Thursday, July 16, 2009

Neutral pH

 

I'm working on the next edition of my textbook. From time to time I'm going to use you (readers) as guinea pigs to try out some new ideas. This is one of those times.

The concept of pH is difficult for students. It's easy for them to memorize the definition—the negative log of the hydrogen ion concentration—but that's not the same thing as understanding what it means.

Textbooks usually tell students that the equilibrium constant (Keq) for the ionization of water is 1.8 × 10-16. They can then calculate the ion product for water (Kw) at 25°C knowing the concentration of pure water (55.5 M). This value (1.0 × 10-14) happens to be a convenient round number, giving rise to the standard pH scale from 1 to 14.

The square root of the ion product for water is the concentration of hydrogen ions ([H+]) and the concentration of hydroxide ions ([OH-]). This concentration is 1.0 × 10-7 or pH = 7.0, which corresponds to neutral pH at 25°C.

It occurs to me that students would have a better understanding of the concept if they were asked to do some calculations on their own rather than just reading the derivations in the textbooks. I propose to add the following problem. How many Sandwalk readers know the answer?
Neutral pH is the pH at which the concentrations of H+ and OH- are equal in aqueous solvent. This pH is 7.0 for pure water at 25°C.

What is the neutral pH in your blood? What is the neutral pH in extremeophiles growing at 0°C or 100°C? (You may have to look up the values of some parameters in the Handbook of Chemistry & Physics).
Post your answers in the comments. You can post anonymously if you want but all the best biochemists will be signing their names.

Don't look at the comments until you come up with your own answer.


25 comments :

  1. If a student does not understand the concept of pH, it is 100% guaranteed that the same student does not understand many other physico-chemical concepts absolutely required for understanding even most basic biochemistry.

    Is biochemistry a remedial course for everything? This is like teaching a multiplication table as an introduction for linear algebra course.

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  2. That said, I don't like your questions. Quite confusing - particularly with regard to calculations. Both blood and cytoplasm are highly buffered and highly concentrated (=> activity is not ~ concentration). And my blood pH is NEVER at neutral pH. So plugging whatever numbers one can find in Handbook of Chemistry & Physics (which is not very easy because the damn thing, last I checked, does not have TOC) is not going to produce meaningful numbers and hardly will contribute to understanding mass action law and logarithm function (which, really, is all that's needed to understand the concept of pH).

    If all you want to test is understanding of the temperature dependence, don't muddle water with blood and extremeophiles and just ask: 7.0 at 25C but higher or lower at 0C? 100C? - Explain the answer.

    The explanation is trivial - water dissociates more at higher temperatures ==> concentration/activity of H+ when it is equal to 0H- is higher. Higher [H+] means lower pH. So there it is - neutral pH is <7.0 at T>25C and >7.0 at T<25.

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  3. I got pH 6.81 at 37°C, pH 7.48 at 0°C and pH 6.13 at 100°C. Ionization goes up with temperature, so -log of [H+] in a neutral solution goes down.

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  4. Piling on from what DK started: what's so special about "neutral" pH that even makes this an interesting question? AFAIK, no proton binding sites also bind (as an alternative) a hydroxyl ion, so the concept of "neutrality" is not really relevant for most (all?) biochemical reactions.

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  5. Hmmm, just to be a contrarian here, I like what Larry's doing, if I understand it correctly. His goal seems to be to get students to see 'neutral' as something different than 'when protons are equal to hydroxyl ions and are thereby neutralized.' That's an easy misconception to grab onto, and I speak as one once so benighted.

    I wouldn't have linked it to data in the HCP, but the aim is a good one.

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  6. [Larry's] goal seems to be to get students to see 'neutral' as something different than 'when protons are equal to hydroxyl ions and are thereby neutralized.'

    I really hope that's not his goal... Because it's NOT something different! The definition of neutrality is indeed a(H+)=a(OH-)
    (where "a(*)" stands for "activity").

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  7. Um, heh, I think my mistake is illustrating the problem that Larry is tackling. FWIW, what I was thinking was 'pH 7' but what I wrote was 'neutral'. I did get the gist of Larry's goal, I think, and the reason I wrote it down wrong is that my cell biological brain has simplified 'neutral' to be equated with 'pH 7'. That, if I'm not mistaken, which is not so unlikely, is the confusion Larry's trying to dispel.

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  8. Isn't it a trick question?

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  9. DK asks,

    Is biochemistry a remedial course for everything? This is like teaching a multiplication table as an introduction for linear algebra course.

    That's a good point. Perhaps we should just assume that all students have a firm grasp of basic chemical concepts before they start taking introductory biochemistry.

    Perhaps we should also assume that they have a firm grasp of basic biology and evolution as well.

