Monthly Archives: October 2014

Year 12 and… what?

Half term is almost with us, hurrah, and I, for one, can’t wait. Lots of sleep lined up.

Whenever I’m planning a lesson, I always like to think of the opening, the lure, the hook. After all, the students are coming in from break, from lunch, from registration, with all kinds of distractions and probably the last thing they’re thinking of is Biology. I want to grab their attention as quickly as possible, get them on task and get them thinking. Projecting an SEM image of an embryo on a pin point – what’s this a picture of? The World War 1 shell casing – anyone know what this is? And so on.

See what you think of this introduction to a Year 12 lesson.

I start by asking if any of them like crosswords. Yes, no, not really. What about cryptic crosswords? Ugh, yuck, no. OK, try this. I project the clue “Beautiful girl in crimson rose(8)”. Huh? What? Don’t get it. So I talk them through how a cryptic clue work and ask leading questions so that they eventually see why the answer is, “rebelled” (8 letters, “belle” inside “red” meaning “rose”). Lovely, elegant clue, with classic misdirection in the defining part. But where’s it going?

Then I say that I’m going to show them my favourite ever cryptic crossword clue, and that they’re going to solve it, and feel really pleased with themselves. It’s HIJKLMNO (5). Bafflement. Consternation. What the…? But they also want to know the answer, they’re intrigued. Suggestions? It’s the alphabet. What, all of it? No, only the middle bit. Describe it. 8 letters in the middle of the alphabet. Which letters? HIJKLMNO. Describe it more succinctly. It’s the bit that starts with H and ends with O. More succinctly than that….

Everyone got it? You will. And that moment of transformation, from utter bewilderment and feeling stupid to understanding the answer is great.

I then switch to the cover of “Aliens Love Underpants”. If you’ve not come across this children’s book, I’d highly recommend it. It’s based on the premise that aliens are here, among us, and they are driven by the urge to steal our underwear. It’s why you can never find a matching pair of sock and why pants go mysteriously missing. When a giant asteroid is heading for earth, the aliens, distraught at the prospect of losing their pants supply, steal a zillion pants, stitch them together in a single gigantic pair of Y-fronts, and ping the asteroid back into space using the elastic power of all that underwear.

Then I show them a picture of Earth flanked by Mars and Venus. If you were an alien, exploring a new solar system in search of a new pants supply, which planet would you choose, and why? They get it. Pants means life. You head for the blue planet, you head for the water. And there’s the key question – why is water essential for life?

I’ve attached the pictures that go with this – I’ve also attached my Water Circus and associated homework assignment. My Water Speed Dating Party, where you constantly mingle and meet a new and rather attractive molecule that you feel a definite attraction to every nano-second, I’ll leave you to imagine…

Have a great half term. I’ll be back in a couple of weeks.


Aliens love underpants

Water Circus revised Sept 2013

Chemiosmosis and DNP; endosymbiosis

I am indebted to one of my colleagues for the following idea – I think it’s brilliant, many of you may already use it, or something similar, but it was new to me and sent me rushing to e-bay to purchase a World War 1 brass shell casing. Not got one in your department? You really should! I would put it up there with our Archaeopteryx fossil cast, our horse front leg bones and our giant brine shrimp tank as being an infallible source of student excitement and curiosity.

Year 13 again, I’m afraid. And as the attached powerpoint shows, it’s the story of the women working in munitions factories in WW1, and the fact that they showed dramatic weight loss (they also turned yellow and were called “canaries”, but that’s another tale). Why? Why? It’s a great example of how to open a lesson with a mystery – it grabs their attention, their imagination, and they get excited because they want to know the answer, they know they’re going to find out the answer, and, if you do it right, they get to work out the answer, which makes it even more satisfying.

So, one of the components of the explosives put into the shells was DNP, or di-nitrophenol. These days, it’s better known as an illegal weight loss pill, and there’s the tragic story of the young Leeds University student who died after taking it. But in the munitions factories it was just a weird and unexplained mystery. What does it do? It acts as a proton channel in the inner mitochondrial membrane. Now why would that make you lose weight? Their ability to explain this is a great test of their understanding of oxidative phosphorylation. You can also link it to brown fat, small babies, and hibernation. So, buy a shell! You can get them for around £10 to £15 on E-bay, and if nothing else, you get the satisfaction of explaining to the school accountant why you’re purchasing WW1 munitions…

…I’m also looking forward to being challenged over my purchase of a bottle of whisky for Year 7 Science. They’ve been studying separation techniques and I set them the challenge of working out how they would separate water and alcohol. As a consolation for not being allowed to actually do it, I’m taking them up to the school kitchen on Friday to teach them how to flambé bananas, which will be deliciously fun, but will also dramatically demonstrate why we don’t distil alcohol in the lab! Flambé bananas, I should add, are the signature dish of Bill, along with fluffy pancakes and slow barbecued lamb.

