Glycolysis, citric acid cycle and oxidative phosphorylation simulation | Hacker News Reader

Glycolysis, citric acid cycle and oxidative phosphorylation simulation

metabolism.plict.nl

37 pointspepachino10 comments

Hmm. I'm an AP Biology student who just started studying cellular respiration. This is interesting, but I simply don't know enough. Could you provide the correct pathway? :P

It's too bad YouTube is under maintenance right now, but I'm uploading a video with the correct pathway... Just hold on a little longer please ;)

The video is online! http://www.youtube.com/watch?v=Eg17e_vvxtA

I studied a Chemical specialization in the secondary school, but this is too difficult for me. I will keep trying, without seeing the video (I already have my two [Pyruvate]s!).

Some comments:

* Add an "undo" button. I'm not sure if it is possible to choose a bad reaction, but I’d like to undo some of the tries. (And perhaps a "restart+areyousure" button.)

* Add a lithe graphic to each molecule, so they look more real.

* Some reactions are too fast, for example [Glucose 6-phosphate] -> [Fructose 6-phosphate] is almost instantaneous, so it took me like a minute to realize that something had happened. You should add some delay and more highlighting.

* The page is very tall, so it is not possible to see at the same time the reactives and the enzymes at the bottom, like [Pyruvate kinase] or [ATP synthase].

* Add an "easy" mode, so that when you pick a molecule, all the possible enzyme targets are highlighted.

* If you put a [ATP] in the [Pyruvate transport] and you don’t got any [Pyruvate] then the [ATP] is splited, but no [Pyruvate] is transported. So you lost a [ATP] :( !! I don’t know if it is biology correct, but I would like that the [Pyruvate transport] is dissable / does nothing when there is no [Pyruvate]. (Same problem with the [NAHD transport].)

* If you put a [ADP] in the [ATP/ADP Translocase] in the Mitochondrial matrix side the [ADP] get stuck until you put a [ATP] in its place. First, it is not possible to remove the [ADP] from the enzyme. Second, I’m not sure, but it looks like that the enzyme is translocating the third phosphate from the [ATP] to the [ADP] on the same side of the membrane.

Nice work.

Thanks for your suggestions! I've implemented a couple of them:

* Added delay for every reaction

* Made the page less tall, everything is smaller now (I'd underestimated the size, working on a 27" iMac)

* The easy mode was already there, enzymes lit up when you picked up a substrate. I've added an extra help now: when you hover over an enzyme, the available substrates light up.

* The transporters are only visible (and usable) if enough ATP/substrate is available

Now it doen’t work in IE8 (javascript error). But it works in Chrome. It looks much better in Chome than in IE8. I think that I didn’t see the enzymes highlighting because of IE8.

Please don’t make the transporters invisible, only disable them.

(I don’t like starting with a Pyruvate, it is like cheating.)

Please let me know if you encounter errors or have questions about the app.

Are there any graphics in the works? It's fun to click around with as-is, but would be a much better learning tool if one could see the sugar chains be broken down etc. Maybe a flash or spark when a phosphate group is removed from an ATP molecule...

That's actually a pretty feasible suggestion! I can't spend too much more time on it because of my education and because the main functionality of the app is finished, but the visualization of the release of energy sounds doable. Ideas on how to do it with pure Javascript/HTML/CSS?

You could do it comic-book style, by just flashing a shiny graphic that says "React!" over the enzyme.

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