1. Chapter 9 The Mutability and Repair of DNA
Outline:
1.replication errors and their repair
2. DNA damage
3.Repair of DNA damage

2. Section 1:replication errors and their repair
Important definations:
Transitions:a kind of the simplest mutations which are pyrimidine-to-pyrimidine and purine-to-purine substitutions
Tranversions:the other kind of mutation which are pyrimidine-to-purine and purine-to-pyrimidine substitutions

3. Point mutations:mutations that alter a single nucleotide
DNA microsatellites: Mutation-prone sequence in human genome are repeats of simple di-, tri- or tetranucleotide sequences, known as DNA microsatellites

4. The Nature of Mutations
Base change substitutions
transitions
transversions

5. Other kinds of mutations(which cause more drastic changes in DNA):
Insertions
Deletions
Gross rearrangements of chromosome
These mutations might be caused by insertion by transposon or by aberrant action of cellular recombination processes.

6. Some Replication Errors Escape Proofreading
The 3’-5’ exonuclease component of replisome only improves the fidelity of DNA replication by a factor of about 100.
But, that’s not enough
The misincorporated nucleotide needs to be detected and replaced, otherwise it will cause mutation.

7. A mutation may be introduced by misincorporation of a base in the first round of replication.In the second round of replication,the mutation becomes permanently incorporated in the DNA sequence.

8. Mismatch Repair Removes Errors That Escape Proofreading
Mismatch repair system:a system that increases the accuracy of DNA synthesis by an additional two to three orders of magnitude.
This system faces 2 challenges:(1)rapidly find the mismatches/mispairs
(2) Accurately correct the mismatch

9. Important parts of mismatch repair system
MutS:a dimer of the mismatch repair protein which detects mismatches
Fuctions of MutS:
1. MutS scans the DNA, recognizes the mismatch from the distortion they cause in the DNA backbone

10. Functions of MutS
2.MutS embraces the mismatch-containing DNA, inducing a pronounced kink in the DNA and a conformational change in MutS itself

11. Crystal structure of MutS

12. Further steps of miamatch repair,we must pay attention to the other two important parts of the mismatch repair system---MutL and MutH

13. How these three parts interact
MutS-mismatch-containing DNA complex recruits MutL, MutL in turn activates MutH, an enzyme causing an incision or nick on one strand near the site of the mismatch. Nicking is followed by the specific helicase and one of three exonucleases.

14. Then we talk about :
how does the E.coli mismatch repair system know which of the two mismatched nucleotides to replace?
(Dam)methylation

15. Dam methylase:the E.coli enzyme that methylases A residues on both strands of the sequence 5`-GATC-3`.
The newly synthesized strand is not methylated by Dam methylase in a few minutes after the synthesis.

16. a.Replication generates hemimethylated DNA in E.coli.
b.MutH makes incision in unmethylated daughter strand.
Dam methylation at replication fork

17. Different exonucleases are used to remove single-strand DNA between the nick created by MutH and the mismatch.

18. MSH proteins MutS homologs
Eukaryotic cells
In fact,eukaryotes have multiple MutS-like proteins with different specificities.
MSH proteins MutS homologs

19. Section 2:DNA Damage
There are mainly three kinds of ways that DNA is damaged:
DNA undergoes damage spontaneously from hydrolysis and deamination
DNA is damaged by Alkylation,Oxidation and Radiation
Mutations are also caused by base analogs and intercalating agents

20. 1st kind, Hydrolysis & Deamination
a.Deamination that Cytosine to Uracil
which explain why DNA contains T instead of U

21. Answer:
If DNA naturally contained uracil instead of thymine,the deamination of cytosine will create a natrual base which the repair system will not easily recognize.

22. 2nd kind,Alkylation Oxidation and Radiation
DNA is subject to attack from Reactive oxygen species (O2-, H2O2, OH•)

23. UV(紫外线) induces a cyclobutane between adjacent thymines

24. 3rd kind,base analogs & intercalating agents
Base analogs: similar enough to the normal bases to be processed by cells and incorporated into DNA during replication.
But they base pair differently, leading to mistake during replication.
The most mutagenic base anolog is 5-bromouracil,an anolog of thymine.

25. 5-bromouracil,base anolog of thymine,can mispair with guanine

26. Intercalating agents
Intercalating agents are flat molecules containing several polycyclic rings that interact with the normal bases in DNA through hydrogen bonds and base stacking.
溴乙锭
原黄素
丫啶橙

27. Section 3:Repair of DNA Damage
There are two consequences of DNA damage:
Some kinds of damage create impediments to replication or transcription
Other kinds of damage create altered bases that cause mispairing which results a permanent alternation to DNA

28. Systems that repair damage to DNA
A repair enzyme simply reverses the damage
Excision repair systems,in which damaged nucleotide is not repaired but removed from DNA(more elaborate step),composed of base excision repair and nucleotide excision repair

29. Systems that repair damage to DNA
Recombinational repair,which is employed when both strands of DNA are damaged,also known as double-strand break repair.(more elaborate)
Translesion DNA synthesis,the last way cells choose

30. Direct reversal of DNA damage
For example,photoreactivation,which directly reverses pyrimidine dimers

31. Direct reversal od DNA damage
Another example,methyltransferase(甲基转移酶) directly removes the methyl group from the O6-guanine residue

32. Base excision repair systems
Base excision repair enzymes—glycosylase(糖基化酶) recognize and remove damaged bases by a base-flipping mechanism,hydrolyzing the glycosidic bond.
DNA glycosylases are lesion-specific.

33. 1.The AP site is created by the hydrolysis of glycosylase bond.
2.AP endonuclease&exonuclease cut out the 5’ phosphate.
3.DNA polymerase fill in the gap.

34. The enzyme
The damaged base which is filpped out
The DNA

35. Nucleotide excision repair systems
What is the difference between the two kinds of excision repair systems?
Also,how does the nucleotide```work?
Recognize distortions to the shape of the DNA double helix
Remove a short single-stranded segment that includes the lesion.
DNA polymerase/ligase fill in the gap.

36. Once encountering a distortion UvrA exits the complex and UvrB melts the DNA to create a single-strand bubble around the lesion.
Next,UvrB recruits UvrC,and UvrC creates two incisions in different positions on one strand.
Finally,DNA polymerase and ligase fill in the gap.

37. Recombinational repair
This is the very essencial way that cells repair double-strand breaks in DNA in which both strands of the duplex are broken.
We call it double-strand break(DSB)repair pathway,which retrieve sequence information from sister chromosome.

38. Translesion DNA synthesis
When cells cannot repair certain lesions,there is a fail-safe mechanism that allows the replication machinery to bypass these sites of damage----translesion synthesis
Translesion synthesis is catalyzed by a specialized class of DNA polymerases that synthesize DNA directly across the damage site.
Translesion polymerase is produced by cell in response to the DNA damage
Translesion polymerases are expressed as part of the SOS response pathway.

39. Crystal structure of a translesion polymerase.

40. Translesion DNA synthesis in E. coli

41. Thank You