DNA replication

Definitions & Key takeaways

DNA replication is the process by which a DNA molecule is copied into two identical DNA molecules. This process is essential to ensure the accurate transmission of genetic information from one generation to the next.

DNA replication occurs in three main steps: initiation, elongation, and termination. Initiation involves the unwinding of the DNA molecule, and it happens thanks to DNA helicase and topoisomerase enzymes. Next, elongation consists of making RNA primers by RNA primase and synthesizing the DNA leading strand by DNA polymerase. In termination, converging replication forks meet, and the whole process is complete.

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At a quick glance, the life of a cell - it’s cell cycle - is pretty routine. It’s either actively dividing, or preparing to divide into two daughter cells.
The cell cycle itself has an interphase, made up of subphases G1, S and G2, during which the cell is preparing for division, and mitosis, during which the cell actively divides.
During the S phase, the cell performs DNA replication - which is when its 46 chromosomes are duplicated so that each daughter cell can get its own copy of the genetic material.
A single chromosome is made up a single DNA molecule that has two strands, which wrap one around one another to form a double helix.
Each single strand of DNA is composed of a sequence of four types of nucleotides - which are the individual letters or building blocks of DNA.
Nucleotides of DNA are made up of a sugar - deoxyribose, a phosphate, and one of the four nucleobases - adenine, cytosine, guanine, and thymine - or, commonly, A, C, G, T for short.
The nucleotides on one strand form hydrogen bonds to complementary nucleotides on the other strand; specifically, A bonds with T via two hydrogen bonds, and C bonds with G, via three hydrogen bonds.
Additionally, the two DNA strands also have a “direction” - meaning, one of them runs from the 3’ end to the 5’ end, while the other one runs from the 5’ end to the 3’ end.
Kinda like two snakes coiled up together, but facing in different directions. DNA replication can be described as semiconservative.
That means that each strand of the double helix acts as a “template”, based on which a new, complementary strand will form.
Eventually the original chromosome will split into two exact copies, each made of one of the original strands, and one of the newly made ones.
Overall, DNA replication has 3 steps: initiation, elongation, and termination. Initiation kicks off when a group of proteins get together to form the pre-replication complex.
This pre-replication complex looks for specific nucleotide sequences along the DNA strand - called origins of replication.
And yes, we’re talking plural! That’s because our DNA strand is so long that DNA replication actually starts in several origins along the chromosomes simultaneously.
These special nucleotide sequences have a ton of A and T bases. Because A and T are joined by only two hydrogen bonds, the enzyme DNA helicase has a relatively easy time separating the two strands.
This creates a replication fork, with the two prongs of the fork being the two strands that are separated from one another.
Single strands of DNA can get a bit unstable, so to help keep them from getting back together again, helper molecules called single stranded DNA binding proteins come in and bind to each of the lonely strands.
Also, as DNA helicase breaks down bonds, the segments of DNA ahead of it start to overwind - meaning, the double helix becomes more tightly wound.
You can try this with a close friend who has braided hair - if you pull the braid apart in the middle then the ends get tighter.
Again - make sure it’s a friend and not a stranger. Overwinding of the DNA can slow down replication, so the enzyme DNA topoisomerase works ahead of DNA helicase to loosen up the tight DNA coils.
It achieves this by gently snapping one strand, loosening the overwinding tension, and then patching it back up, tension free.
The second step is elongation, and for that we need a new enzyme - RNA primase. Yes, you heard that correct, RNA this time.
It’s kinda like DNA, it uses ribose instead of deoxyribose in its nucleotides, and instead of thymine, it uses uracil. So, what RNA primase does is hover around and randomly synthesize small lengths of RNA which are only a few nucleotides long, called RNA primers.
Just by chance, at least one of those RNA primers will be complementary to the opened DNA strand - and it will bind. The enzyme DNA polymerase can then latch onto this short double stranded segment, and from there, the DNA polymerase can add more complementary nucleotides to the template strand.
Now, the DNA polymerase moves in a 3'-5' direction along the template strand, since only the 3’ end offers the -OH group required for synthesis.
The complementary strand in formed in the opposite direction: 5'-3'. As a result, replicating this DNA template strand is smooth sailing, and this new strand of DNA that forms is called the leading strand.
Things are a bit more complicated for the other DNA template strand, that runs from 5’ to 3’. That’s because the RNA primer that’s antiparallel is facing the other way.
For this new strand of DNA to grow towards the replication fork, DNA polymerase would have to add nucleotides to the 5’ end of the primer - but that’s not possible.
To solve this issue, RNA primase lays down a number of primers that bind to different spots along the length of the DNA template strand.
This offers a lot of free 3’ ends! DNA polymerase can then add nucleotides to the 3’ ends of each of these primers.
We call these growing fragments of DNA Okazaki fragments. And they each grow away from the replication fork, until they meet up.
Unfortunately, DNA polymerase can’t join two Okazaki fragments, so they’re joined together by another enzyme - DNA ligase, resulting in a finished strand of DNA called the lagging strand.
Now, the final step of DNA replication is termination. At the end of the chromosome is a region of DNA where there are repeating sequences of TTAGGG nucleotides.
This part of the chromosome is called the telomere. The DNA sequence in the telomere signals the DNA polymerase to hop off of the strand right before replicating the DNA right up to the very end.
Fortunately, the repeating TTAGGG sequences don’t code for anything, so no genes miss out on getting replicated. The telomeres are like those plastic bits on shoelaces - that only exist to protect the shoelace itself.
And the result is that each time the DNA strand is replicated, the new strand is just slightly shorter than the template strand because a bit of the telomere itself is lost.
That, however, means that we have a strictly limited amount of possible divisions available to our cells, before those divisions actually start shortening our genes - which, as you imagine, is bad.
This limit is known as the Hayflick limit. Alright, as a quick recap.
DNA replication occurs in three steps: initiation, elongation, and termination. Initiation starts with DNA helicase and topoisomerase helping to unwind the DNA.
During elongation, RNA primase creates RNA primers, and DNA polymerase creates a leading strand - through a single primer, or a lagging strand, through creation of Okazaki fragments that eventually merge together.
Finally, during termination, the two double strands, each made out of one new and one old strand, separate, slightly shortened at the telomere region.