DNA Replication class 1: General process of DNA replication

“Replication is an enzyme governed process, in which new DNA molecule is formed by the process of semi-conservative DNA replication.” 

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Image credit: MIT technology review

DNA replication is a process in which new DNA is formed (copying DNA). Four new single strands of DNA (2 double helix), are generated in a semiconservative manner of DNA replication. The basic mechanism of replication is almost same in prokaryotic as well as eukaryotic DNA. 

Component of DNA replication

  • Leading and lagging strand
  • Enzymes
  • Primers

Starting DNA replication

DNA replication always starts from specific locations which are called as origins of replication. there are more than one origins of replication present on single DNA molecule. This region of DNA has specific sequences which are always recognized by polymerase for initiation of replication.

The origins of replication are mostly A/T rich sequences. When both strands open up, a Y shaped structure is generated which is called as a replication fork.

Imagine two opposite replication fork on one single circular DNA, it creates a bubble-like structure, termed as a replication bubble. The replication fork moves in opposite direction with the help of enzyme which will discuss in later part of this article.

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Image credit: www.onlinebiologynotes.com

Leading and lagging strands

Replication is initiated at leading strand because the leading strand has free 3’-OH end and is always recognized by DNA polymerase. Here DNA polymerase runs toward the replication fork. On another strand (lagging strand) it runs away from the replication fork.

On the lagging strand DNA polymerase adds nucleotide away from the replication fork. Specialized sequences or fragments, called as okazaki fragments, present on lagging strand helps it to promote synthesis in the exact direction. 

Enzymes

  • DNA polymerase

The polymerase is an enzyme which synthesizes the new DNA strand by adding the nucleotides to the growing DNA strand. It recognizes special sequences present at the origin of replication and bind to that sequences.

  • Helicase

Nucleotides on DNA strands bind with each other by hydrogen bonds. Helicase has specialized properties to unwind DNA stand by breaking the hydrogen bond between two strands. it creates a replication fork and two single strands. 

  • Topoisomerase

It is a group of special kind of enzyme which releases the tension created on rest of the DNA double helix. Imagine you unwind the rope by taking two threads of rope, what happened on rest of the rope? Well, it will winds with each other, right.

A similar mechanism is applied here when DNA helicase unwinds the double helix, tension is increased on rest of the DNA strand (supercoiling)  which is removed by topoisomerase by cutting the double-stranded and single-stranded DNA by two different topoisomerase and further ligates DNA and remove the tension of strands.

  • Primase

Primase synthesized a short RNA primer for starting of replication.

  • DNA ligase

Ligase joins two DNA molecules. the gaps between okazaki fragments and new DNA fragments are joined by ligase.

Primer

Primers are short single-stranded RNA molecules. ActuallyDNA polymerase needs some base to start the replication. It is not possible without RNA primers. RNA primer is synthesized by RNA polymerase and binds to leading strand, at the starting of 3’-OH end.

Double-stranded DNA is open up by helicase and primer is binds at the site of leading strand. DNA polymerase identifies the primer and starts adding nucleotide from 3’-OH to replication fork. Simultaneously, topoisomerase releases the tension by breaking DS DNA and ligase re-joins DNA strand.

Now, at the lagging strand, the opened end is a 5’-P end, hence replication is not possible from that direction. Here polymerase work away from the replication fork. However, still, it isn’t possible to synthesize DNA from the lagging strand.


Attend class: Immunogenetics


Special kinds of small fragments are present on the lagging strand which allows polymerase to work on lagging strand. These fragments are called as “Okazaki fragments”. These fragments are arranged in a tandem manner, hence multiple primers are needed to fill each Okazaki fragments. But a problem can leads to failure in lagging strand replication, floating of DNA polymerase.

A ring-like sliding clamp which is a type of protein, prevent polymerase from floating off. SSP proteins (single-stranded binding protein) are smaller proteins which prevent the binding of DNA strands during helicase activity.

In the end, RNA primers which are actually not a part of DNA strand, are removed with the help of another DNA Polymerase called as DNA polymerase I and the nicks are sealed with ligase.

From the double-stranded DNA molecules, 4 single-stranded exact molecules of DNA is generated.

Though the mechanism of replication is almost similar in prokaryotes and eukaryotes, some molecular differences make it unique which will be discussed in other section, separately. 


Attend class: Extrachromosomal inheritance


Article written by- Tushar Chauhan

Article reviewed by- Binal Tailor