3’ direction means proline while as CCA in 3’→5’
direction means threonine.

TRANSLATION:- is a process in which coded information over mRNA is

used for formation of polypeptide over ribosomes. Main components of
protein synthesis are as follows: a) Ribosomes b) mRNA c) tRNA d)
Amino acids e) initiation factor, elongation factor and termination
factors, f) Enzymes like pettidal transferase, amino acyl synthetase and
pyrophosphatase, g) ions like Mg⁺⁺ and energy in the form of ATP and
GTP.

Ribosomes:- In prokaryotes 70S ribosomes are present while as in

Eukaryotes 80S ribosome is present. Ribosome is made up of 2 sub-
units viz smaller sub-unit and larger sub-unit. Normally 2 sub-units of
ribosomes combine and bind with each other at the time of protein
synthesis in presence of Mg⁺⁺ by a process known as Association. After
the completion of protein synthesis two sub-units separate from each
other by a process called Dissociation. In prokaryotes ribosomes are
free but in eukaryotes most of the ribosomes are attached with the E.R
(larger sub-unit) by Ribophorin I and ribophorin II(Sc-RNA). Larger sub
unit contains E-site or Exit state, P-site or Peptidyle site (donor site) and
A site or amino acyle site.

Larger sub-unit also contains an enzyme peptidyl transferase. It is a

riboenzyme and help in formation of peptide bonds between amino
acids.

Steps In Translation: It completes in 5 steps which are as follows

1. Activation of Amino Acids:- in this step amino acyl synthetase

which is specific for specific amino acids binds with its amino acid in
the presence of ATP as a result amino acid adenylate enzyme
complex is formed and pyrophosphate (2Pi) is released.
 Pyrophosphate breaks into two inorganic phosphates and energy is
released which is utilized for charging amino acid at 3’ end of t-RNA

Aa + E+ ATP → aa – E – AMP + 2Pi ( amino acid adenylate enzyme

complex/ pyrophosphate)

2Pi → Pi + Pi + Energy in presence of Pyrophosphatase.

2. Charging of t-RNA :- t-RNA specific for the activated amino acid

attaches itself with the help of its DHU loop to amino acyle
adenylate enzyme complex. Linkage is established between
Carboxylic group of amino acid and hydroxyl group of t-RNA at 3’
end, resulting in formation of charged t-RNA. Energy for formation
of bond is provided by breaking pyrophosphate (2Pi) in presence of
pyrophosphatase. Once charged t-RNA is formed, enzyme and AMP
is released.
Aa – E – AMP + t-RNA → a.at-RNA + E + AMP (charged t-RNA) in
presence of 2Pi
3. Initiation:- this step requires the help of initiation factors. in
prokaryotes initiation factors are of 3 types IF₁, IF₂ and IF₃ while as
in Eukaryotes initiation factors are pf 9 types.

During initiation, initiation complex is formed. In prokaryotes

initiation complex is formed as follows:

m-RNA + 30S → 30S mRNA (in presence of IF₃)

30S mRNA + aatRNA → 30S m-RNA aa-tRNA (in presence of IF₂)

30S mRNA aat-RNA + 50S→ 70S m-RNA aat-RNA (initiation complex)

in presence of IF₁ and Mg⁺⁺

In Eukaryotes initiation complex is formed as follows

m-RNA + 40S → 40S m-RNA (in presence of eIF₂)

40S m-RNA + aa- tRNA → 40S m-RNA aat-RNA (in presence of eIF₃)
40S m-RNA aa-tRNA + 60S → 80S mRNA aa-tRNA (initiation complex)
(in presence of eIF₁, eIF₄ eIF₆, eIF₅ and Mg⁺⁺).

In initiation complex first charged t-RNA is present at P site. In

prokaryotes first charged t-RNA is f-met t-RNA (formyl methionine)
while as in Eukaryotes first charged t-RNA is met t-RNA (methionine).
Formyl group gives protection to nascent polypeptide chain in
prokaryotes from cytoplasmic enzymes during protein synthesis.