    But there's a slight problem. We know for a fact that students in our introductory biochemistry course do NOT have a solid conceptual understanding of the basic principles of chemistry and biology and that's true of many universities and colleges that use my textbook.

    Part of the problem is that students forget what they learned the year before and part of the problem is that they weren't always taught correctly. That's why we have brief reviews of fundamental concepts such as pH and evolution.

    I wish I didn't have to do this but there's no chance of getting a textbook adopted if I assume that students know what they're supposed to know.

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  10. The idea behind the question was to get students to see that neutral pH varies with temperature and consequently the whole pH scale changes.

    When I did the calculations myself I found that it really helped me understand the concept of pH and it helped me recognize the fact that pH 7.0 was a nice coincidence that only worked at 25 degrees.

    I suspect that only a small number of students will benefit from the problem at the end of the chapter but "small number" is better than zero, no?

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  11. Zwirko asks?

    Isn't it a trick question?

    A "trick question" is a question where the instructor deliberately tries to misdirect students so that they get the wrong answer. Very few instructors do this deliberately but it sometimes happens by accident.

    I did not intend for this to be a "trick question." Would this be better?

    The pH at which the concentrations of H+ and OH- in pure water are equal varies with temperature. Calculate the "neutral pH" at 0C, 37C, and 100C. Consult the table below for the values of the ion product of water at different temperatures.

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  12. Would this be better?
    ...
    Calculate the "neutral pH" at 0C, 37C, and 100C


    IMO, much better!

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  13. Yes, I also think this is much better. Tell them the correct concept, then apply this new knowledge.

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  14. If you want them to better understand it then have them actually do some lab investigations/experimentation on it. If you feel simply doing the calculations are enough I'd say probably not. Just doing calculations is part of the problem of NOT understanding. Incorporate the calculations as part of an inquiry lab. Have them collect, analyze and explain the data.

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  15. As a former student who took a biochemistry class using Dr. Moran's textbook (which I did think was overall well written) I wonder if this is an exercise in futility. While I very much do appreciate it when an author tries to make concepts as clear as possible to students and tries to make the language readable, I do realize the reality is that very few professors teach with the book as their guide.

    I fully admit I rarely did any questions at the end of the chapter, to the point where my exam scores improved when I no longer spent my time doing so. I've noticed in other posts where Dr. Moran is discussing his book that he's talking about concepts that were not introduced to me.

    Also, I like the rewritten question much better. I never did like the questions with superfluous elements in it, occasionally they can help apply it, but I really hope that somebody taking a biochemistry class is able to recognize that the problems apply to real situations. At my alma mater the only students who took the course were biology or chemistry majors so it's not like biochemistry is something they'd never encounter. Especially in this example where it is something so basic as pH.

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  16. Linzel says,

    If you want them to better understand it then have them actually do some lab investigations/experimentation on it.

    That's an interesting comment. It reflects a widespread belief that lab courses—as they are currently run in most universities—contribute to basic understanding of fundamental concepts.

    I don't agree with that belief. As a matter of fact, I think that most undergraduate lab courses may do the exact opposite. They emphasize the "doing" over the "thinking." Some of them don't even require written lab reports any more.

    There are excellent pedagogical reasons for having undergraduate lab courses but the idea that they reinforce fundamental concepts and ways of thinking about the subject isn't supported by pedagogical research.

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  17. Eric says,

    I do realize the reality is that very few professors teach with the book as their guide.

    and ...

    I've noticed in other posts where Dr. Moran is discussing his book that he's talking about concepts that were not introduced to me.

    This is a problem, even in my own department. Many of my colleagues are convinced that their view of the subject is superior to anything that could ever be in a textbook.

    Some of them have been known to adopt a textbook for a course then teach "concepts" that directly conflict with what's in the textbook. This wouldn't be a bad thing if it were treated as a learning opportunity and the lecturers explained why there was another pint of view and why they disagreed.

    But that's not what really happens. What really happens is that the lecturer doesn't even know there's a conflict. Students soon learn that they will be examined on the class notes and not on what's in the textbook. It doesn't matter what the "correct" concept is, all that matters is whether you can give the expected answer.

    I blame the teachers, not the students.

    Sometimes I have to advise students who are being taught one thing in one course and something completely different in another (same subject). I cringe inside when I tell them that they should give one answer in one course and a different answer in another even though they know full well that one of the answers is wrong.

    This is just one of many symptoms that show us how bad undergraduate education has become.

    [Note: I am not saying that the leading textbooks are always right. They certainly aren't. However, as a general rule the material in a textbook has been written by people with some knowledge of what needs to be taught and it has been thoroughly reviewed by independent experts.]

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  18. What is the purpose of having the students work through this problem? Does the concept of "neutrality" even has any the biochemical significance? (IMO, no.) If not, is there a good pedagogical reason why this particular problem is nonetheless *particularly* useful for them to work through? (I think not).

