Nature structure and replication of genetic material
1. Nature structure and replication
of genetic material
Submitted by
J. Venkata Yashwanth
TAM/2019-042
ACHARYA N G RANGA AGRICULTURAL UNIVERSITY
S.V.Agricultural college, Tirupati
Dept. of Genetics and Plant breeding
2. What is genetic material????
Have you people ever wondered why we look similar to our parents
and their characters?
Why some diseases are called inherited diseases and how do they
inherit?
How characters are transferred from parent to offspring's?
The answer is very simple it is due to genetic material
Now the real question is what is that genetic material exactly.
3.
4. Properties of genetic material
Genetic material is a chemical of which are genes composed
Replicated with high fidelity
Inherited with high degree of precision
Able to express itself on development of character
It should store high variable information for gene function
6. Identification of genetic
material
After discovery of Nuclein by Mischer there was hunt to
know what is the genetic material
Experiments of Grifth
Experiments by Avery, Mac leod and Mc carty
Experiments of Hershey and Chase
7. Experiments by Grifth
Grifth discovered the phenomenon of transformation through
s.pneumonieae
Smooth colonies - Strain IIIS – virulent
Rough colonies – Strain IIR – avirulent
Live strains of IIR were injected into mice all mice survived
Live strains of IIIS were injected into mice all mice died
Heat killed IIIS were injected all mice survived
Heat killed IIIS+IIR were injected together then all the mice died
8.
9. Experiments by Avery Mc leod and Mc carty
They carried out experiments invitro conditions in 1944
When live IIR and heat killed IIIS cells were plated on
colony with Anti-IIR gave smooth colonies
They used Proteases DNases and RNases to find out what is
genetic material
From the experiments carried out thy decided that DNA is
the actual genetic material
10.
11. Experiments of Hershey and chase
From this experiment DNA was universally
accepted as genetic material
They used T2 bacteriophage which infects
bacteria
The head coat of bacteriophage is made of
proteins and nucleic material is made up of
DNA
They labelled DNA with P32 protein with
S35
When P32 phage's were cultured in E.coli
for 10 min and centrifuged ghosts particles
were normal and E.coli had P32
Progeny phage's contained P32 DNA
12. In other experiment they cultured S35 phage's with
E.coli for 10 min
The ghosts that were outside consisted of s35 while progeny was normal
By these observations they came to conclusion that DNA is the ultimate
genetic material
13.
14. RNA as genetic material
In several viruses like TMV the DNA is absent in them it
again lead to confusion of genetic material
In 1956 Gierer and Schramm and Frankel-Cornat
independently demonstrated RNA functions as genetic
material
The proteins and RNA from were separated chemically and
injected into Tobacco plant separately
Plants injected with RNA were showing prevalent symptoms
15. Frankel-Cornat and Singer constructed two types of hybrid virus particles
by mixing two different strains
Type A has RNA of Strain A and protein from strain b and type b has
RNA of strain B and protein of strain A
When plants were injected with type a virus they showed symptoms
similar to strain A
When plants were injected with type b virus then they showed symptoms
similar to strain b
By this they concluded that it is RNA that is acting as genetic material
but not proteins
16. Constituents of nucleic acid
Chemical analyses of nuclei acids shown that they are basically
composed of three components
1) Phosphoric acid
2) Pentose sugar
3) Organic base
17. Phosphoric acid(H3po4) – it has three reactive -OH groups among which
two are involved in phospho diester bond with pentose sugar
It makes bonding with 5’c of one and 3’c of neighbouring pentose
molecules
Pentose sugar – it is of two types
Ribose sugar and deoxyribose sugar
Deoxy ribose sugar differs in O atom at 2’c
Always 5’ and 3’ carbons participate in phospho diester linkage and 1’
makes bonds with organic bases
18. Organic bases
They are heterocyclic compounds which contain nitrogen so
they are also called nitrogen bases
They are of two types :- purines and pyrimidines
Pyrimidine bases :- are 6 ringed pyrimidine structures
similar to benzene ring with N- at 1 and 3 carbons and O-
group at 2c position
N at 1 participates in bond with pentose sugar
In cytosine –NH2 group is present at 4c
In uracil – O group is present at 4c
Thymine – it is 5 methyl uracil
19. Purine bases
They are two rings one 5 membered and one 6 membered
N is present at 7th and 9th bases and 9 N participates in bod with
pentose sugar
Adenine – has –NH2 group a 6c
Guanine – has –O group at 6c and –Nh2 at 2C
N bases are have keto and enol tatuo-merisation but mostly they exist in
Keto tautomeric forms
20.
