Water and pH

Most biochemistry takes place in water


There are proteins that work in lipid layers, but the interaction with water is critical to the way biology works. It is the medium in which all the biochemistry takes place, but is also an important chemical player in reactions.
I think you get the first part: the molecules of life are, for the most part, floating in water. Yes, there are some in membranes, but even that depends on the water being on each side of the membrane (remember it is the interaction of the hydrophilic heads of the phospholipid with water and the avoidance of water by the hydrophobic tails that lead to the formation of the lipid bilayer).
Also, you seem to get the idea of how surface tension works, and cohesion and adhesion.
What about the chemistry?
We just learned about dehydration synthesis and hydrolysis. Obviously, the chemistry of water plays a huge role in that. Another main role of water is in acid/base chemistry. pH greatly affects how easily certain reactions proceed and also the shape and function of many proteins.

The central equilibrium:


Water equilib

The big points:
  • There is very little H3O+ and OH- in pure water. The concentration of both is 10-7 Mol/liter.
  • The product of the concentrations of H3O+ and OH- is always 10-14. That is called the "Kw" and is really just an equilibrium constant.
  • For our purposes, acids and bases act by changing the equilibrium position of this equation.
The law of Mass Action says that if I change the concentrations of any one of the components of the equilibrium, the reaction will shift to adjust so that the product of the concentrations of H3O+ and OH- is 10-14. Acids act by adding H+ to the solution, increasing the amount of H3O+ and decreasing the amount of OH-. Bases act by soaking up available H+, which increases the concentration of OH-.
So, if I dissolve HCl in water to a concentration of 0.01 (10
-2 molar) the concentration of H3O+ becomes 10-2 molar (called pH 2) and the concentration of OH- shifts to 10-12 molar (the product of the two is 10-14).
This is what happens in the stomach, for example, where the pH is about 2.
A carboxyl group would release it's H+, doing resulting in the same sort of change as with HCl. An amine could steal an H+ from an H
3O+ and make the pH go up.
Here is a scale I liked that I stole from another website:
http://crescentok.com/staff/jaskew/isr/chemistry/class21.htm

phscale


Buffers:


I didn't get to talk about this in class. A buffer is anything that is a weak acid or base (preferably both) that will give up an H
+ if the pH is above a certain point (different for each buffer) or absorb an H+ if the pH is lower than that point. The result of this is that a solution of water that contains a buffer resists change in pH. Your blood, for example is not pH 5.5 like the water in the room, it is pH 7.4 +/- 0.5 pH units. It is tightly controlled by multiple buffers, including a carbonate buffer system.