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DNA is the foundation of life. It codes the instructions for the creation of all life on Earth. Scientists are now reading the autobiographies of organisms across the Tree of Life and writing new words, paragraphs, chapters, and even books as synthetic genomics gains steam. Quite astonishingly, the beautiful design and special properties of DNA makes it capable of many other amazing feats. Here are five man-made functions of DNA, all of which are contributing to the growing “industrial-DNA” phenomenon.

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The study of minerals is the most fundamental aspect of the Earth and environmental sciences. Minerals existed long before any forms of life. They have played an important role in the origin and evolution of life and interact with biological systems in ways we are only now beginning to understand.

One of the most rapidly developing areas in what is now called ‘geobiology’ concerns the role of microbes in processes both of mineral formation and destruction. For example, the ‘geobacter’ bacteria, shown in the accompanying picture taken in an electron microscope, are not just sitting on an iron oxide mineral surface but interacting with it because it is their method of ‘respiration’ (just as breathing oxygen is ours).

A transfer of electrons between the microbe and the mineral in this case brings about a change in the chemical state of the iron (its ‘reduction’) which also causes the mineral to dissolve. Interactions of this type are now known to play important roles in the release and movement of metals and other elements, including pollutants such as arsenic, at the Earth’s surface.

A very different story linking minerals and the living world concerns the ways that many organisms form minerals to fulfil a particular function, such as providing an external skeleton (shell).

For example, the chalk rock responsible for the ‘White Cliffs of Dover’ in the south of England are almost entirely composed of the remains of microscopic plates of calcite derived from a protective armour around unicellular planktonic algae (‘coccolithophorids’). In many cases the products of such processes of ‘biomineralisation’ are delicate structures of great beauty.

A good example is provided by the (as illustrated) ‘radiolaria’, free-floating single celled organisms found in the upper regions of the water column in the oceans, and  which have skeletons of poorly crystalline (‘opaline’) silica.

Amongst the most remarkable examples of organisms producing a mineral to serve a specific function are the ‘magnetotactic bacteria’. Here the bacterium concerned produces a chain of perfect crystals (see illustration of magnetite crystals), most commonly of magnetite, which make use of the magnetic properties of that mineral. It seems that these organisms use magnetite to become aligned in relation to the Earth’s magnetic field and therefore in the most advantageous position in relation to the sediment-water interface.

One of the most challenging questions in all of science is: ‘How did life on Earth originate’? It is now widely believed that minerals played a key role as catalysts for biochemical reactions and templates for the emergence of the complex biomolecules needed for life. Many different routes have been proposed for the emergence of the first living organisms, almost all have major roles for minerals. These roles may have been in providing catalysts through biomolecule sized cavities in their crystal structures or weathered surfaces. Other routes involve clay minerals as substrates aiding in the formation of the first self-replicating genetic molecules, or look to the environments at, or near, mid-ocean ridges where hot fluids emerge releasing a stream of metal sulphide mineral particles. At the present day, both micro- and macro-organisms utilise chemical energy available in these environments for their metabolisms. Iron sulphide minerals are suggested as the key catalysts in these models.

There are challenging questions in all of these areas, whether it be understanding the electron transfer processes involved when bacteria interact with minerals, the mechanisms involved in biomineral formation, or the complex roles probably played by minerals in the emergence of life on Earth.

In these and many other cases, it is the processes at mineral surfaces which are critically important. Only in recent years has it been possible to study mineral surfaces at a molecular scale. Today, we are at the threshold of a new understanding of the processes taking place at the surface of the Earth which integrates the mineralogical, geochemical and biological realms at the molecular scale. Understanding what happens at surfaces and interfaces at scales from global to molecular is key to that understanding. Here, the emergent field of ‘molecular environmental science’ should provide new insights into the way our planet ‘works’ comparable to the revolutionary advances seen in human biology associated with the genetic code.

Featured image credit: Didimocrytus tetrathalamus, by Tim Evanson. CC-BY-SA-2.0 via Wikimedia Commons.

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This is the third post in our latest regular OUPblog column: SciWhys. Every month OUP editor and author Jonathan Crowe will be answering your science questions. Got a burning question about science that you’d like answered? Just email it to us, and Jonathan will answer what he can. Today: How is the information in a gene used by a cell?

By Jonathan Crowe

In my last two posts I’ve introduced the notion that DNA acts as a store of biological information; this information is stored in a series of chromosomes, each of which are divided into a number of genes. Each gene in turn contains one ‘snippet’ of biological information. But how are these genes actually used? How is the information stored in these genes actually extracted to do something useful (if ‘useful’ isn’t too flippant a term for something that the very continuation of life depends upon).

