Monthly Archives: September 2015

Retrieving the Krebs’ Disaster

Last year (October 16th: Chemiosmosis and DNP) I came clean about an idea that simply hadn’t worked. In my endless search for ways of making students do figure things out for themselves – I had designed an activity whereby they would work out Krebs’ Cycle for themselves.

I wasn’t expecting them to do this completely from scratch! They had already covered ATP, Chemiosmosis, and proton pumping by electrons fed into the ETC by reduced NAD. They knew that the NAD was reduced with hydrogens originally stripped from glucose by dehydrogenase enzymes. They had carried out an investigation with yeast and TTC and interpreted the results (INSERT). And they had met Glycolysis and the Link Reaction, so had met metabolic pathways and the slow tweaking and adjusting of the molecules as each enzyme makes its own small contribution. So the foundation was there. Could they complete the jigsaw?

It looked good on paper. First, a bit of human interest, the story of Krebs fleeing Nazi Germany and finally settling in Sheffield for his entire career because the people were so friendly. Then a list of the various molecules that you find in actively respiring cells (liquidised liver, I believe) – the citrate and the oxaloacetate and so on, along with their basic chemical formula. Next, a brief account of Krebs’ approach – enzyme inhibition followed by measuring the relative concentrations of these molecules. Finally, an outline of what some of the results of the enzyme inhibition.

From that, I reckoned they could figure it out. But when I trialled it on a class of intimidatingly bright students, it failed. They got frustrated and annoyed and ultimately confused. Not great.

At this point, I had two choices. Throw the whole thing in the bin and abandon it as a basically bad idea – and revert to just chalking and talking through the process. Or I could try and figure out why it didn’t work, adjust the exercise accordingly, and try again. Given the inestimable value of giving students ownership of their learning, of the understanding and recall that result from them finding things out for themselves, I opted for the latter.

The trial class had struggled, I realised, because they were trying to account for all of the atoms in the molecules, and couldn’t make any sense of the oxygens. But oxygen is not an important atom to follow in the Krebs’ Cycle – they need to keep track of the carbons and the process of decarboxylation producing CO2 – and they need to appreciate the over-arching importance of dehydrogenation and the production of NADH to power the Electron Transport Chain and thus maintain the proton gradient for chemiosmosis. But oxygen can be safely ignored.

So I went back to the drawing board and re-worked the exercise, summarising the oxygen content of each molecule with (n). Unravelling metabolic pathways a la Hans Krebs

And last week I ran it again. It worked beautifully. They quickly figured out the sequence of the metabolic pathway from the enzyme inhibition results. From there, they deduced that carbon dioxide was being produced as the number of carbon atoms went down AND they identified when dehydrogenation was taking place. To put the icing on the cake, they then figured out that by attaching Acetyl(2C) to Oxaloacetate (4C) it would take them back to Citrate (6C) and the whole thing could start again. It was bloody wonderful.

So I would urge you to try new things. That’s the only way you can find out if they work! Your students will appreciate the effort, even if it’s not 100% successful, and even an apparent disaster will teach you something about your students, your approach, your idea.

Finally, a couple of pictures taken with our Celestron Digital Imager, a bit of kit that is proving so popular with the department that I’ve had to order two more.

cheek cells by Mariablood

These are student slides of blood cells and cheek cells respectively (cheek cells extracted from the micro-centrifuge approach – look how plump, juicy and numerous they are!). With the imager, you can project live microscope work on to your white board, capture images (as here) and even take video footage.

Have a good week!

Sheep Dash and Water update

Last week I wrote about a last minute lesson plan emerging from a fog of exhaustion and panic (a Groundhog moment from the first year of teaching where every single lesson is like that!). I’m pleased to report that the lesson in question was a great success, the Year 8s enjoyed the activity and could almost immediately understand and explain the difference between their two sets of results ( see attached exercise here Sheep Dash experiment). I also made use of the class skeleton and a spare Chromebook to talk them through the sequence of events that take place from the moment that the sheep makesits dash, to their successfully(or not!) clicking the dart gun.

