After studying this chapter, you should be able to:
Identify the elements common in biological matter
Explain the structure and components of an atom
Identify the properties of elements given a periodic table
Define the term isotope and explain how isotopes are used in radiometric dating
State the first and second laws of thermodynamics
Explain the difference between kinetic and potential energy
Elements in Biological Matter
The environment is composed of matter and energy, from the molecules that make up a tree’s cells to the fire that burns down a forest. Understanding environmental issues requires knowledge of chemistry, which is the study of how matter and energy interact.
At its most fundamental level, life is made up of matter. Matter is any substance that occupies space and has mass. Elements are unique forms of matter with specific chemical and physical properties that cannot be broken down into smaller substances by ordinary chemical reactions. There are 118 elements, but only 92 occur naturally. The remaining elements are synthesized in laboratories and are unstable.
Each element is designated by its chemical symbol, which is a single capital letter or, when the first letter is already “taken” by another element, a combination of two letters. Some elements follow the English term for the element, such as C for carbon and Ca for calcium. Other elements’ chemical symbols derive from their Latin names; for example, the symbol for sodium is Na, referring to natrium, the Latin word for sodium.
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, as shown in Table 1. For example, 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. In spite of their 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.
Table 1. Approximate Percentage of Elements in Living Organisms Compared to the Non-living World
Element
Living Organisms
Atmosphere
Earth’s Crust
Oxygen (O)
65%
21%
46%
Carbon (C)
18%
trace
trace
Hydrogen (H)
10%
trace
0.1%
Nitrogen (N)
3%
78%
trace
Atoms
To understand how elements come together, we must first discuss the smallest component or building block of an element, the atom. An atom is the smallest unit of matter that retains all of the chemical properties of an element. For example, one gold atom has all of the properties of gold in that it is a solid metal at room temperature. A gold coin is simply a very large number of gold atoms molded into the shape of a coin and containing small amounts of other elements known as impurities. Gold atoms cannot be broken down into anything smaller while still retaining the properties of gold.
Figure 1. Elements, such as helium, depicted here, are made up of atoms. Atoms are made up of protons and neutrons located within the nucleus, with electrons in orbitals surrounding the nucleus.
All atoms contain protons, electrons, and neutrons (Figure 1). The only exception is hydrogen (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.
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.
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.
Because protons and neutrons each have a mass of 1, the mass of an atom is equal to the number of protons and neutrons of that atom. The number of electrons does not factor into the overall mass, because their mass is so small. However, a neutral (uncharged) atom will have the same number of protons and electrons since their charges must balance each other out.
Properties of Elements
Atomic Number and Mass
Each element has its own unique properties. Each 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 or atomic mass is the number of protons plus the average number of neutrons of that element. Numbers of neutrons in a atom can vary, so the atomic number is a decimal number. It is possible to determine the number of neutrons in an atom by subtracting the atomic number from the mass number. It is important to round the atomic mass to the nearest whole number before subtracting, since there can only be a whole number of neutrons in a single atom.
For example, magnesium (Mg) has an atomic number of 12 and an atomic mass of 24.31. This means a single atom of magnesium has 12 protons and 12 electrons. If we round the atomic mass to 24 and subtract the atomic number, we can conclude that magnesium also has 12 neutrons.
These numbers provide information about the elements and how they will react when combined. Different elements have different melting and boiling points, and are in different states (liquid, solid, or gas) at room temperature. They also combine in different ways. Some form specific types of bonds, whereas others do not. How they combine is based on the number of electrons present. Because of these characteristics, the elements are arranged into the periodic table of elements, a chart of the elements that includes the atomic number and relative atomic mass of each element. The periodic table also provides key information about the properties of elements (Figure 2)—often indicated by color-coding. The arrangement of the table also shows how the electrons in each element are organized and provides important details about how atoms will react with each other to form molecules.
Figure 2. The periodic table shows each element’s one- or two-letter symbol, atomic mass, and atomic number. The atomic number is always a whole number, and the atomic mass is always a decimal number.
Knowledge Check
Isotopes
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 Dating
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 3). 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.
Figure 3. 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.
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.
The second and third energy levels can hold up to eight electrons. The eight electrons are arranged in four pairs and one position in each pair is filled with an electron before any pairs are completed.
Looking at the periodic table again (Figure 2), you will notice that there are seven rows. These rows correspond to the number of shells that the elements within that row have. The elements within a particular row have increasing numbers of electrons as the columns proceed from left to right. Although each element has the same number of shells, not all of the shells are completely filled with electrons. If you look at the second row of the periodic table, you will find lithium (Li), beryllium (Be), boron (B), carbon (C), nitrogen (N), oxygen (O), fluorine (F), and neon (Ne). These all have electrons that occupy only the first and second shells. Lithium has only one electron in its outermost shell, beryllium has two electrons, boron has three, and so on, until the entire shell is filled with eight electrons, as is the case with neon.
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.
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.
The chlorine atom has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons and 18 electrons, giving it a net negative (–1) charge. It is now called a chloride ion. This movement of electrons from one element to another is referred to as electron transfer. As Figure 4 illustrates, a sodium atom (Na) only has one electron in its outermost shell, whereas a chlorine atom (Cl) has seven electrons in its outermost shell. A sodium atom will donate its one electron to empty its shell, and a chlorine atom will accept that electron to fill its shell, becoming chloride. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium) or –1 (chloride) charge.
Figure 4. Elements tend to fill their outermost shells with electrons. To do this, they can either donate or accept electrons from other elements.
