A History Of DNA, Part I: Before the Discovery

Proteins are the biological molecules that make things work in living systems. We could say that they are involved in every process in the cell. They are controllers of biochemical reactions, structural elements that hold parts of the cell together, motors that make things move, signals, and so forth. The function of a protein depends almost entirely on its shape. Its three dimensional shape determines its physical and chemical properties, which in turn allow the protein to serve its unique function. The three dimensional shape of a protein, in turn, depends almost entirely on the linear sequence of the building blocks of life, the amino-acids.

There are 20 kinds of amino-acids. An average protein might have a few hundred amino-acids. So, proteins are the work horses, and their function is determined by its chemical sequence of amino-acids. Now, how do we get a protein of a particular sequence built? To answer this question we need to address two things. First, what is the blueprint that is used to build proteins? Second, how does that molecule actually work?

It is the first question that I want to talk about today. Before we can understand how the code works, we need to understand what the code is made of. I think that we all know the answer today: DNA. Interestingly, though, that was one of the questions that defined molecular biology in the 20th century.

At the very beginning of the 20th century, it was already known to scientist that the code was in genes, which in turn resided in chromosomes. This was known from the work of early cell biologists, Walter Sutton and Theodor Boveri being the most important, who discovered that the particular movement of chromosomes that occurs when cells divide corresponded to patterns of transmission of traits between parents and their offspring. These patters of trait transmission had actually been discovered earlier by the Austrian monk Gregor Mendel.

Cell biologists knew about Mendel’s work, how chromosomes moved, and they developed what now is called the chromosomal theory of inheritance. This theory basically says that the way chromosomes move is somehow related to the way that inheritance occurs, therefore, chromosomes are related to information in cells.

We today know that chromosomes are made of DNA, but how that became a known fact? We must begin by going back to the earlier part of the 20th century, to the work of an English physician named Frederick Griffith. This experiment that I am about to describe really provided the first insight into the chemical nature of genetic information.

Griffith’s Experiment

Griffith was a physician and he wasn’t interested in the molecular basis of inheritance. Instead, he was working on a much more applied problem. He was studying Streptococcus pneumoniae, which is a bacteria that causes pneumonia in humans. What Griffith wanted to do was to develop a vaccine against this particular organism, because the pneumonia caused by it often proved fatal. This was before the advent of antibiotics, of course.

As often it is the case for disease-causing bacteria, there were different strains that varied in their virulence. They varied in how likely they were to induce the disease and cause death. Griffith was working with two strains of Streptococcus pneumoniae. He was working with what we call the S strain on the one hand. This was a very virulent strain. It is called S because if you grow it in a colony, it actually looks kind of shiny and smooth. He had another strain, which he called the R strain, which was non-virulent. If you got the R strain, you might be a little sick but you wouldn’t die. It is called the R strain because the bacteria look kind of rough on the surface.

The important thing to note is that these strains did breed true. In other words, as they reproduced, their offspring had the same properties. S strain bacteria gave rise to more S strain bacteria and so on. It is inferred from that, that the difference between the S strain and the R strain bacteria somehow must be genetically encoded.

What did Griffith do? Griffith was using the approach pioneered by Louis Pasteur, which was to take the organism that you want to develop a vaccine for and kill it. This organism could no longer harm you, but nonetheless, would perhaps induce some sort of immune response if injected in a subject. The idea was to take S strain bacteria, kill them by heating them up, and then take these dead S strain bacteria and inject them into a laboratory mouse, and see if that mouse develops immunity. The mouse wouldn’t die if you injected dead S strain bacteria, but the parts of the bacteria that are injected might nonetheless induce an immune response.

This is a great idea, but it didn’t work. It often doesn’t work. There wasn’t enough left of these dead S strain bacteria to induce an immune response. If you injected these in a mouse, and then injected live S strain bacteria, the mouse would die.

Another common technique that was used then and now to develop vaccines was to eject not only the dead offending organism, but some related organism that was less virulent. In this case, we are talking about the R strain bacteria. The idea is that the live R strain bacteria, because they are alive, would induce the organism to develop a full immune response. That development of a full immune response would somehow pickup some immunity to the dead S strain bacteria. This is a common technique and it often works.

What Griffith did then? He killed some S strain bacteria and injected them in with living R strain bacteria. What he hoped would happen is that the mouse would develop immunity to the S strain, but what happened instead was unexpected, and unfortunate for the mouse, the mouse died. This is a surprising result. What’s being injected into the mouse are dead S strain bacteria, that wouldn’t kill the mouse; and live R strain bacteria, that wouldn’t kill the mouse neither. Nothing was injected in the mouse that should kill it, and yet the mouse died.

