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Biochemistry > DNA Damage and Repair > Flashcards

DNA Damage and Repair Flashcards

1
Q

DNA damage via exogenous sources include ________.

A

Environmental sources such as radiation

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2
Q

DNA damage via endogenous sources include _________.

A

Intracellular processes, ROS, Alkylation, Hydrolysis

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3
Q

Pol delta is responsible for _____.

A

Replication of DNA on lagging strand

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4
Q

Pol epsilon is responsible for _________.

A

Replication of DNA on leading strand

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5
Q

Where are the two checkpoint in the cell cycle?

A
  1. Prior to entrance into S phase (if DNA contains damage)
  2. Prior to entrance into M phase (breaks or damage sites in DNA)
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6
Q

What are the phases of the cell cycle?

A

G1- Cell growth, duplication of organelles, Prep for DNA replication

S- DNA replication

G2- Cell Growth, Duplication of Organelles, Prep Cell Division

M- Mitosis

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7
Q

_____ and _______ are a consequence of faulty/unrepaired DNA.

A

Cancer and Ageing

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8
Q

What is the exonuclease activity of Pol delta and Pol epislon ?

A

3’-5’

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9
Q

What are some sources of DNA legions?

A

ROS (Oxidation and alkylation)

UV light and anti-tumor drugs

Replication Errors

Radiation, anti-tumor drugs, replication fork collapses

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10
Q

DNA replication errors can cause _____.

A

Mismatches

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11
Q

What are the types of DNA lesions? Which one is the most dangerous?

A

SSBs (Single Stranded Breaks)
Oxidized Bases
Bulky lesions
Cross Links
Mismatches
DSBs

DSBs are the worst.

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12
Q

A ________ bond exists between the pentose phosphate sugar and the nitrogenous base while the bond between the sugar and the phosphate groups is called a _______.

A

Glycosidic, Phosphodiester bond

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13
Q

What is the location of the glycosidic and phosphodiester bond?

A

Glycosidic: 1’ of Pentose sugar

(OH/H distinction- 2’)

Phosphodiester: 5’

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14
Q

____________ of cytosine is a ______ DNA damage.

Describe the process of damage.

A

Deamination of cytosine is a spontaneous

Cytosine has an amine (NH2) group. Deamination of it turns the NH2 into an Oxygen which creates a URACIL base.

Uracil is NOT a DNA base.

There will be one mutated and one un-mutated strand during replication of such a strand.

The deaminated strand will create a mutated complementary strand since U binds with A.

The complementary strand of where the C was supposed to be will contain a G. When the complementary strand gets replicated, it will reintroduce a correct cytosine to the strand it creates.

BIG PICTURE: CYTOSINE to URACIL causing replication issues. URACIL strand will base pair incorrectly with an A. Complementary G (to the cytosine that was supposed to be there ) of OG strand will base pair with new cytosine.

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15
Q

____________ of _____ cytosine is a ______ DNA damage.

Describe the process of damage.

A

Deamination, 5-methyl cytosine is a spontaneous DNA Damage.

5- methyl Cytosine has an amine (NH2) group and a neighboring CH3. Deamination of it turns the NH2 into an Oxygen which creates a THYMINE base.

THYMINE is a natural base of DNA so it can escape DNA repair.

BIG PICTURE: CYSTEINE TO THYMINE which binds with alanine

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16
Q

Depurination is a ___________ DNA damage mechanism.

Describe the damage.

A

Depurination is the cleavage of a nucleotide base

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17
Q

Alkylation is the ______________ to DNA ____.

What is a common example of something that can alkylate DNA _______? Describe how it causes damage.

A

addition of ethyl or methyl groups to DNA bases

Nicotine derived nitrosamines can be metabolized by liver and lung. They will bind to a base causing a “bulky group” and can also add methyl as well as other DNA adducts.

This impeded DNA polymerase from performing its function due to the bulkiness of the alkylated DNA strand.

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18
Q

Dimethylnitrosamine, a ________ can cause _______ of DNA ________. How does it do so?

A

carcinogen, alkylation of DNA bases

It gets metabolized by the liver and provides a methyl group that can attach to guanine. This forces Guanine to become O6-methyl guanine.

Guanine normally BPs with cytosine. BUT, O6- methyl guanine BPs with Thymine. This will causing replication issues as the altered Guanine will pair with Thymine now instead of cytosine.

BIG PICTURE: Guanine to O6-Methyl Guanine which BPs with THYMINE.

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19
Q

Alkylated DNA can cause what 3 issues in smokers?

A

Intercalation (Prevent DNA replication by preventing separation)
Interstrand Crosslinking (BPs bind incorrectly with opposing BPs)
Intrastrand Cross Linking (BPs on same side cross link)

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20
Q

Can vapes damage DNA?

A

YES

21
Q

__________ is very susceptible to oxidation creating ______ such as ______

What happens to Guanine?

A

Guanine, ROS such as Peroxides, Hydroxides, Superoxides

Guanine get stripped of an electron (oxidation) creating 7,8,- dihydro-8 Oxoguanine (OxoG).

While OxoG can BP to C, it also base pairs to A which can cause cancer.

22
Q

__________ can also cause ______ and is a product of cigarettes. How does it cause DNA damage?

A

Benzopyrene, oxidation

It covalently attaches it self to guanine and intercalates the strands to prevent DNA base pairing by interrupted H-bonding between G-C.

** Formation of BULKY ADDUCTS**

23
Q

What are the 3 damaging mechanisms of UV light on DNA? Is UV an exogenous or endogenous?

A

Adjacent pyrimidine Dimers (T-T, C-T)

Formation of covalent dimers on C=C double bonds

Defective bp

Exogenous.

