Tuesday, January 03, 2017

The exit exam for biochemistry and molecular biology students

I'm a big fan of teaching fundamental concepts and principles and a big fan of teaching critical thinking. I think the most effective way of accomplishing these objectives is some form of student-centered learning. As I near the end of my teaching career, I wonder how we can tell if we succeed? It should be relatively easy to develop an exit exam for our biochemistry/molecular biology students to see if they grasp the basic concepts and can demonstrate an ability to think critically.

Here are some of the questions we could have on that exam. Each one requires a short answer with an explanation. The explanation doesn't have to be detailed or full of facts, just the basic idea. Students are graded on their ability to think critically about the answers. Many of the questions don't have a simple answer. Can you think of any other questions?
  1. Where do non-photosynthetic chemoautotrophs get their energy?
  2. What is a typical Gibbs free energy change for a metabolic reaction inside a cell?
  3. Why can't you have a lipid monolayer?
  4. Why is DNA supercoiled?
  5. Which pathway evolved first; glycolysis or glucoenogenesis?
  6. Why is methionine an essential amino acid in humans but glutamate is not?
  7. Can humans fix carbon dioxide?
  8. What are the end products of photosynthesis?
  9. How do you create a protonmotive force?
  10. How do some species survive without a citric acid cycle?
  11. Why is some DNA replication discontinuous?
  12. Why does E. coli need so many molecules of RNA polymerase?
  13. Why is the ribosome so big and complex?
  14. Why are there six codons for arginine but only one for tryptophan?
  15. Why is Levinthal's paradox not a paradox?
  16. Why does DNA rich in G/C denature at a higher temperature than A/T-rich DNA?
  17. Why are the amino acids sequences of a typical enzyme different in mice and humans?
  18. If protein folding is spontaneous then why do cells need chaperones?
  19. Why do acids like acetic acid and formic acid have different pKas?
  20. Why did you need to learn about the Michaelis-Menten equation?
  21. How much of your genome is functional?
  22. Why is ATP not an effective allosteric regulator of enzyme activity?
  23. What is flux?
  24. Why isn't it correct to say that ATP is an energy-rich compound?
  25. What was the point of learning about reduction potentials?
  26. Why are transcription and translation separated in eukaryotic cells?
  27. Why did it take so long to evolve an oxygen evolving complex in photosynthesis?
  28. Why is fat better than sugar for storing energy?
  29. Why do we need cholesterol?
  30. Why do eukaryotic genes have introns?
  31. What's the point of homologous recombination?
  32. How can bacteria survive without mitochondria?

I wonder how our own students would do on such an exam?


  1. How do some (anaerobic) eukaryote survive without mitochondria?

  2. Given the following abstract from a paper in this week's JBC, explain how the conclusions of the paper are consistent with the fundamental principles you learned in your course of study.

    1. That could be dangerous since there are quite a few papers that are NOT consistent with fundamental principles. (Not so much in JBC, however.)

    2. It depends on the fundamental principles - those taught in an undergrad course are pretty much universal: redundancy of genetic information, signal amplification and attenuation, the (real) Central Dogma,...

  3. I'm a big fan of teaching fundamental concepts and principles and a big fan of teaching critical thinking. I think the most effective way of accomplishing these objectives is some form of student-centered learning. As I near the end of my teaching career, I wonder how we can tell if we succeed?

    “Education is an admirable thing, but it is well to remember from time to time that nothing that is worth learning can be taught.”
    — Oscar Wilde

    1. "Those who think that nothing worth learning can be taught will never be educated."

      —Larry Moran

  4. #3 is troublesome, as phospholipid monolayers (which I assume is what you meant by "lipid monolayer") exist both artificially and biologically. Phospholipid monolayers are made for a variety of research purposes (usually by layering lipid micelles in an aqueous phase onto a hydrophobic surface). Moreover, a phospholipid monolayer is what surrounds the lipoprotein complexes which are used for lipid/cholesterol transport in our blood (e.g. HDL, LDL) - these essentially solubilize lipids and sterols by surrounding them with a monolayer of phospholipids; the hydrophilic heads point out (blood-exposed) providing solubility, while the hydrophobic tails point inwards (lipid-exposed).