What Griffith found out when he dissected the poor dead mouse was that inside it were living S strain bacteria. He injected dead S strain, and when he took the mouse apart, he found living S strain. What Griffith concluded from this work, and correctly, was that somehow the living R strain bacteria had taken up something from the dead S strain bacteria, and incorporated it into them. That somehow transformed the R strain into the S strain.

Griffith later showed that he didn’t need the mouse. You can do this in a beaker. If you put dead S strain and live R strain bacteria in a beaker, some of the live R strain would become transformed into live S strain.

What’s really interesting from this experiment, in my opinion, is that the material that they incorporated must somehow be genetic material. It must somehow have information in it. How else could the R strain bacteria now become virulent like an S strain bacteria? The difference between S and R had to have something to do with genetically transmitted information. What Griffith did was he left it there. It was only 1929 when he was doing this work. He said that he had discovered what he called the transforming principle.

Our interest in this, and of scientist interested in genetics, is that somehow this transforming stuff must involve genetic material. In my next post we will see how this experiment helped in discovering that DNA is the molecule that holds genetic material in living things.

The Origin of Life, Part II: Polymerization

Okay, let’s go on with the origin of life. In my last post I talked about Miller’s experiment. The significance of this experiment was simply to show that non-biological processes could result in the formation of organic molecules, including amino-acids and nucleotides. These molecules that Miller got, however, were still relatively simple. They thus only represented a first small step.

Amino-acids and nucleotides by themselves don’t get us very far because we need to get these simple molecules linked together. They act as building blocks to make the more complicated stuff that we are really made up of. The technical term for this process is polymerization. In other words, complex organic molecules, like proteins, or DNA, are polymers. They are long chains of building blocks(monomers).

Miller was able to make the building blocks, but living things need those building blocks strung together in polymers.

Ordinarily, in living things today, there are a series of specialized proteins, called enzymes, that are responsible for building these polymers out of the monomeric building blocks. What happened in the early Earth in the absence of these specialized protein machinery that could possibly lead to polymerization?

Polymerization in Laboratory

The first evidence that this was possible came fairly early on in the late 1950’s, and it was worked by Sidney Walter Fox. Fox took Miller’s experiment one step further. He was able to take amino-acids that might have been created in an experiment like Miller’s and get them to start joining together but only under certain conditions. In just the right proportions, in just the right temperature, the right amount of time that you might heat them, he could get short polymers of amino-acids. We call a polymer of amino-acids a protein, but we also call it a polypeptide chain. That’s simply because the chemical bond that link these monomeric amino-acids to form that chain is called a peptide bond.

What Fox was able to do is to get fairly short polypeptides, showing that you can get spontaneous polymerization. The problem was that Fox could only do this under a very narrow range of conditions. In Miller’s work, you could just throw a bunch of stuff into those flasks, and you get some sort of organic molecule. Fox’s work, however, required much more controlled conditions, conditions that are unlikely to have been that of the early Earth.

Origin in Clay?

Fox and a number of other scientists, however, speculated that maybe you could get more spontaneous formation of polymers if you had some sort of non-biological catalyst. A catalyst is just a term that refers to something that makes a chemical reaction run faster. What Fox and others suggested was that maybe there was something that was non-biological that could catalyze these polymerization reactions. Specifically, what they suggested was that perhaps there were certain kinds of clays that acted as inorganic catalysts.

Why clay? It turns out that some kinds of clay, when they dry out, form very regular ladder-like structures. Furthermore, these clays would also have weak electrical charges on their surfaces. These weak electrical charges can adhere organic molecules. The idea here is that sometime in the early Earth, the shores of a primitive ocean had a bed of clay. As organic molecules that were being created in that primitive ocean got accumulated into the shore, they adhered to that clay. And the clay, because of its regular order and the spacing, would increase the probabilities that you get some sort of spontaneous polymerization.

Wow, that’s an interesting idea. Is there any evidence that this could work? We don’t know what the primitive Earth was like at that scale, but it turns out that recent work by James Ferris, who is at the Rensselaer Polytechnic Institute, has shown exactly that this process does work under abiotic conditions. In a laboratory, Ferris and his colleagues have been able to synthesize not only short polypeptides, but also short stretches of DNA from the component building blocks that were created from experiments like those done by Miller.

