5.2: Matter

Matter is the "stuff" found in ecosystems. Technically, matter is defined as anything that occupies space or has mass. Mass is resistance to acceleration. Put more simply, mass is similar to weight, but weight accounts for acceleration due to gravity. Matter moves between biotic and abiotic ecosystem components through biogeochemical cycles. Fully understanding these cycles, requires a background in the particles that comprise matter, atoms.

Atoms and Molecules

Elements are substances that cannot be broken down or transformed chemically into other substances (figure \(\PageIndex{a}\)). A total of 118 elements have been defined; however, only 92 occur naturally and fewer than 30 are found in organisms. The remaining 26 elements are unstable and therefore do not exist for very long or are theoretical and have yet to be detected. Each element is designated by its chemical symbol (such as H, N, O, C, and Na), and possesses unique properties. These unique properties allow elements to combine and to bond with each other in specific ways.

Figure \(\PageIndex{a}\): The periodic table of elements organizes chemical elements based on their properties. Each element is represented by a one- or two-letter symbol. Additionally, the atomic number, name, and atomic mass are listed for each element. Click here for an accessible periodic table of elements. Image by OpenStax (CC-BY)

An atom is the smallest component of an element that retains all of the chemical properties of that element. For example, one hydrogen atom has all of the properties of the element hydrogen, such as it exists as a gas at room temperature and it bonds with oxygen to create a water molecule. Hydrogen atoms cannot be broken down into anything smaller while still retaining the properties of hydrogen. If a hydrogen atom were broken down into smaller particles, it would no longer have the properties of hydrogen. At the most basic level, all organisms are made of a combination of elements. They contain atoms that combine together to form molecules. Molecules can interact to form cells, the structural and functional units of life. In multicellular organisms, such as animals, these cells combine to form tissues, which make up organs. These combinations continue until entire multicellular organisms are formed.

Atoms combine to form molecules. Molecules are chemicals made from two or more atoms bonded together. Some molecules are very simple, like O₂, which is comprised of just two oxygen atoms. Some molecules used by organisms, such as DNA, are made of many millions of atoms. All atoms contain protons, electrons, and neutrons (figure \(\PageIndex{b}\)). The only exception is hydrogen (H), which is typically only made of one proton and one electron. A proton is a positively charged particle that resides in the nucleus (the core of the atom) of an atom and has a mass of 1 and a charge of +1. An electron is a negatively charged particle that travels in the space around the nucleus. In other words, it resides outside of the nucleus. It has a negligible mass and has a charge of –1. Neutrons, like protons, reside in the nucleus of an atom. They have a mass of 1 and no charge. The positive (protons) and negative (electrons) charges balance each other in a neutral atom, which has a net zero charge.

Figure \(\PageIndex{b}\): Atoms are comprised of protons (red with a plus sign, +) and neutrons (yellow) located within the nucleus, and electrons (blue with a minus sign, −)surrounding the nucleus. The nucleus of an atom should not be confused with the nucleus of a cell.

Each element contains a different number of protons and neutrons, giving it its own atomic number and mass number. The atomic number of an element is equal to the number of protons that element contains. The mass number is the number of protons plus the number of neutrons of that element. Therefore, it is possible to determine the number of neutrons by subtracting the atomic number from the mass number.

Chemical Bonds

How elements interact with one another depends on the number of electrons and how they are arranged. When an atom does not contain equal numbers of protons and electrons it is called an ion. Because the number of electrons does not equal the number of protons, each ion has a net charge. For example, if sodium loses an electron, it now has 11 protons and only 10 electrons, leaving it with an overall charge of +1. Positive ions are formed by losing electrons and are called cations. Negative ions are formed by gaining electrons and are called anions. Elemental anionic names are changed to end in -ide. As an example, when chlorine becomes an ion it is referred to as chloride.

