Tag Archives: DNA

Who’s your daddy?

I’m making this the last Burble of this Academic Year. It’s partly a feeling that inspiration is close to running on empty and partly sheer exhaustion. I need a break – as I’m sure you all do too.

I was going to just post some of my favourite pictures of recent work….

…like this spectacular mitosis slide found by a Year 12 student preparing a garlic root tip squash with Orcein stain… (and captured with the Celestron digital microscope imager)

mitosis

… or this fabulous gel, just one from our best ever results with protein electrophoresis. I’m adding to our formidable supply of gel tanks, acquiring enough vertical versions so that we can run more appropriate protein gels with polyacrylamide, but the one on view here is a bog-standard horizontal agarose.

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OK, I wasn’t too impressed with the forensic inquiry of the students – 4 lanes of chicken breast vs 4 lanes of chicken nugget – couldn’t they have included some other parts of the chicken for comparison?!?! – but look at the bands! Photographing with an i-phone or an i-pad also allows for instant fiddling with the picture,  making it black and white and adjusting the contrast to make the bands clearer.

But today was Year 7 Baboon Day, my favourite day of the year.

The full details of this lesson with all the relevant resources can be found here:

Who’s Your Daddy?

So having already role played cuckoos and host birds and rats in Skinner boxes, they now get to role play baboons, whilst half a dozen students try to figure out what’s going on, collect molecular data by “darting” the baboons to get “blood samples” and so on.

All good fun and, as usual, they made splendidly realistic baboons. But the best features of a lesson can sometimes be the unexpected ones. The students cast as scientists had done a great job as field biologists, but were having particular difficulty determining the paternity of the baby baboons. The mothers and babies were fine – the DNA profiles were consistent with their field observations. But who had fathered the offspring?

I couldn’t understand the difficulty. Once you realise that all the bands from a baby must either match bands in the mother or father, so you have to account for all bands present, it’s just a simple logic problem. Isn’t it? But, no, they were baffled. What was the problem? Where was the mental block?

And then one of them had a flash of insight.  Hang on, she said, are baboons different to humans? Can one father have several “wives”?

It was a brilliant moment, a lightbulb moment, one you want to capture and bottle and share with the world. They had been trying to match up mothers and fathers and offspring as discreet, family units. This hadn’t worked and they were getting frustrated and confused. Suddenly, with this new way of looking at the world,  they could make sense of it all. They rapidly worked out that the alpha male was not only the father of 4 of the 6 offspring, but had (shock horror!) sired them with 4 different females.

This is quite sweet – such innocence! such well brought-up students! – but I love anything that startles students out of pre-conceived views of the universe. They had framed baboon society as being essentially the same as conventional, middle class, western human society, and subconsciously made certain assumptions. Which didn’t match the evidence. So something had to give.

Before they left for home, I asked them what they had learned in the lesson. The list was long – dominance hierarchies, stress hormones, grooming behaviour, DNA profiles and how to interpret them, baboon society, field biology, how to communicate without speaking….

And they hadn’t written a single thing down.

Have a great summer. I hope to be back in the autumn with more ideas to share.

 

 

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Strawberry and Coconut genetics

I forget who gave me the idea (I’m afraid I can’t claim it as my own), but if you’re currently extracting DNA from onions with fairy liquid (as my poor, weeping Year 12s used to do), then I’d recommend switching to strawberries and coconut shampoo as I did this year. Smells delicious, looks spectacular DSC_8169 (a little like you’ve liquidised a hamster), and produces prodigious quantities of what they’re happy to accept is DNA (though, truth to tell, most of the white goop is almost certainly pectin).

But onions (cheaper), strawberries (make sure you use coffee filter papers – the goop is too thick to go through standard lab filter paper) or frozen peas (frozen peas, along with onions, are the recommended vegetable of choice for the NCBE), there are ways of telling this story. I saw a teacher recently end the Year 12 Nucleic Acids topic with the DNA extraction exercise, reflecting their belief that practical work is a “just a bit of fun”, tagged on at the end if you’ve got time after the serious business of delivering immaculate notes and diagrams. By then, however, the end product comes as something of an anti-climax because they already know all about it. So what’s the point?DSC_8172

I prefer to do it like this…

Start with the DNA extraction. It’s fun, it’s messy, you can throw in some interesting questions on why you need to use detergent, 60’C water baths, protease and ice cold ethanol, and they end up with great goopy snot-like dribbles of “DNA” – several 1000km of the stuff if you reckon on 1m per cell.

