TEST 3 DNA Repair and Recombination

Question 1

Three types of repair that involve excising of lesion followed by replacement?

Answer 1

Mismatch repair Nucleotide excision repair Base excision repair

Question 2

Mismatch Repair: DNA Methylation Prokaryotes? Humans?

Answer 2

Occurs on adenines, if damage is detected it is excised and replaced using the undamaged strand as a template.

Humans: Occurs at CPG site where C is methylated.

Question 3

What is hemimethylated?

Answer 3

When only the parent strand is methylated.

Question 4

When do HNPCC or Lynch Syndrome result?

Answer 4

When there is an issue with DNA methylation used in mismatch repair.

Question 5

What enzyme methylates the daughter strand?

Answer 5

Dam methylase

Question 6

Process of mismatch repair?

Answer 6

1. Mismatch detected
2. Mut complex forms and binds
3. Forms a nick at the methylation point
4. Removew the DNA from the nick to the mismatch
5. DNA polymerase 3 or SSB fills in the gap and ligase connects them.

Question 7

What is deamination? and what enzyme removes it?

Answer 7

• Spontaneous reaction which converts nucleotides to different structures by removing a amine group and leaving a oxygen.
• Removed by DNA Glycosylase ​​

Question 8

What is the only nitrogenous base that can’t undergo deamination?

Answer 8

Thymine

Question 9

What is the worse form of deamination and why?

Answer 9

• 5-methylcytosine:
  
  • It deaminates to Thymine.
  • Very common in cancer

Question 10

What occurs in Depurination? and how?

Answer 10

Nitrogenous base is detached from the nucleotide, due to water binding.

note: does not occur as often in Ribonucleotides or RNA

Question 11

Base-excision repair what does it do? and steps?

Answer 11

Fixes Deamination and depurination.

1. DNA glycosylase:
   
   • makes an abasic site
     
     • same type of damage as depurination.
   • Specific for each type of of unnatural DNA base.
2. AP endonuclease
   
   • Removes the nucleotide
3. DNA polymerase
   
   • Fills in the long chain
4. DNA Ligase fills the gap.

Question 12

Epigenetic regulation through BER?

Answer 12

1. DNA methyltransferase adds methyl groups
2. TET enzymes change the methyl groups.
3. BER removes the modified methyl group.

Question 13

When is Nucleotide Excision Repair used and steps?

Answer 13

Fixes cross-linking (dimerization) of pyrimidine rings, upon exposure to ultraviolet light.

1. Excinuclease nicks at two different sites.
   
   1. This is a type of endonuclease.
2. DNA helicase separates the two strands
3. DNA poly fills in
4. DNA ligase then seals the gap.

Question 14

What causes Xeroderma Pigmentosum?

Answer 14

Mutation in nucleotide-excision repair

Question 15

What is direct repair and how does it work?

Answer 15

• Directly repairs the damage via chemical reaction that reverts the damage back to the original molecule.
• The cell synthesizes a specific enzyme for just one fix, once complete it is degraded.

Question 16

Type of DNA repair used to fix O6 - Methylguanine - DNA

Answer 16

Direct repair.

Question 17

Type of DNA repair to fix Pyrimidine Dimer.

Answer 17

Direct DNA Repair

Question 18

Why is repairing damage important during DNA replication?

Answer 18

• The lesion may cause a double - strand break
  
  • This is the worst kind of DNA damage a cell can undergo.
• Prokaryotes can’t repair mid replication.

Question 19

Common causes of double straded breaks?

Answer 19

High-energy radiation

Oxidative free radicals

Errors during replication

Question 20

What are the two forms of DSB DNA repair and how are they different

Answer 20

• Non-homol;ogous end joining
  
  • AKA SOS response
  • Extremely error prone, always happens.
• Homologous recombination repair
  
  • BRCA
    
    • abnormal enzymes cause ovarian cancer risk

Question 21

Crispr - Cas9 uses what form of DNA repair?

Answer 21

Homologous and non-homologous repair.

Question 22

Type of DNA repair to repair damage due to tautomerization (wrong nucleotide on the other strand).

Answer 22

Mismatch repair.

Question 23

Repairing damage due to depurination?

Answer 23

Base excision repair

Question 24

Melanoma associated with UV exposure, homemade bait blocked what pathway that caused the tumor?

Answer 24

Nucleotide-excision repair.

Question 25

What are the 3 types of Recombination?

Answer 25

Homologous recombination

Site-specific recombination

DNA transposition

Question 26

Three functions of Homologous recombination?

How is it initiated?

What intermediates are formed?

Answer 26

• Function
  
  • DNA repair, especaily at stalled replication forks.
  • Assists in segregation of chromosomes
  • Enhancement of genetic diversity.
• Initiated: by double-strand breaks
• Intermediates: Holliday intermediates are formed.

Question 27

Describe Unequal crossing over?

Answer 27

Non-homologous sites recombining with each other, causing crossing over where it should not occur.

Can cause short or long chromatids.

Question 28

What is gene conversion?

Answer 28

• Gene Conversion
  
  • Results in the conversion of one allele to the other allele.
  • Has a GC bias.
  • If a cell gets two allels of the same type instead of one of each type this can cause issues if both copies are of a bad type.

Question 29

Allelic gene conversion

Answer 29

Conversion between two alleles of the same gene

Question 30

Conversion between paralogs?

Answer 30

Interlocus gene conversion

Question 31

Explain Site-Specific Recombination

Answer 31

Occurs only at specific sites

Functions in DNA integration and regulation of gene expression.

Question 32

Describe DNA transposition

Answer 32

• Transposons use recombination to move within or between chromosomes
  
  • Immunoglobulin gene rearrangements us a similar mechanism

Question 33

What does DNA methylation do during DNA transposition?

Answer 33

Prevents cleavage