Sunday, February 5, 2012

Biological Revolutions: Abiogenesis Part 2

(Picture from here.)
This is the follow on to the abiogenesis entry I did here. There we talked for probably much too long about containment and how crucial it was to derive modern organisms. Today we're going to talk about the subject dear to our hearts: Okay. We've got a sack for the protoplasm. What the heck are we going to put in it.

Remember the four prerequisites we said we needed to overcome to get to life as we know it today:
  1. Containment: creating the enclosed environment in which the chemical processes can occur. Living systems use a cell for this.
  2. Metabolism: deriving additional material by using energy producing chemical reactions to power energy requiring chemical reactions. Living systems use proteins and, to a limited extent, RNA to do this.
  3. Inheritance: one chemical system has to be able to drive the creation of other chemical systems. Living systems do this by reproduction involving DNA.
  4. Coupling: This joins containment, metabolism and inheritance into a package. Inheritance doesn’t do any good if you’re not inheriting the ability to metabolize. The whole DNA to RNA to Protein complex is how living systems do it.
We talked about containment last time and we can't talk about coupling until we talk about metabolism and inheritance. So. Now we'll talk about metabolism and inheritance.

There are essentially two approaches to abiogenesis models. These are called metabolism first models and replication first models. Historically, approaches to metabolism were first proposed and more recently replication has been making the rounds. We'll start with metabolism.

Metabolism First

J. B. S. Haldane was the first one to suggest that the prebiotic oceans would be significantly different from modern oceans. But in 1952, the Miller-Urey experiment brought it home. In short, Miller and Urey brought together a mixture of water, hydrogen, methane and ammonia and cycled it through a system that periodically sent sparks through it. In short order, they found various interesting biochemical compounds, notably amino acids, were present. This gave experimental heft to the idea. Consequently, several biochemical models of metabolism were then proposed.

Metabolism is, in short, the reproducible extraction of energy from high energy sources (chemical, light, etc.) to produce complex organic molecules. Plants use light to take CO2 and turn it into hydrocarbons that can be used by the plants. Some archae use sulfides produced by geochemical reactions. We take the products of plants or other animals and use them as our high energy sources and produce our own organic molecules. While the high energy source is variable, what must be done is fairly clear. We need to get to a metabolism of sorts and from that metabolism to our metabolism.

All living systems use variants of fermentation and the Kreb cycle to get energy from high energy carbon sources. Plants and sulfur loving bacteria add the step of grabbing a CO2 to get the energy but once they get that high energy carbon compound they use it in a similar fashion.

Any origin story of metabolism has to start with the building up of organic molecules as a consequence of chemical reactions that come from a non-biological origin. The problem to be overcome by all of these models is to create long chain molecules that don't automatically self-hydrolyze back to their constituents. By analogy, spinning a disk doesn't help us since the disk can spin in both directions. What we need is a ratchet that only spins one way. Or, at least spins in one way statistically.

There are a lot of models but I'm only going to talk about three: Eigen's hypercycle model, the iron-sulfur world and thermogenesis.

A hypercycle is a collection of interacting chemical cycles, each of which operate independently. Each of the chemical cycles is self-reinforcing loop and the aggregate represents a net gain in chemical complexity. (Eigen and Schuster's 1978 article is here.) The target of a hypercycle is a quasispecies. This is a collection of cycles that reproduce themselves. In this case, while the metabolism is inherited what we normally think of as reproduction doesn't apply. A hypercycle in a microsphere that grew large enough to break apart into two microspheres, each of which had a full complement of the hypercycle would satisfy the concept.

One way to visualize a hypercycle is as a collection of differently shaped and sized gears. Each gear represents its own little cycle. But the output of one is the input of another. The problem with Eigen and Schuster's original hypothesis was that they had to use nucleotides and proteins o create the process. As such their hypothesis couldn't explain the origin of nucleotides and proteins. 

Enter Günter Wächtershäuser and the iron-sulfur world.

Wächtershäuser proposed that the pioneer organism lived in a volcanic hydrothermal flow. He suggested that mineral based catalytic chemistry could produce all of the polymerization required by abiogenesis. Note that the environment had an abundance of energetic iron and nickel as well as possible cobalt, manganese, tungsten and zinc.

For a moment recall that iron, manganese and zinc are all dietary trace elements in modern systems. Tungsten and cobalt are not. But tungsten is in chromium's column in the periodic table so there is some chemical similarity. Cobalt is not used by us but it is used by bacteria in vitamin B12 synthesis.