21. NUCLEOSIDES
Nitrogen bases are linked with pentose sugar by covalent bonds
between 1’c of sugar and 1c or 9c of nitrogen base
This reaction release one molecule of h2o
When ribose combines with N base it forms Ribo-nucleosides
E.g.:- adenosine guanosine cytidine uridine
When deoxyribose sugar combines with N base it forms deoxy-
nucleosides
E.g.:- deoxy-adenosine deoxy-guanosine deo-cytidine, thymidine
22. NUCLEOTIDES
When phosphate group of phosphoric acid is attached to
nucleoside or deoxy-nucleoside it forms nucleotides or
deoxynucleotides
5’nucleotide – it has free -OH on 3’C
3’nucleotide – it has free -OH on 5’c
5’adenylic acid 5‘guanylic acid 5’cytidilic acid 5’uridylic acid
are examples of ribotides
5’deoxyadynelic acid 5’deoxyguanylicacid 5’deoxycytidilic
aid are example of deoxyribotides
23.
24. The primary structure of DNA
DNA is generally double stranded and each strand is multimer of deoxy-
ribotides and called as polynucleotide
Two nucleotides are joined each other with phospho diester bond
Phosphodiester bond is represented as 5’C-O-P-O-C3’
The 5’C of one nucleotide and 3’C of another nucleotide have free –OH grp
which is used to add deoxy-ribotides and form polynucleotide
In polynucleotides N base sticks out of sugar phosphate backbone
25. THE DNA DOUBLE HELIX
The DNA double helix model was given
by Watson and crick in 1953
Before Watson and crick there were
few scientists who works on model of
DNA
The ability of deoxy-ribotides to
produce polynucleotides was
discovered by Levene
But he proposed that polynucleotides
occurred in a repeated tetranucleotide
sequence
e.g.:- AGTC AGTC …….
26. THE CHARGAFF RULES
Chemical analyses by Chargaff
shown that
Number of purines and number
of pyrimidines are equal in
number
In DNA quantity of A is equal to
quantity of T and quantity of g is
equal to quantity of c
In DNA the number of bases
containing –NH2 groups and
number of bases contain keto
groups are in equivalence
The above stated ones are called
Chargaff rules
27. X ray crystallography by Franklin
The x ray crystallography of
purified DNA by franklin showed
that
It is a multi-stranded with diameter
of about 22A
The groups were spaced at 3.4A
There was occurrence of
repeating unit every 34A
Watson and Crick made use of
both Chargaff rules and x ray
crystallography by franklin in
constructing DNA double helix
28. Features of DNA double helix
DNA molecule is made up of two polydeoxy-ribotide strands
Two strands of DNA are oriented in anti parallel direction
Polynucleotide strand is composed on deoxy-ribotides
joined by phospho diester linkage
The two strands of DNA are complementary (A=T and G=C)
If A≠T and G≠C then the DNA is single stranded
Adenine of one strand pairs with thymine of another strand
with two hydrogen bonds
Guanine of one strand with cytosine of another strand with
three hydrogen bonds
29.
30.
