The substrate can only bind to the active site of the protein in one way. In some enzymes, the substrate fits snuggly into the site, a bit like a 3D jigsaw. In other cases, either the substrate or the enzyme, or both, temporarily change shape a little to enable a tight bind. The binding is usually caused by hydrogen bonds, or other types of weak electrostatic bond. However, some enzymes form temporary nonpolar, and occasionally polar, covalent bonds. Once the active site and the substrate are bound, various processes can occur to start the reaction. Some of these processes involve complex chemistry that is beyond what I can cover here, but others are more easily understood.
When the substrate is forced into a different shape by the enzyme, this puts stress on the covalent electron bonds in the substrate, making them easier to break either by a cofactor, or another part of the protein that can donate or steal protons or electrons. In other cases, the enzyme orients the substrate in such a way it is easier for other molecules involved in the reaction to align and react or join with the substrate. Regardless of the process, the activation energy for the reaction is reduced and the reaction is speeded up.
The increase in the rate of the chemical reactions that enzymes catalyse can be quite remarkable, and sometimes they speed things up by several million times. This is nicely demonstrated by some work on an ancient fossil. Sixty-eight million years ago a female Tyrannosaurus rex died. We don’t know how, but it was one of only a very small number of animals that became fossilized. Remarkably, even some of its muscles and tendons survived. In 2007, Mary Schweitzer, a molecular palaeontologist at North Carolina State University, analysed the tissue and exposed a little of it to an enzyme called collagenase. The enzyme broke down molecules of collagen in the soft tissue in a matter of hours.
Collagen is a tough protein that is central to building a body. It is found in skin, cartilage, tendons and bones. Without collagenase, it is difficult to break collagen down, which is one reason why cartilage and tendons can remain tough and stringy even after meat is cooked, and why these parts of animals are some of the slowest to be broken down by microbes following death. Despite collagen’s known tough properties, Schweitzer’s findings of microscopic remains of soft tissues lasting millions of years were controversial when published, and they remain so. Some independent researchers have been able to replicate some of her findings, while others have not. Science often proceeds like this. Claims that challenge current understanding need multiple independent tests before they are accepted. By no means all researchers in molecular biology or palaeontology are ready to accept Schweitzer and colleagues’ findings, but my reading of the subject is that the pendulum is swinging in her favour. A growing number of scientists, including me, are becoming convinced.
I chose to describe these T. rex findings here, despite their being less strongly supported than the rest of the science described in this chapter. If these findings stand the test of time, they will show that an enzyme can make a reaction happen to a substrate that has been stable for nearly 70 million years. Prior to Schweitzer’s findings, collagenase was known to accelerate the breakdown of collagen by many tens of times, but the T. rex findings suggest it can be even more potent.
Once an enzyme like collagenase has catalysed a reaction it must release the product. Any temporary chemical bonds between the enzyme and the products that have been produced must be broken. Sometimes the rearrangement of charge on the modified substrate may be enough for them to separate and disperse away, but in other cases something more is required. Following the reaction, the enzyme can return to its original, pre-binding shape, helping expel the new product. The enzyme is once again primed to conduct the reaction with a new substrate molecule.
Chemical reactions are governed by the electromagnetic force. If the electromagnetic force was substantially stronger, or weaker, electron shells and the positive and negative charges of cations and anions would be different, and life may not be possible. If atoms held on to their electrons more or less strongly, many chemical reactions would not occur or would require much higher temperatures and pressures to take place. We owe our existence to chemistry, and chemistry works as it does because of the workings of the electromagnetic force.
Although I have only scraped the surface of chemistry in this chapter, I have touched upon how atoms behave, how they share electrons, and why chemical reactions occur and molecules form. These processes are fundamental for you and me to exist. The chemistry of life is not as flamboyant as some of the reactions we encountered that involve highly reactive and explosive compounds, but it is nonetheless astonishing. Scientists have a very deep understanding of how all four forces of nature work, and their hard-won insights into the electromagnetic force means they can predict the outcome of very many reactions before they mix the compounds involved together. Nonetheless, there are aspects that are not well understood.
Chemists cannot yet easily predict many aspects of organic chemistry, the chemistry underpinning life. For example, we do not understand how many reactions that happen within living organisms are controlled and prevented from continually happening. Another thing we do not know, and this is true for all four forces of nature and not just electromagnetism, is why the forces take the strengths they do. Why is the electromagnetic force such that electron shells are spaced as they are, and not closer, or further, from atoms? Is it inevitable that the electromagnetic force is the strength it is, or is it a fluke of our universe? What we do know is that the electromagnetic force defines the chemistry we experience, and that, without chemistry, life could not exist. But it is not the only force that life required to be just right. We needed the weaker force of gravity to allow our solar system to form, and the Earth within it. I now turn to the role of gravity in our existence.
Our Locale
Our universe is truly magnificent, yet one aspect of it is deeply frustrating. It is so large that the prospects of us exploring beyond our immediate backyard are slim. The space probe Voyager 1 was launched in September 1977 when I was nine years old, and it has been travelling for over forty-five years. It is the most distant human artefact from Earth, being about 24 billion kilometres away. A beam of light fired from Earth could reach Voyager 1 in just less than a day. On the scale of the universe, 24 billion kilometres is very close by. Alpha Centauri, the closest star system to our sun, is 4.37 light years away. Voyager 1 is not travelling towards Alpha Centauri, but if it was, at its current speed it would take about 80,000 years to get there.
Our sun is a star, and it, along with the planets around it, forms a star system. Our star system, the solar system, has just one star, the sun. Many star systems have more than one star, and they orbit one another in elaborate dances. The Castor star system, for example, has six stars.