Difference Between Replication Bubble and Replication Fork

 Key Difference – Replication Bubble vs Replication Fork

Replication bubble and replication forks are two structures formed during the DNA replication and the key difference between Replication Bubble and Replication Fork is that the replication bubble is an opening present within the DNA strand during the initiation of replication while replication forks are structures present in the replication bubble that denote the actual occurrence of replication.

In the context of molecular biology, DNA replication is a process where two identical copies of DNA are produced from a DNA molecule. This biological process is the basis of continuity of all life forms and biological inheritance. DNA replication occurs in all living organisms. Replication process consists of different techniques, enzymes, biological compounds, and replication structures that are being established to initiate replication and to process it. The replication bubble and replication forks are such structures that are formed during DNA replication. Both replication bubble and replication fork are present in prokaryotes and eukaryotes.

CONTENTS

1. Overview and Key Difference
2. What is Replication Bubble
3. What is Replication Fork
4. Similarities Between Replication Bubble and Replication Fork
5. Side by Side Comparison – Replication Bubble vs Replication Fork in Tabular Form
6. Summary

What is Replication Bubble?

DNA replication is a process where a DNA molecule replicates and makes a copy of itself. The replication bubble is considered as the opening that is present within the DNA strand during the initiation of replication. The formation of replication bubbles varies in prokaryotes and eukaryotes. Prokaryotes contain a single replication bubble while eukaryotes contain multiple replication bubbles.

The replication bubble has the ability to grow in two directions due to the presence of replication forks. In each replication bubble, there are two replication forks. This is the point where the parental DNA double helix splits. In the context of eukaryotic organisms, they contain a true nucleus. The eukaryotic DNA is linear. Due to this reason, the replication occurs at multiple locations that results in the presence of multiple replication bubbles.

The functioning of the replication bubble occurs with the enzyme DNA helicase that breaks the hydrogen bonds present between the nitrogenous bases of the two parental DNA strands. Single Strand Binding Proteins are attached to the separated parental DNA strands to prevent the reformation of hydrogen bonds.

Figure 01: Replication Bubbles of Eukaryotic DNA

The breaking of hydrogen bonds between the two strands results in relaxation of the double helix and also building up of tension further down the molecule due to unwinding. The enzyme topoisomerase involves in breaking the phosphodiester linkages of the double helix at further downstream of the replication bubble that relieves the tension at those regions through immediate reattachment.

What is Replication Fork?

In the context of the cell cycle, DNA replication occurs at the S phase. The process starts with DNA sequences that are predefined and are termed as replication origins. At these regions, replication bubbles are formed which triggers DNA replication. It was previously mentioned that each replication bubble contains two replication forks. When DNA replication is triggered, replication proteins organize into a structure that resembles a two-pronged fork. Due to the formation of such structure, this is termed as replication fork. These replication proteins coordinate the whole process of DNA replication.

DNA helicase unwinds the double-stranded parental DNA into two single strands by breaking the hydrogen bonds linking the nitrogenous bases of the two strands. This occurs in front of the replication fork and creates single-stranded DNA.

The major functions of the replication fork are DNA unwinding and DNA synthesis. DNA synthesis by the replication fork is achieved with the enzyme DNA polymerase. DNA polymerase links DNA bases in the correct sequence according to complementary base pairing theory.

Figure 02: Replication Fork Components

To prevent the stalling of the replication fork, there is a special protein complex known as replication fork protection complex. The major function of this complex is to re-stabilize if the replication fork is stalled due to any reason and it involves in the coordination of the synthesis of leading and lagging strands and also in replication checkpoint signalling.

What are the Similarities Between Replication Bubble and Replication Fork?

• Both replication bubble and replication fork can be seen during the DNA replication.
• Both structures are common to both prokaryotic and eukaryotic DNA replication.
• Both structures help and trigger the DNA replication.

What is the Difference Between Replication Bubble and Replication Fork?

Summary – Replication Bubble vs Replication Fork

DNA replication is a process where a parent DNA strand gives two identical copies of itself. The replication process consists of different components. Replication bubble is an opening of the DNA strand where initiation of replication takes place. In eukaryotes, multiple replication bubbles are present while in prokaryotes only a single replication bubble is present. Each replication bubble contains two replication forks. A replication fork is defined as a set of replication proteins warned in a two-pronged fork that confirms the initiation of the replication process. The replication fork protection complex is present to restabilize if the replication fork is stalled. Prokaryotes contain a single replication fork complex while in eukaryotes, there are multiple numbers of forks. This is the difference between replication bubble and replication fork.

Reference:

1.“Replication Fork Stalling and the Fork Protection Complex.” Nature News, Nature Publishing Group. Available here 
2.“Replication Bubble: Definition & Overview.” Study.com, Study.com. Available here 
3.“Molecular Mechanism of DNA Replication.” Khan Academy. Available here  

Image Courtesy:

1.’OSC Microbio 11 02 EukRep’By CNX OpenStax, (CC BY 4.0) via Commons Wikimedia 
2.’0323 DNA Replication’By OpenStax (CC BY 4.0) via Commons Wikimedia 

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