Ionic and covalent bonds are strong bonds formed between two atoms. These bonds hold atoms together in a relatively stable state. Ionic bonds are formed between two oppositely charged ions (an anion and a cation). Because positive and negative charges attract, these ions are held together much like two oppositely charged magnets would stick together. Covalent bonds form when electrons are shared between two atoms. Each atom shares one of their electrons, which then orbits the nuclei of both atoms, holding the two atoms together. Covalent bonds are the strongest and most common form of chemical bond in organisms. Unlike most ionic bonds, covalent bonds do not dissociate in water. Hydrogen bonds form when molecules have an uneven distribution of electrons and thus have partially positive and partially negative ends. They are thus attracted to each other (figure \(\PageIndex{c}\)). Technically, hydrogen bonds only occur between hydrogen and either oxygen (O), nitrogen (N), or fluorine (F). Sometimes hydrogen bonds connect different parts or large molecules, as is the case in DNA and proteins. Hydrogen bonds are weaker than ionic and covalent bonds and can break easily. (Note that hydrogen bonds are among the strongest of intermolecular forces, those that occur between molecules, however.)

Figure \(\PageIndex{c}\): Hydrogen bonds form between slightly positive and slightly negative charges of certain molecules, such as water. Each water molecule consists of an oxygen atom (O) connected to two hydrogen atoms (H) by covalent bonds (solid lines). Dashed lines represent hydrogen bonds between water molecules.

Biological Macromolecules

Organisms contain large, organic molecules called biological macromolecules. Organic molecules are those that contain carbon covalently bonded to hydrogen. (In contrast, inorganic molecules lack carbon bonded to hydrogen and are often simpler than organic molecules.) In addition, they may contain oxygen, nitrogen, phosphorus, sulfur, and additional elements.There are four major classes of biological macromolecules: carbohydrates, lipids, proteins, and nucleic acids. Each is an important component of the cell and performs a wide array of functions.

It is often said that life is “carbon-based”. This means that carbon atoms, bonded to other carbon atoms or other elements, form the fundamental components of many of the molecules found uniquely in living things. Other elements play important roles in biological molecules, but carbon certainly qualifies as the “foundation” element for molecules in living things. It is the bonding properties of carbon atoms that are responsible for its important role. Carbon can form four covalent bonds with other atoms or molecules. The simplest organic carbon molecule is methane (CH₄), in which four hydrogen atoms bind to a carbon atom (figure \(\PageIndex{d}\)).

Carbohydrates include what are commonly referred to as simple sugars, like glucose, and complex carbohydrates such as starch. While many types of carbohydrates are used for energy, some are used for structure by most organisms, including plants and animals. For example, cellulose is a complex carbohydrate that adds rigidity and strength to the outer layer of plant cells (the cell walls).

Figure \(\PageIndex{d}\): Carbon can form four covalent bonds to create an organic molecule. The simplest carbon molecule is methane (CH₄), depicted here.

Lipids include a diverse group of compounds that are united by a common feature: lipids are insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of lipids called fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic birds and mammals dry because of their water-repelling nature. Lipids are also the building blocks of many hormones and are an important constituent of the membranes that surround cells and form many of their internal structures.

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. They are all polymers of amino acids. The functions of proteins are very diverse because there are 20 different chemically distinct amino acids that form long chains, and the amino acids can be in any order. Proteins can function in facilitated chemical reactions in organisms, such as photosynthesis, transmitting messages as hormones, causing muscles to contract, and much more. 

Nucleic acids are very large molecules that are important to the continuity of life. They carry the genetic blueprint of a cell and thus the instructions for its functionality. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all organisms, ranging from single-celled bacteria to multicellular mammals. The other type of nucleic acid, RNA, is mostly involved in protein synthesis. DNA and RNA are made up of small building blocks known as nucleotides. DNA has a beautiful double-helical structure (Figure \(\PageIndex{e}\)).

Figure \(\PageIndex{e}\): The double-helix model shows DNA as two parallel strands of intertwining molecules.

Attribution

Modified by Melissa Ha from Matter from Environmental Biology by Matthew R. Fisher (licensed under CC-BY)