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.  

A lifetime's supply of chocolate

"I predict that within one-hundred years, computers will be twice as powerful, 10,000 times larger and so expensive that only the five richest kings of Europe will be able to afford one".

The mind boggling rise of computer technology from abstract plaything of Victorian gentry, to 70s technophobe joke, to inevitable robot overloads, is both marvellous and boringly ubiquitous to my generation, brought up with Windows '95 and Netscape.

For people old enough to remember when a Casio digital watch was both a technological wonder and status symbol of conspicuous consumption however, computer technology holds an uneasy place in there life, occupying both the "it's cool to Google my name" and the "it's scary there's a picture of me when I Google my name" parts of their brains.

Two properties which helped stoke this explosion in computer technology were both the plasticity and "scalability" of computer technology. The plasticity of computer tech is the fact that the "bits" of a computer can really be made of anything - in a "normal" computer it's electricity, but it could be anything given enough imagination. Even things which we don't fully understand - such as quarks.



Lego Vs PlayMobil.

 Scalability describes whether a technology is capable of being grown, or whether it's a stand-alone application. A good analogy is Lego. A Lego model can be pulled apart and reduced to it's basic and easily-understood components, i.e. the bricks, and built and scaled up into more complex structures. Compare this to something like PlayMobil - a "standalone" product which can't be reduced and changed or built upon. Computers are like Lego - they have basic parts which can grow in complexity.

One amazing example which illustrates these two properties was unveiled the other week in the journal Science, a scalable computer - made of DNA (Science 113:1196-1201).

This isn't the first DNA computer, but it definitely shows more promise that previous attempts - which were stand-alone constructs. This new computer can solve the square root of any number up to and including 15 (which is 3.87298335 by the way), and it only takes 7 to 10 hours figure this out - I know impressive right?

Being facetious aside, it's impressive that DNA can be cajoled into achieving this mathamatical feat. But further to this is that the design of this DNA computer is eminently scalable as it is essentially based on the same logic used in computers - Boolean logic.



An AND gate.

Boolean logic is the essence behind the earliest computers and electronics - manifest in a technology called logic gates. If you did GCSE physics, you probably came across these as AND and OR gates in circuit diagrams, but there are plently of exotic logic gates like NOR, NAND, XOR and XNOR.

The basic principle is that the gates takes a various "input" signals and then transforms them into something else, an "output signal". An AND gate (pictured) works when the various input signals (labelled as A and B in the image) are both True - or in binary terms, 1. When this is true, the signal coming from the other side of the AND gate (from wire O) will also be True (or 1). An OR gate alternatively has an output of 1 when either A or B (or both) equal 1.

These logic gates can be wired up in large numbers in various sequences to produce some very nasty and complex circuit diagrams which can achieve wonderfully complex computations. The DNA computer was achieved using some of the most basic properties of DNA to produce logic gates.


Compulsary Image of DNA

 
DNA is a double stranded molecule, with the two complementary strands being highly specific for each other. The DNA computer uses this property by creating DNA nanostructures called "seesaw gates".

Essentially seesaw gates consist of pieces of double-stranded DNA which wait around for a signal - a complementary single-stranded piece of DNA - to reach them. Using some DNA-based jiggery-pokery, the incoming single strand (if sufficiently concentrated) displaces one of the strands inside the seesaw gate, and hybridises to the free strand. The displaced single strand of DNA is then a new signal, which can go to another seesaw gate - and so the signal is propagated throughout the circuit.  

Seesaw gates can be tuned into make their properties more interesting. This is achieved by increasing the concentration of the incoming signal DNA required to cause of strand displacement of the gate DNA. By having a few seesaw gates in order, along with a fluorescence-based (and slightly more complex) "reporter gates", we can produce DNA-based NOT and AND gates.