Wächtershäuser postulated that a sulfur based cycle that resembled the Krebs cycle was possible. Carbon monoxide, ammonia and hydrogen sulfide would pass over catalytic metal compounds under high heat and pressure. This results in the formation of catalytic metallic peptides. Which then can catalyze more interesting compounds. Several of these reactions have been demonstrated experimentally. In addition, it has the added advantage that many of these reactions can occur without cellular containment.

Imagine, for example, if these reactions were occurring in the wall of a hydrothermal vent. Possible in the pores. Possibly in an organic slime. At some further date, the reactions can be encapsulated in a microsphere.

Karo Michaelian went one better. He suggested that we are looking at living systems backwards. He wanted to analyze them on the basis thermodynamics. From that point of view, living systems are unit producers of entropy-- not a surprise, right? Since everything produces entropy. Starting there he suggested that entropy isn't just a byproduct of their chemical reactions; it's the reason for their existence. Living systems arose because they were more efficient at producing entropy than their competition. According to him, nothing much beyond thermodynamics was necessary to cause living systems. They were as natural in their environment as any other chemical reaction. (The original paper is here.)

As an example, he pointed out that RNA and DNA would have existed as chemical compounds pretty much as soon as the temperature of the ocean cooled enough. He pointed out that RNA and DNA both absorb and dissipate UV with a wavelength of about 200-300nm. Which, coincidentally, was the wavelength of UV that fell on the prebiotic earth.

Along with visible light being absorbed by other materials, at the ocean surface, about 1mm depth, such absorption and dissipation would raise the surface temperature of the water about 5-6 C. The temperature of the surface would change on a day/night cycle. RNA and DNA would denature during the higher temperatures of the day. Then, at night when the temperature dropped polymerization would occur using any remaining single stranded molecules as a template. Michaelian's chemistry isn't exactly metabolism and it isn't exactly replication. But it serves as segue to the replication first models.

Replication First

It was long felt that metabolism had to come first since 1) the reactions were less complex and 2) they didn't need RNA or DNA to operate. Both RNA and DNA are problematic. They're complex molecules that are fragile and finicky. It was thought that a more robust system could then incorporate replication later.

That was then. The RNA world is now.

The RNA world hypothesis proposes that the form of life that existed prior to the current form of life was based on ribonucleic acid. The RNA world is based on the proposition that while some nucleotides bind together and break apart, some combinations had catalytic properties that lowered the required energy of their chain's creation. This meant that when these bonds occurred, they were less likely to break apart. This manifested in polymerization of the nucleic acids into RNA. The most efficient molecules were those that best catalyzed their own creation-- opening the opportunity for natural selection of chemical systems. Such catalytic compounds have been found. They are enzymes of a sort and are called ribozymes.

Over time, competition between ribozymes can foster cooperation. Some develop catalytic properties that cause peptides to bind together into small proteins. Proteins are much more efficient enzymes than ribozymes at this and any RNA compound that can synthesize itself and an enzyme out of the soup would certainly have a selective advantage.

One step in protein synthesis, aminoacylation of RNA, has been demonstrated in a short RNA segment. Aminoacylation is one of the chemical reactions used in transfer-RNA and modern protein synthesis.

Coupling Replication and Metabolism

It's a common fallacy among people that there is a single source of things from which all other things derive. Scientists (who are human regardless what some may think) share this fallacy. Sometimes the fallacy is productive-- such as the long pursuit of a unified physics. Other places, such as biology, it often hurts our understanding. If we know anything about living systems and their chemistry it's that if something can be done it probably was. It's a sort of biological analogy of rule 34: if it can happen it did and there's probably porn for it.

So I suspect all of these models and hypotheses occurred at one point or another. Iron-sulfur thermongenic hypercycles ran for millions of years in the RNA world. My bet is on the RNA world since there appears to be a coupling mechanism that occurs as a side effect of a known reaction. But I have a soft spot for iron-sulfur. Just because the idea of all that chemistry in an undersea smoker is very very cool.

We do know is that it changed at some point to the world we now live in. If we had an RNA world it had to change tothe DNA one. So what happened.

Enter Patrick Forterre and his Biology of Extremophiles Laboratory. (Sounds like a band, doesn't it?)

Forterre has suggested that viruses were critical in the push from RNA based life to DNA based life. His hypothesis is that the Last Universal Common Ancestor was RNA based in a world of RNA viruses. Further, that some viruses began using DNA instead of RNA and were selected for given the inherent stabilities of DNA vs. RNA and the fact that the RNA world would only imperfectly defend itself from a DNA virus. But things Go Wrong and some of the DNA remains intact inside a cell filled with RNA and protein machinery.

Thus the prokaryote was born.

But that is a topic for another time.

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