31. This type of pairing is called complementary base pairing
and base pairs are called Watson crick base pairs
Hydrogen bond is weaker bond and denaturation occurs
when ph. is raised in alkaline range
Two strands are coiled in right hand helix forming DNA
double helix
The diameter of this helix is 20A while pitch is 34A
There are 10 bases in a turn at equal spacing of 3.4A
In aqueous medium the non polar groups of bases make
hydrophobic interaction keeping DNA together
32. If we dissolve the DNA in distilled water two strands repel
each other due to negative charge and in aqueous solution
these negative charges are neutralized by Na+ ions and
keeping DNA together
During replication DNA uncoils and single strand individually
participates n replication which avoids error
If there is any error in base pairing during replication then
there is chance of occurring of mutations
The DNA structure explained by Watson and crick is B type
and there are three more forms of DNA found in living
organisms
Apart from B-DNA there are other forms of DNA occurring in
living organisms
33. Forms of DNA
The different forms of DNA are A,B,C and Z
From above forms only Z DNA shows left hand coiling the
remaining three right hand coiling
Dehydrated DNA occurs in form of A DNA it is unusual that
naïve DNA occurs in this B form only
DNA:RNA heteroduplexes and RNA double strands occur in
this A form
B DNA has major and minor grooves and less negative
charge
C DNA is tightly wounded when compared to z DNA
38. Replication of genetic material
There are three methods of replication
1)Dispersive replication
2)conservative replication
3)semi-conservative method of replication
The first two are not accepted as there was no practical
proof but semi conservative model was proven by
experiments of Melson and Stahl by their experiments on
E.coli
40. Semi
conservative
model of
replication
It was proposed by Watson and crick at
time of DNA double helix
The main features of this model are:-
Progressive separation of strands
Complementary base pairing
Formation of phosphodiester bonds with
neighbouring single strands
Each daughter DNA has one strand new
and one strand parent DNA
Sequence of baes on newly synthesized
strand is dictated by template strand from
parent
41. Evidence for semi conservative
replication
It was given by Meselson and Stalh in1958
They used two isotopes of nitrogen, the common 14N and
heavier 15N to label nitrogen in DNA.
The density of N15 was higher (1.724g/cm2 while n14 was
less (1.710g/cm2)
They used caesium chloride(CsCl) equilibrium density
gradient centrifugation as their sedimentation method
When DNA replicates, it incorporates labeled nitrogen atoms
(either 14N or 15N) into DNA molecule, as nitrogen is an
essential chemical component of DNA. Therefore nitrogen
was chosen for labeling of DNA molecule.
42. They grew a culture of E.coli bacteria in a medium that contained
heavier 15N for 14 bacterial generations, which was long enough
to create a population of bacterial cells that contained only the
heavier isotope.
Next, they used the medium containing only 14N labeled
ammonium salts as the sole nitrogen source. So, from that point
onward, every new strand of DNA would be built with 14N than
15N.
Then E.coli were given one generation time and isolated
DNA was extracted from them and subjected to centrifugation
These light and heavy strands can be separated by density
gradient centrifugation in heavy salt solution at 30000 to50000 rpm
for 18 to 72 hours
43.
44. In first generation we can see that all DNA is
intermediate
In second generation DNA half of the strands
were intermediate and half were normal
In each succeeding generation the quantity of
intermediate DNA was reduced to half
All the above results shown that DNA is replicated
by semi conservative method
45.
46.
47. Auto radiography of replicating
E.coli chromosome
At replication fork one DNA molecule occurs to be branched
due to progressive separation of two strands
The presence of replication fork was first shown by
J.Carrins in E.coli
He cultured E.coli cells in presence of 3H-thymidine
He isolated the DNA from them on a filters and affixed on a
glass with photograph emulsions sensitive to beta rays
He observed 0-shaped structures and proposed that semi
conservative replication starts at point called origin and
proceeds in uni direction
48. Replicon
REPLICON: Unit of DNA, capable of DNA replication
independent of other segments of same DNA molecule.
Each replicon has
1. Origin
2. Terminus
Each replicon fires only once in a cell division
Incase of prokaryotes and viral chromosomes, contains single
replicon/ chromosome and incase of eukaryotes multiple
replicons are seen
T7 phages which has 2 replicons but one is non
functional in presence of first
In prokaryotes segregation and replication are same
49. origin
It is sequence of replicon which supports initiation of
replication
In E.coli is identified as genetic loci ORI C
It helps in initiation of replication control of frequency
of events and segregation of replicated chromosome
There are rich in A:T ration helpful in unwinding
The length of E.coli replicon is only 245bp long
In yeast we have autonomously replicated sequences
(A) that is bounded to orc(origin recognition
complexes) which helps in initiation
Three elements (B1 B2 B2) are present I upstream
and any two B and A sequence is necessary to start
replication
50. In eukaryotes, no. of replicons per chromosome varies with
species
Yeast-500
Drosophila-3500
Vicia faba-35000
length of eukaryotic replicon varies with species to species
~40kb in yeast
~100kb in animals
~300kb in vicia
rate of replication rate prokaryotes: 50,000bp/min
eukaryotes: 2000bp/min
No. of detectable replicons vary with developmental stage ,cell
or tissue type. only 15% of replicons seem to be active at one
moment.
