IB DP Biology-D1.1 DNA replication -FA 2025- IB Style Questions For HL Paper 1

Ans:D

To determine which two proteins assist in the unwinding and separation of DNA strands during replication, we need to understand the process of DNA replication and the roles of the proteins listed in the options. DNA replication involves unwinding the double-stranded DNA to form a replication fork, separating the strands, and keeping them apart so that the replication machinery can access the template strands. Let’s break this down and evaluate the options.

### Overview of DNA Replication and Unwinding
DNA replication begins at the origin of replication, where the double-stranded DNA is unwound to form a replication fork. This process involves several key steps and proteins:
1. **Unwinding the DNA**: The double helix must be unwound to separate the two strands, creating a replication fork.
2. **Relieving torsional stress**: As the DNA unwinds, the double helix ahead of the replication fork becomes tightly coiled (supercoiled), and this tension must be relieved.
3. **Stabilizing the separated strands**: Once the strands are separated, they need to be kept apart to prevent them from re-annealing, allowing the replication machinery to access the template strands.

The question specifically asks for proteins that assist in the **unwinding and separation** of DNA strands, so we’ll focus on proteins directly involved in these steps.

### Roles of the Proteins in the Options
Let’s examine the proteins listed in the options and their roles in DNA replication, particularly in prokaryotes (since the options include DNA polymerase III and I, which are prokaryotic enzymes, typically studied in *E. coli*):

– **Helicase**:
– Helicase is an enzyme that directly unwinds the double-stranded DNA at the replication fork. It breaks the hydrogen bonds between the complementary base pairs, separating the two strands and creating the replication fork.
– This is a **key protein** in the unwinding and separation of DNA strands.

– **DNA polymerase III**:
– DNA polymerase III is the primary enzyme responsible for synthesizing new DNA strands during replication in prokaryotes. It adds DNA nucleotides to the growing strand in the 5’ to 3’ direction, working on both the leading and lagging strands.
– While it is essential for replication, DNA polymerase III acts **after** the strands are unwound and separated. It does not play a direct role in unwinding or separating the DNA strands.
– This protein is **not involved** in unwinding or separation.

– **DNA gyrase**:
– DNA gyrase is a type of topoisomerase (specifically topoisomerase II in prokaryotes) that relieves the torsional stress (supercoiling) that builds up ahead of the replication fork as helicase unwinds the DNA. It does this by introducing negative supercoils, which relaxes the DNA and prevents it from becoming too tightly wound.
– While DNA gyrase does not directly unwind or separate the strands at the replication fork (that’s helicase’s job), it **assists the unwinding process** by making it easier for helicase to continue unwinding the DNA without the molecule becoming overly strained.
– This protein **indirectly assists** in unwinding by supporting the process.

– **DNA polymerase I**:
– DNA polymerase I in prokaryotes removes RNA primers (laid down by primase) and replaces them with DNA nucleotides during replication. It also has a proofreading function.
– Like DNA polymerase III, DNA polymerase I acts **after** the strands are unwound and separated, during the synthesis and finishing stages of replication.
– This protein is **not involved** in unwinding or separation.

– **DNA primase**:
– DNA primase synthesizes short RNA primers that provide a starting point for DNA polymerase to begin synthesizing new DNA strands. These primers are necessary because DNA polymerases cannot initiate synthesis de novo.
– Primase works **after** the DNA strands are unwound and separated, as it needs access to the single-stranded DNA to lay down the primers.
– This protein is **not involved** in unwinding or separation.

– **Single-strand binding protein (SSB)**:
– Single-strand binding proteins bind to the separated DNA strands after helicase unwinds them. They coat the single-stranded DNA, preventing the strands from re-annealing (re-forming the double helix) and protecting them from degradation.
– SSBs are critical for **keeping the strands separated** after unwinding, ensuring that the replication machinery (like primase and DNA polymerase) can access the template strands.
– This protein **directly assists** in the separation of DNA strands by stabilizing the unwound state.

### Evaluate the Options
The question asks for **two proteins** that assist in the **unwinding and separation** of DNA strands. Let’s analyze each option:

– **A. Helicase and DNA polymerase III**:
– Helicase directly unwinds the DNA strands, so it fits the criteria.
– DNA polymerase III synthesizes new DNA strands but does not assist in unwinding or separating the strands.
– This option is **incorrect** because DNA polymerase III is not involved in unwinding or separation.

– **B. DNA gyrase and DNA polymerase I**:
– DNA gyrase indirectly assists unwinding by relieving supercoiling ahead of the replication fork, which supports helicase’s unwinding activity.
– DNA polymerase I removes RNA primers and fills in DNA, but it does not assist in unwinding or separating the strands.
– This option is **incorrect** because DNA polymerase I is not involved in unwinding or separation.

– **C. Helicase and DNA primase**:
– Helicase directly unwinds the DNA strands, fitting the criteria.
– DNA primase synthesizes RNA primers after the strands are unwound, but it does not assist in unwinding or separating the strands.
– This option is **incorrect** because DNA primase is not involved in unwinding or separation.

– **D. Single-strand binding protein and DNA gyrase**:
– Single-strand binding proteins (SSBs) assist in the **separation** of DNA strands by binding to the unwound single strands, preventing them from re-annealing and keeping them apart for replication.
– DNA gyrase assists in the **unwinding** process by relieving supercoiling ahead of the replication fork, making it easier for helicase to unwind the DNA.
– Both proteins play roles that support the unwinding and separation of DNA strands: DNA gyrase facilitates unwinding by reducing torsional stress, and SSBs ensure the strands remain separated after unwinding.
– This option is **correct**.

### Why Not Helicase and SSBs Together?
Helicase and single-strand binding proteins (SSBs) are often discussed together as the primary proteins involved in unwinding and separation:
– Helicase unwinds the DNA.
– SSBs stabilize the separated strands.

However, this pairing is not an option. Instead, the question pairs SSBs with DNA gyrase in option D, which also makes sense because:
– DNA gyrase supports the unwinding process by relieving supercoiling, which is necessary for helicase to continue unwinding effectively.
– SSBs ensure the strands remain separated after unwinding.

Both processes (unwinding and keeping strands separated) are critical to the overall task of “unwinding and separation” during replication.

### Conclusion
The two proteins that assist in the unwinding and separation of DNA strands are **single-strand binding protein** (which keeps the strands separated) and **DNA gyrase** (which assists unwinding by relieving supercoiling). This corresponds to option D.

**Final Answer: D**