3.1: Matter

Atoms, Molecules, & Compounds

At its most fundamental level, life is made of matter. Matter is something that occupies space and has mass. All matter is composed of elements, substances that cannot be broken down or transformed chemically into other substances. Each element is made of atoms, each with a constant number of protons and unique properties. A total of 118 elements have been defined; however, only 92 occur in nature and less than 30 are found in living cells. Each element possesses unique properties that allow elements to combine and to bond with each other in specific ways.

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 can bond with oxygen to create a water molecule. Hydrogen atoms cannot be broken down into anything smaller while still retaining the properties of hydrogen. All matter (rocks, stars, or organisms) is made of atoms. Atoms are made of protons and neutrons (which exist in the nucleus of an atom) and electrons (which orbit around an atom).

At the most basic level, all organisms are made of a combination of elements. They contain atoms that combine to form molecules. Molecules are chemicals made from two or more atoms bonded together. How elements interact with one another depends on the number of electrons and how they are arranged. There are three types of basic bonds: ionic bonds, covalent bonds, and hydrogen bonds.

In multicellular organisms, such as animals, molecules can interact to form cells that combine to form tissues, which make up organs. These combinations continue until entire multicellular organisms are formed.

Water is Crucial to Maintaining Life

Do you ever wonder why scientists spend time looking for water on other planets? It is because water is essential to life; even minute traces of it on another planet can indicate that life could exist on that planet or did previously. Water is one of the more abundant molecules in living cells and the one most critical to life as we know it. Approximately 60–70 percent of your body is made up of water. Without it, life as we know it would not exist.

Several important properties of water make it so important to life:

• Water is polar. The hydrogen and oxygen atoms within water molecules form bonds that allow each water molecule to attract other water molecules. Water also attracts other polar molecules (such as sugars) that can dissolve in water.
• Water is an excellent solvent. Because water is polar, other polar compounds and molecules can readily dissolve in it. Water is, therefore, what is referred to as a solvent—a substance capable of dissolving another substance. This makes it an excellent molecule for transporting substances throughout an organism.
• Water stabilizes temperature. The bonds in water allow it to absorb and release heat energy more slowly than many other substances. Temperature is a measure of the motion (kinetic energy) of molecules. As the motion increases, energy is higher and thus the temperature is higher. Water absorbs a great deal of energy before its temperature rises. Increased energy disrupts the hydrogen bonds between water molecules. Because these bonds can be created and disrupted rapidly, water absorbs an increase in energy and temperature changes only minimally. This means that water moderates temperature changes within organisms and in their environments.
• Water is cohesive. Have you ever filled up a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water actually forms a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of cohesion. Water molecules are attracted to each other, keeping the molecules together at the liquid-air (gas) interface, although there is no more room in the glass. Cohesion gives rise to surface tension, the capacity of a substance to withstand rupture when placed under tension or stress. When you drop a small scrap of paper onto a droplet of water, the paper floats on top of the water droplet, although the object is denser (heavier) than the water. This occurs because of the surface tension that is created by the water molecules. Cohesion and surface tension keep the water molecules intact and the item floating on the top. These cohesive forces are also related to the water’s property of adhesion, or the attraction between water molecules and other molecules. This is observed when water “climbs” up a straw placed in a glass of water. Cohesive and adhesive forces are important for sustaining life. For example, because of these forces, water can flow up from the roots to the tops of plants to feed the plant.

Buffers, pH, Acids, and Bases

The pH of a solution is a measure of its acidity or alkalinity. The pH scale ranges from 0 to 14. A change of one unit on the pH scale represents a change in the concentration of hydrogen ions by a factor of 10, a change in two units represents a change in the concentration of hydrogen ions by a factor of 100. Thus, small changes in pH represent large changes in the concentrations of hydrogen ions. Pure water is neutral. It is neither acidic nor basic and has a pH of 7.0. Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. The blood in your veins is slightly alkaline (pH = 7.4). The environment in your stomach is highly acidic (pH = 1 to 2). Orange juice is mildly acidic (pH = approximately 3.5), whereas baking soda is basic (pH = 9.0).

Figure \(\PageIndex{4}\). The pH scale measures the amount of hydrogen ions (H+) in a substance. (credit: modification of work by Edward Stevens)

How is it that we can ingest or inhale acidic or basic substances and not die? Buffers are the key. Buffers readily absorb excess H+ or OH–, keeping the pH of the body carefully maintained in the aforementioned narrow range. Carbon dioxide is part of a prominent buffer system in the human body; it keeps the pH within the proper range. This buffer system involves carbonic acid (H₂CO₃) and bicarbonate (HCO₃–) anion. If too much H+ enters the body, bicarbonate will combine with the H+ to create carbonic acid and limit the decrease in pH. Likewise, if too much OH– is introduced into the system, carbonic acid will combine with it to create bicarbonate and limit the increase in pH. While carbonic acid is an important product in this reaction, its presence is fleeting because the carbonic acid is released from the body as carbon dioxide gas each time we breathe. Without this buffer system, the pH in our bodies would fluctuate too much, and we would fail to survive.

Biological Molecules

Besides water, the molecules necessary for life are organic. Organic molecules are those that contain carbon covalently bonded to hydrogen. They may also contain oxygen, nitrogen, phosphorus, sulfur, and additional elements. There are four major classes of important organic molecules: carbohydrates, lipids, proteins, and nucleic acids. Each 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.

Lipids include a diverse group of compounds that are united by a common feature: they are hydrophobic (“water-fearing”), or insoluble in water, because they are non-polar. Lipids include fats, oils, waxes, phospholipids, and steroids.

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.
• Lipids are also the building blocks of many hormones and are an important constituent of cellular membranes.

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 composed of (polymers of) amino acids. The functions of proteins are very diverse because there are 20 different chemically distinct amino acids that can be combined in any order and in very long strands. Proteins can function as enzymes, hormones, contractile fibers, cytoskeleton rods, and much more. Enzymes are vital to life because they act as catalysts in biochemical reactions (like digestion). Each enzyme is specific for the material (substrate) upon which it acts. Enzymes can function to break molecular bonds, to rearrange bonds, or to form new bonds.

Carbohydrates include sugars and starches. These compounds contain only the elements carbon, hydrogen, and oxygen. Functions of carbohydrates in living things include providing energy to cells, storing energy, and forming certain structures, such as the cell walls of plants. The monomer that makes up large carbohydrate compounds is called a monosaccharide.

Nucleic acids are very large molecules that support 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 the largest trees and mammals, and has a beautiful double-helical structure (Figure \(\PageIndex{6}\)). The other type of nucleic acid, RNA, is mostly involved in protein synthesis and its regulation. DNA and RNA are made up of small building blocks known as nucleotides.

Figure \(\PageIndex{6}\). The double-helix model shows DNA as two parallel strands of intertwining molecules.

Attribution

• Concepts of Biology by OpenStax is licensed under CC BY 4.0. Modified from original by Matthew R. Fisher.