    1. Hmmm ... I didn't think of that. The question should probably be changed to: "Why can't you have cell membranes made of lipid MONOlayers?"

    2. That may fly...unless the students learned about lipid droplets, which form between the leaflets of a bilayer, forming a monolayer-bound "organelle".

    3. what about the membranes of some archaea ?

    4. Monolayers only in a trivial sense, and, in fact, the structure of arechaeal membranes illustrates the principles of the bilayer rather neatly.

    5. of course it is nitpicking, but the question could be more carefully worded

  5. What is the serial number of the starship Enterprise?

    Sorry, couldn't resist. That was the bonus question in one of my theoretical biology courses back in the old days.

  6. On a related subject, I would love to read an article on a list of questions that you have posed in exams that made you laugh.

    For example, I was marking Intro zoology exams and one of the questions was a fill in the blanks. The question was "The Galápagos Islands are of volcanic origin and were named after ________."

    One bright student said "1865". If he had have said "1145", or any similarly distant year, I would have given him full marks.

  7. And a follow-on from my previous comment, I was given half marks on for one of my responses to an invertebrate zoology lab exams. We had to go from station to station and write the genus and species of different slimy creatures pinned on wax dissection trays.

    One had an ascaris round worm but I had a mental gap. Being the smart-ass I was, I wrote on the answer sheet "The great flightless worm of New Guinea".

  8. As a big fan of Dr Moran, it is great pleasure to read his criticism (and his audience's comments here) on science, scientists and exaggerated publications. This is why his blog is one of few that I refer in my Turkish blog (http://bilim-blogu.blogspot.com.tr/) as "Blogs Followed".

    Since I teach Biochemistry (have a pirated PDF copy of his book!), I just copied these great questions. But, before asking to students first I should study myself.
    best wishes and happy new year to everybody on the blog..

  9. Impressive exam, but I remain unclear on Question 22.

    Is it not true that ATP is an allosteric inhibitor of pyruvate dehydrogenase and isocitrate dehydrogenase?

  10. I haven't figured out Question 22.
    "22.Why is ATP not an effective allosteric regulator of enzyme activity?"

    ATP in the reaction catalyzed by Phosphofructokinase 1 acts as its own allosteric inhibitor. PFK1 is allosterically inhibited by PEP, citrate, and ATP.

    and as Tages Haruspex asked:
    "Is it not true that ATP is an allosteric inhibitor of pyruvate dehydrogenase and isocitrate dehydrogenase? "

    1. As I said in my post, the point of the questions is not to see if students know the "right" answer. There may not even be a right answer. The point of the exit exam is to see if students have learned how to think critically about biochemisty and molecular biology.

      The best way to test for this is to ask questions that address common misconceptions or things students may have just blindly accepted without asking themselves whether this makes any sense.

      In this case, students should have grasped some fundamental concepts about ATP. The should know that cells have to maintain a high concentration of ATP relative to ADP because if the two concentrations approach equilibrium values ΔG approaches zero.

      The only way to power reactions in which ATP is a cosubstrate is to keep ATP concentrations high.

      Thus, the concentrations of ATP don't change very much. They can't or the cell would die.

      If that's true, then ATP cannot be an effective allosteric regulator unless the enzyme if fine-tuned to distinguish between a 10% change in concentration. That's beyond the power of most allosteric binding site.

      ADP, on the other hand. Is maintained at a very low concentration. It's concentration can vary by two or three-fold without a drastic corresponding change in ATP concentrations. ADP can be an effective allosteric regulator.

      There are some enzymes that can bind both ATP or ADP at the same site. This is because in the absence of sufficient ADP it will bind the very similar ATP molecule since it's at a high concentration.

      When the ADP concentration rises it displaces the ATP and the activity of the enzyme changes. It's ADP that's the true allosteric effector in such cases.

