DNA Repair

Question 1

What are the primary types of DNA repair mechanisms?

Answer 1

1. Direct Repair – Fixes damage without replacing nucleotides (e.g., photoreactivation).
2. Base Excision Repair (BER) – Corrects small, non-helix-distorting base lesions.
3. Nucleotide Excision Repair (NER) – Removes bulky, helix-distorting lesions.
4. Mismatch Repair (MMR) – Fixes errors missed during DNA replication.
5. Double-Strand Break Repair (DSBR) – Includes homologous recombination (HR) and non-homologous end joining (NHEJ) to repair breaks.

Question 2

How does Base Excision Repair (BER) function?

Answer 2

Step 1: DNA glycosylase removes the damaged base.

Step 2: An AP endonuclease cuts the DNA backbone at the site.

Step 3: DNA polymerase fills the gap with the correct nucleotide.

Step 4: DNA ligase seals the strand, completing the repair.

Question 3

What is the process of Nucleotide Excision Repair (NER)?

Answer 3

Recognition: Complexes detect bulky DNA lesions.

Excision: A helicase unwinds DNA, and an endonuclease removes the damaged section.

Synthesis: DNA polymerase fills in the gap with new nucleotides.
Ligation: DNA ligase seals the DNA strand.

Question 4

What is direct DNA repair, and what are some examples?

Answer 4

Direct repair corrects certain types of damage directly, without nucleotide replacement.

Examples: Photolyase (in bacteria) reverses UV-induced thymine dimers; methyltransferase removes methyl groups from modified bases.

Question 5

Describe the Mismatch Repair (MMR) pathway.

Answer 5

Recognition: Mismatches are recognized by the MutS complex.

Recruitment: MutL complex binds, recruiting endonucleases.

Excision: The incorrect section is removed, and DNA polymerase resynthesizes the correct sequence.

Ligation: DNA ligase seals the repaired section.

Question 6

How does Homologous Recombination (HR) repair work?

Answer 6

Resection: Double-strand break ends are processed to form 3’ overhangs.

Strand Invasion: The 3’ overhang invades a homologous DNA sequence on the sister chromatid.

Synthesis: DNA polymerase synthesizes new DNA using the sister chromatid as a template.

Resolution: Holliday junctions are resolved, restoring the correct sequence.

Question 7

What is Non-Homologous End Joining (NHEJ)?

Answer 7

Binding: Ku proteins bind to double-strand break ends.

Processing: End-processing enzymes may trim the ends to make them compatible.

Ligation: DNA ligase IV, along with XRCC4, joins the ends, often leading to small insertions or deletions.

Question 8

Which enzymes are crucial in DNA repair processes?

Answer 8

DNA Glycosylase – BER.

Photolyase – Direct repair of UV damage (in some organisms).

AP Endonuclease – BER.

DNA Polymerase – BER, NER, MMR, and HR.

DNA Ligase – All pathways, sealing breaks.

Question 9

Why is DNA repair essential for cellular health?

Answer 9

Prevents mutations that could lead to cancer or other genetic diseases.

Maintains genomic stability and prevents chromosomal abnormalities.

Ensures fidelity of genetic information passed to daughter cells during division.

Question 10

What are the two main categories of mutation sources?

Answer 10

1. Endogenous (Internal) – Mutations from internal cellular processes (e.g., DNA replication errors).
2. Exogenous (External) – Mutations from environmental factors (e.g., radiation, chemicals).

Question 11

How can DNA replication errors cause mutations?

Answer 11

During DNA replication, DNA polymerase can sometimes insert incorrect nucleotides, leading to point mutations. If not corrected by DNA repair mechanisms, these errors become permanent mutations.

Question 12

What types of spontaneous chemical changes can lead to mutations?

Answer 12

Depurination – Loss of a purine base (adenine or guanine), creating an abasic site.
Deamination – Conversion of cytosine to uracil, potentially leading to C to T transitions.

Question 13

How does UV radiation induce mutations?

Answer 13

UV radiation causes thymine dimers to form, where two adjacent thymine bases bond, distorting the DNA and disrupting replication. If not repaired, this can cause frameshift mutations.

Question 14

What are chemical mutagens, and how do they cause mutations?

Answer 14

Chemical mutagens are substances that interact with DNA to alter its structure. Examples include:

• Alkylating agents (e.g., EMS) – Add alkyl groups to bases, leading to mispairing.
• Intercalating agents (e.g., ethidium bromide) – Insert between bases, causing frameshift mutations.

Question 15

How does oxidative stress contribute to mutations?

Answer 15

Reactive oxygen species (ROS) generated during cellular metabolism can oxidize DNA bases (e.g., guanine to 8-oxoguanine), leading to mispairing and transversion mutations.

Question 16

What effects does ionizing radiation have on DNA?

Answer 16

Ionizing radiation (e.g., X-rays, gamma rays) can cause double-strand breaks and point mutations by inducing chemical changes in DNA, often resulting in complex mutations or chromosomal rearrangements.

Question 17

How can viruses induce DNA mutations?

Answer 17

Some viruses insert their genetic material into the host genome, disrupting normal gene function and potentially activating oncogenes.

Retroviruses (e.g., HPV) are known to integrate into host DNA, leading to mutations and sometimes cancer.

Question 18

What are transposable elements, and how do they cause mutations?

Answer 18

Transposable elements (or “jumping genes”) are DNA sequences that can move within the genome, potentially disrupting or altering gene function and leading to mutations.

Question 19

How do environmental toxins cause mutations?

Answer 19

Toxins like cigarette smoke contain mutagens (e.g., benzo[a]pyrene) that bind to DNA, causing bulky adducts, which can lead to replication errors and cancer if not repaired.

Question 20

What causes spontaneous mutations?

Answer 20

DNA replication errors (e.g., mispairing)

Spontaneous chemical changes (e.g., deamination or depurination)

Errors during cell division

Question 21

How do DNA replication errors lead to spontaneous mutations?

Answer 21

During replication, DNA polymerase may insert incorrect nucleotides. If not corrected by proofreading, these errors can result in point mutations or small insertions/deletions.

Question 22

What chemical changes can lead to spontaneous mutations?

Answer 22

Common spontaneous changes include:

Depurination – Loss of a purine base, leading to an abasic site.

Deamination – Conversion of cytosine to uracil, causing C to T transitions.

Question 23

What causes induced mutations?

Answer 23

Induced mutations are triggered by environmental agents, including:

• Radiation (UV and ionizing)
• Chemical mutagens (alkylating agents, intercalating agents)
• Biological agents (certain viruses)

Question 24

How does radiation lead to induced mutations?

Answer 24

UV radiation creates thymine dimers that disrupt DNA replication.

Ionizing radiation (X-rays, gamma rays) can cause double-strand breaks and chromosomal rearrangements.