DNA Replication and Repair: Step-by-Step Study Guidance

Study Guide - Smart Notes

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Q1. Which enzyme catalyzes the separation of DNA strands to open the double helix?

Background

Topic: DNA Replication Initiation

This question tests your understanding of the enzymes involved in the first steps of DNA replication, specifically the unwinding of the double helix.

Key Terms:

DNA double helix: The two intertwined strands of DNA.
Enzyme: A protein that speeds up biochemical reactions.
Helicase: The enzyme responsible for unwinding DNA.

Step-by-Step Guidance

Recall that DNA replication requires the two strands to be separated so each can serve as a template.
Think about which enzyme is responsible for breaking the hydrogen bonds between the bases of the two DNA strands.
Consider the role of this enzyme in creating the replication fork, where the DNA is open and accessible for replication.

Try solving on your own before revealing the answer!

Q2. What structures stabilize the single-stranded DNA so that nothing reacts with it before the lagging strand is ready to synthesize?

Background

Topic: DNA Replication - Stabilization of Single Strands

This question focuses on the proteins that protect and stabilize single-stranded DNA during replication.

Key Terms:

Single-stranded DNA (ssDNA): DNA that has been separated and is vulnerable to degradation or unwanted reactions.
Stabilizing proteins: Proteins that bind to ssDNA to prevent it from re-annealing or being degraded.

Step-by-Step Guidance

After the DNA strands are separated, consider what could happen to the exposed single-stranded regions.
Think about which proteins bind to these regions to keep them stable and prevent unwanted reactions.
Recall the specific name of these proteins that are essential for maintaining the integrity of ssDNA during replication.

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Q3. What enzyme catalyzes the synthesis of the RNA primer?

Background

Topic: DNA Replication - Primer Formation

This question tests your knowledge of the enzyme responsible for creating the RNA primer, which is necessary for DNA polymerase to begin synthesis.

Key Terms:

RNA primer: A short segment of RNA that provides a starting point for DNA synthesis.
Primase: The enzyme that synthesizes the RNA primer.

Step-by-Step Guidance

Recall why DNA polymerase cannot start synthesis without a primer.
Think about which enzyme is responsible for laying down the initial RNA nucleotides.
Identify the enzyme that creates the primer so DNA polymerase can extend the strand.

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Q4. What enzyme breaks and rejoins the DNA double helix to relieve twisting forces caused by the opening of the helix?

Background

Topic: DNA Replication - Tension Relief

This question is about the enzyme that manages the supercoiling and tension that occurs as the DNA helix is unwound.

Key Terms:

Supercoiling: The overwinding or underwinding of DNA as it is unwound.
Topoisomerase: The enzyme that cuts and rejoins DNA to relieve tension.

Step-by-Step Guidance

Consider what happens to DNA ahead of the replication fork as the helix is opened.
Think about which enzyme can cut the DNA, allow it to unwind, and then rejoin it.
Recall the name of this enzyme that prevents DNA from becoming too tightly wound.

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Q5. What enzyme holds the DNA in place during strand extension?

Background

Topic: DNA Replication - Processivity

This question tests your knowledge of the protein complex that ensures DNA polymerase stays attached to the DNA during replication.

Key Terms:

Processivity: The ability of an enzyme to catalyze consecutive reactions without releasing its substrate.
Sliding clamp: The protein that holds DNA polymerase in place.

Step-by-Step Guidance

Think about how DNA polymerase could fall off the DNA without assistance.
Recall the protein complex that forms a ring around DNA and keeps polymerase attached.
Identify the specific name of this protein.

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Q6. What enzyme extends the leading strand of DNA during replication?

Background

Topic: DNA Replication - Strand Elongation

This question is about the enzyme responsible for synthesizing new DNA by adding nucleotides to the leading strand.

Key Terms:

Leading strand: The strand of DNA synthesized continuously during replication.
DNA polymerase: The enzyme that adds nucleotides to the growing DNA strand.

Step-by-Step Guidance

Recall the direction in which the leading strand is synthesized (5' to 3').
Think about which enzyme is responsible for adding nucleotides to this strand.
Identify the specific enzyme involved in this process.

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Q7. What enzyme removes the RNA primer and replaces it with DNA?

Background

Topic: DNA Replication - Primer Removal and Replacement

This question tests your knowledge of the enzyme that removes RNA primers and fills the gap with DNA nucleotides.

Key Terms:

RNA primer: Short RNA sequence needed to start DNA synthesis.
DNA polymerase I: The enzyme that removes RNA primers and replaces them with DNA.

Step-by-Step Guidance

Recall why RNA primers must be removed after DNA synthesis.
Think about which enzyme has both exonuclease and polymerase activity to remove RNA and add DNA.
Identify the enzyme responsible for this function.

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Q8. What do you call the sections of lagging strand that must be joined together at the end of the lagging strand’s synthesis?

Background

Topic: DNA Replication - Lagging Strand Synthesis

This question is about the short DNA fragments produced on the lagging strand during replication.

