Life from the ground up: Affixing Atoms into Amino Acids

“If you want to make an apple pie from scratch, you must first create the universe.”

Life is composed primarily of 6 types of atom (or elements); carbon, nitrogen, oxygen, hydrogen, sulphur, and phosphorus. That's it really - and I included sulphur because I was feeling generous. Collectively, these atoms are sometimes refered to as CHON (or CHNOPS). All the other atoms which life uses are just the bells and whistles really - things like potassium, magnesium, and iron give biochemistry an extra kick when it needs to do something in a hurry.



Newts are cool, ok?

 It's remarkable then that life is so diverse. With a toolbox consisting of only 6 fundamental units, life somehow seems to be able to achieve a extraordinary level of diversity and complexity, from newts to newfoundland terriors, whilst only having six fundamental building blocks to do this with.

With this in mind I'm going to start a series called life from the ground up. Life from the ground up is going to be a series of posts about how life can be viewed concurrently in both a reductionist and holistic way. In other words, it's a series on how a handful of atoms can be the root of a disease, the difference between cure and poison, and a cause of speciation.                    

Affixing Atoms into Amino Acids

With only 6 atoms to play with, producing life was always going to be difficult. It's amazing that it happened in the first place, but with the benefit of hindsight, it's probably a good thing that it did. For simplicity I'm going to annex Life (rather arbitrarily) into two realms, into the DNA and Protein domains, and for simplicity's sake (it'll become clear later) I'm going to focus on proteins for the moment.

Proteins are the "do-ers" of the biochemical world. DNA doesn't really do anything, it's a repository of information - which in itself is immensely important - but in isolation DNA would just sit around and not much Life would happen. It's proteins which interact with DNA, allowing it to be read and utilised.  

Proteins, or more accurately enzymes, are the facilitators, capable of achieving chemical slights of hand, enabling chemical reactions to proceed within the cell at speeds several orders of magnitude faster than they would do so uncatalysed. What makes enzymes amazing is their plasticity and their diversity of function - just about every chemical reaction that keeps us ticking over is aided by enzymes.

Where do those six types of atom come in? Well, proteins are exclusively composed of these six elements. With only 6 components, it could be imagined that proteins consist of these atoms in every imaginable configuration. These proteins are huge molecules, consisting of thousands of atoms - surely the diversity of life can be attributed to the innumerable, most likely infinite, number of different ways that these 6 atoms can be joined together, in endless complexity?



Carbon (as graphite), Sulphur, Oxygen Bubbles, Granular Phosphorus, and Liquid Nitrogen. 

 These atoms are joined together in 20-odd ways. Yup, 20 ways, and what's more these 20 ways are all strikingly similar, and are known as amino acids.

It's like asking a painter to paint thousands of pictures of innumerable different things, and giving him oil paints of every conceivable colour, tone and hue, and coming back to find that every image he painted was done in 20 odd shades of purple.  

Here's an amino acid (you can zoom, spin, change the viewing style, go nuts) (oh you need Java enabled):

Above (hopefully) you'll see a 3D copy of the amino acid alanine. In the viewer, carbon atoms are grey, oxygen red, nitrogen blue, and hydrogen are white. Alanine doesn't contain sulphur or phosphorus (in fact phosphorus isn't found really in nascent amino acids), but later on we'll see amino acids with sulphur incorporated, and phosphorus tacked on.

Alanine is one of the simplest of all the amino acids. Amino acids are so called because they have a carboxylic acid group (the red carbon/oxygen end of the molecule) and an amine group (the blue nitrogen end. You can see a carbon atom joining the carboxylic and amine groups, which is known as the C-alpha carbon. Above the C-alpha carbon is another carbon atom with three hydrogen atoms coming off it - known as a methyl group. The methyl group is the only bit that changes between each of the 20 amino acids, and it's known as the R group.

And that's about it. The diversity of the amino acids is found in R groups - of which there are twentyish different types. Next time we'll see how these R groups impact on the character of the amino acids, and we'll get a flavour of how they join up to make proteins.