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AP Biology

the Citric Acid Cycle: Follow the money (electrons)

Classical citric acid cycle image

What makes the Citric Acid Cycle (Kreb’s cycle, TCA cycle) ‘hard’? Misdirection. When most of us sit down to learn something, the first question is usually “what is important here”. When trying to figure out a complicated process (Americans: think about the sport of cricket!), the questions are “What should I be looking at? And what am I seeing when I look there?”. It’s deeply ironic, then, that in looking at Introductory Biology textbooks, it’s incredibly difficult to spot an electron anywhere in representations of the citric acid cycle. This is bizarre, in that the cycle has only two jobs: 1) extract ‘high value’ (energetic) electrons, and 2) be a cycle so it can keep… cycling. A call for electron-watching and some suggestions for teaching electron flow through the citric acid cycle follow (Image source) Continue reading

Interactions in biology: it’s binding all the way down


We use a several terms in IntroBio that all mean the same thing, but may mean little to students in the classroom–‘binding’, ‘specific interaction’, ‘interacts with’, ‘recognizes’. This is particularly dangerous with ‘recognizes’, because newcomers can envision a police line-up: targets appear and we visually choose one. Alternatively, we risk students imagining a somewhat mystical, or at least poorly-defined ‘way’ that molecules have that is beyond their ken. Nothing could be further from the truth; in some ways one of the easiest things to understand is why two molecules ‘stick to’ one another and overcome the force of Brownian motion, at least for a little while.

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Biology: teaching theory vs. teaching practice

learning - theory and practiceHaving participated in teaching biology at a new place, I’ve completed a fresh run as an observer and found myself thinking a lot about introductory biology teaching decisions (the Bob Seger song “Against the Wind” has one of my favorite lines: “Deadlines and commitments/what to leave in… what to leave out.”). It occurred to me that there are two largely separable ways of teaching Introductory Biology that are quite different depending on what we want our students to be able to do. I believe the distinctions are not vastly unlike architects vs. engineers, or theoretical vs. applied physicists. It comes down to whether we want to be exposing our students to the how and why or the how-to and when-to. I’m almost exclusively in the former camp… but if we’re training medical students and technicians for industry, how much of ‘how does this work’ is needed? On the other hand, if we’re trying to attract and prepare P.I. (principal investigator)-level individuals and teach all comers ‘how life works’ alongside the wonders of what has evolved (and how), perhaps I can justify my approach. Continue reading

Pull yourself together! Self-assembly in biology

Double stranded DNA moleculeLists of the ‘characteristics of life’ are a common element in introductory biology early lectures. Generally, these focus on movement, energy conversion, organization, etc.–all legitimate concepts. But the role of self-assembly in biology must not be underestimated; it’s a key feature of the flow of information in the Central Dogma (through the specific partnering of bases), folding of proteins from linear strings of amino acids (readily specified by linear structure of nucleic acids) gives rise to the functioning machines at the heart of almost all cellular work and action, and even membranes, while not members of the Central Dogma club, have function that relies critically on aspects of self-assembly. Without these properties, life would not only be impossible–they’re prerequisites for life to evolve from non-life.

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You might be a mutant if… human mutations and phenotypes

Prototype of womenStudents store Introductory Biology topics in ‘bubbles’, often unrelated to each other or the world the students inhabit. One challenging area where this happens a lot is mutation–how mutations happen, why mutations have consequences, and even the idea that mutations happen to ‘us.’ One of my favorite articles from the popular press had a title similar to “Blue eyes arose through human ‘mutation’ thousands of years ago”, with the word mutation offset in quotes–to indicate blue eye changes aren’t real mutations? In trying to make the concept more concrete and interesting to students, I’ve accumulated a series of human phenotypes (and primary literature sources) that amuse students while also driving key concepts home. The role of mutation in generating diversity and driving evolution is quietly but steadily made as well.

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Molecule display in introductory biology

Molecule display of guanine as it 'feels'Teaching the world of molecules to relative newcomers is challenging because it’s an invisible world with ‘rules’ that don’t always have a 1-to-1 correspondence with the macroscopic world (looking at you, hydrophobicity). A second issue is that while the molecules themselves are concrete things, we discuss them using their labels–A or adenine or glucose or ‘protein’. Too often, students end up with vague notions (or none at all) about these entities. Given that everything in the cell is made of and run by molecules, student success in thinking and understanding is critically dependent on what they’re picturing as molecules. I think care in and improvements of molecule display can go a long way towards making their lives easier and their understandings richer.

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