Section VII - Chapter 27 - DNA Metabolism.ppt

Dna structure, function

1. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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2. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
nd
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DNA Metabolism

3. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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REPLICATION OF DNA
Principles of Replication
1.Copying is accurate
2.Replication is semiconservative
3.Supercoils and DNA topoisomerases
4.Replication fork
5.Replication is simulataneous and
bidirectional
6.DNA synthesis is catalysed by DNA
polymerases

4. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
nd
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Replication fork

5. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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REPLICATION IN PROKARYOTES
Most of the information about the replication
in prokaryotes is obtained from the studies
made on the intestinal bacterium, E.coli.
The process of replication can be studied
conveniently in three stages.
1. Initiation
2. Elongation
3. Termination

6. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Initiation
Helicaseenzymes
Replication fork
Topoisomerases(also called as DNA gyrases)
Single-stranded DNA binding (SSB) proteins
Primer
Primase
DNA polymerase III

7. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Diagrammatic representation of the process of replication

8. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Elongation
Okazaki fragments
DNA polymerase I
Proof-reading ability

9. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Termination
Terminus sequence
DNA polymerase II

10. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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REPLICATION IN EUKARYOTES
There are five distinct DNA polymerases
identified in eukaryotes. They are numbered by
Greek alphabets.
1.DNA polymeraseasynthesises primers for
both leading and lagging strands of DNA.
2.DNA polymerasebhas similar function as
that of DNA polymerase II of prokaryotes –
DNA repair.
3.DNA polymerasegexclusively replicates
mitochondrial DNA.
(Continued…

11. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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4.DNA polymerase dis analogous to that of
DNA polymerase III of prokaryotes. It takes
part in the synthesis of both leading and
lagging strands with an intrinsic proof-
reading activity.
5.DNA polymerase eis comparable in its action
to the prokaryotic DNA polymerase I. It is
involved in the removal of RNA primers of
Okazaki fragments on the lagging strand.
Occasionally, it replaces the DNA polymerase
d and performs its function.
…Continues)
(Continued…

12. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Like bacterial replication, replication in
eukaryotic cells can also be studied in three
stages.
1.Initiation
2.Elongation
3.Termination.
…Continues)

13. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Initiation
Helicases
Topoisomerases
Replication protein A (RPA)
Replication fork
Multiple sites of origin of replication
Primers

14. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Overview of DNA replication on the lagging strand in eukaryotes (leading
strand is not shown) (for abbreviations see the text)

15. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Elongation
Replication factor C (REC)
Proliferating cell nuclear antigen (PCNA)
Sliding clamp
DNA polymerase d
Okazaki fragments
RNase H
FENI (flap endonuclease I)
DNA polymerase e

16. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Termination
Telomeres
Telomerases
RNA dependent DAN synthesis
Reverse transcriptase

17. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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●The differences between the DNA replication
in bacteria and human cells give scope for
developing antibioticsthat target bacterial
replication but do not affect human cells.
Several drugs (e.g. ciprofloxacin, nalidixic
acid) act by inhibiting the enzymes of
bacterial replication.
INHIBITORS OF REPLICATION
(Continued…

18. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Drugs targeting human replication enzymes
such as topoisomerases and telomerases
arrest new DNA synthesis and thus the cell
division. E.g. doxorubicin, adriamycin,
etoposide. Certain nucleotide analogues such
as 6-mercaptopurine and 5-fluorouracil
inhibit human DNA polymerases. They are
also used as anti-cancer drugs.
…Continues)

19. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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CELL CYCLE
•S (Synthetic) phase
•M (mitotic) phase
•Gap1 (G
1) andgap2 (G
2)
•Dormant phase(G0)
•Cyclins
•Cyclin-dependent kinases (CDKs)

20. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Cancer and the cell cycle
Cell cycle in mammalian cells (for abbreviations see the text)

21. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Apoptosis
A programmed cell suicide is referred to as
apoptosis

22. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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The exchange of genetic information between
various DNA segments is known as
recombination. Apart from rearranging genetic
information, it also repairs damaged DNA.
There are two types of recombinations.
RECOMBINATION
1.Homologous recombination:The exchange of
genetic information takes place between
identical DNA sequences (parts of
chromosomes). The most common example is
recombination between the maternal and
paternal chromosomes of a pair.
(Continued…

23. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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2.Non-homologous recombination: In this
type, the exchange of genetic information
occurs randomly (need not be between
identical sequences). Genetic rearrangement
usually takes place by this process
(transposition). It also involves the
experimental installation of foreign DNA into
a host's chromosome.
…Continues)

24. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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A diagrammatic representation of homologous recombination
HOMOLOGOUS RECOMBINATION

25. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Three models have been proposed to explain
homologous recombination.
i)Holliday model
ii)Meselson–Radding model
iii)Double-strand break model

26. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Holliday model of homologous recombination (the areas shown in dotted
boxes are heterologous regions)

27. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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Three types of non-homologous
recombination have been identified.
i)Transposition
ii)Site-specific recombination
iii)Non-homologous end joining.
NON-HOMOLOGOUS RECOMBINATION

28. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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A diagrammatic representation of retrotransposition

29. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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The types of damage inflicted on the DNA
molecule by various physical and chemical
agents (mutagens) are broadly classified into
four categories
DNA DAMAGE
(Continued…

30. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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TYPES OF DNA DAMAGE
…Continues)

31. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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REPAIR OF DNA
Four major repair systems are involved in
rectifying the DNA damage.
1.Mismatch repair
2.Base excision repair
3.Nucleotide excision repair
4.Double–strand break repair.

32. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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MECHANISMS OF DNA REPAIR

33. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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●Even though replication occurs with high
fidelity, defects do occur during copying.
Mismatch repair corrects errors involving
single base pair or a small region of
unpaired DNA
MISMATCH REPAIR

34. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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A diagrammatic representation of mismatch repair

35. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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A diagrammatic representation of base excision repair
BASE EXCISION REPAIR

36. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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●Xeroderma pigmentosum
NUCLEOTIDE EXCISION REPAIR

37. Limited Universities Press Rafi M D: Textbook of Biochemistry for Medical Students (2
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●Double-strand breaks are common during
immunoglobulin gene rearrangement which
are repaired forthwith. Otherwise, double-
strand breaks occur due to the free radicals,
radiation and chemotherapeutic agents.
DOUBLE-STRAND BREAK REPAIR