DNA Repair

Question 1

In what two ways can DNA repair be carried out?

Answer 1

1. By directly repairing the DNA

2. By removing the damaged DNA and replacing it with new DNA

Question 2

In what two ways can E coli repair DNA by undoing the damage by two different repair mechanisms?

Answer 2

1. Photoreactivation (Light Repair)

2. Suicidal enzyme repair of alkylation damage

Question 3

Do human have a photoreactivation repair mechanism?

Answer 3

NO but many other organisms do.

Question 4

What enzyme carries out DNA repair by light repair?

Answer 4

DNA Photolyase

Question 5

What is the substrate of DNA photolyase?

Answer 5

pyrimidine dimers of damaged DNA

Question 6

How is DNA photolyase activated?

Answer 6

It binds to the damaged pyrimidine dimers on the DNA. It is activated when it absorbs light energy in the UVA/blue (>300nm) part of the spectrum.

Question 7

How does the DNA photolyase repair the DNA?

Answer 7

It breaks the pyrimidine dimers to reform monomers

Question 8

How do other organisms including humans repair DNA damage of the alkylation of the O6 in guanine?

Answer 8

directly reversing it

Question 9

How does the suicidal enzyme repair of alkylation damage operate?

Answer 9

The sulfur atom of the cysteine in the enzyme accepts the methyl or ethyl alkyl group. This irreversibly inactivates the enzyme thus reference to “SUCIDE ENZYME”

Question 10

How does the suicidal enzyme in repair of alkylated DNA violate the definition of an enzyme?

Answer 10

The enzyme cannot be regenerated after the reaction.

Question 11

What is this enzyme induced by?

Answer 11

it is a transferase and induced by DNA alkylation

Question 12

What are the two mechanism for repair by excision and replacement with new DNA?

Answer 12

1. Base Excision Repair (BER)

2. Nucleotide Excision Repair (NER)

Question 13

What are the names of all the enzymes involved in BER?

Answer 13

1. DNA Glycosylase
2. AP Endonuclease
3. DNA Phosphodiesterase
4. DNA Polymerase I
5. DNA Ligase

Question 14

What is the function of DNA GLycosylase?

Answer 14

Breaks the glycosidic bond between the damaged base and its sugar exposing the damaged base.

Question 15

WHat os the function of AP Endonuclease?

Answer 15

Recognized the AP site and nicks the DNA on the 5’ of the AP site.

Question 16

After DNA Glycosylase breaks the glycosidic bond between the damages base and sugar what site is left?

Answer 16

AP site which is an apurinic or apyrimidinic site that is a sugar without its purine or pyrimidine base.

Question 17

What is the function of the DNA phosphodiesterase?

Answer 17

Removes the AP sugar phosphate

Question 18

WHat is the function of DNA Pol I?

Answer 18

Degrade the DNA in the 5’—>3’ direction while in with new DNA

Question 19

What is the function of DNA Ligase?

Answer 19

Seals all the remaining nicks

Question 20

What is the enzyme acting in nucleotide excision repair?

Answer 20

excinuclease

Question 21

What is the function of excinuclease?

Answer 21

Cuts on either side of the damaged DNA to remove an oligonucleotide that is a 12-13mer in bacteria and a 24-32mer in eukaryotes

Question 22

After the excision is made in the nucleotide excision repair what is the next step?

Answer 22

DNA Pol I fills in the gap in the DNA and Ligase seals the nick.

Question 23

Most of the damage in E coli is repaired by what method?

Answer 23

nucleotide excision repair

Question 24

What are the two mechanisms of NER that occurs in humans?

Answer 24

1. GLobal Genome NER

2. Transcription-coupled NER

Question 25

What is a major difference between Global Genome NER and Transcription-couple NER in humans?

Answer 25

Global Genome NER can repair any lesion (damage) throughout the genome. Transcription-coupled NER is confined or restricted to transcribed strands in genetically active parts of the genome.

Question 26

Where does most of the information involving Global Genome NER come from?

Answer 26

The study of the disease Xeroderma pigmentosum (XP)

Question 27

People with Xeroderma pigmentosum (XP) are more vulnerable to what?

Answer 27

They are extremely sensitive to sunlight and are THOUSANDS times more likely to develop skin cancer if exposed.

Question 28

Why are XP patients so extremely sensitive to sunlight?

Answer 28

XP cells are defective in NER and therefore cannot repair helix-distorting DNA damage which includes pyrimidine dimers.

Question 29

What is the complete mechanism of global genome NER?

Answer 29

XPC recognized the distortion in the helix and binds to it. This induces DNA melting around the damage. RPA binds to the undamaged DNA strand across from the damage. TFIIH, a DNA helicase, causes additional melting. RPA helps position 2 endonucleases (XPF complex and XPG) on each side of the damage and they clip the DNA. An oligonucleotide containing the damage is excised. DNA Pol Epsilon or Delta fills int he gap with good DNA DNA Ligase seals the final nick

Question 30

What molecule recognizes the damage in transcription-coupled NER?

Answer 30

RNA Polymerase instead of XPC in global genome NER

Question 31

When RNA Polymerase recognized the damaged DNA what happens?

Answer 31

RNA Polymerase will stall at the damaged DNA leaving a region of melted DNA. The factors associated with global genome NER then are utilized to repair the damage.