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4.1: Matter

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    Atoms, Molecules, Compounds

    At its most fundamental level, life is made up of matter. Matter 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 naturally, and fewer than 30 are found in living cells. 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 \(\ce{H}\), \(\ce{N}\), \(\ce{O}\), \(\ce{C}\), and \(\ce{Na}\)), and possesses unique properties. These unique properties 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 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 subatomic 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. 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.

    At the most basic level, all organisms are made of a combination of elements. They contain atoms that combine together to form molecules. 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. All atoms contain protons, electrons, and neutrons (Figure below). The only exception is hydrogen (\(\ce{H}\)), which is 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.

    clipboard_ef67ef65fa3feb89e864bc8beec21ef2a.png
    Figure \(\PageIndex{1}\): Atoms are made up of protons and neutrons located within the nucleus, and electrons surrounding the nucleus.

    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.

    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.

    Isotopes are different forms of the same element that have the same number of protons, but a different number of neutrons. Some elements, such as carbon, potassium, and uranium, have naturally occurring isotopes. Carbon-12, the most common isotope of carbon, contains six protons and six neutrons. Therefore, it has a mass number of 12 (six protons and six neutrons) and an atomic number of 6 (which makes it carbon). Carbon-14 contains six protons and eight neutrons. Therefore, it has a mass number of 14 (six protons and eight neutrons) and an atomic number of 6, meaning it is still the element carbon. These two alternate forms of carbon are isotopes. Some isotopes are unstable and will lose protons, other subatomic particles, or energy to form more stable elements. These are called radioactive isotopes or radioisotopes.

    Evolution in Action

    Carbon-14 (14C) is a naturally occurring radioisotope that is created in the atmosphere by cosmic rays. This is a continuous process, so more 14C is always being created. As a living organism develops, the relative level of 14C in its body is equal to the concentration of 14C in the atmosphere. When an organism dies, it is no longer ingesting 14C, so the ratio will decline. 14C decays to 14N by a process called beta decay; it gives off energy in this slow process. After approximately 5,730 years, only one-half of the starting concentration of 14C will have been converted to 14N. The time it takes for half of the original concentration of an isotope to decay to its more stable form is called its half-life.

    Because the half-life of 14C is long, it is used to age formerly living objects, such as fossils. Using the ratio of the 14C concentration found in an object to the amount of 14C detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined. Based on this amount, the age of the fossil can be calculated to about 50,000 years (Figure below). Isotopes with longer half-lives, such as potassium-40, are used to calculate the ages of older fossils. Through the use of carbon dating, scientists can reconstruct the ecology and biogeography of organisms living within the past 50,000 years.

    clipboard_ec53ada7c3e2fa116a1aca3371ef924e5.png
    Figure \(\PageIndex{2}\): The age of remains that contain carbon and are less than about 50,000 years old, such as this pygmy mammoth, can be determined using carbon dating. (credit: Bill Faulkner/ NPS)

    Chemical bonds

    How elements interact with one another depends on how their electrons are arranged and how many openings for electrons exist at the outermost region where electrons are present in an atom. Electrons exist at energy levels that form shells around the nucleus. The closest shell can hold up to two electrons. The closest shell to the nucleus is always filled first, before any other shell can be filled. Hydrogen has one electron; therefore, it has only one spot occupied within the lowest shell. Helium has two electrons; therefore, it can completely fill the lowest shell with its two electrons. If you look at the periodic table, you will see that hydrogen and helium are the only two elements in the first row. This is because they only have electrons in their first shell. Hydrogen and helium are the only two elements that have the lowest shell and no other shells.

    Not all elements have enough electrons to fill their outermost shells, but an atom is at its most stable when all of the electron positions in the outermost shell are filled. Because of these vacancies in the outermost shells, we see the formation of chemical bonds, or interactions between two or more of the same or different elements that result in the formation of molecules. To achieve greater stability, atoms will tend to completely fill their outer shells and will bond with other elements to accomplish this goal by sharing electrons, accepting electrons from another atom, or donating electrons to another atom. Because the outermost shells of the elements with low atomic numbers (up to calcium, with atomic number 20) can hold eight electrons, this is referred to as the octet rule. An element can donate, accept, or share electrons with other elements to fill its outer shell and satisfy the octet rule.

    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. 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. For example, sodium only has one electron in its outermost shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons and only 10 electrons, leaving it with an overall charge of +1. It is now called a sodium ion.

    Ionic and covalent bonds are strong bonds or interactions that require a larger energy input to break apart. When an element donates an electron from its outer shell, as in the sodium atom example above, a positive ion is formed. The element accepting the electron is now negatively charged. Because positive and negative charges attract, these ions stay together and form an ionic bond, or a bond between ions. The elements bond together with the electron from one element staying predominantly with the other element.

    Another type of strong chemical bond between two or more atoms is a covalent bond. These bonds form when an electron is shared between two elements and are the strongest and most common form of chemical bond in living organisms. Covalent bonds form between the elements that make up the biological molecules in our cells. Unlike ionic bonds, covalent bonds do not dissociate in water.

    The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds. The electron from the hydrogen atom divides its time between the outer shell of the hydrogen atom and the incomplete outer shell of the oxygen atom. To completely fill the outer shell of an oxygen atom, two electrons from two hydrogen atoms are needed, hence the subscript “2” in \(\ce{H2O}\). The electrons are shared between the atoms, dividing their time between them to “fill” the outer shell of each. This sharing is a lower energy state for all of the atoms involved than if they existed without their outer shells filled.

