DNA Replication: Creating your Genome

DNA is the genetic material, the code for life. Think of it as the instruction manual of our cells. It essentially holds all the information our cells need to function properly so it’s existence is pretty important. That is why such intricate procedures must take place in replicating said DNA. Any harm or damage or loss of this DNA could very well have detrimental effects to our cells, and by extension our health. For this reason, DNA replication is a very vital process and so it’s important we understand the steps properly and in doing so we learn a little bit more about ourselves as well!

 To start off with, let’s recap the structure of DNA. As you may already know from prior knowledge, DNA stands for deoxyribonucleic acid; hence the abbreviation DNA. The structure of DNA is a double helix, think of it like a twisted ladder rotated on its axis. If we look at just one of these strands and focus our attention to the DNA monomer itself, you will notice DNA is made up of 3 components: a sugar, a phosphate group and a nitrogen-containing base. DNA -unlike its counterpart  RNA- consists of the pentose sugar Deoxyribose. This is where the ‘Deoxyribose’ part of the name comes from. It’s a nucleic acid which basically are naturally occurring chemical compounds that serve as the primary information-carrying molecules in cells and make up the genetic material. That’s it’s name sorted. Thinking back to our analogy of the twisted ladder rotated on its axis, the rungs of the ladder are the interaction of the 2 bases of both the DNA strands. The scientific term for this is complementary base pairing and the bonding between these base pairs is hydrogen bonding. The purine bases pair to a pyrimidine base which is complementary to it; so adenine (A) binds with thymine (T) and cytosine (C) with guanine (G). The rails on the side come from the phosphodiester bonds between the phosphate groups and the pentose sugar deoxyribose. That’s the basic structure of DNA .

DNA replication takes place in the S phase of the cell cycle, it’s simply the phase were all the DNA in a cell is replicated to prepare for the events of mitosis.The process is catalysed by a variety of enzymes, the main being DNA polymerase . There are many DNA polymerases and it is actually DNA polymerase III which goes forward with the whole replication process. The other polymerases are used mainly for the enzyme’s proofreading capabilities, namely for the purpose of repairing incorrect base attachments. They do this through the exonuclease activity of the enzyme. This basically allows the enzyme to remove successive nucleotides from the end of a polynucleotide molecule. As already mentioned, there are many DNA polymerases and they all have slightly different roles to play in the whole process and we will now look at some of their actions and activities. Starting with DNA polymerase I, this enzyme has exonuclease capabilities as a means of proofreading for the DNA strand. What this essentially means is that it removes the incorrectly matched bases and replaces them with the correct bases, enabling it to simply try again. This can happen in both the 3’ to 5’ direction and 5’ to 3’ direction and depending on however which way it works, the process is slightly different. In the 5’ to 3’ direction  it acts in the same direction of the polymerising activity and can remove mononucleotides or up to 10 nucleotides at a time. This type of exonuclease activity involves the removal of RNA primers at the end of replication.  Whereas in the 3’ to 5’ direction, it can only remove one mononucleotide at a time. This action of exonuclease activity involves the polymerase reversing direction (moving from synthesising 5’ to 3’ to 3’ to 5’) and replacing it with a correct base.   Now there are 3 steps that take place in DNA replication: Initiation, elongation and termination. And we will go through these steps in detail in the following paragraphs. 

Initiation:

In the initiation phase, the DNA exists in its usual state, the famous DNA double helix. In this form the DNA isn’t able to be replicated so the double strand must be broken. This is the role that DNA helicase plays. It’s an enzyme (notice the ‘-ase’ part of its name) that breaks the hydrogen bonds within the strand to unwind the helix structure. Then something called primase (a type of RNA polymerase) catalyses a short segment of RNA -known as a primer- which is complementary to the template strand of DNA. The primer is essential as DNA polymerase cannot begin the DNA replication process and cannot occur without the addition of the initial primer. This primer is removed during the elongation however, due to the exonuclease action of DNA polymerase.

Elongation:

In the elongation phase, nucleotides are added to the ever increasing newly formed DNA. As we have already discussed, the DNA double helix is antiparallel. Thus when unwinding of the helix occurs, one strand goes 5’ to 3’ and the other 3’ to 5’. The 3’ to 5’ strand contains DNA polymerase that runs continuously making a new strand which is in the direction 5’ to 3’. However if we look at the 5’ to 3’ strand, multiple DNA polymerases are needed to synthesise the new strand of DNA. This is because DNA polymerase only works in the 3’ to 5’ direction (thus synthesising the new strand in the 5’ to 3’ direction) and DNA helicase acts in the opposite direction causing fragments in the sequence. These fragments are known as Okazaki fragments. The strand cannot be left in this state however. All the Okazaki fragments must be glued together and this is catalysed by the actions of DNA ligase. Therefore the strand which consists of many okazaki fragments glued together is called the lagging strand and the strand synthesised continuously is called the leading strand.

Termination:

The final step in DNA replication. As during the whole process more than one DNA helicase is used to unwind the DNA double helix and several points in a cell, there are many replication forks-sites of DNA replication- formed as a result. The aforementioned forks and the DNA polymerase will of course eventually meet. The point at which the two forks meet are all joined by DNA ligase (with the help of primase) and present are two new continuous DNA molecules. These strands formed are described as being ‘semi-conservative’ as half the DNA present in these strands are from the original DNA strand whereas the other half of the DNA strand is newly synthesised. Hence the term ‘semi-conservative replication’.

There’s a small detail not to be overlooked when thinking about DNA replication and that is the existence of telomeres. They have a vital and often overlooked role in DNA replication. Their main purpose is to prevent degradation of the DNA sequence and for protection purposes. Briefly, telomeres consist of repeats of the 6 base pairs TTAGGG at the ends of the chromosome arms. This repeated sequence can be repeated many thousands of times over in the DNA sequence. These clusters help protect the integrity of the DNA sequence and allows replication of the extreme ends of DNA. The one downside however, as more and more replication takes place, the telomeres are slowly used up. Therefore, the older a cell gets, the more susceptible the DNA strand is to degradation and mutation. However there are ways to extend these telomere strands. This can be done by using telomerase. It extends the telomeres on the far ends of the DNA strand. Enzymes bind to a special RNA that contains a sequence complementary to the telomeric repeat, it extends the overhanging strand of telomeres DNA using this complementary RNA template. Once the overhang is long enough, a matching strand- made by normal DNA replication machinery- and thus producing the double strand of the telomere section. 

DNA replication is a vital process needed for cellular growth, and without it we wouldn’t be able to pass on our hereditary material which constitutes all instructions the cell needs to function. It allows accurate replication and ensures every new cell, whether it is a growing embryo or replacing a damaged cell, ensures that they all have the same genetic material. 

References

https://teachmephysiology.com/biochemistry/cell-growth-death/dna-replication/

https://courses.lumenlearning.com/microbiology/chapter/dna-replication/

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