mRNA Translation (Advanced)

Like I said man, whatever helps you sleep at night. Even if it's a straw man like an unreferenced assertion about unnamed people in the 18th century. p.s. which part is the clockwork? the ticker tape with the encoded data, or the part that reads it? whole thing?: ▶ this video edit: Probably none of those since rhibosomes were discovered in the 1950s it seems.

Only tangentially related, but because they are so amazing here are a few videos that illustrate the process of transcription (creating mRNA from DNA) and translation (creating a protein from mRNA). link ▶ this video The common complaint with these videos is that everything is more complex. One thing that isn't evident is that these specific videos (built mostly by Drew Barry) actually model a lot of other molecules to create a more realistic physical environment with brownian motion and whatnot. Then the irrelevant molecules are simply made transparent in the rendering. Obviously it's still much much more complex (eg the constant stream of ATP used to drive many of these operations is not illustrated). There are these and many more great illustrations/explanations at WEHImovies on youtube link

Some amazing animations that show some of the primary operations related to DNA: Transcription (copying sections of DNA into RNA) - link Translation (turning messenger RNA into proteins) - ▶ this video RNA Splicing (removing non-coding sections of mRNA) - link DNA Wrapping & Replication(two part video) - link One thing I would encourage folks to do as you listen to the narration of these is to consider any time words are used that imply agency and remember that these are basically blobs of magnets in a jostling goo. You'll find the names Drew Berry and WEHI referenced in most of these. There are many more stunning and IMHO profoundly informative examples of biological machinery from them on youtube.

These might interest you then: 3d visualizations of cellular processes in real time. I was shown them in my intro to biology class, which filled me with the same interest. Transcriptase: link DNA polymerase: link The Ribosome: ▶ this video

This is a great animation of the life cycle of an HIV virus. It’s not exactly what happens with the pandemic virus but it gives you a good idea of the complexity of the process of viral reproduction (vaccine or immune response isn’t covered here): link Animation of transcription from mRNA: ▶ this video

Wow Looks like it is analogous to having a header on a TCP packet. [0] Here is an animation of mRNA encoding translated to proteins inside a ribosome. [1] "The ribosome is composed of one large and one small sub unit that assemble around the messenger RNA, which then passes through the ribosome like a computer tape. The amino acid building blocks, that's the small glowing red molecules, are carried into the ribosome attached to specific transfer RNAs; that's the larger green molecules also referred to as tRNA. The small sub unit of the ribosome positions the mRNA so that it can be read in groups of three letters known as a codon." Very analogous indeed. [0] link [1] ▶ this video

It’s broader than that actually, this is a generalized protein factory. This is how mRNA is created by the cells in your body to create the proteins needed to keep you alive (aka transcription): link This is how mRNA is then used to create proteins, either from strands manufactured by your own cells, those coming from viruses that have infected your body, or from mRNA vaccines (aka translation): ▶ this video Not directly related, but here is an amazing video showing how HIV infection works, including parts you will now recognize from the above: link

Apologies if I spam this stuff too much but I'm so intrigued by the dynamic complexity of this whole thing. The following three videos describe the process of DNA Transcription (copying a single gene's worth of RNA from the DNA strand), Translation (subject of TFA, creation of the protein from that RNA), and Replication (the process of making a complete copy of DNA for purposes of cell division. Keep in mind that the functional components you see in here are themselves (generally) proteins that are created (and have evolved) by a similar process. Transcription - link Translation - ▶ this video Replication - link

>On the other hand, the ribosome is an amazingly complex machine Just a bit: Transcription - link Translation - ▶ this video Replication - link It's not clear to me how much these features can be degraded without destroying the ability for organisms to reproduce with heritable traits. Also, when listening to these videos, ask yourself 'how' and 'why' any time an action is described. For example, the following parenthetical questions from a small chunk of the 'Translation' video: "The addition of each amino acid is a three-step cycle; (Why three step?) First the tRNA enters the ribosome at the A-Site (Why does it only enter at the A-Site? How are other options prevented and/or made inconsequential? Was it always this way? How did the features of the A-Site evolve for this to happen. What happened before this? ), and is tested for a codon / anti-codon match with the mRNA. (How is the tRNA tested? What happens when it fails the test or is missing the amino acid? What is the energy budget of this test and what are the specific features of the ribosome, RNA, tRNA and amino acid that make it possible? What happened before this testing was done? How did we get from the lack of ability to test and the ability to test?) Next, provided there is a correct match, the tRNA is shifted to the P-Site (What is the mechanism of this shifting? Why does it only go one direction? What is the energy budget of this process and how is it powered? How do we prevent multiple tRNA from shifting or keep

It always bothered me that in the standard explanations of how these processes work it always seemed that reaction ingredients would somehow magically seek each other out, such as in videos like this where the amino acids arrive at the ribosome in order: ▶ this video The molecules really do move randomly, not magically, and it's just that they go so fast and are so numerous and collide so often that even random chance puts the right molecules in the right place many times per second. This article was a revelation when I first read it and I'm quite disappointed that this was never explained properly in my entire school life.

Indeed. I had read about it before but viewing these visualizations blew my mind: link (DNA transcription) ▶ this video (mRNA translation) link (DNA replication)

The RNA->protein translation process is pretty awesome. Here's a very informative video: ▶ this video Also Wikipedia page on the ribosome has a good description if you're patient enough to read through.

I wonder what T.S.Eliot would say about a robot winning a prize named after him? "Poetry is not a turning loose of emotion, but an escape from emotion; it is not the expression of personality, but an escape from personality. But, of course, only those who have personality and emotions know what it means to want to escape from these things."[1] -- T.S. Eliot from 'Tradition and the Infividual Talent' In this essay, Eliot uses the metaphor of chemistry to describe the poetic process. However, I think using the metaphor of the chemical process inside the ribosome is a better analogy. The poet's mind takes a finite amount of emotions and feelings as there are a finite amount of condons which can be processed through a ribosome in an infinite number of ways to create all sorts of proteins [2] as the poet can move the reader to experience new feelings. Whereas a computer can test if a new protein will bind to a cell or act in a certain way, the computer doesn't have the ability to quantify if a reader is experiencing a new feeling or epiphany. Or perhaps, a person can be placed in a MRI machine so the computer can have a feed back loop. A good example of the artistic process that T.S.Eliot described is how George Lucas, who has said in interviews that T.S.Eliot has influenced his work, stitched together several scenes from dog fights in WWII movies [3] using physical images of things that are familiar to the audience like planes and words, "I got him," to create a new feeling for p

link "modern medicine" isn't perfect, it's good and getting better every day, but we have a long way to go. Plus, we don't know for sure what modifying our DNA does. It might affect certain things, but it might also have unknown consequences. There is a ton of trial and error in science, and you don't want to have too many errors in your body, else it leads to cancer and other horrible things. Lots of mice have given their lives to ensure that we and our children live awesome healthy lives. Thank you lab-rats (and other animals), you have suffered for our benefit (though you didn't have much of a choice). Also, it's really really difficult and really tiny, ▶ this video but there are several teams working on it and many other approaches.