    When polar covalent bonds containing a hydrogen atom form, the hydrogen atom in that bond has a slightly positive charge. This is because the shared electron is pulled more strongly toward the other element and away from the hydrogen nucleus. Because the hydrogen atom is slightly positive (δ+), it will be attracted to neighboring negative partial charges (δ–). When this happens, a weak interaction occurs between the δ+ charge of the hydrogen atom of one molecule and the δ– charge of the other molecule. This interaction is called a hydrogen bond. This type of bond is common; for example, the liquid nature of water is caused by the hydrogen bonds between water molecules. Hydrogen bonds give water the unique properties that sustain life. If it were not for hydrogen bonding, water would be a gas rather than a liquid at room temperature.

    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 or did exist on that planet. 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 simply would not exist.

    • WATER IS POLAR. The hydrogen and oxygen atoms within water molecules form polar covalent bonds. The shared electrons spend more time associated with the oxygen atom than they do with hydrogen atoms. There is no overall charge to a water molecule, but there is a slight positive charge on each hydrogen atom and a slight negative charge on the oxygen atom. Because of these charges, the slightly positive hydrogen atoms repel each other and form the unique shape. Each water molecule attracts other water molecules because of the positive and negative charges in the different parts of the molecule. Water also attracts other polar molecules (such as sugars) that can dissolve in water and are referred to as hydrophilic (“water-loving”).
    • WATER STABILIZES TEMPERATURE. The hydrogen 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 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 AN EXCELLENT SOLVENT. Because water is polar, with slight positive and negative charges, ionic compounds and polar molecules can readily dissolve in it. Water is, therefore, what is referred to as a solvent—a substance capable of dissolving another substance. The charged particles will form hydrogen bonds with a surrounding layer of water molecules.
    • 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. In cohesion, water molecules are attracted to each other (because of hydrogen bonding), 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. It is even possible to “float” a steel needle on top of a glass of water if you place it gently, without breaking the surface tension. 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. You will notice that the water appears to be higher on the sides of the straw than in the middle. This is because the water molecules are attracted to the straw and therefore adhere to it. 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). Acids are substances that provide hydrogen ions (\(\ce{H+}\)) and lower pH, whereas bases provide hydroxide ions (\(\ce{OH-}\)) and raise pH. The stronger the acid, the more readily it donates \(\ce{H+}\). For example, hydrochloric acid and lemon juice are very acidic and readily give up \(\ce{H+}\) when added to water. Conversely, bases are those substances that readily donate \(\ce{OH-}\). The \(\ce{OH-}\) ions combine with \(\ce{H+}\) to produce water, which raises a substance’s pH. Sodium hydroxide and many household cleaners are very alkaline and give up \(\ce{OH-}\) rapidly when placed in water, thereby raising the pH.

    clipboard_ec51dd6b80db8160f00d1580286ff7bc8.png
    Figure \(\PageIndex{3}\): The pH scale measures the amount of hydrogen ions (\(\ce{H+}\)) 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 \(\ce{H+}\) or \(\ce{OH-}\), 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 (\(\ce{H2CO3}\)) and bicarbonate (\(\ce{HCO3-}\)) anion. If too much \(\ce{H+}\) enters the body, bicarbonate will combine with the \(\ce{H+}\) to create carbonic acid and limit the decrease in pH. Likewise, if too much \(\ce{OH-}\) 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

    The large molecules necessary for life that are built from smaller organic molecules are called biological macromolecules. There are four major classes of biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids), and each is an important component of the cell and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s mass. Biological macromolecules are organic, meaning that they contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, phosphorus, sulfur, and additional minor elements.

    Carbon

    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, if not most, 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 bonding

    Carbon contains four electrons in its outer shell. Therefore, it can form four covalent bonds with other atoms or molecules. The simplest organic carbon molecule is methane (\(\ce{CH4}\)), in which four hydrogen atoms bind to a carbon atom (Figure below).

    fig 4.1.4.jpgFigure \(\PageIndex{4}\): Carbon can form four covalent bonds to create an organic molecule. The simplest carbon molecule is methane (\(\ce{CH4}\)), depicted here

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

    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, arranged in a linear sequence. 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. For example, proteins can function as enzymes or hormones.

    Enzymes, which are produced by living cells, are catalysts in biochemical reactions (like digestion) and are usually proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts. Enzymes can function to break molecular bonds, to rearrange bonds, or to form new bonds.

    Nucleic acids are key macromolecules in the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus, but instead use an RNA intermediary to communicate with the rest of the cell. Other types of RNA are also involved in protein synthesis and its regulation. DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group. Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to a phosphate group. DNA has a double-helical structure (Figure below).

    fig 4.1.5.jpgFigure \(\PageIndex{5}\): The double-helix model shows DNA as two parallel strands of intertwining molecules.

    It is composed of two strands, or polymers, of nucleotides. The strands are formed with bonds between phosphate and sugar groups of adjacent nucleotides. The strands are bonded to each other at their bases with hydrogen bonds, and the strands coil about each other along their length, hence the “double helix” description, which means a double spiral. The alternating sugar and phosphate groups lie on the outside of each strand, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase, and these bases pair; the pairs are bound to each other by hydrogen bonds. The bases pair in such a way that the distance between the backbones of the two strands is the same all along the molecule.

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