[CrimpJiggler]

I've been studying a fair bit of biosynthesis recently and notice that all kinds of things get phosphorylated before catabolic reactions occur. I can see that phosphorylating makes hydroxy groups better leaving groups, but I also see that various molecules get phosphorylated before different reactions occur in other positions of the molecule. An obvious one is how linear monosaccharides get phosphorylated on both ends, then suddenly they can just split in two. But its everywhere, shikimic acid gets phosphorylated at the 3-hydroxy group, then the 6-hydroxy group suddenly becomes much more reactive. What exactly does it do to the electron distribution to the molecule to alter reactivity so greatly? I've already heard of ATP being a high energy molecule and I hear the first stage of photosynthesis is all about generating high energy molecules but I don't know why this is. Also, what about molecules like DMAPP which have two phosphate groups attached?

[Irlanur]

I think the most obvious thing you forgot is the huge charge change. If you phosphorylate something you get a huge negative charge which can e.g. change the shape of the protein or mark a small molecule to be recognized by a molecule.

[Babcock_Hall]

You are asking a very, very big set of questions.  Phosphorylation/dephosphorylation can make/destroy a signaling molecule such as fructose 2,6-bisphosphate (sometimes called a third messenger).  Phosphorylation can make a poor leaving group into a good leaving group, as happens in many biosynthetic  reactions, such as glutamine synthetase.  The splitting of ATP by this enzyme also changes the overall thermodynamics of the process.  Phosphorylation/dephosphorylation regulates many enzymes, presumably through conformational changes brought about by the changes in size, electrostatics, and H-bonding of the phosphorylated form versus the desphosphorylated form of the same enzyme.  Frank H. Westheimer wrote an article called "Why Nature Chose Phosphates" that might be a good place to start.

With respect to the biosynthesis of chorismate, I am not sure exactly what you are asking.  Enzymes may choose to phosphorylate one hydroxyl group over another on the basis of complementarity to their active sites.  In any case, do not trust the diagram below.  The structures of EPSP and chorismate are incorrect: what is shown as a ketone group is actually a vinyl group.
http://openi.nlm.nih.gov/detailedresult.php?img=3018139_1471-2164-11-628-1&req=4#

[Yggdrasil]

I've been studying a fair bit of biosynthesis recently and notice that all kinds of things get phosphorylated before catabolic reactions occur. I can see that phosphorylating makes hydroxy groups better leaving groups, but I also see that various molecules get phosphorylated before different reactions occur in other positions of the molecule. An obvious one is how linear monosaccharides get phosphorylated on both ends, then suddenly they can just split in two.

I haven't studied the other reaction pathways in detail, but for glycolysis, the first phosphorylation step (glucose --> glucose-6-phosphate) helps cells take up glucose from the environment.  By phosphorylating glucose, you prevent it from being able to exit the cells through glucose transporters that do not recognize glucose.   The second phosphorylation event (fructose-6-phosphate --> fructose-1,6-bisphosphate) is basically for the same reason.  The retro-aldol cleavage catalyzed by aldolase in glycolysis produces two triose sugars.  These trioses are much more membrane permeable and are able to leak out of the cell if not phosphorylated.  Phosphorylating f6p to create f1,6bp ensures that both triose products of aldolase are phosphorylated and will not leak out of the cell.

If you're interested in understanding the chemical logic behind glycolysis, here's a nice review article with a lot of great, insight into the subject: http://www.nature.com/nchembio/journal/v8/n6/full/nchembio.971.html