#dna replication

So, for my biology class I am supposed to write a short "day in the life" story about DNA.

The first half problem is, I've been playing portal 2 and watching games like Poppy Playtime and the Stanley Parable. For some strange reason, I find Portal (specifically Portal 2 multiplayer) extremely inspiring in the way that no matter how many times you fail, you get back up (put back together by the reassembly machine) and continue your mission no matter how demeaning, rude, or sarcastic GLaDOS is to you (and you even have fun doing it despite the bleak circumstances). And I find The Stanely Parable incredibly thought provoking and an amazing story about the monotony that life can be if you always live up to the expectations of society by living a "normal" life.

These pieces of info are important for later.

As for the second half of the problem, do you know what happens to DNA during the cell cycle???

It's in a double helix right? Well that helix is untwisted and zipped apart/torn in two by an enzyme called Helicase. DNA gets ripped. in. half. and I am supposed to turn this into a short "day in the life" story for a school assignment without making my teacher and classmates worry about my mental health?

Anyway, DNA is then held apart from itself by SSB proteins. (It is prevented from reuniting with its other half, the love of its life. They are never to be together again)

Then it gets bits and pieces of RNA and other stuff added to it that will be turned into a new DNA strand. (It is turned into a host for the fragments that will become a clone replacement of its past lover)

This happens to each DNA strand (our main character DNA strand here is forced to watch their former partner go through the same horrific process)

And then each identical DNA helix is taken and put into separate cells when the cell replicates. (Not only does our DNA strand get ripped from their lover and given a clone replacement while being forced to watch their previous other half go through it too, they are then sent to completely different buildings where this will likely happen to them again unless they die before it can take place)

And it has this happen while coding for all sorts of functions and genes (managing an office?)

And to top it all off, this is its fate. Its destiny. This life is inevitable for DNA. This is what it was made to do, and it has no say in the matter nor any means of doing anything else with its life because it quite literally doesn't have any other function.

To tie this into Portal 2 multiplayer and the Stanley Parable:

The constant getting destroyed and rebuilt that DNA goes through is reminiscent of the way Atlas and Peabody get destroyed and reassembled during testing

And the way DNA goes through the exact same thing every single day of its life reminds me of the way Stanley's entire job was to press buttons when told to and we have no idea how long he did that before the story in the game took place. At least I don't know how long it was. The existentialism from the Stanley Parable is similar to the existentialism from DNA replication.

Or maybe none of this is connected and I'm actually insane. One can never know.

I still have to write a semi normal story about a day in the life of DNA and I have no idea how I'm going to do it...

You may not have even an itch in your dad's pants a few decades ago, but you were an egg in your mom's ovary.

What I'm trying to say is that females are born with all the (precursors to) eggs they will ever have (about 400 of them), while males continue to produce gametes throughout their life. I'm talking about MEIOSIS!

Meiosis makes four cells (each with half the original DNA) and is involved with sexual reproduction. Mitosis makes two identical cells and is necessary for life.

Consists of creating an exact replicate of itself; each strand serves as a template for synthesizing a complementary strand; this replication process is semi-conservative. The new DNA has formed thanks to enzymes called DNA polymerases; this needs a primer synthesizing DNA from the 5' to 3' end. This process also includes other enzymes such as DNA ligase, DNA primase, DNA helicase, and topoisomerase, "this process takes us from one starting molecule to two "daughter" molecules, with each newly formed double helix containing one new and one old strand" (Clark, Douglas, Choi, 2018).

Let's talk about the differences between DNA replication in eukaryotes and prokaryotes. We could start by saying that prokaryotic organisms have circular chromosomes with a less extensive coiling structure than eukaryotic chromosomes. The replication process begins with a specific sequence of nucleotides called the origin of replication which has approximately 245 base pairs rich in AT sequences; the helicase is responsible for breaking the double helix in two and unwind the hydrogen bonds between the hydrogen base pairs, the ATP hydrolyzing process is necessary because requires energy.

This process requires three essential types of enzymes, DNA polymerase I, which acts later in the process. DNA polymerase II is used to repair, and DNA polymerase III acts by providing new nucleotides one by one doing it in the 3' to 5' direction. "Topoisomerase binds at the region ahead of the replication fork to prevent supercoiling or over-winding" (Clark, Douglas, Choi, 2018).

On the other hand, we have replication in eukaryotes which although it starts in a similar way to prokaryotes, the process in eukaryotes has a pre-replication phase which contains proteins that initiate the process, "the leading strand is continuously synthesized by the enzyme pol δ, the lagging strand is synthesized by pol ε" (Clark, Douglas, Choi, 2018). Here the genome is much larger than in prokaryotes, so the replication process is slower, making a ratio of 50 to 100 nucleotides per second; DNA polymerases have the names pol α, pol β, pol γ, pol δ, and pol ε.

Their DNA is packaged when chromatin fibers begin to condense around proteins called histones, which condense to form linear chromosomes. The end of which are called telomeres which are non-coding DNA sequences for a particular gene and protect the information from being deleted as the cell divides. A highly regulated DNA replication process is found in eukaryotes and almost always involves extracellular signals to coordinate specialized cell divisions in different tissues of multicellular organisms. Cyclins are synthesized during the G1 process of the cell cycle, and external signals trigger their synthesis. To facilitate the synthesis of the S-phase proteins, DNA polymerases, and thymidylate synthesize, cyclins form complexes with cyclin-dependent kinases (CDK). The cells are primed for DNA replication during the S process by these complexes(Tabancay & Forsburg, 2006).

"In the final stage of DNA replication, the enzyme ligase joins the sugar-phosphate backbones at each nick site. After ligase has connected all nicks, the new strand is one long continuous DNA strand, and the daughter DNA molecule is complete" (DNA Replication in Eukaryotes, 2020). The environment in which they live; prokaryotes are not formed by cells, so they do not need complex machinery to function, however eukaryotes that are usually multicellular need a more complicated process because their requirements are higher, this is why more enzymes and fewer nucleotides are involved in eukaryotes and fewer enzymes and more nucleotides per second in each case.

References

Clark, M. A., Douglas, M., & Choi, J. (2018). Biology 2e. OpenStax.

DNA Replication in Eukaryotes. (2020, August 15). Retrieved March 2, 2021, from

https://chem.libretexts.org/@go/page/13293

OpenStax, Concepts of Biology. OpenStax CNX. May 18, 2016

http://cnx.org/contents/[email protected]:2ousESf0@5/DNA-Replication

Rye, C., Wise, R., Jurukovski, V., DeSaix, J., Choi, J., &; Av, Y. (2016). Biology. Houston, TX: Openstax.

Tabancay, A. P., & Forsburg, S. L. (2006). Eukaryotic dna replication in a chromatin context. Current Topics

in Developmental Biology, 129-184. doi:10.1016/s0070-2153(06)76005-7

Simple Explanation of DNA Replication

Introduction to DNA/RNA DNA or Deoxyribose Nucleic Acid is the motherboard of every living thing. It is a double helix structure comprised of a Phosphate and sugar (Deoxyribose) backbone that is connected by 5′-3′ phosphodiester bonds. Attached to the backbone is the main genetic material that codes for the synthesis of proteins and other structures. These important molecules are called…