2.10: Introduction to Atoms and Elements - Biology

2.10: Introduction to Atoms and Elements - Biology

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What you’ll learn to do: Define atoms and elements

You’re probably familiar with the concept of atoms. Before you can understand chemical reactions, you must first understand the way that atoms work.

Over the years, scientists have used different models to visualize atoms as our understanding has changed. You may be familiar with a few of the models in Figure 1. In this course, we we largely use the Bohr model.

Percent and fraction essentially tell you the same thing, they describe the ratio of a part of the whole. Because a chemical compound has a constant composition, which is defined by is molecular or compound formula, the fraction of each type of element must be constant. For example, water has 3 atoms, one hydrogen and two oxygens. So the fraction of oxygen is 1/3 (33.3%) and the fraction of hydrogen is 2/3rd (66.7%), as exemplified in the left pie chart of Figure (PageIndex<1>). But water weights 16 times as much as hydrogen and so if you could weigh a water molecule, the mass of oxygen would be 16 Daltons, while that of the two hydrogens would be 2 Daltons, so on a mass basis, water if 88.9% oxygen and 11.1% hydrogen. So when we say the fractional or percent composition, we need to identify how we are determining it. Usually, but not always, chemists use percentage for mass and fraction for moles (number of particles).

Mole Fraction/Percent of Water Mass Fraction/Percent of Water

Figure (PageIndex<1>): Mole (left) and mass (right) fractions (or percentages) of oxygen and hydrogen in water.

So, is water mostly oxygen or hydrogen? Well, that depends on how you look at it. If you are counting atoms, it is mostly hydrogen. If you are measuring the mass, it is mostly oxygen.


Elements in various combinations comprise all matter, including living things. Some of the most abundant elements in living organisms include carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. These form the nucleic acids, proteins, carbohydrates, and lipids that are the fundamental components of living matter. Biologists must understand these important building blocks and the unique structures of the atoms that comprise molecules, allowing for cells, tissues, organ systems, and entire organisms to form.

All biological processes follow the laws of physics and chemistry, so in order to understand how biological systems work, it is important to understand the underlying physics and chemistry. For example, the flow of blood within the circulatory system follows the laws of physics that regulate the modes of fluid flow. The breakdown of the large, complex molecules of food into smaller molecules—and the conversion of these to release energy to be stored in adenosine triphosphate (ATP)—is a series of chemical reactions that follow chemical laws. The properties of water and the formation of hydrogen bonds are key to understanding living processes. Recognizing the properties of acids and bases is important, for example, to our understanding of the digestive process. Therefore, the fundamentals of physics and chemistry are important for gaining insight into biological processes.

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    The Periodic Table of Elements

    The different elements are organized and displayed in the periodic table. Devised by Russian chemist Dmitri Mendeleev (1834–1907) in 1869, the table groups elements that, although unique, share certain chemical properties with other elements. The properties of elements are responsible for their physical state at room temperature: they may be gases, solids, or liquids. Elements also have specific chemical reactivity, the ability to combine and to chemically bond with each other.

    In the periodic table, shown in Figure 3, the elements are organized and displayed according to their atomic number and are arranged in a series of rows and columns based on shared chemical and physical properties. In addition to providing the atomic number for each element, the periodic table also displays the element’s atomic mass. Looking at carbon, for example, its symbol (C) and name appear, as well as its atomic number of six (in the upper left-hand corner) and its atomic mass of 12.11.

    Figure 3. The periodic table shows the atomic mass and atomic number of each element. The atomic number appears above the symbol for the element and the approximate atomic mass appears below it.

    The periodic table groups elements according to chemical properties. The differences in chemical reactivity between the elements are based on the number and spatial distribution of an atom’s electrons. Atoms that chemically react and bond to each other form molecules. Molecules are simply two or more atoms chemically bonded together. Logically, when two atoms chemically bond to form a molecule, their electrons, which form the outermost region of each atom, come together first as the atoms form a chemical bond.

    Watch this video for a more in-depth introduction to the periodic table:

    3.2 What are living things made of?

    If we took a sample of all living matter, put it in a blender, and further broke it down into its simplest parts we would have the elements. Currently 94 elements have been identified on earth. All matter that we know of is made up of one or more of these elements. You may have seen these elements listed in a periodic table like the one below (note the table has 118 elements – those past number 94 have been made by researchers and may or may not exist in nature).

