Prokaryotic cells divide by pinching in two
Fig. 10-CO, p.240
Learning Objectives
1. What Is the Flow of Genetic Information in the
Cell?
2. What Are the General Considerations in the
Replication of DNA?
3. How Does the DNA Polymerase Reaction Take
Place?
4. Which Proteins Are Required for DNA
Replication?
5. How Is DNA Replicated in Eukaryotes?
The Central Dogma
The flow of genetic information in biological
systems.
Fig. 10-1, p.241
It states that in all living organisms, the
genetic information is stored in chromosomal
DNA. The flow of genetic information occurs
in one direction from DNA  RNA  Protein
The eukaryotic cell cycle
Fig. 10-18, p.256
DNA Replication
In this process the two polynucleotide chains
of DNA are separated and each is copied
in a complementary manner to produce
daughter polynucleotide chains .
Each daughter DNA molecule will contain
one polynucleotide comes from the
parental DNA and the other chain is newly
formed ( semiconservative replication)
Experimental evidence for semiconservative replication. Meselon-Stahl Experiment
1958 ( In Prokaryotes )
Fig. 10-3, p.243
Fig. 10-2, p.242
DNA replication must occur in order to faithfully
transmit genetic material to the progeny of any cell or
organism.
DNA replication takes place during S phase of the cell
cycle.
Transcription is the process by which the information
contained in a section of DNA is transferred to a newly
assembled piece of messenger RNA (mRNA).
Translation a process in which proteins can be
synthesized using the information in mRNA as a
template .
• In eukaryotic genome there is no similar
linear relationship between genetic
information carried in DNA and proteins
expression, which was observed in
prokaryotic system
• Occasionally, genetic information flows
from RNA to DNA (in reverse of normal
transcription). This is known to occur in the
case of retroviruses, such as HIV.
DNA replication
• In prokaryotes like E. coli , the replication
starts at fixed point called the origin and
proceeds bidirectional along the
chromosomal DNA (both directions) until
the whole circular DNA is completely
replicated. By then the replication process
is terminated at certain point on DNA.
Fig. 10-4a, p.244
Fig. 10-5a, p.245
Fig. 10-5b, p.245
Mechanism of DNA replication in Prokaryotes
• Relaxation of complex super structure of
chromosomal DNA
• Inside bacteria the circular double helix DNA
is present in super helical form in which the
DNA is further twisted in more circles. The
relaxed double helix is called a secondary
structure and the complex super helix called
tertiary structure. The super helix is needed
to pack the DNA in small space inside the cell
but it is not suitable form for starting DNA
replication. So, the first step in starting DNA
replication is the relaxation of super coiled
DNA by making small cut (nicking) with the
enzyme Topoisomerase (Gyrase).
DNA replication involves 3 stages
Initiation, elongation and termination.
1.Initiation:
• Initiation of DNA replication starts by the binding
of the initiator factor protein DnaA at the initiation
point in DNA, which recognizes a repeat 9 A-T
base pair rich region. The binding of this protein
helps in local unwinding double helix DNA at the
initiation point by the enzyme helicase. After
local unwinding the two single strands DNA are
kept separated and not folded back again by
single strand binding proteins.
Formation of bubble origin point
• The separation of the two DNA strands
expand the DNA region at the origin point
to form a bubble shape area that help in
the incorporation of deoxynucleotides to
synthesis new DNA strands.
II. Elongation of new DNA
• At the bubble area, local unwinding and
replication will grow in two opposite directions so
that both polynucleotides are copied
simultaneously .This polynucleotides growth
form a Y-shaped replication fork at each
direction site of DNA replication (2 replication
forks).
• Since, the DNA synthesis occurs in 5′ to 3′
direction, one strand called the leading strand,
can be synthesized continuously while the other
called the lagging strand, must be synthesized
backward discontinuously in short fragments
(Okazaki fragments) which are later joined to
make one long piece.
Properties of prokaryotic DNA polymerase
enzymes
• There are 3 different types of prokaryotic DNA
polymerases ,called pol I,pol II, pol III.Only pol
I and III are involved in DNA replication while
pol II function is limited to DNA repair of
damaged DNA.The pol I enzyme has slower
activity than pol III enzyme.
• Each DNA polymerase enzyme has two types
of activities, polymerization and nuclease
activities.
Table 10-1, p.246
The dimer of β-subunits of DNA polymerase III bound to DNA
t
Fig. 10-7, p.246
1) Polymerization activity
• Add deoxynucleotids ( as monophosphate)
from triphosphates deoxyncleotides , using
energy liberated from the hydrolysis of
pyrophosphates (the process is called
polymerization).The monophosphate
deoxynuleotides are connected by
phosphodiester linkage in 53 direction.