Ionic Bonds
There are four types of bonds or interactions: ionic, covalent, hydrogen bonds, and van der Waals interactions. This chapter will only discuss ionic and covalent bonds. 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. When Na+ and Cl–ions combine to produce NaCl, an electron from a sodium atom stays with the other seven from the chlorine atom, and the sodium and chloride ions attract each other in a lattice of ions with a net zero charge.
Covalent Bonds
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 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. The hydrogen molecule, oxygen molecule, and carbon dioxide molecule are three other common molecules with covalent bonds (Figure 5).
Figure 5. The hydrogen molecule, oxygen molecule, and carbon dioxide molecule are all formed by sharing electrons between atoms. Hydrogen has a single covalent bond, sharing two electrons. Oxygen and carbon dioxide have double covalent bonds, sharing four electrons.
Knowledge Check
Energy
In general, energy is defined as the ability to do work, or to create some kind of change. Energy exists in different forms. For example, electrical energy, light energy, and heat energy are all different types of energy. To appreciate the way energy flows into and out of biological systems, it is important to understand two of the physical laws that govern energy.
Thermodynamics
Thermodynamics refers to the study of energy and energy transfer involving physical matter. The first law of thermodynamics states that the total amount of energy in the universe is constant and conserved. In other words, there has always been, and always will be, exactly the same amount of energy in the universe. Energy exists in many different forms. According to the first law of thermodynamics, energy may be transferred from place to place or transformed into different forms, but it cannot be created or destroyed. The transfers and transformations of energy take place around us all the time. Light bulbs transform electrical energy into light and heat energy. Gas stoves transform chemical energy from natural gas into heat energy. Plants perform one of the most biologically useful energy transformations on earth: that of converting the energy of sunlight to chemical energy stored within organic molecules. Some examples of energy transformations are shown in Figure 6.
Figure 6. Shown are some examples of energy transferred and transformed from one system to another and from one form to another. The food we consume provides our cells with the energy required to carry out bodily functions, just as light energy provides plants with the means to create the chemical energy they need.
The challenge for all living organisms is to obtain energy from their surroundings in forms that they can transfer or transform into usable energy to do work. Living cells have evolved to meet this challenge. Chemical energy stored within organic molecules such as sugars and fats is transferred and transformed through a series of cellular chemical reactions into energy within molecules of ATP. Energy in ATP molecules is easily accessible to do work. Examples of the types of work that cells need to do include building complex molecules, transporting materials, powering the motion of cilia or flagella, and contracting muscle fibers to create movement.
A living cell’s primary tasks of obtaining, transforming, and using energy to do work may seem simple. However, the second law of thermodynamics explains why these tasks are harder than they appear. All energy transfers and transformations are never completely efficient. In every energy transfer, some amount of energy is lost in a form that is unusable. In most cases, this form is heat energy. Thermodynamically, heat energy is defined as the energy transferred from one system to another that is not work. For example, when a light bulb is turned on, some of the energy being converted from electrical energy into light energy is lost as heat energy. Likewise, some energy is lost as heat energy during cellular metabolic reactions.
An important concept in physical systems is that of order and disorder. The more energy that is lost by a system to its surroundings, the less ordered and more random the system is. Scientists refer to the measure of randomness or disorder within a system as entropy. High entropy means high disorder and low energy. Molecules and chemical reactions have varying entropy as well. For example, entropy increases as molecules at a high concentration in one place diffuse and spread out. The second law of thermodynamics says that energy will always be lost as heat in energy transfers or transformations.
Living things are highly ordered, requiring constant energy input to be maintained in a state of low entropy.
Knowledge Check
Potential and Kinetic Energy
When an object is in motion, there is energy associated with that object. Think of a wrecking ball. Even a slow-moving wrecking ball can do a great deal of damage to other objects. Energy associated with objects in motion is called kinetic energy (Figure 7). A speeding bullet, a walking person, and the rapid movement of molecules in the air (which produces heat) all have kinetic energy.
Now what if that same motionless wrecking ball is lifted two stories above ground with a crane? If the suspended wrecking ball is unmoving, is there energy associated with it? The answer is yes. The energy that was required to lift the wrecking ball did not disappear, but is now stored in the wrecking ball by virtue of its position and the force of gravity acting on it. This type of energy is called potential energy (Figure 6). If the ball were to fall, the potential energy would be transformed into kinetic energy until all of the potential energy was exhausted when the ball rested on the ground. Wrecking balls also swing like a pendulum; through the swing, there is a constant change of potential energy (highest at the top of the swing) to kinetic energy (highest at the bottom of the swing). Other examples of potential energy include the energy of water held behind a dam or a person about to skydive out of an airplane.
Figure 7. Still water behind a dam has potential energy; moving water, such as in a waterfall or a rapidly flowing river, has kinetic energy.
Potential energy is not only associated with the location of matter, but also with the structure of matter. Even a spring on the ground has potential energy if it is compressed; so does a rubber band that is pulled taut. On a molecular level, the bonds that hold the atoms of molecules together exist in a particular structure that has potential energy. The fact that energy can be released by the breakdown of certain chemical bonds implies that those bonds have potential energy. In fact, there is potential energy stored within the bonds of all the food molecules we eat, which is eventually harnessed for use. This is because these bonds can release energy when broken. The type of potential energy that exists within chemical bonds, and is released when those bonds are broken, is called chemical energy. Chemical energy is responsible for providing living cells with energy from food. The release of energy occurs when the molecular bonds within food molecules are broken.
Knowledge Check
Attributions
Introduction to Atoms and Elements. Authored by: Shelli Carter and Lumen Learning. Provided by: Lumen Learning. License: CC BY: Attribution