    Figure 3.2 The Periodic Table of the Elements.

    However, out of those 94 elements, the vast majority (over 98%!) of the human body (and the bodies of other plants and animals) is made up of only 6 of them. These most common biological elements are carbon, hydrogen, oxygen, nitrogen, calcium, and phosphorus.

    Figure 3.3 The main elements that compose the human body are shown from most abundant (by mass, not by fraction of atoms) to least abundant.

    What we are made of

    Astronomer Neil DeGrasse Tyson speaks about the beauty of what we are made of in this video:

    When you look at the ingredients of the universe the #1 ingredient is hydrogen, next is helium…oxygen, carbon nitrogen. … What are we made of?… The fact that you rank the atoms in the human body, with the exception of helium, which is chemically inert…(look at the top ingredients of the human body)…[it] matches the universe.

    So we’ve learned in the last 50 years that, of course, not only do we exist in this universe, it is the universe itself that exists within us.”

    One tiny piece of an element is called an atom. An atom is the smallest portion of an element that has the properties of that element. An atom contains a nucleus with positive and uncharged particles (protons and neutrons, respectively), and has negatively charged electrons that circle the nucleus.

    Figure 3.4 An atom’s charges

    The electrons of one atom can interact with electrons of other atoms and form chemical bonds. When two or more atoms of the same or different elements bond together they form molecules. The way these atoms are arranged into molecules impacts their properties and functions. One of the simplest molecules you may be familiar with is water, a molecule in which two hydrogen atoms are bound to an oxygen atom.

    In biological organisms there are some important categories of molecules (called biomolecules) that are found in all forms of life. We will highlight a few of the biomolecule categories here, including:

    1. By 2012rc. Own work. Notes and font fixed: The Photographer, CC BY 3.0. &crarr
    2. By OpenStax College - Anatomy & Physiology. CC BY 3.0 &crarr

    Common Elements

    Let's work with the alphabet idea again. If you read a book, you will find words on each page. Letters make up those words. In English, we only have twenty-six letters, but we can make thousands of words. In chemistry, you are working with almost 120 elements. When you combine them, you can make millions of different molecules.

    Molecules are groups of atoms in the same way that words are groups of letters. An "A" will always be an "A" no matter what word it is in. A sodium (Na) atom will always be a sodium atom no matter what molecule it is in. While atoms from different elements have different masses and structures, they are all built with the same parts. Electrons, protons, and neutrons are the basic subunits for all atoms across the Universe.

    Everything in the universe is made up of atoms. Atoms are the smallest units of matter, and the different types of atoms make up different elements. They can exist on their own, or bonded together in molecules.

    The subatomic particles that make up atoms are protons, neutrons, and electrons. Elements have unique properties and atomic structures. All atoms of the same element have the same number of protons. The universe of elements and their properties are charted in the periodic table.

    A preview of each game in the learning objective is found below.

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    2.1 What is Organic Chemistry?

    2.2 Elements, Atoms, and the Periodic Table

    Elements and Abundance

    Atomic Theory

    Subatomic Particles

    Protons Determine the Identity of an Element

    Isotopes and Atomic Mass

    Electrons and the Periodic Table of the Elements

    Features of the Periodic Table

    2.3 Chapter Summary

    2.4 References

    2.1 What is Organic Chemistry?

    Have you ever wondered why some plants can be used to make medicines while others are toxic and can kill you? Or why some foods are thought of as healthy while others are bad for you? Or how beverages like beer, cider and wine are made? This course is designed to introduce the reader to fundamental concepts in Organic Chemistry using consumer products, technologies and services as model systems to teach these core concepts and show how organic chemistry is an integrated part of everyday life.

    Organic chemistry is a growing subset of chemistry. To put it simply, it is the study of all carbon-based compounds their structure, properties, and reactions and their use in synthesis. It is the chemistry of life and includes all substances that have been derived from living systems. The application of organic chemistry today can be seen everywhere you look, from the plastic making up components of your computer, to nylon which make up your clothes, to macromolecules and cells that make up your very body! Organic chemistry has expanded our world of knowledge and it is an essential part of the fields of medicine, biochemistry, biology, industry, nanotechnology, rocket science, and many more!

    To begin our discussions of organic chemistry, we need to first take a look at chemical elements and understand how they interact to form chemical compounds.