The building blocks for this process
are 5'-ribonucleoside triphosphates,
and pyrophosphate released as each
phosphodiester bonds made.
RNA primer
DNA polymerases cannot initiate synthesis of a
complementary strand of DNA on a totally singlestranded template. Rather, they require an RNA
primer that is, a short, double-stranded region
consisting of RNA base-paired to the DNA
template, with a free OH-group on the 3'-end of
the RNA strand .This OH group serves as the first
acceptor of a nucleotide by action of DNA
polymerase. In de novo DNA synthesis, that free
3'-hydroxys provided by the short stretch of RNA,
rather than DNA.
Primase
A specific RNA polymerase, called primase
synthesizes the short stretches of RNA
(approximately ten nucleotides long) that are
complementary and antiparallel to the DNA
template. In the resulting hybrid duplex, the U in
RNA pairs with A in DNA. These short RNA
sequences are constantly being synthesized at the
replication fork on the lagging strand, but only one
RNA sequence at the origin of replication required
on the leading strand.
Primosome
Prior to the beginning of RNA primer synthesis on
the lagging strand, a prepriming complex of
several proteins assembled and binds to the
single strand of DNA, displacing some of the
single-stranded DNA-binding proteins. This
protein complex, plus primase is called the
primosome. It initiates Okazaki fragment
formation by moving along the template for the
lagging strand in the 5’ 3’ direction, periodically
recognizing specific sequences of nucleotides
that direct it to create an RNA primer thats
synthesized in the 5’  3’ direction (antiparallel to
the DNA template chain).
• 2) Exonuclease activity:
Repeated cutting of single nucleotide from the
terminal end of a polynucleotide
• 3-Exonuclease activity: Removal of
polynucleotide sequence in 35 direction
from the terminal end associated with pol III
activity.
• 5- Exonuclease activity: Removal of
polynucleotide sequence in 53 direction
from the terminal end, associated with pol I
activity.
DNA polymerase I proofreading removes nucleotides from the
3’ end of the growing DNA chain.
Fig. 10-11, p.250
The 5’3’ exonuclease activity of DNA polymerase I can remove
up to 10 nucleotides in the 5’ direction downstream from a 3’-OH
single –strand nick
Fig. 10-12a, p.252
Mechanism of DNA synthesis at each
Replication Fork
1)-Leading strand
RNA primase enzyme creates a short primer
RNA with free 3' end ( 10 RNA nucleotide
sequence) .
DNA polymerase III enzyme - uses a single
parent strand of DNA as a template to add new
nucleotides to the 3' OH end of initially
incorporated RNA primer.
• The addition is continuous according to the
base pairing rule.
• If a mismatch is accidentally incorporated,
the polymerase is inhibited from further
extension. Proofreading removes the
mismatched nucleotide and extension
continues. The mismatched nucleotides are
remove by the exonuclease activities of DNA
polymerase III.
• Later , DNA polymerase I removes the RNA
primers and replaces them by DNA pieces
leaving a small gap of free 3' OH and 5’ OH
ends to be sealed by DNA ligase .
2)-Lagging strand
DNA polymerase is unable to work directly on the
lagging strand because it lacks a free 3- OH end on the
existing DNA strand.
The new strand is synthesized in short discontinuous
segments, each segment consists of RNA primer formed
by primase and replicated DNA piece (Okazaki
fragments) about 100-200 DNA nucleotides in length
formed by DNA polymerase III similarly to the leading
strand except that the addition takes place in backward
direction
Later the polymerase I removes the RNA primers and
replace them by DNA fragments leaving gaps .
Ligase enzyme seals the gaps as described before..
Reiji Okazaki
(1930 –1975)
• was a pioneer Japanese molecular biologist, known for his
research on DNA replication and especially for describing the
role of Okazaki fragments which he discovered working with
his wife Tsuneko in 1966.
• Okazaki was born in Hiroshima, Japan. He graduated in 1953
from Nagoya University, and worked as a professor there
after 1963. He died of leukemia (due to Atomic bombings of
Hiroshima) in 1975 at the age of 44; he had been
heavily irradiated in Hiroshima when the first atomic
bomb was dropped. His wife, Tsuneko, won the L'OréalUNESCO Awards for Women in Science in 2000 for her work.
Final results of replication at the
fork level
III.Termination:
Termination requires that the progress of the DNA replication
fork must stop at a specific locus on DNA. This process
involves the interaction between two components:
(1) A termination site sequence in the DNA
(2) A protein which binds to this sequence to physically stop
DNA replication.