I’m afraid my idea for getting students to work out the Krebs Cycle flopped rather badly. That’ll teach me to never share an idea before I’ve tested it! Not only did it not work, they got terribly confused about everything and I had to wade in and do some heavy duty lifting to rescue things. It’s been modified now, and I’ll try it again next year, but much more carefully…

Nick and I are currently both trying to get a working model of chemiosmosis going, like the one Brian Cox showed on his programme I can’t remember the name of. Acid and water separated by some visking tubing with a couple of electrodes – a battery, basically – should be able to power a small motor. Mine didn’t even power a small LED and we ended up with about a litre of 0.1M HCl on the floor. Ahem. The origin of life needs a little more work…

One thing that does work is Endosymbiosis with Year 12. After a little background on the history of life and that crucial moment when complicated cells first appeared, I introduce them to Lynn Margulis (see attached sheet) and her idea. They then have to make some predictions about mitochondria based on this suggestion – and then find out if these predictions are true. It can take them a while to figure out what I mean by “prediction” but they will all suggest the presence of plasmids, ribosomes, binary fission, size/shape and susceptibility to antibiotics. The best of them will even predict that mitochondria should have two membranes, which is always a champagne moment.

Have a great week.


Munitions and DNP

TEM bacteria vis plant cells

Lynn Margulis and Endosymbiosis

Cheeky Year 9 microscopy

Do you look at cheek cells with Year 9? It never works, right? Oh, alright, I know there’s some disagreement on this. Bill swears it works every single time. I, on the other hand, have never, ever, ever found even a single cheek cell from the usual SwabYourInnerUpperCheekWithACottonBud technique. Seriously, not one. Even when rigorously following the Burnett Protocol. I had pretty much given up on it. After all, there are so many more interesting, findable cells out there – all the protoctists, sperm cells (no, not what you think – we get them from a cattle breeding centre), and so on. On the other hand, apart from red blood cells, it’s about the only cell of theirs they get to see, and there’s something quite soulful about watching a cluster of you slowly dying on a slide… and reflecting that that tiny dark blue smudge contains all the information needed to make another you.

So, what to do? Well, we carry out PCR with our Year 13s and after mixed results with eyebrow hair root cells, we got spectacular improvement with cheek cells obtained with a saline rinse. And it struck me, hey, look at that cell pellet in the centrifuge tube! It must be full of….. 5 minutes later, I was looking at ridiculous numbers of cheek cells under the microscope. 70 in a single HP view. Over 1000 in a single MP view. Lovely great plump juicy obvious unmissable clumped cheek cells. No more fruitless hunting around a slide!

And it was great. The Year 9s were slightly put off by the saline rinse, but gamely went for it. I encouraged really vigorous rinsing for one minute, accompanied by scraping the inside cheeks with their teeth. Three 60 second twirls in the mini-centrifuge gave a huge cell pellet. Extract it with the end of a split spill (makes a nice little paddle for scooping it up), on to slide, stain, and there are actually so many cells that you have to gently squish them flat with the cover slip. Highly recommended.

And relentlessly pursuing my objective of making my students do all the work, I came up with this idea for covering Krebs cycle. This can be rather dry, even with the wonderful John Kyrk website animations, so what can you do? Well, how about getting them to interpret the results, just as we do for Calvin’s results on Light Independent reactions? I’ve attached the exercise – let me know what you think!

That’s it for now. Have a great week!


Unravelling metabolic pathways a la Hans Krebs

Poking the brain; ATP introduction; chemiosmosis

All good things come to an end and my Year 13s and I were both very sad to finish the Behaviour topic last week. Still, we were able to launch straight into Bill’s brilliant Poke the Brain interactive powerpoint and next week they’ll be dissecting squid to locate stellar ganglia and giant axons, so motivation levels should stay high (even if the lab stinks of squid for days afterwards).

