MCAT DNA repair mechanisms practice questions

What is Base Excision Repair (BER)?

A DNA repair mechanism that corrects single-base lesions in DNA.

Key enzyme in BER?

DNA glycosylase: removes damaged bases.

True or False: BER can fix bulky DNA adducts.

False. BER specifically targets small base lesions.

Fill in the blank: The first step in BER involves __________.

Recognition and removal of damaged base.

What follows DNA glycosylase action in BER?

AP endonuclease cleaves the sugar-phosphate backbone.

Compare BER and NER.

BER: single base damage; NER: bulky lesions.

Cause → Effect: DNA damage caused by reactive oxygen species leads to __________.

Base mutations repaired by BER.

Which enzyme fills in the gap after base removal in BER?

DNA polymerase synthesizes the new nucleotide.

True or False: DNA ligase seals nicks in the DNA backbone during BER.

True. DNA ligase is crucial for completing the repair.

What is the role of AP endonuclease?

It creates a nick in the DNA backbone at the apurinic/apyrimidinic site.

Short Example: How does DNA glycosylase identify damaged bases?

It scans DNA and recognizes altered base structures.

Which type of damage is commonly repaired by BER?

Deamination, oxidation, and alkylation of bases.

Fill in the blank: In BER, after the gap is filled, __________ joins the ends.

DNA ligase.

List the steps in BER.

- Base removal - AP site formation - Nicking - Gap filling - Ligation

True or False: BER is error-prone and leads to mutations.

False. BER is generally accurate in correcting errors.

What is the role of DNA polymerase in BER?

It synthesizes the correct base to replace the removed one.

What is Nucleotide Excision Repair (NER)?

NER is a DNA repair mechanism that removes bulky DNA lesions, such as those caused by UV light.

List the key steps in NER.

- Damage recognition - Excision of damaged DNA - DNA synthesis - Ligation of DNA strands

True or False: NER only repairs single-strand breaks.

False. NER repairs bulky lesions and helix-distorting damage, not just single-strand breaks.

What enzyme is responsible for recognizing DNA damage in NER?

XPC protein complex recognizes damaged DNA and initiates NER.

Fill in the blank: The endonuclease that excises damaged DNA in NER is called ____.

XPF/ERCC4 and XPG/ERCC5.

Cause → Effect: What happens when NER is defective?

Increased susceptibility to UV-induced skin cancers, such as xeroderma pigmentosum.

Compare NER and Base Excision Repair (BER) processes.

NER repairs bulky lesions; BER fixes non-helix-distorting base damage.

What is the role of DNA polymerase in NER?

DNA polymerase synthesizes new DNA to fill in gaps after excision.

Name a key protein involved in the NER pathway.

XPC protein is crucial for damage recognition.

True or False: NER can fix all types of DNA damage.

False. NER is specific for bulky lesions; it cannot repair all damage types.

What happens during the 'incision' step of NER?

Endonucleases cut the DNA strand on both sides of the damaged segment.

Fill in the blank: NER is particularly important for repairing damage from _____.

UV radiation.

What is the function of the helicase in NER?

The helicase unwinds the DNA to allow access for repair enzymes.

Describe the role of ligase in NER.

Ligase seals the nicks in the DNA backbone after repair synthesis.

List two diseases associated with defective NER.

- Xeroderma pigmentosum - Cockayne syndrome

What type of damage does NER primarily address?

Helix-distorting damage such as thymine dimers.

What is mismatch repair (MMR)?

MMR is a DNA repair mechanism that corrects base pair mismatches that occur during DNA replication.

Key enzymes involved in MMR?

- MutS: detects mismatches - MutL: links detection to repair - MutH: cleaves the daughter strand

True or False: MMR corrects DNA damage caused by environmental factors.

False. MMR specifically corrects replication errors, not damage from environmental sources.

Fill in the blank: MMR prevents the __________ of mutations during DNA replication.

accumulation

Compare MMR and NER.

MMR fixes replication errors, while NER repairs bulky DNA lesions and distortions.

What triggers the activation of MMR?

The presence of mismatched base pairs detected by MutS proteins.

Role of MutH in MMR?

MutH identifies the newly synthesized DNA strand and cleaves it to initiate repair.

What types of mismatches does MMR correct?

MMR corrects insertions, deletions, and base substitutions that lead to mismatched pairs.

True or False: MMR is essential for all organisms.

True. MMR is conserved across many species and is crucial for DNA fidelity.

What happens if MMR is defective?

Defective MMR can lead to increased mutation rates and is associated with certain cancers, such as Lynch syndrome.

Cause → Effect: MMR deficiency leads to __________.

increased microsatellite instability

What is the role of exonuclease in MMR?

Exonuclease removes the erroneous nucleotides after MutH has cleaved the strand.

Identify a key difference between MMR and Base Excision Repair.

While MMR corrects mismatched bases, Base Excision Repair fixes damaged or inappropriate bases.

Short example of MMR in action.

During DNA replication, if adenine pairs with cytosine, MutS will detect this mismatch and activate repair mechanisms.

True or False: MMR operates only in prokaryotes.

False. MMR is present in both prokaryotic and eukaryotic cells.

Name one disease associated with MMR defects.

Lynch syndrome (hereditary non-polyposis colorectal cancer).

What is a double-strand break (DSB)?

A DSB is a type of DNA damage where both strands of the DNA helix are severed, potentially leading to genomic instability.

True or False: Non-homologous end joining (NHEJ) is error-prone.

True. NHEJ can introduce mutations because it directly ligates broken ends without template guidance.

Homologous recombination (HR) requires what type of DNA?

It requires a homologous template, usually the sister chromatid, to accurately repair the break.

Fill in the blank: NHEJ is most active during _____ phase.

G1 phase.

Comparison: NHEJ vs. HR.

- NHEJ: fast, error-prone. - HR: slower, high fidelity.

What proteins are key in NHEJ?

Key proteins include Ku70/80, DNA-PKcs, and Ligase IV.

Cause → Effect: DSBs can lead to cancer.

Unrepaired DSBs can cause chromosomal rearrangements, leading to tumorigenesis.

What role does RAD51 play in HR?

RAD51 facilitates strand invasion of the homologous template and promotes DNA pairing.

True or False: HR requires cell cycle specificity.

True. HR primarily occurs in the S and G2 phases when sister chromatids are available.

What enzymes initiate NHEJ?

Ku proteins recognize DSBs and recruit DNA-PKcs to the site.

Fill in the blank: The 5' overhangs are filled in during _____.

NHEJ process.

How does HR ensure fidelity in DNA repair?

HR uses a homologous template to guide accurate repair, reducing errors.

What happens during the exonuclease step in HR?

Exonucleases trim the ends of the broken DNA to create single-stranded overhangs for strand invasion.

Define: DNA-PKcs.

DNA-PKcs is a kinase that plays a critical role in the NHEJ pathway by phosphorylating target proteins.

What is the significance of the Holliday junction?

The Holliday junction is a key intermediate in HR, allowing for the exchange of genetic material between homologous chromosomes.

Differentiate between DSB repair pathways: NHEJ vs. HR.

- NHEJ: faster, no template. - HR: slower, uses template.