Question

If you could engineer an activity into DNA polymerase to allow both strands to follow the replication fork, what would this additional activity be? a. the ability to begin DNA synthesis without a primer b. the ability to proofread in the \(5^{\prime} \rightarrow 3^{\prime}\) direction c. the ability to synthesize DNA in the \(3^{\prime} \rightarrow 5^{\prime}\) direction d. the ability to synthesize DNA without using a template

Short answer

The most appropriate feature to be engineered into DNA polymerase in order to allow both strands to follow the replication fork is the ability to synthesize DNA in the \(3^{\prime} \rightarrow 5^{\prime}\) direction (Option C). This would enable both leading and lagging strands to be synthesized in the same direction, streamlining the replication process.

Step-by-step solution

Understand DNA replication

During DNA replication, a replication fork forms where the parent DNA double helix unwinds and separates into two single strands. The leading strand is synthesized continuously in the 5' to 3' direction, following the replication fork. However, the lagging strand is synthesized discontinuously in short segments called Okazaki fragments, in the 5' to 3' direction but away from the replication fork.

Evaluate Option A

Option A suggests that the DNA polymerase has the ability to begin DNA synthesis without a primer. However, the primer is essential for initiating synthesis as it provides a starting point for the synthesis of new DNA strands. Although this feature could be beneficial in some circumstances, it wouldn't help both strands to follow the replication fork.

Evaluate Option B

Option B suggests the ability to proofread the DNA sequence in the 5' to 3' direction. Although proofreading is important for maintaining the accurate replication of the DNA sequence, it doesn't solve the issue of allowing both strands to follow the replication fork.

Evaluate Option C

Option C suggests the ability to synthesize DNA in the 3' to 5' direction. This could potentially solve the issue as it would allow both leading and lagging strands to be synthesized in the same direction, enabling them to both follow the replication fork. This feature could simplify the replication process and solve the problem.

Evaluate Option D

Option D suggests the ability to synthesize DNA without using a template strand. However, the template strand is required for complementary base pairing, which is essential for the accurate replication of the DNA sequence. Synthesizing DNA without a template wouldn't address the issue of both strands following the replication fork.

Choose the correct answer

Upon evaluating the given options, it's clear that option C - the ability to synthesize DNA in the 3' to 5' direction - is the most appropriate feature to be engineered into DNA polymerase in order to allow both strands to follow the replication fork.

Key concepts

DNA Polymerase

DNA polymerase is the chief enzyme responsible for DNA replication, playing a crucial role in cellular division and the transmission of genetic information from one generation to the next. It adds nucleotides, the building blocks of DNA, to a growing strand of DNA by adhering to the principle of complementary base pairing. The DNA polymerase can only add nucleotides in the 5' → 3' direction, which means it adds new bases to the 3' end of the existing strand.

One significant aspect of DNA polymerase is its need for a primer to initiate the replication process. A primer is a short RNA sequence that provides a starting point for the DNA polymerase. Without this primer, DNA polymerase cannot start replicating a strand of DNA from scratch. This fact is crucial for understanding why DNA polymerase alone cannot replicate both strands in the direction of the replication fork without a primer (Option A).

Furthermore, DNA polymerase possesses a proofreading ability to correct errors in the newly synthesized DNA strand. This ensures the high fidelity of DNA replication, though this function is not directly related to the directionality of replication and does not address the issue of lagging strand synthesis (Option B).

Okazaki Fragments

Okazaki fragments are short DNA sequences that are synthesized on the lagging strand during DNA replication. Due to the unidirectional nature of DNA polymerase, which can only add nucleotides in a 5' → 3' orientation, the lagging strand, which unwinds in the 3' → 5' direction at the replication fork, must be synthesized in a series of small segments moving away from the fork.

These fragments are produced as the DNA polymerase periodically reinitiates synthesis after each RNA primer is laid down by primase. Once an Okazaki fragment is completed, DNA polymerase is released, a new primer is synthesized further down the lagging strand, and the process starts again. Multiple Okazaki fragments are eventually linked together by the enzyme DNA ligase to form a continuous strand. The development of these fragments represents a critical workaround for the inherent directionality constraint of the DNA polymerase enzyme and is a pivotal component in the semi-discontinuous replication process.

Replication Fork

The replication fork is a Y-shaped structure that forms during DNA replication when the double helix unwinds. At this site, the two parent DNA strands separate, initiating the formation of new complementary DNA strands.

The replication fork has two sides: the leading strand and the lagging strand. The leading strand is synthesized smoothly and continuously, moving with the replication fork, as this direction is compatible with the DNA polymerase activity (5' → 3' synthesis). However, to replicate the opposite strand, known as the lagging strand, the process is more complex due to the 3' → 5' orientation of this template. This necessitates synthesizing DNA discontinuously in the form of Okazaki fragments, as described earlier.

If it were possible for DNA polymerase to synthesize in the 3' → 5' direction (Option C), both the leading and lagging strands could theoretically follow the replication fork. This would eliminate the need for the production of Okazaki fragments, significantly simplifying the replication process and potentially increasing efficiency.