Question

Define and indicate the significance of (a) Okazaki fragments, (b) DNA ligase, and (c) primer RNA during DNA replication.

Short answer

Answer: The three components related to DNA replication are (a) Okazaki fragments, (b) DNA ligase, and (c) primer RNA. Okazaki fragments are short sequences of nucleotides produced on the lagging strand, allowing complete replication of both DNA strands. DNA ligase is an enzyme that connects the Okazaki fragments, ensuring accurate copies of the original DNA molecule. Primer RNA facilitates the initiation of DNA replication on both the leading and lagging strands by providing a starting point for DNA synthesis.

Step-by-step solution

(a) Okazaki fragments

Okazaki fragments are short sequences of nucleotides (around 100-200 nucleotides in eukaryotes, and 1,000-2,000 nucleotides in prokaryotes) that are produced on the lagging strand of DNA during replication. This is because DNA replication happens in the 5' to 3' direction, and the lagging strand is synthesized discontinuously in small stretches, which are later joined together. The significance of Okazaki fragments is that they allow the progression of DNA replication on the lagging strand in the 3' to 5' direction, ensuring complete replication of both DNA strands.

(b) DNA ligase

DNA ligase is an enzyme that plays a crucial role in joining the Okazaki fragments on the lagging strand during DNA replication. It forms phosphodiester bonds between the individual fragments, sealing the gaps and creating a continuous DNA strand. The significance of DNA ligase is that it ensures the completion of replication by connecting the discontinuous fragments on the lagging strand, making sure that the newly synthesized DNA molecules are intact and accurate copies of the original DNA molecule.

(c) Primer RNA

Primer RNA, or RNA primer, is a short sequence of RNA nucleotides that is synthesized by an enzyme called primase. The RNA primer acts as a starting point for DNA synthesis by providing a free 3'-OH group to which the DNA polymerase can add new DNA nucleotides. Unlike DNA polymerase, primase can synthesize the RNA primer without needing a pre-existing strand with a free 3'-OH group. The significance of primer RNA is that it allows the initiation of DNA replication on both the leading and lagging strands and ensures proper synthesis of the new DNA molecules. Once the replication is complete, the RNA primers are removed and replaced with the corresponding DNA nucleotides, and DNA ligase seals the remaining gaps.

Key concepts

Okazaki Fragments

During DNA replication, the two DNA strands are separated, and each strand serves as a template for the formation of a new complementary strand. However, replication must occur in a specific direction, from the 5' to the 3' end. This presents a challenge for the replication of one of the two strands, known as the lagging strand.
Okazaki fragments are short sequences of DNA nucleotides crucial for the synthesis of the lagging strand. On the lagging strand, replication is not straightforward because the replication machinery moves away from the replication fork. Therefore, it's synthesized discontinuously in short sections – these are the Okazaki fragments.
These fragments play a vital role as they allow the DNA polymerase to replicate DNA in sections moving back toward the replication fork, despite the continuous progression of the replication machinery in the opposite direction. Without Okazaki fragments, accurate and complete replication of the lagging strand wouldn't be possible.

• Short DNA segments formed on the lagging strand
• Enable DNA replication in a 3' to 5' direction on the lagging strand
• Later joined to form a continuous DNA strand

DNA Ligase

DNA ligase is like the glue in the DNA replication process, especially for the lagging strand. After the DNA is initially replicated, the Okazaki fragments on the lagging strand are left as separate pieces, not yet forming a full, continuous DNA strand.
DNA ligase comes into play to resolve this issue. This essential enzyme facilitates the formation of phosphodiester bonds between the Okazaki fragments, effectively stitching them together. By doing so, DNA ligase ensures that the newly synthesized DNA is a continuous and complete strand, just like its original template.
The job of DNA ligase is crucial because any gaps between Okazaki fragments could lead to errors in the DNA sequence, which might result in problems for the organism.

• Seals the gaps between Okazaki fragments
• Forms phosphodiester bonds
• Ensures the DNA strand is continuous

RNA Primer

The synthesis of a new DNA strand cannot start from scratch; it needs a small piece of RNA called the RNA primer to get started. This primer is synthesized by the enzyme primase.
An RNA primer is essential because DNA polymerases (the enzymes that synthesize DNA) cannot start forming a new strand on their own. They need a free 3'-OH end to attach the first nucleotide. The RNA primer provides exactly this, giving DNA polymerase a starting point.
Once the initial segment of an RNA primer is laid out, DNA polymerase can extend this primer with DNA nucleotides, effectively laying down new DNA in the proper direction. Eventually, the RNA is replaced with DNA, ensuring that the entire strand is DNA after the replication process finishes. This process ensures that both the leading and lagging strands are synthesized accurately.

• Short RNA sequence laid at the start of synthesis
• Provides 3'-OH group for DNA polymerase
• Replaced with DNA after replication is complete