IMG_0830 IMG_0827

I’m following that up with a simplified version of Bill’s marvellous Brain Injury exercise (also see last year) which is an excellent example of how you can turn what could be a dull lesson in information delivery into a lesson of learning and discovery. It’s based on the fact that most of what we know about brain function was originally deduced from linking an injury to a specific region of the brain (stroke being the classic example), to the symptoms that follow. Students “damage” localised areas of the brain and are told the resulting symptom(s) – they then try to infer what that part of the brain does. (brain injuries) It’s also a great illustration of the potential of Powerpoint, where the direction of the lesson is determined by the students’ choices, not by the linear construction of the slideshow. Have a go! It’s strangely addictive, even when you know the answers….

The new Year 12s are adjusting to life at A-level. I talked last Year (22nd October) on my introduction to Water (which is also my introduction to the A-level course). One girl this year got the HIJKLMNO(5) clue in less than a second (literally!) which given that I normally expect this to take 5-10 minutes, rather threw my lesson plan. But once the water circus and the water properties homework is out of the way, I then go back to the importance of the solvent properties, particularly the idea that metabolic reactions take place in solution. I talk about the origins of life. I talk about Miller and Urey and show them this (amino acids intro it’s another one of Bill’s splendid animated Powerpoints), stressing the idea that in certain conditions, complex organic molecules can arise spontaneously out of simple ones. But there’s a problem….

I herd them all into a corner of the lab. You’re all complex organic molecules, I say, amino acids and nucleotides and stuff, all in solution, pouring out of that cold vent in the ocean floor. The rest of the lab is the big wide ancient ocean, 3.5 billion years ago. If you could only bump into each other, we could get life kick started! But what happens….?

It’s lovely. They all drift apart, sub-consciously (perhaps) recalling Year 9 lessons on Diffusion, until they’re evenly spread throughout the “ocean”. I stop them. What’s happened???? Why can’t you bump into each other???? Oh no! Life is never going to happen… unless…. What else must we have? They instantly see the need for some kind of enclosing structure to stop them diffusing irrevocably apart. What do we call that enclosing structure? A cell membrane! Aha! And what property, I say, must a cell membrane emphatically NOT have????

This last question usually requires a few seconds thought…. Someone might suggest “permeability”, which is fine – I praise the answer and then park it for a future lesson – but what else? Given what they’ve just done, what property must the membrane NOT have? Yep, that’s right, it must not be soluble in water. Which means it must be made out of something…? Hydrophobic. Can they think of any common hydrophobic organic molecules….?

This launches us into Lipid chemistry and the background to cell membranes, one of my favourite topics on this or any other specification.

I structure it this way because I like the story, the logical sequence (rather than sticking water into a random lesson half way through the course), and the evolutionary context. I like the way it stresses the primary role of a membrane – which helps when we come on to compartmentalisation – and I always like getting them up out of their chairs and doing something, even if it’s just role-playing an amino acid in an ancient ocean….

Lesson Planner’s Block

Welcome back to Biological Burblings, and welcome to a new academic year. I hope you all had wonderful summers.

It’s been the usual hectic start to the autumn term. Not one, but TWO (joy) days of INSET, or professional development, or whatever you want to call it (I could think of a few choice words….). Then a day of students in school but no teaching. And then, on the Friday, I took 27 Year 13 students to darkest Somerset for the Biology Field Trip and a full set of ecological Practical Skills Assessments. More joy.

Actually, the field trip is a genuine joy. Nettlecombe Court ( is a glorious setting, an old red sandstone stately home surrounded by deep valleys and ancient woodland and some of the biggest trees I’ve ever seen anywhere. The students are invariably brilliant, we always seem to catch the best of the early September sunshine, there are endless cups of tea and cake, and it’s a gentle way of easing back into the term after the summer holiday. With the abolition of PSAs (I have a bottle of champagne set aside for when I mark the very last one of these wretched distortions of scientific inquiry), there is no longer a compelling reason to organise a field trip, but I’m pretty confident we’ll retain it. It’s popular, successful and enjoyable and – with the OCR Biology A course – there needs to be some ecological investigation in the practical portfolio. I rather like the idea of letting students ask their own questions and design their own investigations. What are other people thinking?

