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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

A machine to teach with: ATPase as a core cellular mechanism

Angry cartoon firecrackerBoth studies and common sense indicate that common threads running through our teaching provide students with reinforcement of both thread components and the things they connect. This approach also highlights conveying principles rather than fact collecting as our learning objective. The details of a basic ATP hydrolysis reaction illustrate both key principles (how enzymes actually implement their abstract aspects [speed up reaction; lower reaction barrier], roles for specific amino acids and protein folding), value of understanding chemistry in thinking about biology) as well as providing students with a tool that they’ll see over and over… and over again: the core mechanism is found in nucleotide addition, kinase and phosphatase reactions, pre-mRNA splicing, the timing mechanisms of GTPases [tubulin, EF-Tu, GPCRs], and… oh yeah: virtually every ATP-driven or -coupled reaction in the cell!

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What’s important about… ATP?

Every Intro Bio student can cite ATP as ‘the energy currency of the cell’… but what do we mean by that? And why does it play that role? These are important questions, and they deserve answers. And real ones, not invocation of the mystical ‘high energy bonds’.

Perusing Wiki for an image to link for ATP, I’m surprised to find how many directly imply that the ‘value’ is in the bond between two phosphates. I think suggesting that this is the case does a disservice to students’ ability to analyze and understand. We’ve taught them by now that bonds are simply shared pairs of electrons. Blaming the bond for the potential energy inevitably raises the question “Is it the electrons that are special? If not, what is it about the bond?”. No and nothing.

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