What's great about this method is it's scalibility - just string together the NOT and AND gates and you too can create a DNA computer. What's more is that stringing up about 30 of these seesaw gates can produce a circuit which can produce the square root for 15 numbers - imagine what can be done with 300 or 3000 seesaw gates! Entire fully understood DNA computers could , if robust enough, be used to create synthetic life in an entirely comprehensive and determinate way.  

PCR to the People

"If you want to change the world in some big way - that's where you should start - biological molecules." - Bill Gates

Molecular biology is starting to undergo a cultural change - moving from labs to garages and spare rooms. Soon every man and his dog will soon be meddling with molecular biology in a vision which is reminiscent of the the 1980s computer-garage-hackers - who were so last millennium by the way.

At the heart of this movement is the hope that the manipulation of DNA, the operating system of the cell, which was once so mind-bogglingly-Nobel-Prize-winningly complex that it was the preserve of Professors and PhDs only, is gradually becoming facile, and may one-day be commonplace. It's a gradual distillation of the disciplines of recombinant DNA production and synthetic biology into workaday and useful "tools". 

I use the word tool in an abstract sense, rather than a hammer and spanner sense, in the way that a PC is a tool - a facilitator for (hopefully) greater things. Extending the analogy of computer technology, people don't really need to understand the concepts of binary and logic circuits to print off an essay from Word '95 - and the same can be said for synthetic biology. If the world of molecular biology was standardised enough, and familiar enough, and most importantly cheap enough, people would be able to manipulate (and create) biology to their heart's content.  

Facilitating this movement from lab space to loft space are two movements. 

First, molecular biology is pretty open source - and the hope is that it will become increasingly open source. Extraordinary useful resources, little things like the Human Genome for example, are essentially open to Joe Public - even if it's difficult for Joe Public (or myself for that matter) to make head or tail of the information presented. Programs which present the information in a sensible and utilitarian manner however are all over the web - are are extremely helpful. Other databases, such as the PDB which focuses on different (but not necessarily separate) areas of molecular biology, are popping into existence all the time - with a basic prerequisite of open access for all. These databases are the raw material for the budding garage DNA enthusiast - it's a library is to an aspiring authors. Garage DNA meddlers - just like authors - can cut and paste DNA from databases to create new and inventive organisms. 

An OpenPCR machine - for $512 you too can make copies of DNA!

Second, is that the price of manipulating DNA is gradually moving into the amenable zone. Reading or "sequencing" DNA is almost becoming redundantly inexpensive. The individual letters (known as bases) of a string of DNA can be read for far less that $0.01 each. Within the decade (if not sooner) it is believed that sequencing your 3 trillion bases long genome could be $1,000 (or less - if the dollar is still in existence by 2020 and not replaced with renminbi). In 2020 you'll probably be able to spit in a tube, or swab your cheek, send it off mail order, and hey presto in a few days you'll have your genome sent back to you on a futuristic floppy disk.  To put this in perspective, the sequencing of the first Human Genome took the best part of 21 years and three billion dollars. Other applications are abound; hand-held DNA sequences may make it quicker to sample the DNA of an unknown species of plant rather than look it up in a field guide. Producing your own DNA (now as oligonucleotide synthesis) however is still more expensive and labour intensive, but there are plenty of plans to overcome this. And as my old pal Craig Venter showed, synthesising an entire genome is within the realms of possibility - although rather out of the price range of (presumably) you and (definitely) I.

When manipulating DNA, sequencing DNA, and synthesising DNA becomes easy and affordable interesting things are set to happen. When what was once a major limitation of "programming" biology is removed, the whole arena becomes infinitely more accessible. Imagine early computer programmers worrying about how much each line of code cost the programmer to write or even read - it would have been an omnipresent inhibitor to everyone's creativity. When the cost-constraints for tinkering with DNA are a relic of the past - that's when coming home from work and playing with the genome of the organism your designing in your garage becomes a possibility.