The proteins and DNA that Ferris and other have produced are not functional. These are strings of monomers that have been polymerized, but they don’t make any sense. It’s not like a string that would do anything like a real biological molecule might. Nevertheless, it is a start. We can postulate that biological polymers could arise spontaneously.

So, let’s imagine that we have complex polymers. Let’s imagine that we’ve got a primitive ocean brimming with a whole bunch of organic polymers, what has been called the primordial soup. Let’s imagine that even some of these polymers, by chance, have come together as strings that might even have some sort of useful biological function, like modern polymers. Where do we go from there?

The experiments of Miller, Fox, Ferris and others had shown that this is possible, but even with all of this we still don’t have anything approaching what we would want to call life. Why not? Because we know that the organic molecules that make us up are not just a jumble of things floating around in a primordial soup, they are highly ordered. They come in highly ordered packages. This is going to be the subject of my next post, cells. Stay tuned.

Return from Polymerization to The Origin of Life

The Origin of Life, Part I; Miller's Experiment

As Richard Dawkins puts it, “the theory of evolution is about as much open to doubt as the theory that the Earth goes round the sun”. We can also be sure that all of the diverse forms of life we see around us today have arisen from some common, primitive, single original living entity. Our first problem is, then, how this living “thing” originated. In 1953, Stanley Miller conducted his famous (or infamous) experiment. At the time he was a graduate student at the University of Chicago. For decades, scientists had speculated whether the complex organic compounds characteristic of living things could have somehow been generated spontaneously on the early Earth. Spontaneous generation of organic compounds can’t happen today. This is because organic compounds are too fragile.

It is possible that, given enough time, a complex compound might just come together. If it did, however, it would immediately be taken apart. This is because today our planet is just filled with oxygen. Oxygen breaks down organic compounds. Oxygen pulls electrons out of organic compounds and turns them into inorganic compounds.

How can we even get the formation of any kind of organic compound, if as soon as anything begins to arise by chance, it is immediately taken apart? Well, this one is easy. If oxygen is bothering you, just get rid of it.

Before the Miller-Urey experiment, two scientists, Alexander Oparin and J.B.S. Haldane, independently suggested that the early Earth actually did not have much or any oxygen. Oxygen is all around us in the atmosphere, but they suggested that when the planet was formed, the first atmosphere that developed was entirely composed of just a few gases: hydrogen, methane, ammonia and water vapor. This would be as the atmospheres of the moons of other planets that have been described.

Oparin and Haldane independently suggested that the problem of spontaneous generation of organic compounds wasn’t really a big deal, because the early Earth did not have an oxidizing atmosphere. To test this hypothesis, what Miller did was set out to reproduce the conditions presumed to exist on the early Earth before life have arisen, and see if he could get the spontaneous production of organic compounds.

A Simple Experiment, Powerful Results

Miller’s experiment was set up this way: He had two flasks connected by a series of glass tubes. He had a lower flask in which he put water, and he heated this water gently with a little flame. He would cause the water to evaporate and create water vapor, which would circulate into a higher flask. In the upper flask, Miller also added a number of other gasses. He created an atmosphere similar to the one of the early Earth, consistent of hydrogen, methane, ammonia and wáter vapor.

The Experiment. Souce: Wikipedia.

Miller also exposed the gases in this upper chamber to a lot of energy by putting two electrodes that would create electrical sparks. He knew that he needed energy to create any kind of compound, certainly organic compounds.

This is actually a pretty simple experiment, and you can almost do this in your own house. All of these materials are easily available. You could replicate Miller’s experiment and results, which were spectacular. In only a couple of days, he found he could synthesize a whole range of different organic compounds, including some very complex ones, like amino-acids.

The scientific community immediately set out to replicate this. Many people replicated the experiment and it quickly became clear that depending on starting conditions, it was possible to spontaneously, without any preexisting organic molecule, produce all of the amino-acids that are normally found in living material. Most intriguingly of all, you could create nucleotides, which are the building blocks of nucleic acids, DNA and RNA.

The implication of Miller’s experiment and those that followed was that there appeared to be no trouble at all for complex organic compounds to arise spontaneously on the inorganic early Earth. This is a first stepping stone to the origin of life from non-living matter.

On the other hand, as exciting as this result was, the organic compounds that Miller created were still relatively simple compared to the stuff that we are made of. What else do we need to get something that we would call “living”? We have to take our synthesis of organic compounds even farther, beyond these organic building blocks, to get the varied extremely complex molecules that living systems are really made of. We will see how that was possible in the early Earth next time.

Return from Miller's Experiment to the Origin of Life