    2.2 Elements, Atoms, and the Periodic Table

    Elements and Abundance

    An element is a substance that cannot be broken down into simpler chemical substances. There are about 90 naturally occurring elements known on Earth. Using technology, scientists have been able to create nearly 30 additional elements that are not readily found in nature. Today, chemistry recognizes a total of 118 elements which are all represented on a standard chart of the elements, called the Periodic Table of Elements (Figure 2.1). Each element is represented by a one or two letter code, where the first letter is always capitalized and, if a second letter is present, it is written in lowercase. For example, the symbol for Hydrogen is H, and the symbol for carbon is C. Some of the elements have seemingly strange letter codes, such as sodium which is Na. These letter codes are derived from latin terminology. For example, the symbol for sodium (Na) is derived from the latin word, natrium, which means sodium carbonate.

    Figure 2.1: Elements. Some examples of pure elements include (A) Bismuth, Bi, a heavy metal is used as a replacement for lead and in some medicines, like pepto-bismol, the antidiarrheal and (B) Strontium, Sr, a major component in fireworks. (C) All of the elements that have been discovered are represented on the Periodic Table of Elements, which provides an elegant mechanism for not only displaying the elements, but describing many of their characteristics.

    The elements vary widely in abundance. In the universe as a whole, the most common element is hydrogen (about 90%), followed by helium (most of the remaining 10%). All other elements are present in relatively minuscule amounts, as far as we can detect. On the planet Earth, however, the situation is rather different. Oxygen makes up 46.1% of the mass of Earth’s crust (the relatively thin layer of rock forming Earth’s surface), mostly in combination with other elements, while silicon makes up 28.5%. Hydrogen, the most abundant element in the universe, makes up only 0.14% of Earth’s crust. Table 2.1 “Elemental Composition of Earth” lists the relative abundances of elements on Earth as a whole and in Earth’s crust. Table 2.2 “Elemental Composition of a Human Body” lists the relative abundances of elements in the human body. If you compare Table 2.1 “Elemental Composition of Earth” and Table 2.2 “Elemental Composition of a Human Body”, you will find disparities between the percentage of each element in the human body and on Earth. Oxygen has the highest percentage in both cases, but carbon, the element with the second highest percentage in the body, is relatively rare on Earth and does not even appear as a separate entry in Table 2.1 “Elemental Composition of Earth” carbon is part of the 0.174% representing “other” elements. How does the human body concentrate so many apparently rare elements?

    The relative amounts of elements in the body have less to do with their abundances on Earth than with their availability in a form we can assimilate. We obtain oxygen from the air we breathe and the water we drink. We also obtain hydrogen from water. On the other hand, although carbon is present in the atmosphere as carbon dioxide, and about 80% of the atmosphere is nitrogen, we obtain those two elements from the food we eat, not the air we breathe.

    Atomic Theory

    The modern atomic theory, proposed about 1803 by the English chemist John Dalton, is a fundamental concept that states that all elements are composed of atoms. An atom is the smallest part of an element that maintains the identity of that element. Individual atoms are extremely small even the largest atom has an approximate diameter of only 5.4 × 10 −10 m. With that size, it takes over 18 million of these atoms, lined up side by side, to equal the width of your little finger (about 1 cm).

    Most elements in their pure form exist as individual atoms. For example, a macroscopic chunk of iron metal is composed, microscopically, of individual iron atoms. Some elements, however, exist as groups of atoms called molecules. Several important elements exist as two-atom combinations and are called diatomic molecules. In representing a diatomic molecule, we use the symbol of the element and include the subscript 2 to indicate that two atoms of that element are joined together. The elements that exist as diatomic molecules are hydrogen (H2), oxygen (O2), nitrogen (N2), fluorine (F2), chlorine (Cl2), bromine (Br2), and iodine (I2).

    Subatomic Particles

    There have been several minor but important modifications to Dalton’s atomic theory. For one thing, Dalton considered atoms to be indivisible. We know now that atoms not only can be divided but also are composed of three different kinds of particles with their own properties that are different from the chemical properties of atoms.

    The first subatomic particle was identified in 1897 and called the electron. It is an extremely tiny particle, with a mass of about 9.109 × 10 −31 kg. Experiments with magnetic fields showed that the electron has a negative electrical charge.