We returned late on Monday, so actual teaching didn’t start for me until Tuesday. Four days of lessons later and I already feel exhausted….

….but we’re up and running. This year I have three Year 13 classes, two Year 12 classes, a Year 7 and a Year 8, as I continue my self-appointed task to re-write the KS3 Scheme of Work. So I’ve got no iGCSE teaching at all. The Year 12s are underway with the new A-level, but still starting with Water – see my blog from 22nd October last year for ideas on this. A colleague of mine also had the wonderful idea of freezing equal volumes of water and olive oil in separate plastic cups. The comparison of volume after freezing is dramatic and, better still, the frozen olive oil cube sinks like a stone in liquid olive oil.

I teach both sides of the Year 13 course, so two groups have tackled Squiggle Chemistry, where they figure out Chemiosmosis for themselves using the same evidence that Peter Mitchell used (Squiggle Chemistry) whilst the other one has launched into maggot innate behaviour experiments and the chance to try out their new found statistical knowledge. For any of you who don’t like teaching statistics, try introducing the Chi2 test with the opening from Rosencrantz and Guildenstern Are Dead, by Tom Stoppard. If you don’t know the play, here’s one version of the first scene ( And here’s the script
The play starts with the two characters gambling by flipping a coin – which has come down Heads 85 times in a row. The winning character, Rosencrantz, who gets a gold coin every time it comes down Heads, is a bit embarrassed but clearly not too bothered. Guildenstern, however, is deeply disturbed, not because he’s lost a shed-load of money, but because there’s something funny with the fabric of the universe. A coin cannot come down Heads 85 times in a row….I ask the students at what point they would stop playing. And introduce the idea that statistics is basically just a way of finding out if you’re being cheated – or if something funny is going on. It’s also a nice way of thinking about alternative explanations – if something doesn’t match your Expected, how could you explain it? Loaded coin? Double headed coin? He’s lying?

As for the KS3 classes, I’m reviewing and revising the Year 7 lessons that I wrote last year, whilst writing an entirely new SoW for the Year 8s. I love the excitement and creativity of generating new lesson plans, but because the Science lessons are standardised across the two year groups, it also means I’m planning new lessons for 3 other teachers who, understandably, want to know they’re getting something good and reliable. That’s quite stressful. I can go into my own lesson completely unprepared and improvise, busk, entertain, distract. But I can’t expect other people to do the same.

And on Thursday night it almost came unstuck. I was shattered, absolutely cream crackered, barely able to keep my eyes open, only just awake. And I had to have a new lesson ready for the next day. I knew what I wanted to do – something on the Nervous System to link to the work they had already done on muscles and bones. But my mind was blank. I scribbled down some random thoughts on how to introduce the topic. But what then? I wanted some kind of experimental investigation that would be fun and different and memorable. The old course was extraordinarily content heavy – masses and masses of facts to be delivered and regurgitated on demand. I want to pull it to the other end of the spectrum – no notes, not much talk, lots of Learning By Doing. But it wasn’t happening for me. My mind was completely blank. Sure, there’s lots of stuff out there, but I was reluctant to steal stuff from the iGCSE course, even if part of me was saying, “oh, just do the ruler reaction time practical, or the skin sensitivity practical.”

But I had no inspiration. So I got up and walked around and did the washing up and turned the children’s lights out and got my stuff ready for the next day….

And then went back to my desk and wrote a lesson plan based around the Sheep Dash game Which would be quicker, to dart the sheep by watching them? Or darting the sheep when they hear a friend say “baaa” when they see a sheep run across. There’s data to collect, means to calculate, graphs to draw, comparisons to make and explanations to explain. It’s not the greatest lesson in the world, but they’ll talk about it when they go home and I’ve bought an extra week to think of the next two lessons….