L3: DNA Damage & Repair (farook)

Question 1

DNA damage can be either in

Answer 1

Question 2

True or false?

DNA damage is a unnatural occurring process in a cell.

Answer 2

False, a naturally occurring process in a cell.

Question 3

When DNA damage occurs, what recognizes and corrects the damage?

And what happens if the damage was not repaired?

Answer 3

the DNA repair system is what recognizes and corrects the damage, If the damage is not repaired, it will create a mutation during DNA replication.

Question 4

What are the factors known to mutations?

Answer 4

Question 5

During DNA replication, what can naturally make an error and create mismatch nucleotides?

And how is it normally fixed?

Answer 5

• During DNA replication, DNA polymerase III can naturally make an error and creates mismatch nucleotides.
• However, the 3’ to 5’ exonuclease subunit of the DNA polymerase proofreads and corrects the mismatch error.

What makes the error: DNA polym III
Who fixes it: 3’ to 5’ exonuclease

Question 6

For proofreading, list who does the proof reading and where?

Answer 6

Question 7

Summarize how a mutation is created due to error in proof reading & mismatch?

Answer 7

1. When DNA polymerase fails to correct error, the next
   defense mechanism is DNA repair system
   (DNA mismatch repair system recognizes and corrects the mismatch nucleotides)
2. If the mismatch repair system even fails to correct the error, it will create a permanent mutation.

(Elly ta7at is just a further explanation for ur understanding)

• During replication, the uncorrected mismatched nucleotides (G to T) will create a permanent mutation in the genome as follows:

One strand: A:T
Mutant: G:C

Question 8

What is depurination and how does it occur?

Answer 8

• Depurination refers to the loss of purines (G or A) from a nucleotide
• Depurination occurs through spontaneous hydrolysis reaction.

Question 9

During depurination, will the backbone of the strand be affected?

Answer 9

Only the base is removed, it will still have the backbone of the phosphate and sugar molecule

Question 10

How does depurination induce mutation ?

Answer 10

• Depurinated site (Sugar & P) will be recognized
and corrected by the DNA repair enzymes (Endo/exo nucleases, ligase, blah blah blah)

• If depurinated site is not removed, DNA
polymerase skips the depurinated site during
replication and creates a deletion mutation

• The depurinted nucleotide will eventually be
removed in successive replications creating a
permanent deletion mutation in one copy.

Question 11

Spontaneous hydrolysis causes what mutations?

Answer 11

Deamination & Depurination

Question 12

What is deamination and what causes it?

Answer 12

• Deamination refers to the loss of amino group (NH2).
• It occurs due to spontaneous hydrolysis.

Question 13

How does a deamination create transition mutation?

Answer 13

• Loss of amino group from methylcytosine creates Thymine.
• If repair system fails to repair the thymine, it creates a transition mutation (cytosine to thymine) during replication.
• Wild strand (il og strand) will have C-G
• Mutant strand will have T-A

Question 14

Pyrimidine (C) to Pyrimidine (T) change is called _________________?

(Talking abt deamination)

Answer 14

Pyrimidine (C) to Pyrimidine (T) change is called transition mutation

Question 15

• Depurination creates a ______________
• Deamination creates a ______________

Answer 15

• Depurination creates a deletion mutation
• Deamination creates a mismatch mutation

Question 16

• ______________ creates a mismatch mutation
• ______________ creates a deletion mutation

Answer 16

• Deamination creates a mismatch mutation
• Depurination creates a deletion mutation

Question 17

Both depurination and deamination are caused by…

Answer 17

Spontaneous hydrolysis.

(Explanation: Usually hydrolysis is used for hydrolyzing many enzymes are proteins but by mistake it hydrolyzes the nucleotides)

Question 18

List the names of the bases and what they turn into when they get deaminated

Answer 18

Question 19

Adenine bases exist in common and rare
tautomers forms, list them

Answer 19

T & G: keto➡️enol
A & C: amino➡️imino

Question 20

How can Tautomers create a transition mutation ?

