DNA: Cytosine

Of the four nucleobases in DNA, cytosine is the simplest to model. Its angular geometry is two dimensional and it has just a single six-sided ring. Here’s the molecular model done the Wikipedia way:

It’s not that hard to make a cytosine molecule from scratch using the molecular modeling tool kit, but why not look at some Sketchup tricks to speed up the process of making models? We can do that by recycling parts of the models that we’ve made previously.

So let’s start with our previous model of the benzene ring and add and subtract as necessary to make cytosine. If you didn’t make and save a copy of benzene yourself, I’ll upload a model to the Google Sketchup Warehouse.

So we start with benzene:

Orienting the model so that it looks like the wikipedia example of cytosine, we delete everything in our benzene model that’s different from cytosine:

This looks like a real mess, but now it’s simple to modify. First let’s put in the nitrogen atoms:

Now, we could copy bonds from the tool kit and orient accordingly. But why not simply copy from the molecule itself, where the bonds are already in the correct orientation?

Like so:

(Notice I snuck in the oxygen molecule too.)

Finally, we want to attach the amine group at the top. What is the amine group? Just a branch with a nitrogen and two hydrogen atoms. Again, rather than raid the tool kit and orient bonds, let’s simply copy and group the pre-oriented parts of the molecule thus far:

And so, adding hydrogen atoms, we get:

Here’s the wikipedia model again for comparison:

It may seem at first that the tricks we used to construct the cytosine model out of the benzene model apply only to the realm of making models in Sketchup, but if you think about it, maybe nature works this way too. That is, using chemical processes rather than mouse commands, maybe nature starts with benzene molecules and transforms them into cytosine molecules by removing carbons and oxygens and adding nitrogens and oxygens, and then capping with an amino group. Yes? No? Well, something to think about.