51.
52. Terminus
Prokaryotic replicon's have two terminus in general
E.coli has terA terC terD terE
Termination requires tus gene product which recognizes ter
sequence and
Tus gene has contra helicase activity
Replication fork moves 10 times faster than the replication
In prokaryotes generally replication and transcription takes
place simultaneously
55. Replication in prokaryotes
INITIATION:
DNA replication begins from origin. In E coli, replication origin is
called OriC which consists of 245 base pair and contains DNA
sequences that are highly conserved among bacterial replication
origin. Two types of conserved sequences are found at OriC,
three repeats of 13 bp (GATRCTNTTNTTTT) and four/five
repeats of 9 bp (TTATCCACA)
About 20 molecules of dna A proteins binds with 9 mer repeats
along with ATP which causes DNA to wraps around dna A
protein forming initial complex. The dna A protein and ATP
trigger the opening of 13 mer repeats forming open complex.
58. Two copies of dna B proteins (helicase) binds to 13 mer repeats.
This binding is facilitated by another molecule called dna C. The
dna B-dna C interaction causes DNA B ring to open which binds
with each of the DNA strand. The hydrolysis of bound ATP
release DNA C leaving the DNA B bound to the DNA strand.
The binding of helicase is key step in replication initiation. dna B
migrates along the single stranded DNA in 5’-3’ direction causing
unwinding of the DNA.
The activity of helicase causes the topological stress to the
unwinded strand forming supercoiled DNA. This stress is relieved
by the DNA topoisomerase (DNA gyrase) by negative
supercoiling. Similarly, single stranded binding protein binds to
the separated strand and prevents reannealing of separated
strand and stabilize the strand.
The DNA polymerase cannot initiate DNA replication. So, at first
primase synthesize 10±1 nucleotide (RNA in nature) along the 5’-
3’ direction. In case of E.coli primer synthesized by primase starts
with ppp-AG-nucleotide. Primer is closely associated with dna B
helicase so that it is positioned to make RNA primer as ssDNA of
lagging strand.
59.
60. 2. ELONGATION:
I. Leading strand synthesis:
Leading strand synthesis is more a straight forward process which
begins with the synthesis of RNA primer by primase at replication
origin.
DNA polymerase III then adds the nucleotides at 3’end. The leading
strand synthesis then proceed continuously keeping pace with
unwinding of replication fork until it encounter the termination
sequences.
II. Lagging strand synthesis:
The lagging strand synthesized in short fragments called Okazaki
fragments. At first RNA primer is synthesized by primase and as in
leading strand DNA polymerase III binds to RNA primer and adds
dNTPS.
On this level the synthesis of each okazaki fragments seems straight
forward but the reality is quite complex
61.
62. Mechanism of Lagging strand synthesis
The complexity lies in the co-ordination of leading and lagging strand
synthesis. Both the strand are synthesized by a single DNA polymerase
III dimer which accomplished the looping of template DNA of lagging
strand synthesizing Okazaki fragments.
Helicase (Dna B) and primase (Dna G) constitute a functional unit within
replication complex called primosome.
DNA pol III use one set of core sub unit (Core polymerase) to synthesize
leading strand and other set of core sub unit to synthesize lagging strand.
In elongation steps, helicase in front of primase and pol III, unwind the
DNA at the replication fork and travel along lagging strand template along
5’-3’ direction.
DNA G primase occasionally associated with DNA B helicase synthesizes
short RNA primer. A new B-sliding clamp is then positioned at the primer
by B-clamp loading complex of DNA pol III.
63.
64. When the Okazaki fragments synthesis is completed, the replication
halted and the core sub unit dissociates from their sliding clamps
and associates with new clamp. This initiates the synthesis of new
Okazaki fragments.
Both leading and lagging strand are synthesized coordinately and
simultaneously by a complex protein moving in 5’-3’ direction. In this
way both leading and lagging strand can be replicated at same time
by a complex protein that move in same direction.
Every so often the lagging strands must dissociates from the
replicosome and reposition itself so that replication can continue.
Lagging strand synthesis is not completes until the RNA primer has
been removed and the gap between adjacent Okazaki fragments
are sealed. The RNA primer are removed by exonuclease activity
(5’-3’) of DNA pol-I and replaced by DNA. The gap is then sealed by
DNA ligase using NAD as co-factor.