Again, I should stress that if you want a higher percentage of real DNA, then onions or frozen peas are better, but given that we’re not going to sequence/amplify/carry out X-ray crystallography with the extracted material, I’m happy with my strawberries. The key learning point, apart from interpreting the extraction design, is that cells contains loads of this stuff, so it must have some really important function.

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OK, so there it is, DNA. What next? Well, there’s obviously loads of it, so it presumably has some importance to cells, but what exactly does it do and how exactly does it do it? They’re motivated to find out more so I send them off to think through some of the classic experiments that identified DNA as the molecule of inheritance.DNA experiments exercise

Next lesson, it’s time to explore the structure. You could just tell them, of course, but why not get them to work out the structure for themselves? I do no more than tell them that nucleic acids are polymers of nucleotides, and sketch the structure of a simplified nucleotide for them. They then do exactly what Watson and Crick did – cut out card models and try to fit them together.DNA model instructions DNA model parts (tip: make sure your sugar/phosphates are on a different colour card to your organic bases). Again, I must cite my sources – this is another of Bill’s typically brilliant creations.

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What makes this wonderful to watch is that even if they can remember A-T and C-G from (i)GCSE, they can now see why it has to be that pairing – A to T to 2, C to G to 3 (say it out loud), is my tip for remembering the number of hydrogen bonds.

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We then bring all the nucleotides together in a large class molecule…

DSC_8202…and I play them the clip from DNAi where Jim Watson recalls the moment when they saw it  – the morning of February 28th, 1953. I tell them he got a Nobel prize for doing what they’ve just done – if you make your students feel brilliant, then they will do brilliant things.

We go back to the model and discuss it. What can they see? They can see that, to put it together, the two strands have to run anti-parallel. They can see the symmetry that the purine/pyrimidine pairing gives. It’s easy to point out the 3’ 5’ direction. I mention the footnote to the original Nature paper – “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material”

Can they see it as well? Yes they can! That base pairing means each half is a template for the other may be half remembered from (i)GCSE, though not with the clarity provided here. The hydrogen bonds which provide such a ready means of unzipping the molecule are also starkly obvious. Their next homework will be interpreting the design and results of Meselson and Stahls’ beautiful experiment. DNA Replication Meselson Stahl prep Meselson Stahl experiments

And so on. We hang our model from the ceiling and attempt to make it 3D and helical. It comes in very useful when explaining PCR to the Year 13s.

In the next lesson, when I finally give them a simplified diagram to label, DNA basic structure the detail they recall and include is fantastic. Because they figured it all out for themselves while I made a coffee and fed the hamsters.

Lego proteins

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A lego crayfish, as built by my eldest son when he was 6

I had the idea for the following lesson when I was trying to come up with a good analogy for ribosomes for Year 11. We were teaching AQA GCSE biology at the time (shudder – never again) and ribosomes were on the spec. No objections from me; I’m all for making the GCSE cell a bit more interesting, and it’s easy enough to label some dots on the cell diagram and attach an annotation, “site of protein synthesis.” But I wanted to go beyond the label and learn approach. I wanted to help the students actually understand what went on at a ribosome – as always, a student who understands something has, de facto, learned it, and will be pleasantly surprised when they come to revise the topic.

But to understand what goes on at a ribosome, you need to understand what a protein is. You need to have an idea of what they’re made of, and what their role in the body is. Most of this, of course, doesn’t get touched on until A-level. OK, yes, a GCSE student will be vaguely aware that proteins are “building blocks” (though, boy, doesn’t that sell proteins short! If I was ATP synthase, I would be mortified at being described as a mere “building block”) needed for growth and repair. Some may even recall from the digestion topic that proteins are made of amino acids, but none of this helps with actual understanding. After all, what is an amino acid? At this level, it’s all too vague and abstract, and the vague abstraction is rendered even more difficult by complicated technical terms.