Answer 20

Question 21

What are tautomers?

Answer 21

Tautomers are nucleotide isomers that
spontaneously interconvert by proton shift (ya3ni from their common to rare form w il 3aks), a chemical reaction called tautomerization.

Question 22

ROS (reactive oxygen species):

1. Where do they come from?
2. They pair with?
3. What are its effects?

Answer 22

1. Natural metabolism releases reactive oxygen species, they come from the mitochondria and are highly reactive.
2. ROS base pairs with other molecules in a cell including DNA
3. It damages or alters the nucleotides in DNA.

Question 23

Explain ROS mediated DNA damage and its Mutagenic mechanism

(Shnu ysawee bl dna and how it turns into a mutation)

Answer 23

(The pic is a summary bas here’s the detailed explanation)

1. ROS species primarily base pairs with guanine and converts it into 8-hydroxyl guanosine (8-OHdG)
2. DNA damage repair enzymes recognize 8OHdG and corrects the error.
3. If The repair system fails, DNA polymerase assumes it is thiamine (T) fa it inserts Adenine (A) instead of (C)
4. Therefore, during the next replication, y9eer transversion mutation from G to T

Question 24

Give me the best example for a

1) transition mutation
2) transversion mutation

Answer 24

Question 25

Quick recap: Mnu il purines w mnu il pyrimidines?

Answer 25

Question 26

ROS species primarily binds with?

Answer 26

Guanine

Question 27

\_\_\_\_\_\_\_\_\_\_\_\_ is the most common type of DNA damage caused by UV irradiation.

Answer 27

Thymine dimer

Question 28

Thymine dimer is the most common type of DNA damage caused by \_\_\_\_\_\_\_\_\_\_\_\_

Answer 28

UV irradiation.

Question 29

Thymine dimers are examples of what kind of DNA damage?

Answer 29

Structural damage of the DNA

Question 30

Thymine dimers are caused by what DNA damage factor?

Answer 30

Exogenous factors

Question 31

Explain the mechanism of thymine dimer mutations?

Answer 31

1. UV light attacks the two adjacent thymine bases and cross links between carbon atom positions 5 & 6 of two adjacent thymine bases. 2. This causes the bending of the DNA and disrupts the bonding of these two thymine with their complimentary adenine nucleotides. 3. Repair enzymes recognize and correct the damage. 4. If the repair enzymes fail to correct the errors, it will create mutations during replication.

Question 32

What corrects oxidative deamination?

Answer 32

Base excision repair mechanism

Question 33

What does the base excision mechanism repair?

Answer 33

Oxidative deamination (E.g. cytosine➡️uracil)

Question 34

What is the difference between endo and exonucleases?

Answer 34

Endonuclease: cuts a nucleotide from the inside, flanking the mismatch. Exonuclease: cleaves from the end

Question 35

Describe the mechanism of the Base excision repair of DNA after cytosine gets deaminated:

Answer 35

1. The enzyme uracil DNA glycosylase removes the uracil created by spontaneous deamination in the DNA 2. An endonuclease cuts the backbone near the defect 3. 5’-3’ exonuclease of poly I removes a few bases/nucleotides 4. The defect is filled in by the action of a DNA polymerase I 5. The strand is rejoined by a ligase, which attaches them by creating a phospodiester bond

Question 36

Which mechanism fixes damage caused by physical agents (thymine dimers)?

Answer 36

Nucleotide excision repair

Question 37

Nucleotide excision repair removes the \_\_\_\_\_\_\_\_\_\_induced by \_\_\_\_\_\_\_\_\_\_\_\_\_\_.

Answer 37

Nucleotide excision repair removes the thymine dimers induced by ultraviolet light (UV).

