Environmental Chemistry

Figure 2.2 from Biology 2e (Openstax). Note the relatively large protons and neutrons in the nucleus of the atom and the electrons that circle it. Download for free at http://cnx.org/contents/8d50a0af-948b-4204-a71d-4826cba765b8@15.43.

The number of protons, neutrons, and electrons at atom possesses defines it and how it interacts with other atoms. The number of protons an atom has is called its atomic number and defines the type of atom, or element. For example, the element hydrogen always has 1 proton, while the element carbon always has 6 protons. As of now, atoms with between 1 and 108 protons have been found in nature or created in labs. These elements are charted on the periodic table, and each has an accepted symbol. For example, carbon is abbreviated C, and oxygen is abbreviated as O.

Protons are considered them to have an atomic mass of 1. Neutrons also have a mass of 1, while electrons are so small they are considered to have negligible mass. The number of protons and neutrons is called the atomic mass of an element. Elements may have different forms, or isotopes, that differ in the number of neutrons they possess and thus have different atomic weights. For example, Carbon-13 (C-13) has 6 protons and 7 neutrons, while C-12 has 6 protons and 6 neutrons. Isotopes may differ over time or space and thus may be useful in determining facts about a specimen. For example, oxygen isotope analysis can be used to estimate the age of ice cores, and isotopes that are found in structures (otoliths) in the ears of fish that accumulate as fish grow can be used to estimate where they lived as juveniles.

The number of electrons is important for determining how atoms will interact with other atoms. Atoms (of the same or different element) can share electrons via covalent bonds to form molecules; these molecules are formed during chemical reactions. Molecules that contain atoms of more than one element are called compounds. Compounds may have different chemical properties (property that do not depend on the amount of substance, such as boiling point) than their constituent atoms and can not be broken into smaller pieces except through chemical processes. This differentiates them from a mixture, which is a combination of two or more items that can be separated through physical processes (such as filtering). Although not explored fully here, atoms can also lose or gain electrons and become charged particles, or ions.

Compounds that contain at least one carbon-carbon or one carbon-hydrogen bond are typically considered organic molecules. Carbon is able to form 4 covalent bonds with other atoms due to number of electrons it has and how they rotate around the nucleus. This allows carbon atoms to form chains with other carbon atoms and other atoms, and carbon chains form the basis of the molecules of life on our planet. Major types of carbon chains that are also organic compounds include carbohydrates (starches and sugars) that are often used as active or transitional energy. Photosynthesis, for example, is a chemical reaction that takes place in the leaves of plants where carbon from the air combines with water in the presence of sunlight to produce oxygen (an important byproduct!) and glucose, a carbohydrate. This reaction stores energy from the sun by forming bonds between carbon atoms. When organisms require energy, these bonds can be broken to release the stored energy. Lipids, such as fats and oils, serve as longer-term repositories for energy that can be converted to carbohydrates as needed. Lipids are also the building blocks of steroids and and some hormones, or signalling molecules that allow cells to communicate and control processes with-in an organism. Nucleic acids are what make up our genetic material; DNA, for example is a nucleic acid. Proteins form the actual physical framework of organisms, such as collagen and bone, and also make up enzymes, or molecules that enable chemical reactions such as photosynthesis to occur; some hormones are also composed of proteins. All proteins are composed of twenty amino acids; a few of these can't be produced from other sources by humans and thus are essential nutrients that we need to survive. In general, organic materials organisms require for survival are known as vitamins.

Inorganic molecules are also important to life. Water, for example, is an essential inorganic molecule. Inorganic molecules that organisms require for survival are called minerals.

Understanding the chemical identity of molecules is important across multiple scales in ecology. Organisms must acquire or create these biological molecules to survive, which means they must intake energy (which we often measure as calories) and certain molecules (such as the essential amino acids mentioned above). This means that consumption must serve the dual needs of energy and molecule intake. This explains why we have nutrition labels on our food! These dual needs can also lead to interesting outcomes. For example, aphids and other insects eat the sugar-rich sap of plants. While this a high-energy food source, it has very low amounts of protein in it, so aphids must consume large amounts of sap to meet their protein requirements. This means they intake and must expel excess energy in the form of sugar. This has led to a digestive system that produces a sugar-rich waste called honeydew that is actually consumed by other animals. Honeydew production can also lead to mutualisms, or mutually beneficial relationships among organisms. For example, some ant species protect (or farm!) aphids to gather the honeydew they produce!

Organisms can also produce molecules that influence species interactions. For example, organisms can produce chemical cues (pheromones) that help mates find them or influence behaviors. These chemical cues can be particularly important for organisms with limited vision. For example, some nocturnal (active at night) moths can smell a mate over four miles away! Prey can use molecules produced by predators to identify risk; for example, mud crabs can determine a blue crab is nearby based on the presence of trigonelline and homarine in their urine (Poulin et al 2018).