So what could I do? I wanted an analogy, something familiar and comfortable, to show that you can make different things with the same basic blocks. Hmmm, blocks. Something like… lego. Could they build things with lego? But how could I link this to ribosomes?

And then I stumbled upon these. http://www.lego.com/en-us/creator/products/3in1models and had my eureka moment.

Hopefully, you can immediately see the analogy I planned to use. 3 in 1 kits? In other words, you can make 3 different things from the same basic building blocks, depending on which instructions you follow….?

I promptly ordered a dozen sets (3 sets of four different ones; they’re pleasingly cheap) to make up enough for a class with one lego kit between two students. I cut up and laminated the different versions of the instructions – each pair of students gets just one of the versions. I set it all up in advance of the lesson so that…

… the students come into the lab and CANNOT BELIEVE THEIR EYES. They stop and look at me. Is that really LEGO ON OUR DESKS? They look around. Yes, it really is LEGO!!!. They look at me again. Really? REALLY? Is this for us? You want us to play with… LEGO???

I don’t think I’ve ever made a class of students happier. Indeed, at that point I didn’t really care whether the lesson was going to work or not. Anyway, once they got over the shock, they gleefully throw themselves into it, and for 15 happy minutes they follow the instructions and build their particular version of whichever kit they’ve got (the helicopter, or the aeroplane, or the racing boat, or whatever). There’s no rush here; they’re having fun – let them take their time, play with the models, whatever.

Once they’re all assembled, it’s time to tackle the biology. Now it’s crucially important at this stage not to rush the explanation. I’ve heard teachers say that the demo, the practical, the lego is just a bit of fun, some light relief to break up the monotony of diligently taking notes, but this couldn’t, in my view, be more wrong. Yes, the lego is fun, of course it is, but it’s also got to stimulate curiosity and questions, otherwise the learning outcome is lost. This, for me, is where the real lesson planning comes in, working out your questions in advance. You want a line of answerable questions that will lead the students to the right answers without you ever actually just telling them…

Now, chances are that they’ve not been thinking much about Biology while they’ve been building their backhoe loader, so…

….get all the models onto a single desk and gather the students around.

Start by asking, “So, what’s all this about, then?”

Huh?

Well, this is a Biology lesson. Why have I got you all making lego?

They won’t know, obviously, but they’re refocused, and they should be curious. Yeah, what is this all about?

Group models from the same kit together. Get them to describe their model.

What’s that?

It’s a rescue helicopter!

What’s it for?

For rescuin’.

What’s that?

It’s a digger.

What’s it for?

For diggin’.

And so on.

So you’ve built loads of different models, all with very different shapes and functions, but made out of basically the same stuff (if it’s from the same kit, it’s exactly the same stuff). What are the things that you build in your body? What are the things that do things in your body? What are you made of?

And so they gradually start to see that the lego models are the equivalent of proteins – can they think of any examples? In Year 11, they should, with a little prompting, be able to arrive at all kinds of enzymes, some hormones, keratin and collagen, muscle, maybe even antibodies …. diggers and helicopters, aeroplanes and speedboats, racing cars and dump trucks…

So what do the individual bits of lego represent?

Huh?

Well, what are proteins made of?

Aha, amino acids.

Right. And where does all this assembly take place? In other words, what were you yourselves representing?

Ribosomes.

Oh, but how did you know which model to build?How does a ribosome know which protein to make?

We had instructions.

So you did. What do those laminated sheets represent?

Huh?

Inside a cell, instructions, information, what form is it in?

Oh, DNA.

And so on.

As I say, I use it with Year 11, but it could be equally useful with Year 12, or even Year 13 – no-one is ever unhappy to play with lego!

A few practical points:

  • The lego bits are tiny – keep each kit in a shallow plastic tray to minimise the risk of losing “amino acids”.
  • Get the students to disassemble the models at the end, or your poor technician will spend hours doing it.

OK, that’s enough for now, and for 2014.

Have a splendid holiday and I’ll be back in the first or second week of January 2015.