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3 Matter and Life
Learning Outcomes
Understand the concept of atoms, ions, and molecules and their basic structure.
Be able to describe and explain different bonding types: ionic, covalent, metallic, van der Waals interactions, and hydrogen bonding.
Understand and give examples of the role of these bonding types in biological systems.
Understand phase diagrams and the unusual characteristics of the water phase diagram.
Understand how phase diagrams can be used to understand planetary environments and their suitability for liquid water.
Describe extreme states of matter, including plasma and degenerate matter.
Understand some of the interactions between matter and light that are important to astrobiology.
Be able to calculate the energy, frequency, and wavelength of light absorbed or emitted for given energy level changes of electrons in atoms and thus the implications for absorption and emission spectroscopy of stars and exoplanets.
3.1 Matter and Life
At the heart of our understanding of physical processes in the Universe, including the principles that govern the assembly of life, is our knowledge about the structure of matter. The structure of matter, including the interactions of atoms and molecules, may not seem to be directly linked to astrobiology. However, to understand how the molecules of life are assembled, we need to understand how atoms associate and the types of associations that occur. Ultimately, it is the binding between individual atoms, ions, and molecules that results in the complex array of structures we call life.
Knowledge of the structure of matter can also provide us with a basis to question how universal the characteristics of life might be. Are all living things, if they exist elsewhere, made in the same way?
A grasp of the structure of matter is also enormously helpful for understanding why biological systems are constructed in particular ways. Why don't organisms make widespread use of solid metals in their assembly? How does a gecko attach to a window? How are the two strands of the genetic material DNA put together? These questions, which might seem detached and even obscure, will be answered by the end of this chapter. You will discover that what unites these questions is an understanding of the bonding between atoms, ions, and molecules, and how those bonds are used to perform certain tasks in living things.
The application of this information to astrobiology is that it allows you to go beyond what seem to be parochial Earth-based questions into the underlying principles that govern living things.
3.2 Life Is Made of “Ordinary” Matter
The matter from which stars, planets, and life are made is probably less than 5% of all the matter in the Universe. That may come as a surprise. Most of the rest of the matter of the Universe is thought to be in more elusive forms such as Dark Matter. The properties of so-called Dark Matter are not known, but this matter was hypothesized to exist to explain certain properties of galaxies, such as their rotation, that cannot be explained without assuming there is a lot more matter in the Universe than the 5% we are familiar with. It is called Dark Matter because of its apparent lack of interaction with electromagnetic radiation (which is one factor that makes it difficult to detect).
In addition, Dark Energy is an elusive form of energy thought to permeate the Universe and has been hypothesized to exist to complete theories about the expansion rate of the Universe. These other types of matter and energy that are thought to exist in the Universe are cosmological areas of science that are hugely interesting. However, as far as we know, they have no direct relevance to life, although of course they are thought to influence the characteristics of the Universe in which life exists.
We will not consider these other forms of matter further in this textbook. Instead, this whole book focuses on the part of the Universe that we call ordinary matter or baryonic matter. It is usually just called “matter.”
The basic building blocks of matter are atoms, themselves constructed from subatomic particles. An atom has a nucleus, which is surrounded by electrons. Apart from hydrogen, which has a single proton, the nucleus of atoms is made of two subatomic particles: protons, which are positively charged, and neutrons, which have no charge. They have very small masses: the proton is 1.672 × 10−27 kg; the neutron is 1.675 × 10−27 kg. Protons and neutrons are themselves made of elementary particles, called quarks. An elementary particle is a particle that cannot be broken down any further, so they represent the basic building blocks, if you like, of matter. Quarks fall into the domain of the scientific field of particle physics. Although, like the cosmological questions raised earlier, this is an enormously interesting area of science, we will not spend any more time on it here. The electrons that surround the nucleus are negatively charged and they are elementary particles (Figure 3.1).
Figure 3.1 A very simplified depiction of the structure of a typical atom showing the nucleus and electrons. Note that this is not to scale. The electrons are in orbitals about 10 000 times further out than the diameter of the nucleus. Electrons occupy energy levels, depicted here as circles.
3.3 The Atomic Nucleus
In the nucleus of any given atom, the total number of protons is given by Z. This is also called the atomic number. The number of protons defines the element. So, for instance, in the biologically important atom carbon, the number of protons is 6. The element has an atomic number of 6. This defines it as the element carbon.
The nucleus also contains neutrons (a total number N). For any given atom, the atomic mass is the total number of protons and neutrons. In all stable elements, there are at least an equal number of neutrons as protons,
