Wikipedia:Reference desk/Archives/Science/2019 June 26

= June 26 =

DNA Replication
Help from biologists required: I am in the process of generating a video to show the basics of DNA replication. The video will (in acceptable volume) be published in a relevant article of the en:WP. As I am not sure that I understand the concept of 3´to 5´vs 5´to 3´I need some WP editor with specific knowledge to verify that my little film shows a correct process of replication. Thank you for any help / critique and advise. --Cookatoo.ergo.ZooM (talk) 13:48, 26 June 2019 (UTC) PS: I may have to split the video into shorter, maybe 60" clips to achieve some reasonable quality, but that is temporarily irrelevant. PS2:  You may have to click twice;  for unknown reasons, the fist click shows but a black window.


 * Our article didn't have a figure I wanted, so I numbered the one we had and put it at the right. Polymerases work by breaking off some phosphates and linking the remaining phosphate of a nucleotide to a 3' end, so DNA strands grow at the 3' end under nearly all situations where replication is going on.  The strands form a double helix pointing in opposite directions.  Oh ... and as for the video, I'm afraid you have to scrap it entirely.  It's just not the way it works -- you don't have large regions of side-by-side "double helix" without the helix. Wnt (talk) 15:40, 26 June 2019 (UTC)
 * Besides, the nucleic acid double helix contains a major groove and minor groove of different widths Gem fr (talk) 16:35, 26 June 2019 (UTC)

Hi, User:Wnt and thank you for the advice. I will modify the design and resubmit. The first attempt at abiogenesis was a total failure. And for all we know, the current attempt (executed in online reality) may be doomed, as well 😈 --Cookatoo.ergo.ZooM (talk) 13:07, 27 June 2019 (UTC) PS: I will ignore that helices are not symmetrical and uneven gaps / grooves are the result. This is not an exercise in molecular geometry. --Cookatoo.ergo.ZooM (talk) 13:14, 27 June 2019 (UTC)
 * Obviously you have to decide what level of detail to include and what the academic level of your target audience is. One confusing aspect is that in the polymerase reaction, there are dozens of loose A/T/G/C diffusing into the active site and then the correct one attaches with the rest simply dissapearing. It's true that there are lots of available bases of all types, but either they should bounce in and out (with only the correct one sticking) or else only the correct one should ever come in. You've also lost the whole visual idea of the need for the polymerase activity, which as you note is important for getting the strands to build. As illustrated, it seems its role is just to get the correct base-pairing, not also for attaching the new base to the previous part of the chain. Maybe retain the backbone, so it can "bond to the backbone" once it pairs with the base? If the backbone is made of arrows (rather than just a tube), then you can even illustrate the antiparallel difference between leading and lagging and the directionality of the replication, which you mention and is a major idea. DMacks (talk) 13:57, 27 June 2019 (UTC)

Thank you, user:DMacks. I like your suggestion of switching the tubular backbones to antiparallel helical arrays of arrows to indicate the 3´/ 5´ logics of leading (continuous) / lagging (Okazaki) strand replication. This seems intuitive visual semantics. I have to experiment how to achieve that, but that is my problem. I expect a spot of brain storming in my Gothically vaulted regular winebar next to our cathedral will provide divine inspiration (or, at least, medication for ensuing frustration) 🤢. And yes, the A/T/C/G blobs floating in and miracolously evaporating is clumsy and dilletant rubbish. This needs to be tightly modelled. A spot more brainstorming. Your comments have been very constructive. Muchly obliged. --Cookatoo.ergo.ZooM (talk) 16:10, 27 June 2019 (UTC)
 * Have you see the WP:Videowiki tool? Doc James  (talk · contribs · email) 19:21, 27 June 2019 (UTC)
 * Note abiogenesis is the original origin of life, not any replicative process. Likely some RNA-like nucleotides were involved, but certainly not helicase! Wnt (talk) 14:53, 28 June 2019 (UTC)

Re abiogenesis: Sorry, this was just an infantilistic joke. Humour, I perceive, is a non-overlapping magesterium to the Popperian school of scientific methodology. --Cookatoo.ergo.ZooM (talk) 16:41, 29 June 2019 (UTC)