(IN)ORGANIC

"I can make urea without needing to have kidneys, or anyhow, an animal, be it human or dog."-Friedrich Wöhler

It’s becoming apparent that there’s something special about life. Thermodynamically, cosmologically, probabilistically – life seems to overcome the inherent obstacles which would make any sane person question the likelihood of their own existence. Yet amongst this grandeur, wonder and humbling beauty, a question hangs over the entire affair – what is life? Pinpointing the exact moment when lifeless, inanimate matter transforms into a living entity is difficult, and a question which needs answering - fast. When laboratory created life, artificial intelligence, and human augmentation all seem inevitable rather than an impossible there is a lingering doubt - when does the inorganic become organic? What’s alive and what’s not?

Historically, ascribing a material or chemical as part of life or not was an unambiguous affair – the two great kingdoms of organic and inorganic chemistry were supposed to be unequivocally separate. Vitalism, a belief that living things were of a different constitution to inert matter, underwent a resurgence in the early 19^th century on the discovery of chemicals such as chlorophyll, which had no known comparably complex inorganic counterpart. Life was chemically complex, irreproducible, and beyond the chemical abilities of man.

However, chemicals which were once intrinsically aligned as components of life came to have their allegiances questioned. Urea is something which we’re all reassuringly familiar with as a component of urine. At a molecular level urea consists of an atom each of oxygen and carbon, a couple of nitrogen atoms, and a smattering of hydrogen – atoms as natural and abundant in life as it comes. To question whether urea is organic is elementary, almost pedantic, isn’t it? A chemical produced by my wonderfully fleshy body can be classed as organic indisputably.

But urea can also be produced inorganically – by heating the undeniably chemically sounding potassium cyanate and ammonium chloride. Is the urea produced by this reaction, known as the Wöhler Synthesis, organic? What if I also told you that urea can be produced in a test tube with the hydrolysis of arginine to ornithine using the catalyst arginase? Although this may sound inorganic, but it’s the exact reaction that occurs in each and every one of our body’s cells countless times, requiring all that micturition.

Urea is but one of a multitude of biochemically relevant molecules which can be whipped up in a lab over the course of an afternoon. Even the crowning glory of life – DNA, can be manufactured to order, pieced together with a machine comparable in size and complexity to that of a breadmaker.

So is urea inorganic or organic, a thing of life or the lab? Does the source of our urea make a difference? I’m sure that some sources of urea are preferable to others, but is our glossy catalogue-ordered DNA part of the rich tapestry of life, or an inferior doppelganger - incapable of fully realising the potential of naturally synthesised DNA? Are these chemicals natural or not?

It’s a distinction which is becoming increasingly redundant. As was widely reported in the press, Craig Venter’s “artificial life” – an experiment which essentially swapped organically produced DNA for DNA made in the lab – illustrated that artificially produced DNA seems to be just as capable as the organic.

Just as the Wöhler Synthesis undermined Vitalism – experiments like Venter’s are at the forefront of deciding what we choose to describe as part of life, and what (if any) reverence we choose to ascribe to it. The truth is that atoms give very little thought to whether they are in blood or bottle rockets (iron), in pyrotechnics or plants (magnesium), or are found in chalk or cheese (calcium). If the conditions are correct, atoms may conspire to make some “life” happen. Is this breadmaker-made DNA, produced in a “non-canonical” manner, part of biology? Does it break the contiguity of life?

It’s a problem with wide implications. If DNA produced artificially is classed as organic, where does that leave transgenic animals (animals produced using DNA from multiple genomes – the source of images depicting glowing green rabbits)? Surely if I add two pieces of organically made DNA together, the resultant verdant rodent is organic – and yet our gut feeling rejects this as inorganic.

It’s becoming apparent that science is able to blur the once distinct line of natural and unnatural with increasingly unnerving ease. Deciding what is part of our inherited biology – Life 1.0, and what is not - may help allay public fear over the newest advances in science. If we can accept that human endeavours which dabble in the stuff of biology - from “Frankenstein Foods” to limb regeneration – are wholly separate from Life 1.0, and are man-made artifices of nature, the acceptance and incorporation of new technologies may be far easier.