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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.

(Image source:

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Problem solving perspectives: questions determine answers

If we look at problem-solving as “figuring out something truly novel” as opposed to “grinding out an answer Figure with faces if seen as black; a vase if seen as whiteusing different insertions for the variables”, the game gets much more complicated… and there’s a lot more to ‘teach’ and to discover. I’ve posted a number of different “derived wisdoms” elsewhere (Polya, me, thinkBio’s problem-solving games directory), now I want to highlight a specific example about a general principle: “The way represent a problem defines the answers we can come up with.” Take the famous figure on the right. If presented as “Look at the black images; what do you see?” most come up with a pair of faces. If asked “What is depicted in white?” you see the goblet. The derived challenges are: how do we make sure we cast problems correctly? and how do you ‘unsee’ an initial finding?  Continue reading

Great experiments: Crick hypothesizes wobble pairing

Robotic hand with DNAToo often, biology is presented as gathering data and letting it lead us. While this is a valid and important component, there are also many glorious examples where the thinking came first and directed the experimentation. Many of the great experiments in biology came about this way–Meselson and Stahl (semi-conservative replication), Hershey-Chase (the Blender experiment, or ‘who is the genetic material)… and some that are more abstract–Pauling’s proposal of the alpha helix and beta sheet… and a number of Crick’s hypotheses. This post covers his prediction that efficiencies would be achieved in the tRNA pool through wobble pairing: relaxing orientation of the participants in a basepair to allow one base to partner with several others. Continue reading

What’s in tRNA structure: all alike; each unique

Too often we overlook the tough job that tRNAs do, seeing them only as the handmaidens of translation: matching up with mRNA; delivering a specific amino acid place on their heads by synthetases, arriving at the ribosome to first take the chain and then be stripped of it… These tiny (~100 nte.) elves  perform a series of amazing sleights-of-hand: sometimes they must all be the same (the ribosome must deal similarly with all of them); at other times, unique (codon matching) and still other times, as ‘family members’ (all those ‘serviced’ by a single tRNA synthetase. Just how much recognition-surface and information is stamped onto a tRNA?

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I’m back baby: thinkBio rises Phoenix-like

After a long hiatus, I’m going to be dedicating a lot of the next six months (Feb-August 2017) to this site. Major projects include getting the first chapters of the Intro Bio eText usable (scientific method & Central Dogma players), porting more things to Web platforms (both the ‘VocabuWary‘ and Chapter Review tools are trembling on the edge of readiness), and updating the 3D menagerie to consolidate the tricks I’ve learned and start to realize the vision of letting students operate the viewing of and almost touch the molecules of life.