You know there are many things that you are exposed to during your life that you think "I can't wait until this is over, I'm never dealing with this again." In science I have found that I said "I will never work on this" or "I will never take this approach or use this methodology." only to find myself working on that using that approach and methodology. CRAP. It has gotten to the point where I find myself not verbalizing such things as it may curse me into doing things I initially find dull or tedious. I will say that when I have been working in an area or using a method I had previously considered anathema, it is with excitement or a certain amount of passion, because I came into it to learn something new about a problem I had been studying. pH is one of those things.
pH is better known as how acidic or basic something is. Acid has a low pH and base has a high pH. pH is really a mathematical term meaning -log[H+] or -log of the concentration of hydrogen ions. pH is something you learn about in general chemistry in high school and college. You find yourself doing some math problems and using acids and bases to bring some solution to a given pH or adding acid and bases to a solution and taking a plethora of measurements to determine the buffering capacity. (This latter procedure involves opening the spigot on the acid/base solution and trying to hit the pH you're looking for as quickly as possible, usually you overshoot, have to add the opposite acid/base, and repeat). So why do we care?
In biology, pH is one of those issues all cells have to deal with. Well, they could die instead. My work is focused, in large part, in understanding how Candida albicans, a fungal pathogen, responds to pH. The reasons are historical....I identified the pathway that senses pH and allows Candida to respond appropriately to changes in environmental pH. I identified the pathway first, then figured out what it did...so my interest is in the pathway and pH turned out to be an acquired interest. Over time my appreciation for pH has grown dramatically, not from a chemistry perspective that's always been what it is, but from the biological implications. First, most organisms can live in a relatively small range of pH. Normally we think of pH in the range of 2-14 although extremely acidic solutions can have a pH of ~ -5! This range may seem small, but remember pH is measured on a log scale, so the difference between pH 2 and pH 14 is the same as the difference between 100 and 10,000,000,000,000. Most organisms can grow over a small range of pH (2-3 pH units) and survive over a slightly greater range (4-5 pH units). Our body fluids are maintained at a pH ~7.4, however conditions such as acidiosis occur with an arterial blood pH <7.3 and alkalosis occurs with an arterial blood pH >7.5. C. albicans can be grown in the lab from pH 2-10. The range may be greater, but this is the limit that we analyzed. All solutions have a pH and all organisms grow in or are contained in fluids (yes even us). What is interesting is that the process of being alive generates chemicals that make solutions more acidic and more basic. So, a living organism can and will change the pH of the environment it finds itself in. Our bodies are well buffered, in other words we contain mechanisms to keep the pH of fluids such as blood at 7.4 in response to these chemicals. Remember these are chemicals (metabolites) we generate ourselves, this isn't some pollutant from the environment. Finally, I should point out pH matters to a cell. Most proteins a cell makes has a pH optima around 7, however there are many exceptions. For example, cells in that grow in an acidic environment secrete proteins that function best in an acidic environment (but even these cells maintain an internal pH of ~7, so the internal proteins work best at pH ~7). Helicobacter pylori, which lives in your stomach is a good example. Also, some digestive enzymes in your spit work best at acidic pH so are not very functional until you swallow. Suffice it to say that environmental pH is an important stress that all cells must deal with (or as said previously die). Further, cells can change the pH of the surrounding environment. So cells must be able to adapt quickly to environmental pH or suffer the consequences.
You might ask, how can cells change the pH of the environment? Well there are many ways, but the simplest and most widely known is through glucose metabolism. Glucose is the sugar of choice for most organisms on the planet, it is a great source of carbon, which we need for virtually every molecule within our cells, it is also a great source of energy. A cell converts glucose into a bunch of ATP, which is then used to allow most other cell processes to happen, such making proteins, moving things in and out of the cell, etc. ATP is the currency the cell uses to get things done. When cells use glucose they generate a molecule called NADH from NAD. Unfortunately there is a finite supply of NAD, so when it is all converted to NADH, then cell cannot use anymore glucose. Thus, no more carbon and no more energy. However, cells can recycle NADH back to NAD in two general ways. One is fermentation (Yes that fermentation). The process of fermentation allows NAD to be recycled without the use of oxygen. To recycle NADH back to NAD, electrons (damnit not physics!) are taken from NADH and given to another molecule making it into something different. Often it is pyruvate, which conveniently enough is the last thing made when glucose is broken down for energy. So the cells can recycle NADH and use the end-product of glucose metabolism to do it. Life is sweet. When pyruvate picks up these electrons, recycling NAD to be used for more glucose metabolism, it is changed into something else. If we are lucky (and currently I am enjoying some luck) it is converted to ethanol, this is how beer and wine come about. If we are unlucky it is converted to lactic acid, this is why are muscles burn after prolonged exercise. Lactic acid is acidic, DUH, which our bodies/muscles do not like so much. So we make a lot of acid in our bodies, which is dealt with, but some pain ensues temporarily. The same thing happens to microbes, they can make lots of acid, such as lactic acid, although other microbes make other things (and this is important, which Ill try to blog about another time). In effect, microbes by secreting acid into the environment can make the environment more acidic. If they could not respond to this appropriately, they would kill themselves, and who wants that?
So you see, pH matters in biology. Not just to make sure your reagents are correct so your experiments work but because life causes changes in pH, which life responds to, which changes the pH, which life responds to, which......repeat until your head explodes.
Idiosyncratic Thinking: a computer heuristics lecture
10 hours ago in Doc Madhattan