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1434: Classroom Puzzle: Phosphates in Biology

Closed since almost 5 years ago

Intermediate Pilot


September 27, 2017
Max points

Note: Due to player feedback and an excessive number of bugs, this puzzle was closed early and is worth zero points.

Welcome to the first of the U. of Denver educational puzzles! In this puzzle, students will be asked to fold an RNA structure to help learn about the distinct chemical and structural properties of phosphorous in nucleic acids. Phosphates are essential to the structure of the RNA backbone; after enabling "Show advanced GUI" in General Options, try adjusting the View options to Stick mode with CPK colors to see the chemical structure of the RNA backbone. The RNA used for this puzzle is a section of Xist RNA, which is very important in gene transcription and cancer, but whose tertiary structure is still unknown. See if you can find a high-scoring structure for this RNA!

U. of Denver students will be asked to read two articles alongside this Foldit puzzle. The first is a landmark 1987 paper by Frank Westheimer discussing the unique role of biological phosphates; the second is a controversial 2010 paper by Wolfe-Simon et al. suggesting arsenic as a viable substitute for phosphorus.

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bkoep Staff Lv 1

Typically, when the results of a scientific experiment challenge established theory, other scientists will try to replicate those results or design experiments to test alternate hypotheses.

The controversial arsenate paper has spawned some great follow-up research in this vein, such as the following two reports, which suggest alternate explanations for the results of Wolfe-Simon et al.:

SaraL Lv 1

as this is not a standard protein, please exercise caution when using recipes. You may either break the puzzle or cause the program to crash.

SaraL Lv 1

Do not use:

-Ideal SS

This includes any recipe that does the same. It will cause the program to crash.

Susume Lv 1

The user interface should help the player discover what actions are available. Leaving enabled actions that are not relevant (and crash the program) is poor UI practice (and drives players nuts).

Keeping hidden actions that actually work is also a mistake: in selection interface, whether you select something or not, the Shake button does not appear. However, the "S" hotkey (which many players don't know about) does make shake run, and it is good for points. If I can shake, show me the shake tool.

Btw Shake runs on all segments (whatever they are called in RNA), rather than only on selected ones; idk if that is on purpose or not.

Susume Lv 1

To see hydrogen bonds, turn on show bonds (non-protein) in view menu.

The sequence of this piece of RNA is GGUUUUGUGAGUUAUUGCACUACC.

In lua, when using structure.GetAminoAcid(n) on an RNA molecule, foldit returns a 2-letter abbreviation for base n ("ra", "rc", "rg", or "ru").

Wikipedia has a page on secondary structure of RNA, with a few pictures of shapes that RNA can make:

More pics of shapes RNA can make - scroll down to the "secondary structure" section:

alwen Lv 1

But it's REALLY interesting to have something new to play with!

I'm using CPK and Sphere view and trying to stick red areas to blue ones.

Susume Lv 1

In proteins, you can select one segment and use left/right arrows to step through the sidechain positions. In the RNA, the left/right arrows seem to step through positions of the lone oxygen that hangs off the pentagon, rather than the positions of the large sidechain. Moving the large sidechain would be more useful.