Key Terms:

Lagging strand: The strand synthesized discontinuously.
Okazaki fragments: Short DNA segments on the lagging strand.

Step-by-Step Guidance

Recall why the lagging strand is synthesized in fragments.
Think about the name given to these fragments.
Identify the term used for these sections.

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Q9. What enzyme catalyzes the joining of Okazaki fragments?

Background

Topic: DNA Replication - Fragment Joining

This question tests your knowledge of the enzyme that seals the gaps between Okazaki fragments.

Key Terms:

Okazaki fragments: Short DNA pieces on the lagging strand.
DNA ligase: The enzyme that joins these fragments.

Step-by-Step Guidance

Recall why Okazaki fragments need to be joined.
Think about which enzyme forms phosphodiester bonds between fragments.
Identify the enzyme responsible for this process.

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Q10. Which is the correct model of DNA replication?

Background

Topic: DNA Replication Models

This question is about the three proposed models for DNA replication and which one is correct.

Key Terms:

Semiconservative model: Each new DNA molecule has one old and one new strand.
Conservative model: One molecule is entirely old, one is entirely new.
Dispersive model: DNA is a mix of old and new segments.

Step-by-Step Guidance

Recall the three models proposed for DNA replication.
Think about the evidence from the Meselson-Stahl experiment.
Identify which model is supported by experimental data.

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Q11. Where would you expect to find a telomere?

Background

Topic: Chromosome Structure

This question is about the location and function of telomeres in chromosomes.

Key Terms:

Telomere: Repetitive DNA sequence at the end of chromosomes.
Chromosome: DNA molecule with associated proteins.

Step-by-Step Guidance

Recall the structure of a chromosome.
Think about where telomeres are located and their function.
Identify the specific region of the chromosome where telomeres are found.

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Q12. What enzyme can extend the end of chromosomes so that they chromosomes don’t get shorter every time DNA replication takes place?

Background

Topic: Telomere Maintenance

This question is about the enzyme that adds DNA to the ends of chromosomes to prevent shortening.

Key Terms:

Telomerase: The enzyme that extends telomeres.
Telomere: Protective DNA sequence at chromosome ends.

Step-by-Step Guidance

Recall why chromosomes get shorter during replication.
Think about which enzyme can add DNA repeats to chromosome ends.
Identify the enzyme responsible for this function.

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Q13. What enzyme begins the DNA proofreading process?

Background

Topic: DNA Replication - Proofreading

This question is about the enzyme that checks for errors during DNA synthesis.

Key Terms:

Proofreading: Checking for and correcting errors during DNA replication.
DNA polymerase: The enzyme with proofreading activity.

Step-by-Step Guidance

Recall how errors can occur during DNA synthesis.
Think about which enzyme can detect and correct mismatched bases.
Identify the enzyme that initiates proofreading.

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Q14. What kind of repair takes place if DNA polymerase fails to correct an error in the DNA replication?

Background

Topic: DNA Repair Mechanisms

This question is about the repair system that fixes errors missed during replication.

Key Terms:

Mismatch repair: The system that corrects errors after replication.
DNA polymerase: The enzyme that sometimes misses errors.

Step-by-Step Guidance

Recall what happens if proofreading fails during replication.
Think about the repair system that scans DNA for mismatches after replication.
Identify the name of this repair mechanism.

Try solving on your own before revealing the answer!

Q15. What is mutation that happens to DNA when exposed to UV light?

Background

Topic: DNA Damage and Mutation

This question is about the specific type of mutation caused by UV radiation.

Key Terms:

Thymine dimer: A mutation where two adjacent thymine bases bond together.
UV radiation: Causes DNA damage.

Step-by-Step Guidance

Recall what happens to DNA when exposed to UV light.
Think about the specific bases affected by UV radiation.
Identify the name of the mutation formed.

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Q16. Sometimes DNA is damaged during non-replication times, such as by UV radiation. What kind of enzymes help repair thymine dimers that get produced during this UV radiation exposure?

Background

Topic: DNA Repair - Thymine Dimer Correction

This question is about the enzymes that fix thymine dimers caused by UV light.

Key Terms:

Thymine dimer: DNA damage caused by UV light.
Nucleotide excision repair: The process that removes and replaces damaged DNA.

Step-by-Step Guidance

Recall the process that removes damaged DNA segments.
Think about the enzymes involved in cutting out and replacing thymine dimers.
Identify the type of enzymes responsible for this repair.

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Q17. What genetic condition causes young people to get skin cancer because they are unable to repair any of the damage done by UV radiation?

Background

Topic: DNA Repair Deficiency Disorders

This question is about a genetic disorder that impairs DNA repair, leading to increased cancer risk.

Key Terms:

Genetic disorder: A disease caused by mutations in DNA.
Xeroderma pigmentosum: A condition where DNA repair is defective.

Step-by-Step Guidance

Recall the consequences of defective DNA repair mechanisms.
Think about the name of the disorder that results in extreme sensitivity to UV light.
Identify the genetic condition associated with this phenotype.