Category Archive: Teaching

Aug 10

A graph to show

A graph to show [CC-BY-SA-3.0 Steve Cook]

I’ve never been sure where “a graph to show…” comes from. As far as I can tell, A-level specifications don’t use or specify this wording, and you wouldn’t typically see it in a figure legend in a scientific paper. But if you ask first-year students to put a title on a graph without any further guidance, almost every one of them will default …

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Jul 10

Phage vs. host

Phage vs. host [CC-BY-SA-4.0 Steve Cook]

For a recent schools’ outreach day, I put together a card-game based around the arms-races that develop between bacterial hosts and their viruses (bacteriophages). It’s mostly just a bit of fun, but if anyone finds it useful or can suggest improvements (or just make them! I release this under a CC-BY-SA-4.0 license) I’d be happy to hear them.

Dec 16

Stentorian

Stentor sp. [CC-BY-SA-3.0 Steve Cook]

We had the annual “looking at muck down a microscope” practical last week. As usual, the best thing we saw was a ciliate in some pond water, in this case a little trumpet animalcule: Previous winners: Vorticella and Lacrymaria. The Ciliata really are the phylum that keeps on giving.

Oct 16

Teardrops of the swan

Lacrymaria olor [CC-BY-SA-3.0 Steve Cook]

Last year, the most marvellous thing we saw in the pond-water microscopy practical was a ciliate, and this year the prize goes to that same clade. Ciliates don’t disappoint. This is Lacrymaria olor, the “teardrop of the swan”. It’s a predator, like the Vorticella from last year, but rather than sitting rooted to the spot, Lacrymaria is …

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Oct 09

The Wason card problem

Wason cards [CC-BY-SA-3.0 Steve Cook]

The Wason card problem is a well-known psychological test that probes how people think about hypothesis testing. The version I use in one of my first-year lectures is shown below. I think the original version used letters and numbers, but I’m a biologist, so obviously I use pictures of dead pets instead of numbers. We …

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Aug 09

Enzymes provide alternative routes to product with a lower activation energy

Hydrogen peroxide decomposition [CC-BY-SA-3.0 Steve Cook]

An enzyme lowers the activation energy for a reaction Like a previous post, the problem here is not so much that this idea is flat-out wrong, but that it’s very prone to misinterpretation. Text-books often state that an enzyme, or any other catalyst, lowers the activation energy of a reaction. The activation energy for a reaction (written …

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May 01

The Michaelis-Menten model is not applicable to most enzymes in a cell

Sigmoidal kinetics [CC-BY-SA-3.0 Steve Cook]

Enzymes in cells can be modelled using the Michaelis-Menten model Enzymes can be, and often are, modelled by the Michaelis-Menten (well, Briggs-Haldane) model: v = vmax · [S] / (KM + [S]) Where: v is the velocity of the enzyme, which is the rate at which product accumulates vmax is the maximum velocity of the enzyme (i.e. …

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Apr 23

Metabolic pathways don’t really have end products

Metabolic pathways [CC-BY-SA-3.0 Zephyris from w]

The end product of glycolysis is pyruvate This, and equivalent statements about other metabolic pathways: The products of Krebs cycle are ATP/GTP, NADH and carbon dioxide are not exactly wrong, but they are easily over-interpreted in a way that leads to misunderstanding. They are also  easily swallowed as explanations without considering quite what ‘end product’ …

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Apr 09

Enzymes don’t necessarily increase the rate at which products are formed

An enzyme increases the rate of product formation What happens if you add the enzyme malate dehydrogenase to a mixture of of its substrates NAD and malate (both at 1 mM for the sake of argument)? A brief look on BRENDA indicates that the reaction malate dehydrogenase catalyses is: malate + NAD → oxaloacetate + …

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Apr 09

The product of succinate dehydrogenase is ubiquinol not reduced flavin

Succinate dehydrogenase [CC-BY-SA-3.0 Steve Cook, based on PDB 1NEK: Yankovskaya, V., Horsefield, R., Tornroth, S., Luna-Chavez, C., Miyoshi, H., Leger, C., Byrne, B., Cecchini, G., Iwata, S. (2003) Architecture of succinate dehydrogenase and reactive oxygen species generation. Science 299:700-704 doi: 10.1126/science.1079605]

Succinate dehydrogenase (SDH) produces reduced flavin (FADH2) as a product This misconception is so widespread, even the exam boards get it wrong. Page 41 of the Edexcel GCE specification for A-level biology (2008 onwards) states that students should be able to… Describe the role of the Krebs cycle in the complete oxidation of glucose and formation …

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