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Biochemistry🧪 > L3: DNA Damage & Repair (farook) > Flashcards

L3: DNA Damage & Repair (farook) Flashcards

1
Q

DNA damage can be either in

A
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2
Q

True or false?

DNA damage is a unnatural occurring process in a cell.

A

False, a naturally occurring process in a cell.

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3
Q

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

And what happens if the damage was not repaired?

A

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.

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4
Q

What are the factors known to mutations?

A
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5
Q

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

And how is it normally fixed?

A
  • 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

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6
Q

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

A
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7
Q

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

A
  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

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8
Q

What is depurination and how does it occur?

A
  • Depurination refers to the loss of purines (G or A) from a nucleotide
  • Depurination occurs through spontaneous hydrolysis reaction.
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9
Q

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

A

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

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10
Q

How does depurination induce mutation ?

A

• 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.

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11
Q

Spontaneous hydrolysis causes what mutations?

A

Deamination & Depurination

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12
Q

What is deamination and what causes it?

A
  • Deamination refers to the loss of amino group (NH2).
  • It occurs due to spontaneous hydrolysis.
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13
Q

How does a deamination create transition mutation?

A
  • 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
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14
Q

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

(Talking abt deamination)

A

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

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15
Q
  • Depurination creates a ______________
  • Deamination creates a ______________
A
  • Depurination creates a deletion mutation
  • Deamination creates a mismatch mutation
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16
Q
  • ______________ creates a mismatch mutation
  • ______________ creates a deletion mutation
A
  • Deamination creates a mismatch mutation
  • Depurination creates a deletion mutation
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17
Q

Both depurination and deamination are caused by…

A

Spontaneous hydrolysis.

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

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18
Q

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

A
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19
Q

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

A

T & G: keto➡️enol
A & C: amino➡️imino

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20
Q

How can Tautomers create a transition mutation ?

A
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21
Q

What are tautomers?

A

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.

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22
Q

ROS (reactive oxygen species):

  1. Where do they come from?
  2. They pair with?
  3. What are its effects?
A
  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.
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23
Q

Explain ROS mediated DNA damage and its Mutagenic mechanism

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

A

(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
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24
Q

Give me the best example for a

1) transition mutation
2) transversion mutation

A
25
Q

Quick recap:

Mnu il purines w mnu il pyrimidines?

A
26
Q

ROS species primarily binds with?

A

Guanine

27
Q

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

A

Thymine dimer

28
Q

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

A

UV irradiation.

29
Q

Thymine dimers are examples of what kind of DNA damage?

A

Structural damage of the DNA

30
Q

Thymine dimers are caused by what DNA damage factor?

A

Exogenous factors

31
Q

Explain the mechanism of thymine dimer mutations?

A
  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.
32
Q

What corrects oxidative deamination?

A

Base excision repair mechanism

33
Q

What does the base excision mechanism repair?

A

Oxidative deamination

(E.g. cytosine➡️uracil)

34
Q

What is the difference between endo and exonucleases?

A

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

Exonuclease: cleaves from the end

35
Q

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

A
  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
36
Q

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

A

Nucleotide excision repair

37
Q

Nucleotide excision repair removes the __________induced by ______________.

A

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

38
Q

Explain how Nucleotide Excision Repair works

A
  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
39
Q

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

A

Base excision repair

40
Q

The activity of which DNA polymerases are found in

  1. Base excision repair mechanism
  2. Nucleotide excision repair mechanism
  3. Mismatch repair mechanism
A

DNA polymerase I:

  1. Base excision repair mechanism
  2. Nucleotide excision repair mechanism

DNA polymerase III:
3. Mismatch repair mechanism

41
Q

Mismatch repair mechanism corrects?

A 
Mismatch repair (MMR) corrects the mis-incorporated
bases that can arise during DNA replication.
42
Q

Describe how the mismatch repair mechanism works

A
  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).
  1. DNA polymerase III synthesizes and fills the gap
  2. Ligase ligates the gap.
43
Q

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

A
  1. MutS
  2. MutL
  3. Mut H

(Mut is basically short for mutation)

44
Q

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

A

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.

45
Q

True or false?

The principles for all systems are different

A

False

Explanation:
46
Q

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

A

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

47
Q

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

A
  1. Missense mutation
  2. Non-sense mutation
  3. Silent mutation
  4. Frame shift mutation
48
Q

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

A

Missense mutation

49
Q

CAG (Glycine ) to TAG (stop codon)

Is an example of what mutation?

A

Nonsense mutation

50
Q

Explain each one:

  1. Missense mutation
  2. Non-sense mutation
  3. Silent mutation
  4. Frame shift mutation
A
51
Q

Missense/deletion in the promoter region causes?

A
52
Q

Missense mutation in the coding region alters?

A
53
Q

Deletion mutation in coding region can affect?

A
54
Q

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

A
  1. Xeroderma pigmentosum (XP)
  2. Antaxia-telangiectasia
  3. Hereditary non polyposis colon cancer
55
Q

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

A
56
Q

Defects in Base excision repair causes?

A

Ataxia-telangiectasia

57
Q

Defects in Mismatch repair system causes?

A

Hereditary Nonpolyposis Colon Cancer

(HNCC)

58
Q

Defects in Nucleotide Excision Repair causes?

A

Xeroderma Pigmentosum (XP)

59
Q

DEFECTS IN…

  1. Nucleotide base excision repair
  2. Mismatch repair system
  3. Base excision repair

CAUSES THESE DISEASES:

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

Biochemistry🧪 (7 decks)

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