In-Depth General Biology/1. The Inorganic Chemistry of Life

1. THE INORGANIC CHEMISTRY OF LIFE

Orion Nebula. Located some 60 Light Years form Earth, this nebula visible in north hemisphere during winter with the unaided eye is a factory of stars. Every day, gas and dust collpases and forms new stellar systemas, with planets that may harbour life. The Sun and Earth surely came from a nebula like this 4,500 billion years back, as the result of a supernova which synthesized lots of the heaviest elements of the universe (like gold, mercury, lead and uranium), while giving birth to stars which produce in their cores carbon, oxygen and nitrogen - the elements of life - by burning hydrogen and helium, their fuel. As Carl Sagan once put eloquently, we're made of star stuff.

Learning objectives

1. You will be able to define matter, atom and element
2. You will understand and be able to recite the structure of atoms and isotopes
3. You will be able to read the Periodic Table and predict properties of elements
4. You will understand how electrons form bonds between molecules
5. You will understand the process of chemical reactions, moles, and how to read chemical equations and formulas
6. You will understand importance of chemical equilibrium in biological systems
7. You will understan principles of inorganic nomenclature and their importance on living beings

The big questions

1. How do atoms define the behaviour of living matter?
2. How do chemical reactions affect living beings?
3. What's the importance of chemical equilibirum in life?
4. Are there any inorganic compounds of importance for living beings?

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Everything in the universe consists of atoms, which are the fundamental components of matter, though not the smallest. Matter possesses mass, which is the amount of matter contained within, and volume, which is the space it occupies. Matter can be categorized into pure substances and mixtures. Pure substances are the foundational building blocks of matter, including elements and compounds, while mixtures are combinations of different types of compounds. Life is organized using these building blocks as a starting point.

ATOMS AND ELEMENTS

Universe is made of atoms. Atoms are the building blocks of matter and the universe. We can define them as the smallest unit presenting the chemical properties of an element. Elements are the smallest substances of all, which cannot be separated in smaller components by any chemical or physical means. We currently know 118 chemical elements, but only around 90 are natural, and the rest are synthesized artifically. Living beings on Earth are made of six basic elements: carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur. Other elements like iron, calcium, potassium, molibdene, and magnesium are called trace elements and are only present in small quantities when compared with the most abundant elements (Table 1).

Table 1. Quantity and percentage of chemical elements on humans and other living beings
Name	Chemical symbol	Percentage of Body Mass in Humans
Carbon	C	18.5%
Hydrogen	H	9.5%
Oxygen	O	65.0%
Nitrogen	N	3.3%
Phosphorus	P	1.0%
Sulfur	S	0.3%
Calcium	Ca	1.5%
Potassium	K	0.4%
Sodium	Na	0.2%
Chlorine	Cl	0.2%
Magnesium	Mg	0.1%

We order them in a grpahic representation called Periodic Table of Chemical Elements, organized in eighteen columns and seven rows which indicate some of the atom properties. Elements have trends we can follow and predict when looking at the periodic table. Some of these trends we'll study later.

Atomic structure

Figure 1. An helium atom. This is a representation of an helium atom. The nucleus is minuscule when compared to the rest of the structure. Protons (in red) and neutrons (in purple) are located at the center, while the big dark extension symbolizes the electron cloud. An helium atom has only one orbital 1s with two electrons.

Figure 2. Strong Nuclear Force. Protons and neutrons are hadrons: particles made up of smaller particles. In this case, they are baryons, made of three quarks. Quarks appear as small coloured circles, and their type and disposition changes respect to the nucleon (a particle that integrates an atomic nucleus). The small zig-zaggy lines in white-yellowish color are the gluons, and they bind quarks in position, being responsibles of strong nuclear interactions.

Atom comes from greek, meaning "undivisable", coming from the original idea proposed by Democritus, who speculated in a sort of mental experiment that after cutting subsequently in halves a sand grain, a point would be reached where the grain cannot be divided more. John Dalton took the idea in the 19th centruy and postulated his atomic theory. Atoms, basically are composed of three subatomic particles, particles smaller than an atom, called electron (with negative electric charge), proton (with positive electric charge) and neutron (no charge at all). Protons and neutrons stick together in the center of the atom, in a small region called atomic nucleus (Figure 1). Given protons have the same electric charge, they would repel each other, so they stick next to neutrons, who are uncharged, using strong nuclear force. Strong nuclear force comes from small elemental particles conforming protons and neutrons, called quarks, which bond thanks to gluons, particles that act like glue or adhesive (Figure 2). Electrons circle the nucleus at high velocities forming an electron cloud.

Electrons do not follow a predetermined orbit or trajectory, a phenomena called Heissenberg Uncertainty Principle: is not possible to predict fully the state in which a particle finds itself without altering, modifying or unknowing some results, like speed and position. We can only predict where they might be most of time. Electrons usually exist in three-dimensional spaces inside the electron cloud, called orbitals, and each one can be filled up with two electrons at max. This is called Pauli Exclusion Principle. Electrons have a propery called spin, similar to the spin of a ball or a giroscope (their angular moment). The value of their spin is half a spin (1/2 spin). Thus, to complete their spin, they arrange in pairs. We say then that electrons are paired. This also explains why there can only be two electrons in each orbital. There are four kinds of orbital: s (like a sphere), p (like a dumbell), d and f (like flowers), as seen in (Figure 3). Electrons have certain energy level, and can occupy orbitals with the same level of energy. Orbitals with the seme energy level make electronic shells, each with a limit in electron quantity, and represented by a letter ranging from K to Q (Table 2). Electrons in the most outermost shells are called valence electrons, and they're the most energetic of them all, something necessary as it allows to form chemical bonds and create molecules.

Figure 3. Orbitals. Orbitals are 3D regions where it's possible to find most of time (90% of time) electrons in the electron cloud. It's possible to distinguish four main kinds of orbitals. In the atoms that form life, only s and p orbitals are of significance. In middle families (transition metals and rare earths), d and f orbitals come into play. These last orbitals also have complex axis and planes of orientation.

Table 2. Electronic shells
Shell	Max. N° of electrons
K	2
L	8
M	18
N	32
O	32
P	18
Q	8
Total max.	118 electrons

Atoms have discrete units of energy: we say they're quantizised. And atoms can "jump" between shells when they receive and energy imput. For example, when an electorn absorbs a photon of high energy (like UV or Purple light), the electron will get excited (it's energy level will increase) and will reach a new shell proportional to the energy input (Figure 4). If the electron emits another photon, this time of low energy, it will return to it's original state of lowest energy possible (called ground state). The implications this has in biology are important, as this electron excitation ultimately leads to photosynthesis (Go to Chapter XX)