CHAPTER 21: Unit 6. DNA Replication

In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the basis for biological inheritance.

DNA Replication.

DNA replication is the process by which DNA makes a copy of itself during cell division. The first step in DNA replication is to ‘unzip’ the double helix structure of the DNA’s Molecule. The purpose of DNA replication is to produce two identical copies of a DNA molecule. This is essential for cell division during growth or repair of damaged tissues. DNA replication ensures that each new cell receives its own copy of the DNA.

Reference:
https://www.youtube.com/watch?v=TNKWgcFPHqw

Stages of DNA replication

There are three main steps to DNA replication: initiation, elongation, and termination. In order to fit within a cell’s nucleus, DNA is packed into tightly coiled structures called chromatin, which loosens prior to replication, allowing the cell replication machinery to access the DNA strands1.    InitiationDuring initiation, proteins bind to the origin of replication while helicase unwinds the DNA helix and two replication forks are formed at the origin of replication. During elongation, a primer sequence is added with complementary RNA nucleotides, which are then replaced by DNA nucleotides.DNA synthesis is initiated at particular points within the DNA strand known as ‘origins’, which are specific coding regions. These origins are targeted by initiator proteins, which go on to recruit more proteins that help aid the replication process, forming a replication complex around the DNA origin. There are multiple origin sites, and when replication of DNA begins, these sites are referred to as Replication Forks.Replication begins at a location on the double helix known as “oriC” (Replication of the bacterial chromosome initiates at a single origin of replication that is called oriC. This occurs via the concerted action of numerous proteins, including DnaA, which acts as an initiator) to which certain initiator proteins bind and trigger unwinding. Enzymes known as helicases unwind the double helix by breaking the hydrogen bonds between complementary base pairs, while other proteins keep the single strands from rejoining. The “topoisomerase” proteins surround the unzipping strands and relax the twisting that might damage the unwinding DNA. The cell prepares for the next step, elongation, by creating short sequences of RNA called primers that provide a starting point of elongation.Within the replication complex is the enzyme DNA Helicase, which unwinds the double helix and exposes each of the two strands, so that they can be used as a template for replication. It does this by hydrolysing the ATP used to form the bonds between the nucleobases, therefore breaking the bond between the two strands.DNA Primase is another enzyme that is important in DNA replication. It synthesises a small RNA primer, which acts as a ‘kick-starter’ for DNA Polymerase. DNA Polymerase is the enzyme that is ultimately responsible for the creation and expansion of the new strands of DNA.

Figure above is DNA Replication

Reference: https://courses.lumenlearning.com/boundless-biology/chapter/dna-replication/

2. ElongationOnce the DNA Polymerase has attached to the original, unzipped two strands of DNA (i.e. the template strands), it is able to start synthesising the new DNA to match the templates. This enzyme is only able to extend the primer by adding free nucleotides to the 3’-end of the strand, causing difficulty as one of the template strands has a 5’-end from which it needs to extend from.With the primer as the starting point for the leading strand, a new DNA strand grows one base at a time. The existing strand is a template for the new strand. For example, if the next base on the existing strand is an A, the new strand receives a T. The enzyme DNA polymerase controls elongation, which can occur only in the leading direction. The lagging strand unwinds in small sections that DNA polymerase replicates in the leading direction. The resulting small “Okazaki fragments” can contain 1,000 to 2,000 bases in bacteria, but eukaryotes — organisms having cells with nuclei — have fragments of only 100 to 200 bases. The fragments terminate in an RNA primer that is subsequently removed so that enzymes can stitch the fragments into an elongating strand.

Figure above: The double helix is un’zipped’ and unwound, then each separated strand (turquoise) acts as a template for replicating a new partner strand (green). Nucleotides (bases) are matched to synthesize the new partner strands into two new double helices.

3. TerminationThe process of expanding the new DNA strands continues until there is either no more DNA template left to replicate (i.e. at the end of the chromosome), or two replication forks meet and subsequently terminate. The meeting of two replication forks is not regulated and happens randomly along the course of the chromosome.Once DNA synthesis has finished, it is important that the newly synthesised strands are bound and stabilized.  With regards to the lagging strand, two enzymes are needed to achieve this; RNAase H removes the RNA primer that is at the beginning of each Okazaki fragment, and DNA Ligase joins two fragments together creating one complete strand.After elongation is complete, two new double helices have replaced the original helix. During termination, the last primer sequence must be removed from the end of the lagging strand. This last portion of the lagging strand is the telomere section, containing a repeating non-coding sequence of bases. Enzymes snip off a telomere at the end of each replication, leading to shorter strands after each cycle. Finally, enzymes called nucleases “proofread” the new double helix structures and remove mispaired bases. DNA polymerase then fills in the gaps created by the excised bases.Now with two new strands being finally finished, the DNA has been successfully replicated, and will just need other intrinsic cell systems to ‘proof-read’ the new DNA to check for any errors in replication, and for the new single strands to be stabilized.

Figure Above: Generic illustration of replication initiation (A-B), elongation (C-D), and five events that are unique to replication termination (D-G). The replicative DNA helicase is depicted without reference to a specific translocation mechanism; RNA primers are in red. The order of the termination events is hypothetical.

Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6386472/

Reference:
https://www.youtube.com/watch?v=TNKWgcFPHqw