      Scientists have gotten confused by this effect because they can isolate enzymes that are free of ATP or ADP. When they add ATP in vitro they see an effect on activity so they assume ATP regulates activity. What they fail to appreciate is that inside the cell ATP will always be bound unless it's displaced by ADP (or something else).

      I don't care if students buy into this explanation or not. They are free to describe the problem but offer some way out of the conundrum. They are free to mention possible exceptions where ATP might actually be an allosteric effector.

      I just want to know if they've thought about it and if they understand the problem.

    2. Thank you very much for taking time to respond with such a detailed explanation. That was very informative. Thanks again Dr. Moran.

  11. Thought provoking! Thank you for your interesting response which obliged me to revisit my Lehninger & Stryer

    Couple of points:

    Allosteric inhibition by ATP can fall under the rubric of recruiting a kinase... which I believe can be exquisitely sensitive to subtle variation in ATP concentrations

    Meanwhile I was wondering about your take on the following quote:

    In many bacteria, the funneling of two-carbon fragments into the cycle also is controlled. The synthesis of citrate from oxaloacetate and acetyl CoA carbon units is an important control point in these organisms. ATP is an allosteric inhibitor of citrate synthase. The effect of ATP is to increase the value of KM for acetyl CoA. Thus, as the level of ATP increases, less of this enzyme is saturated with acetyl CoA and so less citrate is formed."


    Was Stryer in error?

    Would your caveats regarding the differences in substrate concentrations of in vivio vs in vitro scenarios apply here?

    1. Here's what I wrote in my textbook (p. 407).

      Citrate synthase catalyzes the first reaction of the citric acid cycle. This would seem to be a suitable control point for regulation of the entire cycle. ATP inhibits the enzyme in vitro, but significant changes in ATP concentration are unlikely in vivo; therefore, ATP may not be a physiological regulator. Some bacterial citrate synthases are activated by α-ketoglutarate and inhibited by NADH.

      It doesn't make much sense to regulate the activity of citrate synthase by ATP. You may think that the only purpose of the citric acid cycle is to oxidize acetyl-CoA and generate NADH for use in making ATP.

      That's not true. The pathway is essential for amino acid synthesis and may other processes in a normal cell. Many of these other pathways require ATP.

      Most citrate synthases are not affected by ATP in vitro. In most species it seems to be NADH that counts as the effective allosteric regulator (but not in mammals).

      Furthermore, there are studies in the scientific literature showing that activity might be regulated by ADP and/or AMP and these effectors are much more likely to be the true allosteric regulators in vivo. In that case, inhibition by extremely high concentrations of ATP in vitro might simply reflect weak binding of an ADP analogue.

      Not only that, there are papers showing that while ATP may inhibit the reaction in vitro, the in vivo (in siitu) enzyme is insensitive to ATP concentrations.

      There is no simple characterization of regulation of citrate synthase that applies to all species, or even some broad classes such as mammals or bacteria. I decided to avoid getting into a detailed discussion of the problems in my undergraduate textbook.

      However, there are many other textbooks and websites that claim, authoritatively, that citrate synthase is allosterically regulated by ATP so I thought I should mention that these claims might not be true.

      I know you probably don't care, but biochemistry textbooks often copy each other so that errors and mistakes get propagated without any fact-checking. The problem is especially severe in basic metabolism because most textbook authors don't like the subject and don't bother keeping up with the latest scientific literature. That's why the description of basic metabolic pathways has hardly changed since the 1970s.

      There's an additional problem associated with this phenomenon. Any textbook that attempts to update information and publish a correct description of a reaction that conflicts with the other textbooks is likely to be rejected by most teachers who assume that the oddball is wrong and the majority of textbooks are correct.

  12. No no... please do not take me wrong! I share your frustration how texts will often copy each other's errors in deference to educators who do not know better.

    Your expertise in Biochemistry is matched by your clarity in explanation.

    Thank you! I stand deep in your debt.

    Your explanation how citrate synthase is crucial in other metabolic pathways also renders moot my query of regultion by kinase. I am delighted you took the time to correct me.