65. Termination:
Eventually the two replication fork of circular E. coli chromosome meet
at termination recognizing sequences (ter).
The Ter sequence of 23 bp are arranged on the chromosome to create
trap that the replication fork can enter but cannot leave. Ter sequences
function as binding site for TUS protein.
Ter-TUS complex can arrest the replication fork from only one direction.
Ter-TUS complex encounter first with either of the replication fork and
halt it. The other opposing replication fork halted when it collide with the
first one. This seems the Ter-TUS sequences is not essential for
termination but it may prevents over replication by one fork if other is
delayed or halted by a damage or some obstacle.
When either of the fork encounter Ter-TUS complex, replication halted.
Final few hundred bases of DNA between these large protein
complexes are replicated by not yet known mechanism forming two
interlinked (catenated) chromosome.
66.
67. Initiation
The first steps is the formation of pre-initiation replication complex (pre-
RC). It occurs in two stage. 1st stage requires, there is no CDK activities.
It occur in early G1 phase. It is known as licensing but licensed pre-RC
cannot initiate replication at G1 phase. 2nd stage is binding of ORC
(origin recognition complex).
The replication begins with binding of ORC to the origin. ORC is a
hexamer of related protein and remains bounded even after DNA
replication occurs. Furthermore ORC is analogue of prokaryotic DNA A
protein.
After binding of ORC to origin, cdc6/cdc18 and cdtl coordinate the
loading of MEM (mini chromosome maintenance) to origin.
MEM complex is thought to be major eukaryotic helicase.
After binding of MEM complex to pre-RC, cdtl get displaced. Then DdK
phosphorylates MEM, which activates its helicase activity. Again DdK
and CdK recruit another protein called cdc45 which then recruit all the
DNA replicating protein such that the origin get fired and replication
begins.
68. 2. Elongation:
DNA polymerase δ synthesizes and adds dNTPs at 3’ end of RNA
primer.
The leading and lagging strands are synthesized in the similar
fashion as in prokaryotic DNA replication.
3.TERMINATION:
At the end of DNA replication the RNA primer are replaced by DNA
by 5’-3’exonuclease and polymerase activity of DNA polymerase ε.
Exonuclease activity of DNA polymerase removes the RNA primer
and polymerase activity adds dNTPs at 3’-OH end preceding the primer.
In case of bacteria, with circular genome, the replacement of RNA
primer with DNA is not a problem because there is always a preceding
3’-OH in a circular DNA.
69. But in eukaryotic organism with linear DNA, there is a problem.
When RNA primer at 5’ end of daughter strand is removed, there is not
a preceding 3’-OH such that the DNA polymerase can use it to replace
by DNA. So, at 5’ end of each daughter strand there is a gap (missing
DNA). This missing DNA cause loss of information contain in that
region. This gap must be filled before next round of replication.
For solving this end replication problem; studies have found that
linear end of DNA called telomere has G:C rich repeats. These
sequence is known as telomere sequence. These repeats of telomere
sequence is different among different organisms. Telomere in human
cell consists of repeats of TTAGGG/AATCCC. Each species has its own
species specific telomere repeats. These telomere sequence don't
codes anything but it is essential to fill the gap in daughter strand and
maintain the integrity of DNA.
70.
71. Telomere replication: end replication problem
in Eukaryotic DNA
There is an enzyme found in eukaryotic cell called
telomerase.
Telomerase is a DNA polymerase (RNA dependent DNA
polymerase) which adds many copies of telomere sequence at 3’-
OH end of template strand. Like other DNA polymerase,
telomerase also adds deoxyribonucleotide at 3’-OH end. Unlike
other DNA polymerase, telomerase adds DNA at 3’-OH end of
parent strand not at the daughter strand and also it synthesizes
the same sequences over and over in absence of template
strand.
First telomerase binds to 3’-OH end of parent strand by
hybridization between its AACCCCAAC RNA sequences and
TTGGGG DNA sequences (telomere sequences of Tetrahymena).
The telomerase adds TTG at 3’ end of parent strand. After
adding TTG sequences, telomerase translocate along 5’-3’ end of
parent strand. Now the telomerase adds GGGTTG to 3’ end by
using its CCCAAC sequence. Again telomerase translocate and
adds GGGTTA
72. This process is continued for
many time. The parent strand
become more longer than
daughter strand. Now RNA
polymerase (PRIMASE)
synthesize RNA primer by copying
the parent strand in 5’-3’ direction
using telomere sequence as
template.
