In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritance.

1. DNA REPLICATION
Saveena Solanki
Biotechnologist

2. • DNA replication in most eucaryotic cells occurs
only during a specific part of the cell division
cycle, called the DNA synthesis phase or S
phase
The four successive phases of a standard eucaryotic cell
cycle. During the G1, S, and G2 phases, the cell grows
continuously. During M phase growth stops, the nucleus
divides, and the cell divides in two. DNA replication is
confined to the part of interphase known as S phase. G1 is
the gap between M phase and S phase; G2 is the gap
between S phase and M phase

3. • Telomerase Replicates the Ends of Chromosomes
• a special problem when the replication fork
reaches an end of a linear chromosome:
• there is no place to produce the RNA primer
needed to start the last Okazaki fragment at the
very tip of a linear DNA molecule.
• Eucaryotes solve it in an ingenious way:
– they have special nucleotide sequences at the ends of
their chromosomes,
– which are incorporated into telomeres and attract an
enzyme called telomerase

4. • The telomerase synthesizes a new copy of the
repeat, using an RNA template that is a
component of the enzyme itself.
• The telomerase enzyme otherwise resembles
other reverse transcriptases, enzymes that
synthesize DNA using an RNA template

5. The structure of telomerase. The telomerase is a protein RNA complex that carries an RNA
template for synthesizing a repeating, G-rich telomere DNA sequence. Only the part of the
telomerase protein homologous to reverse transcriptase is shown here (green). A reverse
transcriptase is a special form of polymerase enzyme that uses an RNA template to make a DNA
strand; telomerase is unique in carrying its own RNA template with it at all times

6. DNA Repair
• Without DNA Repair, Spontaneous DNA
Damage Would Rapidly Change DNA
Sequences
• a spontaneous reaction called depurination
and deamination occurs due to thermal, UV
radiation etc.

7. A summary of spontaneous alterations likely to require DNA repair.
The sites on each nucleotide that are known to be modified by
spontaneous oxidative damage (red arrows), hydrolytic attack (blue
arrows), and uncontrolled methylation by the methyl group donor S-
adenosylmethionine (green arrows) are shown, with the width of each
arrow indicating the relative frequency of each event

8. Depurination and deamination. These two reactions are the most frequent
spontaneous chemical reactions known to create serious DNA damage in cells.
Depurination can release guanine (shown here), as well as adenine, from DNA. The
major type of deamination reaction (shown here) converts cytosine to an altered DNA
base, uracil, but deamination occurs on other bases as well. These reactions take place
on double-helical DNA; for convenience, only one strand is shown.

9. DNA Damage Can Be Removed by More Than One
Pathway
• The first pathway, called base excision repair, involves
a battery of enzymes called DNA glycosylases, each of
which can recognize a specific type of altered base in
DNA and catalyze its hydrolytic removal.
• There are at least six types of these enzymes, including
those that remove
– deaminated Cs, deaminated As,
– different types of alkylated or oxidized bases,
– bases with opened rings,
– and bases in which a carbon carbon double bond has been
accidentally converted to a carbon carbon single bond.

10. Apurinic/apyrimidinic (AP) endonuclease

11. • The second major repair pathway is called
nucleotide excision repair
• This mechanism can repair the damage
caused by almost any large change in the
structure of the DNA double helix.
• Ex. pyrimidine dimers (T-T, T-C, and C-C)

12. • DNA helicase ,
• DNA polymerase and
• DNA ligase repair the region.

13. DNA Rearrangements
• Homologous recombination results in the reassortment
of genes between chromosome pairs without altering
the arrangement of genes within the genome.
• In contrast, other types of recombinational events lead
to rearrangements of genomicDNA.
• Some of these DNA rearrangements are important in
controlling gene expression in specific cell types;
– others may play an evolutionary role by contributing to
genetic diversity.

14. • General recombination (also called
homologous recombination) allows large
sections of the DNA double helix to
– move from one chromosome to another, and
– it is responsible for the crossing-over of
chromosomes

15. • General recombination is essential for the
maintenance of chromosomes in all cells,
– and it usually begins with a double-strand break
that is processed to expose a single-stranded DNA
end.
• Synapsis between this single strand and a
homologous region of DNA double helix is
catalyzed by the bacterial RecA protein and its
eucaryotic homologs, and
– it often leads to the formation of a four-stranded
structure known as a Holliday junction.

16. General recombination. The breaking and
rejoining of two
homologous DNA double helices creates two
DNA molecules that have
"crossed over." In meiosis, this process causes
each chromosome in a germ
cell to contain a mixture of maternally and
paternally inherited genes

17. A heteroduplex joint. This structure unites
two DNA molecules
where they have crossed over. Such a joint is
often thousands of nucleotides
long.