Many (but not all) genes act as recipes for a family of biological molecules called proteins: they literally tell the cell what the ingredients for a particular protein are, and how they should be combined to create the protein itself. (Proteins have a range of essential roles in the human body. Some act as building materials for different components of the body, such as the keratin we find in our hair and nails. Others act as molecular transporters: haemoglobin, which is found in our red blood cells, carries oxygen from our lungs to other parts of the body. A family of proteins called the enzymes are arguably the most important, however. Enzymes cajole different chemicals in our body into reacting with one another. Without enzymes, our bodies would be unable to generate energy from the food we eat (and you’d not be reading this blog post).)

So, somehow, the information stored in a DNA molecule is deciphered by the cell and used as the recipe for a protein. But how?

To answer this question, let’s take a journey inside the cell. We can imagine a cell to be like a factory, but one that has been divided into a series of physically separated compartments. Unlike a factory filled with air, a cell is filled with a jelly-like fluid called the cytoplasm, which surrounds the various compartments enclosed within it. In an earlier post I likened a genome to a biological library. And, inside the cell, this library is stored within a particular compartment called the nucleus.

I mentioned earlier that genes often act as recipes for proteins. But here comes a bit of a quandary: chromosomes – and the genes they contain – are locked away inside the cell’s nucleus. By contrast, proteins are manufactured by the cell in the cytoplasm, outside of the nucleus. So, for the genetic information to be used, it has to get out of nucleus and into the cytoplasm. How does this happen? Well, if we’re in a library with a book that contains information we really need, but we’re unable to take the book out of the library, we might make a photocopy of the page that holds the information we’re after. To get the information it needs out of the nucleus and into the cytoplasm the cell does something remarkably similar. The chromosome containing the gene of interest has to stay inside the nucleus, so the cell makes a copy of the gene – and that copy is then transported to where it is to be used: out of the nucleus and into the cytoplasm.

The copy of the gene generated during this cellular photocopying is made not of DNA but of a close cousin called RNA. RNA is made of three of the same building blocks as DNA – A, C and G. Instead of the T found in DNA, however, RNA uses a different block represented by the letter U (for ‘uracil’). Despite this

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Today we’d like to introduce our latest regular OUPblog column: SciWhys. Every month OUP editor and author Jonathan Crowe will be answering your science questions. Got a burning question about science that you’d like answered? Just email it to us, and Jonathan will answer what he can. Kicking us off: What is DNA and what does it do?

By Jonathan Crowe

We’ve all heard of DNA, and probably know that it’s ‘something to do with our genes’. But what actually is DNA, and what does it do? At the level of chemistry, DNA – or deoxyribonucleic acid, to give it its full name – is a collection of carbon, hydrogen, oxygen, nitrogen and phosphorus atoms, joined together to form a large molecule. There is nothing that special about the atoms found in a molecule of DNA: they are no different from the atoms found in the thousands of other molecules from which the human body is made. What makes DNA special, though, is its biological role: DNA stores information – specifically, the information needed by a living organism to direct its correct growth and function.

But how does DNA, simply a collection of just a few different types of atom, actually store information? To answer this question, we need to consider the structure of DNA in a little more detail. DNA is like a long, thin chain – a chain that is constructed from a series of building blocks joined end-to-end. (In fact, a molecule of DNA features two chains, which line up side-by-side. But we only need to focus on one of these chains to be able to understand how DNA stores its information.)

There are only four different building blocks; these are represented by the letters A, C, G and T. (Each building block has three component parts; one of these parts is made up of one of four molecules: adenine, cytosine, guanine or thymine. It is these names that give rise to letters used to represent the four complete building blocks themselves.) A single DNA molecule is composed of a mixture of these four building blocks, joined together one by one to form a long chain – and it is the order in which the four building blocks are joined together along the DNA chain that lies at the heart of DNA’s information-storing capability.

The order in which the four building blocks appear along a DNA molecule determines what we call its ‘sequence’; this sequence is represented using the single-letter shorthand mentioned above. If we imagine that we had a very small DNA molecule that is composed of just eight building blocks, and these blocks were joined together in the order cytosine-adenine-cytosine-guanine-guanine-thymine-adenine-cytosine, the sequence of this DNA molecule would be CACGGTAC.

The biological information stored in a DNA molecule depends upon the order of its building blocks – that is, its sequence. If a DNA sequence changes, so too does the information it contains. On reflection, this concept – that the order in which a selection of items appears in a linear sequence affects the information stored in that sequence – may not be as alien to us as it might first seem. Indeed, it is the concept on which written communication is based: each sentence in this blog post is composed of a selection of items – the letters of the alphabet – appearing in different sequences. These different sequences of letters spell out different words, which convey different information to the reader.

And so it is with the sequence of DNA: as the sequence of the four building blocks of DNA varies, so too does the information being conveyed. (You may well be asking how the information stored in DNA is actually interpreted – how it actually determines how an organism develops and functions – but that’s a topic for a different blog post.)

You may be wondering how on earth ju