The DNA polymerase can now
extend the primer in 5’-3’ direction
by adding deoxyribonucleotide to
3’ end.
The primer is now removed and it
won’t be replaced because it is an
extra sequence added by copying
telomere sequence.
Finally the integrity of daughter
strand is maintained.
73.
74. Enzymes or proteins involved in
DNA replication
DNA replication involves several proteins and enzymes
Many of these are identified by study of mutants
In E.coli DNA E DNA N DNA X and DNA Z Code for four out of
seven polypeptides of complete DNA polymerase III enzyme
Genes involved in DNA replication are studied by isolating series
of temperature sensitive mutants called DNA mutants
They cease DNA replication when temperature is increased to
42*degrees which are of to types
Quick stop DNA mutants
Slow stop DNA mutants
75. DNA polymerase
Also called DNA replicase that synthesizes new strand of
DNA
Its activity was first observed by Kornberg in 1956
It cannot initiate synthesis but adds nucleotides to free 3-
OH on primer end
It has property of proof reading
They are aging classified into prokaryotic and eukaryotic
polymerases
76. Prokaryotic polymerases
DNA polymerase I or korenberg enzyme
It has 3 function )5’—3’ polymerase 2)5’—3’ exonuclease 3)
3’—5’ exonuclease
Exonuclease activity is observed in different regions
3’—5’ exonuclease is essential in proof reading and 5’—3’
exonuclease removes DNA hat is affected by uv light
chemicals etc.
It has unique property to initiate replication at a nick in
strand of DNA duplex this property of nick translation
DNA polymerase II has same activity but mainly act as
DNA repair
77. DNA polymerase III
It has 5’—3’ polymerase and 3’—5’ exonucleases activity
and responsible for in vivo replication
In eukaryotes γ form of DNA polymerase is present in
mitochondria
Pol α primes the replication in both the strands
δ and ε form of polymerases are terminatory in nature
Pol β is monomer and carries out high fidelity excision
repair
78. Primase
It catalyses synthesis of RNA primers
Primases are rna polymerases that synthesis 11-12 base
pairs
Primases of E.coli and some viruses have Dna G a single
polypeptide that associates with plication complex
In eukaryotes the same function is performed by pol α and
extends the primers as DNA strand then it is replaced by
pol δ and pol ε
79. Polynucleotide ligase
This enzyme important in DNA replication and repair
Its's forms phosphodiester linkage between ‘phosphoryl
group of one nucleotide and -3OH group of immediate
nucleotide
DNA ligase seals the nick that is left by DNA polymerase I
during DNA repair and among okazaki fragments
Endonucleases :- restriction endo nuclease produces cut
in DNA at only specific bases
E.g.:- phage θX174
It introduces a nick in surrounding DNA damage leaving free 5’
end for DNA polymerase I to cleave off the damaged
80. Helicase
An enzyme that separate's two DNA strands
It is multimer which has two conformations one that binds with
DNA duplex and one that binds with single stranded DNA
1 ATP molecule is hydrolysed for unwinding 1 base pair
Further it may be 3’—5’ helicase or 5’—3’ helicase
Single stranded binding proteins (SSB) proteins
SSB proteins binds to single stranded DNA and prevents
forming duplex
It binds to DNA as replication fork advances and mutants that
lack ssb function are defective in repair and recombination
Pilot proteins are synthesized by virus DNA that decides to go
replication or transcribed by rna
81. Replication of genetic rna
Direct replication of rna
In many viruses like polio virus influenza viruses direct
replication of rna by rna primed rna synthesis
It is RNA dependent rna polymerase
It requires a rna template mg++ ions and triphosphate ribo-
nucleotides
The replication of ss rna produces both + and – strands but
only the + strands are packaged into virions
82. Replication via DNA
In some viruses called as tumour inducing virus rna first
synthesis complementary DNA which is transcribed into rna
It is done by rna dependent DNA polymerase or reverse
transcriptase
This DNA helps for integration of viral genetic material into
host
Some viruses can remain as pro virus or cause cancerous
cells
Such virus are called oncogenic viruses