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DNA Replication: The Process

This process is the foundation of who we are—without it, our cells could not reproduce, and we wouldn’t be able to live. I’ll run through the basic process, then let the proteins do the talking for me.

Essentially, in replication, the double helix is unwound in two separate strands by the enzyme helicases, which break the hydrogen bonds between the base pairs. The base pairs are explained, ready to serve as a template for the synthesis of new strands. The place where the helix is being unwound is called the replication fork. The replication fork has a bunch of enzymes swarming all over it, including DNA polymerase which synthesises new nucleotides to whack down like train tracks as the helix unwinds.

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However, DNA polymerase can only add new nucleotides in a 5’ to 3’ direction, so one strand is going to get left out. An enzyme can just zip over the top strand and synthesise a matching one since it’s facing the right direction, and it’ll keep going as the strand keeps unwinding because the enzyme is moving left. But the bottom strand has to be synthesised in a 3’ to 5’ direction too, which is in the opposite direction to the way the helix is unwinding, away from the replication fork. So we’ve got these bits constantly being exposed at the fork.

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Instead of synthesising continuously like the top strand, the bottom strand has to be synthesised discontinuously—little bits at a time, starting at the replication fork and moving until they reach the last fragment. These fragments are called Okazaki fragments, and in humans, they’re only made in stretches of 100-200 nucleotides. These fragments then have to be stitched together by an enzyme called ligase, creating one long continuous strand.

Because the bottom strand has to wait for the replication fork to open up a bit before it can start synthesising fragments, the process takes slightly longer—so it’s called the lagging strand, while the top strand is called the leading strand.

Another problem faced by the lagging strand is the creation of RNA. See, DNA polymerase, which synthesises new nucleotides and thus creates the new strands, actually lacks the ability to initiate the process. It can’t start strands out of nothing—it needs to have something to build off of. So, an enzyme called RNA primase is given the job of creating a short, initial stretch of nucleotides. Then DNA polymerase latches on and happily zips off.

In the leading strand, the RNA primase needs to do its job just once, and DNA polymerase chugs along continuously. But in the lagging strand, RNA primase constantly has to create new initial chains of nucleotides—one for each fragment. As you can probably imagine, this is a nightmare—because it means that between every Okazaki fragment, there are bits of RNA, disrupting your DNA strand.

So, before the Okazaki fragments can be stitched together by ligase, these RNA bits have to be removed.

Finally, once all this is done and the lagging strand has been patched up, we have two DNA molecules: each one with one parent strand, and one daughter strand, as per the semi-conservative model. Pretty neat, huh?

Next time: the super-long explanation of the mechanisms behind it all.

Body images sourced from Wikimedia Commons

Further resources: Crash Course: DNA Structure and Replication


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Transcription

DNA is the genetic information of the cell—the blueprints for how every protein in your body is built, dictating the sequences of amino acids. However, although our genes provide the blueprints, they don’t directly build the proteins. That job is delegated to the ribosomes, the cell’s protein-synthesising machinery.

But in eukaryotes, the DNA never leaves the nucleus, and ribosomes are in the cytoplasm. There needs to be some mechanism for getting DNA’s information to the ribosome—and mRNA (messenger RNA) does the job.

Messenger RNA (mRNA) is a strand of RNA that holds the faithful translation of the protein-building instructions of DNA. Remember that RNA is a nucleic acid just like DNA, but it differs in three man ways:

  1. Its main sugar is ribose, not deoxyribose.
  2. It only has one strand, not two.
  3. Its nucleotides are Adenine, Uracil, Cytosine and Guanine—so A pairs with U instead of T, and C pairs with G like in DNA.

mRNA is created by an enzyme called RNA polymerase, which uses a strand of DNA as a template. This process is called transcription, and there are three stages.

1. Initiation

  • RNA polymerase binds to the DNA strand at a very specific sequence of nucleotides, called the promoter. RNA polymerase can’t actually recognise the promoter sequence by itself, so it uses the help of something called the TATA box.

2. Elongation

  • RNA polymerase begins to move along the DNA strand, unwinding the helix by breaking the hydrogen bonds between the DNA’s nucleotides. The base pairs are exposed and are paired with RNA nucleotides: A with U, T with A, G with C, C with G.
  • Behind RNA polymerase, the freshly synthesised RNA strand peels away from the template, and the DNA double helix reforms (hydrogen bonds are usually pretty keen to snap back together).

3. Termination

  • The RNA polymerase has to be given a signal to stop transcription. In prokaryotes, there’s a terminator sequence in the DNA just like the promoter sequence, and the RNA polymerase recognises it and detaches.
  • In eukaryotes, however, there’s this extra step where pre-mRNA is created—almost like a draft of the real mRNA. RNA polymerase transcribes a signal sequence on the RNA, which cause associate proteins to cut the pre-mRNA free. The polymerase, however, keeps on transcribing for a few hundred nucleotides—bit of a waste, really, because the RNA it creates is usually just digested by an enzyme.

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So, what’s up with this pre-mRNA business in eukaryotes? Basically, before it’s sent out as a genetic message to the cytoplasm (where all the ribosomes are), enzymes modify the pre-mRNA. This is called RNA processing. The ends are given a “cap” and a “tail” to protect them and aid with attachment later, and bits from the transcript are cut out and the remaining bits are spliced together.

Imagine your friend has just given you a copy of their short story to edit. There are some parts you really like, but there are other parts that are utterly unnecessary to the plot. So before you give it back to them, you make some edits—you delete the side-adventure about the runaway cat, you remove the misogynistic old uncle, and then bridge the gap between the scenes. The story is a whole lot cleaner and more efficient now.

That’s basically what happens in RNA processing. There are sections of a DNA sequence called introns that are non-coding—they don’t actually code for any amino acid sequence, they’re just there, scattered amongst the rest. Whatever they say is not expressed in protein building. The other regions are called exons, which are coding and are expressed. In RNA processing, enzymes do some editing, splicing out those useless intron sequences and stitching the exons up seamlessly.

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So the mRNA that is sent out into the cytoplasm,all grown up and off to synthesise proteins, is an abridged version of the original DNA sequence: a continuous coding sequence.

Next, we’ll learn about how proteins are assembled: translation.

Body images sourced from Wikimedia Commons

Further resources: DNA Transcription video