4. Elongation:- During elongation charged t-RNA come at A site and

polypeptide chain is formed. In Prokaryotes 3 types of elongation
factors are present viz EF-Tu, EF-Ts, EF-G. in eukaryotes there are 2
types of elongation factors. in prokaryotes charged t-RNA comes at
A site with the help of EF-Tu and EF-Ts.

Peptidal transferase acts as charged t-RNA at P site and releases its

amino acid. After that it forms peptide bond between the carboxylic
group of amino acid present at P site and the amino group of amino
acid present at A site. In order to free A site from charged t-RNA
ribosomes show movement over mRNA in 5’-3’ direction and this
process is called as translocation, it occurs in presence of EF-G and
GTP. Thus EF-G is also sometimes called as Translocase. In Eukaryotes
charged t-RNA are placed at A site by eEF₁ while as translocation
occurs in presence of eEF₁. Elongation continues till non sense codon
appears at A site.

5. Termination:- of polypeptide occurs when non sense codon, anti-

sense codon, comes at A site. In prokaryotes termination occurs in
presence of 2 releasing factors viz RF₁, RF₂. RF₁ recognizes UAA and
UAG terminator codons while as RF₂ recognizes all the 3 terminator
codons.

Post Translational Modifications : - Polypeptides formed during

translation show 1⁰ level structure and at that time they are unstable.
Nascent polypeptides under goes folding in presence of a specialized
proteins called Chaperons and become stable by attaining 2⁰ level or
3⁰ and quaternary level.

GENE REGULATION

The mechanism which stimulates the expression of some genes and

inhibits the expression of others in a cell is known as expression of
gene regulation or simply contraction. On the basis of activity there
are two types of genes:-

1. House Keeping or Constitutive Genes :- These are those types of

genes which work continuously as their products are required
continuously. Hence do not require switch on or switch off
mechanism e.g. Respiratory genes.
2. Non- Constitutive Genes/ Specialist genes / Luxury genes :- These
are those genes which do not work continuously, hence require
switch off mechanism e.g. Digestive genes.

Gene regulation is of two types

1. Positive Gene Regulation :- it is that gene regulation in which the

specialist gene becomes functional in the presence of inducer
(chemical substance).
2. Negative gene regulation :- It is that gene regulation in which
specialist gene switches off in the presence of chemical substance
called repressor. The former is also known as inducible gene
regulation while as later is known as repressible gene regulation.
Jacob and Monad proposed that specialist gene acts as an operan.
Operan is the segment of DNA containing structural genes,
operator genes, promoter genes and regulator genes.

Lac operan in E-Coli

Lac operan in E coli was discovered by Jacob and Monad. It is an

inducible operan. It contains structural genes, operator genes,
promoter genes and regulator genes.
1. Structural Genes :- there are 3 structural genes in E coli operan
namely as Z, Y and A. Gene Z codes for enzyme β-galactosidase which
breaks lactose into glucose and galactose. Gene γ codes enzyme lac
permase which increases the permeability so that more lactose
enters into E coli cell and gene A codes for enzyme transacetylase
which brings utilization of toxic substances in E-coli cells.
2. Operator gene :- It directs the synthesis of mRNA on structural gene.
In presence of lactose, the operan is switched on. The lactose binds
with repressor, thus do not block the path of RNA polymerase. The
RNA polymerase moves over the operator gene and reaches to
structural gene where it forms mRNA through transcription.
3. Promoter gene: It acts as initiation signal or recognition Centre of
RNA polymerase as RNA polymerase remains associated with
promoter gene. When the operan is switched on, it moves over
operator gene and forms RNA.
4. Regulator gene: It is the gene which synthesizes repressor. In the
absence of lactose, the repressor gets attached with operator gene
and blocks the path of RNA polymerase. With the result operan is
switched off.