In bacteria this protein is named the DNA replication
terminus site-binding protein.
Because bacteria have circular chromosomes, termination of
replication occurs when the two replication forks meet each
other on the opposite end of the parental chromosome.
In E. coli the chromosomal DNA replication takes about 40
minutes to replicate the 4000 kb size of DNA. Therefore
each fork replicates 2000 kb in 40 min. or ~ 50 kb/min or
~1000 bases/sec.
Why Does DNA Contain Thymine & Not Uracil ?
p.251a
The incorporation of thymine instead of uracil helps ensure that the DNA is replicated
faithfully.
p.251b
General features of a replication fork
Fig. 10-10, p.249
Table 10-3, p.250
END Part I
Eukaryotic DNA replication
• Eukaryotic genome is more complex than
prokaryotic genome. For example human
genome is composed of 30,000-40,000
genes, and each gene is segmented into two
types of DNA pieces, exons and introns ,Each
gene has on average between 5 and 8 exons,
8000 base-pairs.
• Exon: DNA segment which after
transcription to RNA codes directly to
peptide units of a polypeptide, i.e which `is
expressed in protein' (200 base-pairs on
average, in human genome)
• Intron: DNA segment which is not directly
expressed for protein, involved in regulation,
splicing and other unknown functions each
2000 bp's on average, in human genome.
Cell cycle in eukaryotes
• Actively dividing eukaryote cells pass through a
series of stages known collectively as the cell
cycle: involving interphase stage between each
two mitosis. The interphase stage itself includes
3 phases represented by two gap phases (G1
and G2); and S (for synthesis) phase, in which
the genetic material is duplicated. The two gaps
are preparative periods for cell division and an
opportunity for the cell to make decision whether
to go in to division or not. In the M phase a
nuclear division takes place before it is followed
by cell division that occurs in cytokinesis
• In the S phase. DNA synthesis replicates the
genetic material and each chromosome
becomes having two sister chromatids.
Therefore, only in this period of the
interphase that DNA replication occurs which
is a necessary step before the cell decides to
go in to division(without DNA replication there
is no cell division).In human the S period is
carried out for about 8 hours in an average
total cell cycle period of around 20 hours.
• Eukaryotic DNA synthesis is similar to
synthesis in prokaryotes, except for some
complexity. In eukaryotic cells:
• there is more DNA than prokaryotic cells
• the chromosomes are linear
• the DNA complexes with proteins
Eukaryotic replication initiated at many
points
• Because the eukaryotic genome is so large
(about 100 times the size of bacterial DNA), it
would take days to replicate the whole length of
eukaryotic chromosome using the same single
initiation point as in prokaryotes.
• Therefore, many initiation points ( about 10,000
in human) are found in each eukaryotic
chromosome instead of one, with replication
forks moving in opposite directions away from
each initiation point until they meet in the middle
between each two initiation points. The initiation
point is called a replicons which do not need
specific termination sequences.
Fig. 10-4b, p.244
• Not all replicons are activated
simultaneously. Rather, clusters of 20-80
adjacent replicons are activated
throughout S phase until the whole
chromosome is completely replicated.
• The rate of eukaryotic DNA replication is
much slower than E. coli, with only 100200 nucleotides bases/sec are replicated
in eukaryotic Okazaki fragments.
However, the majority of replication forks
results in the whole genome being
replicated in only about 8 hours. Histones
for packaging the DNA are synthesized
simultaneously with DNA replication to
bind the new DNA.
Enzymes involved in eukaryotic DNA
replication
1.DNA Polymerase α
• Initiation the synthesis of RNA primer (about 2030 ribonucleotides) then adds DNA to the RNA
primers
• It has low processivity (efficiency) of DNA
synthesis and has no 35 exonuclease activity .
2.DNA Polymerase δ
• The principal DNA polymerase in eukaryotic DNA
replication which has 35 exonuclease activity.
• When it complexes with PCNA (Proliferating Cell
Nuclear Antigen) it becomes highly processive.
Additional Proteins Involved in
Eukaryotic DNA Synthesis
• DNA helicase: the enzyme which carries out partial
unwinding of double helix DNA at the initiation point
before the starting of DNA replication
• PCNA (Proliferating Cell Nuclear Antigen)
Provides high processivity to DNA Polymerase δ
• RPA (Replication Protein A)
• ssDNA-binding protein that facilitates the
unwinding of the helix to create two replication forks.