    The vast majority of life forms on earth are subjected to temperature changes that are biochemically significant, and one way this occurs is by affecting the affinity of key proton-binding sites. So the general issue is important and worth teaching. But the affect of temperature on the pH of pure water is of only minor importance (and its relation to the pOH is irrelevant). As DK correctly points out, real biological fluids are chock full of proton buffers that will swamp the temperature effects on water. Moreover, several of those “buffers” will, in fact, be the sites where changes in biochemical activity are directly mediated. Furthermore, cells have active processes that tightly and strongly *regulate* the proton concentration in a dynamic environment. Thus, an exercise where the student looks up an equation in the CRC handbook and plugs in a few temperatures to determine a biologically irrelevant parameter (neutrality of pure water) strikes me as pedagogically pointless.

    A problem that dealt with a real (or a pseudo-real) system could provide better insight in the general phenomenon (temperature dependence of proton-binding sites) *and* its biological relevance. For example, positing a hypothetical enzyme whose activity is directly related to whether a proton is bound at a simple binding site, and having them calculate activity vs temperature, would (IMO) be a more valuable exercise.

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  19. Possibly just a pet peeve, but the scale image at the left of this post can get misleading when you leave the bounds of aqueous solution chemistry. There's nothing stopping one from having a solution with negative pH, but the graphic that shows it gives the impression that you can't go lower. I guess it doesn't matter in the biochemical world, but this is another thing that people often take for granted with the classical view of pH.

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  20. To Divalent:

    What is the purpose of having the students work through this problem? [snip the rest]

    Look, you are missing a point. The point is, the whole education system is royally fucked up with no "system" to be found anywhere. Larry is trying to work "within the system" and teach who he can however he can no matter the failings of the system as a whole. That's what he is paid to do, after all (I hope).

    The point is, it is routinely possible to take Biochemistry course without knowing what entropy is or being able to solve a quadratic equation. The point is, 90% of Biochemistry course takers are faking it - they WILL NOT understand the bulk of the course, they just need a "right" grade. The point is, the devaluation process in higher education is advancing steadily. These days, for everyone who cares, BS accounts essentially for nothing other than that a person survived a bunch of random classes, MS means someone is above average but something is weird, and PhD means someone may be passably good at what he/she professes to know.

    Here is where, IMHO, a root problem lies: Higher education is a good business and society values higher education. As an eventual consequence of this, about 10X more than necessary and sensible attend universities.

    The result is that a 90% of underqualified people are paying customers and the offering eventually conforms to customer base. Meet Larry M.: In order to make a [good] living, he has to explain things that, under the normal circumstances, should have never ever been his business to explain.

    Even worse: If Larry does not have a tenure, it is in his best interests to inflate the grades and graduate as many non-deserving graduate students as he possibly can.

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  21. Divalent asks,

    What is the purpose of having the students work through this problem?

    The point is to try and get students to understand the concept of pH rather than just memorizing some formulae.

    The fact that you are so concerned with "relevance" and practical applications troubles me. I'm not interested in how temperature affects various processes inside the cell. The temperature calculations were merely a hook to get students to think about pH and what it really means.

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  22. Larry: "The point is to try and get students to understand the concept of pH rather than just memorizing some formulae."

    Well, maybe that explains why nobody does the exercises at the back of your textbook. :) Sending them off to hunt down a CRC Handbook to calculate an arbitrary and biochemically meaningless parameter at different temperatures doesn't seem (to me) to be the best route to give them an intuitive sense of what pH is. (The “neutral pH in your blood”?)

    But what do I know? I'm not a textbook author. OTOH, I think a lot about maximizing the value of a student's time and effort in a course. And it seems to be that there are more biologically relevant example systems you could use to achieve the same purpose. Ones that would have the collateral benefit of also exposing them to something important about biochemical reactions in living cells in nature.

    BTW, IMO pH is difficult because of the “p”. Why not use molarity (like with every other ion in biological solutions)?

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  23. Divalent asks,

    BTW, IMO pH is difficult because of the “p”. Why not use molarity (like with every other ion in biological solutions)?

    What exactly do you mean? Do you mean we should replace pH with -log [H+]?

    BTW, I discuss the origin of the "little p" in my book. Did you find it useful?

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  24. I never did like the questions with superfluous elements in it, occasionally they can help apply it, but I really hope that somebody taking a biochemistry class is able to recognize that the problems apply to real situations.

    Has it occurred to you that one purpose of questions like (the original form of) Larry's is to help you learn to figure out which elements are germane and which are superfluous? And that this is a rather important skill in science, to put it mildly?

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  25. My CRC Handbook dates from the second millennium (ca. 1962?). So the any insight it might provide is equally dated, isn't it?

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