Question 38

Explain how Nucleotide Excision Repair works

Answer 38

1. Thymine dimer is formed 2. UV specific endonuclease (uvrABC excinuclease) recognizes and cleaves the damaged strand 3. DNA polym I fills the gap by synthesizing new DNA, using the intact strand as a template 4. DNA ligase seals the remaining gap by joining the old and new DNA

Question 39

The enzyme uracil DNA glycosylase is found in which DNA damage repair mechanism?

Answer 39

Base excision repair

Question 40

The activity of which DNA polymerases are found in 1. Base excision repair mechanism 2. Nucleotide excision repair mechanism 3. Mismatch repair mechanism

Answer 40

DNA polymerase I: 1. Base excision repair mechanism 2. Nucleotide excision repair mechanism DNA polymerase III: 3. Mismatch repair mechanism

Question 41

Mismatch repair mechanism corrects?

Answer 41

``` Mismatch repair (MMR) corrects the mis-incorporated bases that can arise during DNA replication. ```

Question 42

Describe how the mismatch repair mechanism works

Answer 42

1. First, MutS recognizes the mismatch + recruits MutL 2. MutL then recruits MutH, an endonuclease. 3. MutH cuts the DNA strand flanking the mismatch. ``` 4. Exonuclease 1 chews all the nucleotides in the small DNA fragment (flanking mismatch site). ``` 5. DNA polymerase III synthesizes and fills the gap 6. Ligase ligates the gap.

Question 43

In E coli, MMR system involves three major proteins? What are they?

Answer 43

1. MutS 2. MutL 3. Mut H (Mut is basically short for mutation)

Question 44

In principle, all the three repair mechanisms operate in the same manners:

Answer 44

1) Protein recognizes the altered bases 2) Endonuclease cuts the DNA strand flanking the altered base. 3) Exonuclease chews the cut nucleotides 4) DNA polymerase synthesizes new complementary strand 5) Ligase seals the gap.

Question 45

True or false? The principles for all systems are different

Answer 45

False

Question 46

In which region where if a mutation occurs, it wouldn’t really make any differences?

Answer 46

If the mutation occured in the telomeres (non coding regions), ma yafrig. But if it occurred in the coding region, especially in the exons… r7na feeha

Question 47

If the DNA alterations are not repaired by the repair systems, what are the types of mutations possibly and permanently created in a gene?

Answer 47

1. Missense mutation 2. Non-sense mutation 3. Silent mutation 4. Frame shift mutation

Question 48

Histidine (CAT) to Proline (CCT) Is an example of what mutation?

Answer 48

Missense mutation

Question 49

CAG (Glycine ) to TAG (stop codon) Is an example of what mutation?

Answer 49

Nonsense mutation

Question 50

Explain each one: 1. Missense mutation 2. Non-sense mutation 3. Silent mutation 4. Frame shift mutation

Question 51

Missense/deletion in the promoter region causes?

Answer 51

Question 52

Missense mutation in the coding region alters?

Answer 52

Question 53

Deletion mutation in coding region can affect?

Answer 53

Question 54

What are the Human disorders associated with due to failure in DNA repair system ?

Answer 54

1. Xeroderma pigmentosum (XP) 2. Antaxia-telangiectasia 3. Hereditary non polyposis colon cancer

Question 55

What are the Human disorders associated with due to failure in DNA repair system ? Describe them?

Answer 55

Question 56

Defects in Base excision repair causes?

Answer 56

Ataxia-telangiectasia

Question 57

Defects in Mismatch repair system causes?

Answer 57

Hereditary Nonpolyposis Colon Cancer | (HNCC)

Question 58

Defects in Nucleotide Excision Repair causes?

Answer 58

Xeroderma Pigmentosum (XP)

Question 59

DEFECTS IN… 1. Nucleotide base excision repair 2. Mismatch repair system 3. Base excision repair CAUSES THESE DISEASES:

Answer 59

1. Nucleotide base excision repair: Xeroderma Pigmentosum (XP) 2. Mismatch repair system: Hereditary Nonpolyposis Colon Cancer (HNCC) 3. Base excision repair: Ataxia-telangiectasia