How does high altitude affect brewing chemistry? Up here in Denver (5280') or even higher in the mountains (some towns in Colorado are 9000' and higher), water does different things. In Denver, water boils at around 202˚F (~94.4˚C).
How do these atmospheric changes affect things like hop utilization, mash temperature, etc?
Mashing shouldn't be affected by the altitude. However, hop utilization at lower temperatures is fairly significant. Ray Daniels republished a correction factor in homebrewdigest here.
Depending on what part of Denver you live, you'll see about an 18% - 20% reduction in utilization versus that at sea level.
The biggest difference I noticed brewing in Denver wasn't that my beer was less hoppy, though - it was the electrical-tape flavor from the chloramine in Denver water. So hopefully you've already taken care of that.
Carbonation will be effected, if you are force carbonating in the keg. Up the CO2 pressure by about 10%, shake it a lot, and have the brew very cold (I used to live in Laramie and at 7200 ft, beer went flat REALLY fast unless you kept it around 35-38oF). Here is a link to a carbonation table that I have found to be useful: http://www.winning-homebrew.com/support-files/kegcarbonationchart.pdf
