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..