24
Q

UV radiation can cause __________ bonding. This forms a shape called.

A

adjacent T-T bonding , Cyclobutane Pyrimidine Dimer

T’s bond on same STRAND.

25
Q

Is blue light irradiation safe?

A

Blue light falls under “visible light”. It generates oxygen radicals (ROS) at levels so low that the body can deal with the oxidative stress.

26
Q

DSBs are ___________ so there is __________. It is caused by ____ and can lead to _____.

It interferes with _______.

A

Double stranded breaks , there is no template strand for repair

gamma irradiation and X-rays

can lead to breakdown of chromosomes and chromosomal rearrangement.

Interferes with DNA replication and transcription

27
Q

What is a well-known example of the impacts of gamma irradiation? What disease was seen commonly?

A

1986 Ukraine

Chernobyl Disaster

Thyroid Cancer

28
Q

How does gamma radiation cause ______?

A

DSBs

Indirectly, gamma irradiation impact water and causes the generation of ROS’s which can cause SSBs or cause a DNA to lose a base (abaisc) via depurination.

Directly, gamma irradiation can cause SSBs or cut straight through both strands to create DSBs.

29
Q

Getting X-rays in an office cause more radiation exposure than taking a walk outside.

A

FALSE

We don’t need lead aprons anymore but its up to the dentist to decide.!

30
Q

What are the 5 major DNA Repair Mechanisms?

A

Excision Repair
Direct Repair
Double Strand Break Repair
Translesion Synthesis
Mismatch repair

31
Q

DNA repair pathways are similar in prokaryotes and eukaryotes. True or False

A

True

32
Q

What are the major enzymes of Base Excision Repair?

What are the major lesions repaired?

A

Glycosylase
AP (apurinic/apyriminidic) endonuclease
DNA polymerase
Ligase

Uracil, OxoG, O6-methyl-G , SSBs

33
Q

Steps of Base Excision Repair

A
  1. Damage in DNA strand will be recognized.
  2. Glycosylase will cleave the glycosidic bond between the base and the sugar.
  3. AP endonuclease will cut the phosphodiester bond to create a gap
  4. DNA polymerase fills in the gap and seals it.
34
Q

What are the important enzymes needed for Nucleotide Excision Repair?

What damages does it fix?

A

DNA nuclease
Helicase
DNA Polymerase
Ligase

Pyrimidine Dimers, bulky adducts

35
Q

Steps of Nucleotide Excision Repair

A
  1. Scan for DNA damage
  2. Cut around region using DNA nuclease
  3. Helicase removes segment with lesion
  4. DNA polymerase fills in gap, ligase seals up the phosphodiester bond.
36
Q

What is Xeroderma pigmentosum?

A

Children are born with a problem that does not allow repair of thymine pyrimidine dimers.

Makes them extremely UV sensitive.

37
Q

Transcription Coupled Excision Repair (TC-NER)

A

Nucleotide excision repair is coupled to RNA transcription.

This normally occurs when the deletion coincides with a location that is a protein coding gene.

RNA polymerase will halt at site of damage and recruit CSB protein. RNA polymerase exits the DNA and allows NER factors to repair the damage before RNA polymerase restarts transcription.

38
Q

Direct repair involves _______ DNA polymerase activity.

A

NO

39
Q

What are the major enzymes of Direct Repair?

A

DNA Photolyases : Uses visible light to cleave pyrimidine dimers

Methyltransferase: Transfers methyl group from O6-Guanine to a cysteine residue within protein.

40
Q

Where are DNA photolyases found?

A

In bacteria! Not humans! This is why we have NER to repair pyrimidine dimers.

41
Q

What are the three ways DSBs can be repaired?

What else can these mechanisms repair?

A

Homologous Recombination (HR)
Non-homologous end Joining (NHEJ)
Alternative NHEJ

CAN ALSO REPAIR SSBs , Inter and Intrastrand crosslink

42
Q

How does homologous recombination repair DSBs? When can it be done

A

At S and G2 phases before mitosis

During DNA replication, chromosomes are replicated. If there is a break in DNA in one chromosome, information from the intact sister chromatid can be copied and placed into the broken region.

43
Q

What genes are critical for homologous recombination repair?

A

BRCA1 and 2

They recruit proteins to form a bridge to bring DNA from the sister chromatid to the broken region.

Also cause Breast Cancer

44
Q

Homologous recombination damage repair is only possible when there is an existing sister chromatid copy. What happens if the cell has already divided and damage is not repaired?

A

NHEJ

It simply pushes the broken strands together and cleave any loose single strands of DNA.

This cleavage may be in an important REGION!

Can be done in all cell cycle changes.

45
Q

Translesion DNA Synthesis

What is it and how effective is it?

A

Low fidelity DNA polymerases will insert nucleotides across from a DNA lesion that has not or cannot be removed from replication fork pathway.

BIG chance of mutations such as mispairing

NO exonuclease activity.

46
Q

What is mismatch repair (MMR)

A

Corrects mismatched undamaged bases in DNA. AKA spelling error

Not truly a lesion; wrong base was added

47
Q

How does MMR work in E.Coli ?

A

In E.Coli

When DNA is being added, bases are not normally methylated. MMR deals with the methylated strand (parental) of DNA to find the mismatch and repairs it on the unmethylated strand, newly-synthesized.

When a mismatch occurs, a bulge is created, a cut is made on the unmethylated strand, repaired with DNA polymerase and assembled via ligase.

48
Q

In cancer, tumor cells can lose the ability to repair mismatched base pairs because ______.

A

They lack the genes needed to repair them.

48
Q

Dental Application of DNA Damage and Repair

A

Oral Cancer (Increase of HPV)
Dry Mouth

Biochemistry (18 decks)

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