19. DNA synapsis catalyzed by the RecA protein. In vitro experiments show that several
types of complex are formed between a DNA single strand covered with RecA protein
(red) and a DNA double helix (green). First a non-base-paired complex is formed, which
is converted through transient base-flipping to a three-stranded structure as soon as a
region of homologous sequence is found. This complex is unstable because it involves
an unusual form of DNA, and it spins out a DNA heteroduplex (one strand green and
the other strand red) plus a displaced single strand from the original helix (green). Thus
the structure shown in this diagram migrates to the left, reeling in the "input DNAs"
while producing the "output DNAs.“ The net result is a DNA strand exchange

20. A Holliday junction

21. • Site-Specific Recombination
• In contrast to general homologous
recombination,
– which occurs at any extensive region of sequence
homology,
– site-specific recombination occurs between
specific DNA sequences and can proceed via
either of two distinct mechanisms
– (1) Transpositional site-specific recombination
– (2) Conservative site-specific recombination

22. • Transposition via DNA Intermediates
• Site-specific recombination occurs between two
specific sequences that contain at least a small
core of homology.
• In contrast, transposition involves the movement
of sequences throughout the genome and has no
requirement for sequence homology.
• Elements that move by transposition, are
called transposable elements, or transposons.

23. • They are divided into two general classes,
depending on whether they transpose
– via DNA intermediates or via RNA intermediates.
• Enzyme involved in transposition, transposase.
• Transposase introduces a staggered break in
the target DNA and cleaves at the ends of
the transposon inverted-repeat sequences.

24. • Following the cleavage of transposon and
target site DNAs,
– transposase joins the overhanging ends of the
target DNA to the transposable element.
• The resulting gap in the target-site DNA is
repaired by DNA synthesis,
– followed by ligation to the other strand of the
tranposon.

25. Replicative transposition. In the course of replicative
transposition, the DNA sequence of the transposon is copied by
DNA replication. The end products are a DNA molecule that is
identical to the original donor and a target DNA molecule that has
a transposon inserted into it. In general, a particular DNA-only
transposon moves either by the cut-andpaste pathway shown in
or by the replicative pathway. However, the two mechanisms have
many enzymatic similarities, and a few transposons can move by
either pathway

26. Two types of DNA rearrangement produced by conservative sitespecific
recombination. The only difference between the reactions in (A) and B) is the relative
orientation of the two DNA sites (indicated by arrows) at which a site-specific
recombination event occurs. (A) Through an integration reaction, a circular DNA
molecule can become incorporated into a second DNA molecule; by the reverse
reaction (excision), it can exit to reform the original DNA circle. (B) Conservative site-
specific recombination can also invert a specific segment of DNA in a chromosome

27. • In vertebrates, site-specific recombination is
critical to
– the development of the immune system,
– which recognizes foreign substances (antigens)
– and provides protection against infectious agents.

28. • There are two major classes of immune
responses,
– which are mediated by B and T lymphocytes.
• B lymphocytes secrete antibodies
(immunoglobulins)
– that react with soluble antigens;
• T lymphocytes express cell
surface proteins (called T cell receptors)
– that react with antigens expressed on the surfaces of
other cells

29. • diverse antibodies (and T cell receptors) are
– encoded by unique lymphocyte genes that are
formed during development of the immune
system
– as a result of sitespecific recombination between
distinct segments of immunoglobulin and T cell
receptor genes.

30. How Cells Read the Genome: From DNA to
Protein

31. • When the cell needs a particular protein, the
nucleotide sequence of the appropriate
portion of the immensely long DNA molecule
in a chromosome is first copied into RNA (a
process called transcription).
• It is these RNA copies of segments of the DNA
that are used directly as templates to direct
the synthesis of the protein (a process called
translation)

32. • Transcription Produces RNA Complementary
to One Strand of DNA
• The enzymes that perform transcription are
called RNA polymerases.

33. • Although RNA polymerase catalyzes essentially the
same chemical reaction as DNA polymerase, there are
some important differences between the two enzymes.
• First, and most obvious, RNA polymerase catalyzes the
linkage of ribonucleotides, not deoxyribonucleotides.
• Second, unlike the DNA polymerases involved in DNA
replication, RNA polymerases can start an RNA chain
without a primer.
• This difference may exist because transcription need
not be as accurate as DNA replication

34. • Cells Produce Several Types of RNA
• small nuclear RNA (snRNA) molecules direct
the splicing of pre-mRNA to form mRNA,
• ribosomal RNA (rRNA) molecules form the
core of ribosomes,
• and that transfer RNA (tRNA) molecules form
the adaptors that select amino acids and hold
them in place on a ribosome for incorporation
into protein

35. • Signals Encoded in DNA Tell RNA Polymerase
Where to Start and Stop
• A detachable subunit, called sigma (σ) factor,
is largely responsible for its ability to read the
signals in the DNA that tell it where to begin
transcribing

36. • when the polymerase slides into a region on
the DNA double helix called a promoter, a
special sequence of nucleotides indicating the
starting point for RNA synthesis, it binds
tightly to it.
• The polymerase, using its sigma factor,
recognizes this DNA sequence by making
specific contacts with the portions of the
bases that are exposed on the outside of the
helix

38. • How do the signals in the DNA (termination
signals) stop the elongating polymerase?
• For most bacterial genes a termination signal
consists of a string of A-T nucleotide pairs
preceded by a two-fold symmetric DNA
sequence, which, when transcribed into RNA,
folds into a "hairpin" structure.
• As the polymerase transcribes across a
terminator, the hairpin may help to wedge open
the movable flap on the RNA polymerase and
release the RNA transcript from the exit tunnel