A giant map of metabolic pathways | Hacker News Reader

A giant map of metabolic pathways

biochemical-pathways.com

96 pointscel1ne17 comments

It would be great to have this detail of map for immunology...but we can't grind up cells to meaningfully isolate and test enzymes as quickly as the old biochemists because so much depends on signaling the 'state' of the intact cell, like whether certain genes/proteins are in an on or off state, which in turn seems to depend on a never-ending abyss of factors like what other cells are nearby or what media you're trying to grow them in. A sharp contrast to many basic metabolic pathways which have to be available ('on') at most times in most cells could be studied without needing as much or any DNA/RNA analysis back in the day. Sigh.

I think maps like this beautifully illustrate how complicated biology is. Now add in things like what the parent mentions such as cell state, external signalling systems and it gets worse. Much of this chart was mapped out using E. coli, S. cerevisiae (budding yeast) and other single celled organisms.

It gets much much more complicated when you have multi-celled organisms. It also gets much more complicated when you recognize that many of those arrows are equilibria, so the reaction can actually go backwards under certain circumstances. And virtually every signalling system controlling these activities is an equilibrium. The interaction of all these systems makes biology incredibly difficult to understand in the kind of rigorous, systemic, mathematical way we would like to.

Also each of the reactions shown is the intended reaction only, it doesn't show all the side products, side reactions, impurities, and what happens when things break.

I don't know anyone ever try to make a detailed immunology map will become, but I always assume them explodingly huge. I never took a second look into immunology after reading the first chapter of an immunology textbook

Honestly kegg is more useful because it's interactive and hyperlinked and contains species specific information (identified genes in genomes)

http://www.genome.jp/kegg-bin/show_pathway?hsa01100

Paper versions of the Roche metabolic pathway map have been on at least one -80 freezer in every biology lab I've ever worked in.

I remember the many, many hours I spent during my undergrad learning just parts of this. I felt quite proud when I had committed the Krebs cycle to memory and then somewhat crushed when I later saw it in context.

gotta follow this up with a shout-out to flux balance analysis https://en.wikipedia.org/wiki/Flux_balance_analysis I'm TAing intro Bio right now, and I really wish teaching metabolism with toy FBA models was generally part of the pedagogy: http://www.nature.com/nchembio/journal/v8/n6/full/nchembio.9... (my apologies, that probably isn't open access). I think it would go a long way towards getting students to think about metabolism rather than just memorizing it, and it might be a good way to also teach the strengths and limitations of modeling.

For years I had this as a poster on my wall. Very humbling when you occasionally get the idea that some non trivial biological cause and effect must be straight forward.

How did you get it? I emailed them at some point asking if I could buy it somewhere, and got a one liner back more or less telling me to get lost.

You can just order it online - it's free.

http://www.roche.com/sustainability/for_communities_and_envi...

Click on image below "Order the Poster".

In response, I received:

"Roche Life Science will no longer provide printed copies of the Biochemical Pathways Charts. These charts are now available for viewing online only at Explore the Pathways.

Regards,

Roche Life Science"

That was way back. Mid 80ies. Bought it in a campus book store.

These used to be up in a slightly different, less nice for humans, but easy to scrape UI.. So I did and stitched them together. 16870 x 12000 @ 300DPI came out at 56x40in

Any chance of getting a copy of this from you?

Nice! Another great site with gorgeous pathways is the Small Molecule Pathway Database (http://smpdb.ca).

Also another good map: http://www.sigmaaldrich.com/technical-documents/articles/bio...

Wish this was available as a couple of nice PDFs

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