My other Year 13s are grappling with Respiration. This is a nice example of the importance of narrative and flow in teaching. As always, I’m looking for ways to get the students to do all the work while I make a coffee. I start with a quick round of Heads, Shoulders, Knees and Toes to warm things up. What did they need to do this? Lots of energy! Where do they get this energy from? Food! At this point, burn some sugar or scream a jelly baby. The jelly baby is more dramatic, but the burning sugar allows you to ask questions. What’s it doing? What’s the reaction? What are the waste products? What’s the equation? Remind you of anything? So why can’t we release energy like this in our cells? Compare the flaming sugar dish with a tube of yeast quietly bubbling away.

Then I show them the attached PP. Again, it’s designed to make them think. What’s this? (blank looks of panicked incomprehension!). Come on, you did this in Year 12. Oh, it’s glucose. No, it’s not, but right idea – look again. Oh, it’s a pentose sugar. Possibilities? Ribose or deoxyribose. Right. Next slide. What have I done to it? Added a phosphate. To which carbon? (wonderfully creative guesses at this point). Next slide. What’s this? If they’re switched on, they’ll identify an organic base. They might even be able to name it. What have we made? Eventually, they’ll stumble upon the right answer (stressed in the PP). What have I done now? Added a phosphate! And now?

ATP is a phosphorylated nucleotide.

I then use Guy Brown’s Energy of Life analogy of ATP as a gun. What does this look like? A handgun. What do guns do? Fire bullets. Click, and bang, the 3rd phosphate flies off with a big yellow flash. What happened? Release of energy. Right. If I want to fire the gun again, what do I need to do? Re-load it. But if I released energy when I fired it, what do I need to do to reload it? Put in energy. Where does that energy come from? Your food….

Show them the clip from Hidden Life of the Cell where the virus is moved along the cytoskeleton with motor proteins. It includes relevant and useful info on mitochondria.

Homework is then to find out about how ATP powers active transport, translation and kinesin (because they love the little motor proteins in The Hidden Life of the Cell).

Next lesson, they work out the basics of Chemiosmosis using the same experimental evidence as Mitchell (see attachment – and, by the way, how does anyone isolate a mitochondrial inner membrane, never mind do experiments with it?!?!?). Then we explore the concept in a bit more detail (see PP attached) and look at various animations. John Kyrk’s is probably the best. I also use a water turbine as a demo to give an analogy – deeply satisfying.

I keep challenging them with questions. After they’ve labelled up the Chemiosmosis sheet, what’s the obvious question? Blank looks. All these protons! Diffusing into the matrix! To power that little rotor! What’s going to happen? Ah, they get it. Things diffuse to equilibrium. So what have you got to do? Pump them back! What do we call that? Active transport. How do we normally power that? This is always a good moment as they try to make sense of a contradiction. Using ATP? But that’s what you’re trying to make… So, what’s powering this active transport? Where does the energy come from to pump the protons? Oh, glucose oxidation…

At this point I get them to do the TTC Fuschia Fizz experiment (attached) with no other background theory, and they draw some basic conclusions from that. I then get them to build a molymod glucose and ask them to oxidise it. But where’s the oxygen? Think redox. What else could you do? Oh, strip off the hydrogens. What are you left with? Carbon and oxygen. What happens to that? Excreted as CO2. Look at all that hydrogen! What could you do with it? Reduce something. Which then links to their TTC observations. I also like to explode lots of hydrogen balloons at this point.

Then it’s into the ETC, with NAD delivering the hydrogens stripped from glucose to power the proton pumps. Once you’ve done all that, you can finally look at how the glucose is broken down.

If you’re still with me (sorry, this is very long and rambling!) you’ll notice that it’s all in reverse. I think it works better than starting with glycolysis, because if you start at the beginning, there’s no sense of where you’re going and it’s hard to make sense of the point of all that reduced NAD.

Sometimes it’s better to tell a story backwards. Here’s a poster done by a student to bring it all together and show how all the separate stages connect.


That’s quite enough from me. Open Evening tomorrow, staff vs girls rounders at lunch, and Ultimate Frisbee club this afternoon. 4 weeks into the autumn term and I’ve never felt so tired!

Have a good weekend


brain injuries


ATP intro

Fuschia Fizz

Fuschia Fizz Mark Scheme

Squiggle Chemistry