Study Guide

Acids and Bases Themes

  • Chemistry of Enzymes

    Acids and Bases in Enzymes

    Many acids and bases are highly toxic and there's no way they would get along inside the cells of your body. Strong acids and bases could probably explode some cells much like this exploding watermelon. However, relatively weak acids and bases are everywhere in biology and help cells do some amazing chemistry.

    On example of weak acids and bases in action is their use by enzymes to catalyze many of the vital biochemical reactions going on all the time within cells. Enzymes are nature's most common nano-machines. They are large molecules consisting of a long string of amino acids that folds up into a precise structure. Scientists can take pictures of enzymes using X-rays (see below) to get an overall map of how the amino acid string is folded up and to find the location where the enzymes interact with the chemicals that need catalyzing. This special location is called the active site. The active site is where all the amazing chemistry happens that is needed to keep reactions going faster than they would otherwise. 


    An X-ray crystal structure of an enzyme. (Image from here.)

    Enzyme active sites contain an arsenal of amino acid side chains that interact with the reactant molecule(s) undergoing catalysis, better known as the substrate(s) of the enzyme. Amino acid side chains are the parts of the amino acid that do not participate in the bonds that make up the long chain. There are 20 different common amino acids, each with their own side chain. One of the most deadly weapons in the active site arsenal is an amino acid side chain that can transfer or accept protons from the substrate.

    Of the 20 common amino acids, several of them have side chain groups that can act as acids or bases. These acidic or basic amino acid side chains are called "general acids" or "general bases" in the context of the enzyme. It turns out that in order to react many substrates need to pick-up or lose a proton in order to get to the products side of the equation. Enzymes make this happen faster by having weak acids and bases in the active site to transfer the needed protons like a super-quick ball boy shuttles tennis balls back and forth during a match. Saved yet again by acids and bases.

  • Chemistry of Blood

    Blood as a Buffer

    Everyone knows that aliens have extremely corrosive and acidic blood, which is why you would never want to harm an alien should you ever run into one. What you probably didn't realize was that Earthlings (yes, you) also have acids and conjugate bases in their blood.

    For your body and cells to function properly, your blood must be maintained at a very specific pH value: pH 7.4, which is slightly basic. Several buffers contained in the blood maintain this pH. One of the most interesting buffers in blood is the bicarbonate buffer system consisting of the acid H2CO3 and its conjugate base HCO3-. How does the body get this buffer into the blood? Take a deep breath because you're about to learn the shocking truth.

    Did you take a deep breath? If you did, you just lowered the concentration of your blood's biocarbonate buffer system by exhaling CO2. CO2 levels control the bicarbonate buffer because gaseous CO2 in the lungs is in equilibrium with dissolved CO2 in the blood (see figure below). This equilibrium is linked to the bicarbonate buffer equilibrium because dissolved CO2 can form H2CO3 by taking up H2O in the blood stream. A third equilibrium between H2CO3 and HCO3- forms the buffer system. H2CO3 is a weak acid because it can release its proton to form HCO3-.

    When you exercise, the lactic acid produced by muscle tissue causes a build up of H+ in the blood. Without the biocarbonate buffer system this process would eventually turn your blood very acidic and that would obviously have dire consequences for your fragile little blood vessels. They are not built to withstand the corrosive and toxic properties of acidic solutions. Thankfully, when H+ begins to build up, HCO3- acts like all good buffers do—by absorbing the free H+. This shifts the equilibrium to the H2CO3 side. As a result, the second equilibrium between H2CO3 and CO2 shifts toward the CO2 side. The build up of CO2 in the blood gets released into the lung air space making you breath heavier.

    One reason exercise results in heavy exhalation is that exhalation is needed to keep the blood pH balanced. The opposite process happens when you're sitting around watching YouTube videos. This causes minimal exhalation, keeping plenty of CO2 around in the lung air space to supply the bicarbonate buffer system. Ultimately, the balance of CO2 by your exhale and inhale rate serves to balance the buffering system that keeps the pH of your blood very near 7.4 at all times.