Tag Archives: molymods

Friends, Romans, countrymen, lend me urea

A few weeks ago I burbled on how I use Molymods to enable Year 10 students to work out the balanced equation of aerobic respiration. Today I did something similar with Year 13, as we start to explore the liver.

As with all such activities, I encourage them to take photographs with their phones as they go along, which they can use for reference/revision.

I started by asking each student to make an amino acid from basic Molymod atoms and bonds. Once the initial panic/hilarity subsided (“what? remember something from AS?!?!!?), they actually did OK, perhaps needing a reminder on what to use for the C=O bond. And although most, understandably, went for glycine, there was an alanine and a serine for variety.

So, a load of amino acids swirling around. They’ve been absorbed in the small intestine and taken to the liver via the hepatic portal vein for processing. They’re being plucked from the sinusoid by the hepatocytes – what could the liver cells do with them?

OK, so they’re the raw ingredients for proteins, perhaps they’ll get converted into enzymes or muscle or membrane proteins or electron carriers or whatever.

But what if there’s too many? The liver can’t store excess amino acids – and the amine group is toxic. What’s going to happen? We talk about deamination. I tell them it requires an oxygen atom and produces ammonia.

They then use their amino acid and an oxygen atom to build the products, and use that to write out the equation.

What have they made? Along with the ammonia molecule, I tell them they’ve made a keto acid. Keto acids can be respired, but if the body is forced to use protein for respiration (in diabetes, anorexia, Atkins diet…) then too much keto acid goes into the blood. Why is this a problem?

We talk about keto-acidosis, bad breath and other interesting distractions.

But what about the ammonia?

We pass round a dilute ammonia bottle and take a sniff. Even the dilute stuff is pretty eye-watering (the concentrated version takes the back of your head off!). And you’re making this in your liver! What do you do with it?

Yes, it’s got to be excreted. So I ask them to react two of their ammonia molecules with one carbon dioxide to form a water molecule and one other molecule…

They dutifully work through the reaction with the models and figure out the equation.

Hmmmm, what’s this? They’ve built a brand new molecule! What could it be?

The chemists gamely tried to name it – di-amine-carbonyl? But eventually a light bulb goes on in someone’s brain and they realise what they’ve made.

What I like about this is that they build a molecule of urea without knowing that that’s what they’re doing or what the structure of urea actually is. It transforms the dry ornithine cycle into something immediately interesting and relevant and hands on, and they can use their photos for reference when they eventually sit down to learn it.

Next week, blood!

Good Golly, Miss Molymod

Just a quick idea this week as I was working on the George learns to walk page.

Do your GCSE students struggle to remember the balanced formula equation for respiration?

Try this.


Draw a molecule of glucose on the board and get them to build a molymod version (in pairs). They enjoy this. It’s a challenge and they’ve got to concentrate.

Get them to count the atoms. Link this to the formula for glucose.


Now give each pair 10 (it’s important that it’s 10!) oxygen molecules.


Burning (i.e. oxidising) things in oxygen gives what waste products? Carbon dioxide and water.

So get them to completely oxidise their glucose molecule, using as many oxygens as they need, to give carbon dioxide and water.



Look at the molecules they’ve built now. How many carbon dioxides? How many waters? And how many oxygens did you need? Can’t remember? Well, how many have you got left from the 10?

You could line the molecules up and get them to take a photo with their phone. Or get them to take photos as they go along.


But, and here’s the thing, they remember the balanced formula.