
A giant map of metabolic pathways - cel1ne
http://biochemical-pathways.com/
======
medymed
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.

~~~
entee
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.

~~~
imaginenore
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.

------
dnautics
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](http://www.genome.jp/kegg-
bin/show_pathway?hsa01100)

------
lunchladydoris
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.

------
rotexo
gotta follow this up with a shout-out to flux balance analysis
[https://en.wikipedia.org/wiki/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...](http://www.nature.com/nchembio/journal/v8/n6/full/nchembio.969.html)
(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.

------
jonsen
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.

~~~
dhoe
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.

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

[http://www.roche.com/sustainability/for_communities_and_envi...](http://www.roche.com/sustainability/for_communities_and_environment/philanthropy/science_education/pathways.htm)

Click on image below "Order the Poster".

~~~
ethbro
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"

------
Terribledactyl
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

~~~
TheSpiceIsLife
Any chance of getting a copy of this from you?

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

------
vasili111
Also another good map: [http://www.sigmaaldrich.com/technical-
documents/articles/bio...](http://www.sigmaaldrich.com/technical-
documents/articles/biology/interactive-metabolic-pathways-map.html)

------
bane
Wish this was available as a couple of nice PDFs

