What is matter?

Everything on Earth is made of matter. Matter is the “stuff” that gives everything its substance or mass. If it takes up space and you can weigh it - it’s made of matter. Matter can be a solid like your body, a liquid like water, or a gas like the atmosphere.

The four elements common to all living organisms are oxygen (O), carbon (C), hydrogen (H), and nitrogen (N). In the non-living world, elements are found in different proportions, and some elements common to living organisms are relatively rare on the earth as a whole. The atmosphere is rich in nitrogen and oxygen but contains little carbon and hydrogen, while the earth’s crust, although it contains oxygen and a small amount of hydrogen, has little nitrogen and carbon. Differences in abundance, all elements and the chemical reactions between them obey the same chemical and physical laws regardless of whether they are a part of the living or non-living world.

To understand how elements come together, we must first discuss the smallest component or building block of an element, the atom. This is the smallest unit of matter that retains all of the chemical properties of an element. An atom is composed of two regions: the nucleus, which is in the centre of the atom and contains protons and neutrons, and the outermost region of the atom which holds its electrons in orbit around the nucleus

Protons have a positive electrical charge (+1), have mass, and are found in the centre, or nucleus, of the atom.
Neutrons have no charge (0), or are neutral, have mass, and are found in the nucleus of the atom
Electrons have a negative electrical charge (–1), have virtually no mass, and orbit the nucleus of the atom.

Atoms of each element contain a characteristic number of protons and electrons. The number of protons determines an element’s atomic number and is used to distinguish one element from another. The number of neutrons is variable, resulting in isotopes, which are different forms of the same atom that vary only in the number of neutrons they possess. Together, the number of protons and the number of neutrons determine an element’s mass number

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The electron shell diagram (known as the Bohr model) shows the atom as a central nucleus containing protons and neutrons, with the electrons in circular orbitals at specific distances from the nucleus. These orbits form electron shells or energy levels, and these energy levels are designated by a number and the symbol “n.” Electrons fill orbitals in a consistent order: they first fill the orbitals closest to the nucleus, then they continue to fill orbitals of increasing energy further from the nucleus. If there are multiple orbitals of equal energy, they will be filled with one electron in each energy level before a second electron is added. The electrons of the outermost energy level determine the energetic stability of the atom and its tendency to form chemical bonds with other atoms to form molecules.

Molecules form the structures of cells and carry out cellular functions. Chemical bonds within and between biological molecules are important to their structure. Molecules are formed by the chemical bonding of atoms

There are several types of chemical bond:

Strongest = covalent bond
Weakest = non-covalent bond

Some atoms are more stable when they lose or gain electron and become ions. The outermost electron shell fills entirely making them more stable. In this case the number of electrons does not equal number of protons, so ions have a net charge

Cations = positive
Anions = negative

Ionic attractions are bonds formed as a result of the electrical attraction between ions bearing opposite charges. Ions can form bonds that result in stable solid compounds, e.g. sodium chloride (NaCl)

Compounds with a polar covalent bond have regions that have a partial negative charge and regions with a partial positive charge. A molecule with such a charge difference is called a dipole. Any polar molecule can interact with other polar molecules through the weak (δ+ to δ–) attractions of hydrogen bonds. If a polar molecules interact with polar water molecules and become soluble = hydrophilic. Non-polar molecules aggregate with one another rather than with the polar water molecules = hydrophobic

Functional Groups

Certain small groups of atoms, called functional groups, occur frequently in biological molecules. Each functional group has specific chemical properties, and when it is attached to a larger molecule, it confers those properties on the larger molecule; one of these properties is polarity.

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Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning. Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding of an enzyme to its substrate.