• RFC (Replication Factor C) binds PCNA at the end
of the primer
• FEN1/RTH1 (flap endonuclease 1/RAD two
homologue 1) exonuclease complex
Leading strand synthesis
1) Starts with the primase activity of DNA Pol α to put
down RNA primer in 5’
3’-direction
2) The same enzyme adds a piece of DNA to the primer
3) RFC binds PCNA at the end of the primer
4) PCNA displaces DNA Pol α.
5) DNA polymerase δ binds to PCNA at the 3’ ends of
the growing strand to carry out polymerase switching to
highly processive DNA synthesis activity.
The RFC mediates the polymerase switching by helping
in the
a) Assembly of PCNA
b) Removal of DNA Pol α
c) Addition of DNA Pol δ
Lagging strand synthesis
1) Starts off the same way as leading strand synthesis
2) RNA primers synthesized by DNA polymerase α every 50
nucleotides and consist of 20-30 nucleotides RNA
3) DNA polymerase δ switching as before to extend the RNA
primers and generating Okazaki fragments
4) When the DNA Pol δ polymerizes the RNA primer of the
downstream Okazaki fragment, RNase H1 removes all but the
last RNA nucleotide of the RNA primer
5) The FEN1/RTH1 exonuclease complex removes the last RNA
nucleotide
6) DNA Pol δ fills in the gap as the RNA primer is being
removed
7) DNA ligase joins the Okazaki fragment to the growing strand
Telomeres problem during human DNA
replication
• Telomeres present at the ends of linear
chromosomal DNA and consist of long
area of short repeating sequences
TTGGGG ->->->->- to protect the integrity
and stability of human chromosomes.
During DNA synthesis these chromosome
ends cannot be replicated with DNA
polymerase.
This sequence of TTAGGG is repeated
approximately 2,500 times in humans. In
humans, average telomere length declines
from about 11 kilobases at birth to less
than 4 kilobases in old age, with average
rate of decline being greater in men than
in women.
Telomeres are found at the termini of
chromosomes. The end of a telomere inserts back
into the main body of the telomere to form a T-loop
• Since DNA can only be synthesized at the 3'end of a pre-exiting DNA or RNA chain,
there is no available mechanism for achieving
DNA synthesis all of the ways to the end of the
lagging strand. Once the primer in the last
Okasaki fragment is removed by a 5' to 3'
exonuclease it is not possible to replace it with
DNA. This is because the 5 - ends of the
lagging strands does not have enough space to
put a new primer with free 3'-hydroxyl group
and therefore it is not copied completely.
• After maturation of Okazaki fragments,
there is a primer gap
This problem does not occur with the
leading strand which can undergo complete
replication round. If this phenomenon is
repeated over many rounds of replication,
some of the chromosomes will gradually
develop major shortening in their ends.
Correction of the chromosome ends by
the enzyme Telomerase
Telomerase enzyme is a ribonucleo protein complex containing
RNA-dependent DNA polymerase activity and 450-nucleotide
RNA. It can act as a reverse transcriptase enzyme by using its
own repetitive RNA sequence (AAAACCCC ) as a template to
add a repeat complementary sequence of TTAGGG to the 3OH end of leading strand in telomeres of human DNA. This
addition step by telomerase is repeated several times until an
extend 3- end of the DNA is formed. In this case the role of
telomerase enzyme is ended leaving gap in the 5- phosphate
end of the opposite lagging DNA strand .This gap will be filled
later by primase (adding short RNA primer ) and combined
actions of DNA polymerase and ligase activities..
• Some somatic cells lack telomerase
activity and therefore, their telomeres get
shorter with each cell division (About 50
bases are lost from each telomere every
time a cell divides) which may end up with
cell death. To the contrary cancer cells
may have high activity of telomerase
enzyme that increases their survivals,
• Telomerase: Terminates the process of
DNA replication only at the telomere ends
of chromosomal DNA by adding many
repeat units that can not be recognized by
the replication complex.
p.259a
p.259b
p.258a
Telomere replication (asterisks indicate sequences at the 3’ end that cannot
be copied by conventional DNA replication
p.258b
Model for initiation of the DNA replication cycle in
eukaryotes
ORC is present at the replicators throughout the cell
cycle. The pre-replication complex (pre-RC) is
assembled through sequential addition of the RAP
(replication activator protein) & RLFs (replication
licensing factors ) during a window of opportunity
defined by the state of cyclin-CDKs.
Phosphorylation of the RAP,ORC,and RLFs triggers
replication.
After initiation, a post-RC state is established, and the
RAP & RLFs are degraded.
Model for initiation of the DNA replication cycle in eukaryotes
Fig. 10-19, p.257
The basics of the eukaryotic replication fork
Fig. 10-21, p.261
Table 10-4, p.257
Table 10-5, p.260
END
Part II