    By 1920, experimental evidence indicated the existence of a second particle. A proton has the same amount of charge as an electron, but its charge is positive, not negative. Another major difference between a proton and an electron is mass. Although still incredibly small, the mass of a proton is 1.673 × 10 −27 kg, which is almost 2,000 times greater than the mass of an electron. Because opposite charges attract each other (while ‘like’ charges repel each other), protons attract electrons (and vice versa).

    Finally, additional experiments pointed to the existence of a third particle, called the neutron. Evidence produced in 1932 established the existence of the neutron, a particle with about the same mass as a proton but with no electrical charge.

    We understand now that all atoms can be broken down into subatomic particles: protons, neutrons, and electrons. Table 2.3 “Properties of the Subatomic Particles” lists some of their important characteristics and the symbols used to represent each particle. Experiment have shown that protons and neutrons are concentrated in a central region of each atom called the nucleus (plural, nuclei). Electrons are outside the nucleus and orbit about it because they are attracted to the positive charge in the nucleus. Most of the mass of an atom is in the nucleus, while the orbiting electrons account for an atom’s size. As a result, an atom consists largely of empty space. (Figure 2.4 and 2.5).

    Fig 2.4 The anatomy of an atom. The protons and neutrons of an atom are found clustered at the center of the atom in a structure called the nucleus. The electrons orbit the nucleus of the atom within an electron cloud, or the empty space that surrounds the atom’s nucleus. Note that most of the area of an atom is taken up by the empty space of the electron cloud.

    Fig 2.5 The path of the electron in a hydrogen atom. Electrons are not in discrete orbits like planets around the sun. Instead there is a probability that an electron may occupy a certain space within the electron cloud (a) The darker the color, the higher the probability that the hydrogen’s one electron will be at that point at any given time. (b) Similarly, the more crowded the dots, the higher the probability that hydrogen’s one electron will be at that point. In both diagrams, the nucleus is in the center of the diagram.

    Protons Determine the Identity of an Element

    As it turns out, the number of protons that an atom holds in its nucleus is the key determining feature for its chemical properties. In short, an element is defined by the number of protons found in its nucleus. The proton number within an element is also called its Atomic Number and is represented by the mathematical term, Z (Fig 2.6). If you refer back to the Periodic Table of Elements shown in figure 2.1, you will see that the periodic table is organized by the number of protons that an element contains. Thus, as you read across each row of the Periodic Table (left to right), each element increases by one proton (or one Atomic Number, Z).

    Fig 2.6 Structure of the Periodic Table. Each element on the periodic table is represented by the atomic symbol (Cu for Copper), the Atomic Number in the upper lefthand corner, and the Atomic Mass in the righthand corner.

    Isotopes, Allotropes, and Atomic Mass

    How many neutrons are in atoms of a particular element? At first it was thought that the number of neutrons in a nucleus was also characteristic of an element. However, it was found that atoms of the same element can have different numbers of neutrons. Atoms of the same element that have different numbers of neutrons are called isotopes (Fig. 2.7). For example, 99% of the carbon atoms on Earth have 6 neutrons and 6 protons in their nuclei about 1% of the carbon atoms have 7 neutrons and 6 protons in their nuclei. Naturally occurring carbon on Earth, therefore, is actually a mixture of isotopes, albeit a mixture that is 99% carbon with 6 neutrons in each nucleus. Isotope composition has proven to be a useful method for dating many rock layers and fossils.

    Fig 2.7 Isotopes of Hydrogen. All hydrogen atoms have one proton and one electron. However, they can differ in the number of neutrons. (a) Most hydrogen atoms onlycontain one p+ and one e- and no neutrons (b) A small amount of hydrogen exists as the isotope deuterium, which has one proton and one neutron in its nucleus, and (c) an even smaller amount contains one proton and two neutrons in its nucleus and is termed Tritium. Note that Tritium is unstable isotope and will breakdown over time. Thus, Tritium is a radioactive element.

    Most elements exist as mixtures of isotopes. In fact, there are currently over 3,500 isotopes known for all the elements. When scientists discuss individual isotopes, they need an efficient way to specify the number of neutrons in any particular nucleus. The atomic mass (A) of an atom is the sum of the numbers of protons and neutrons in the nucleus (Fig. 2.6). Given the atomic mass for a nucleus (and knowing the atomic number, Z, of that particular atom), you can determine the number of neutrons by subtracting the atomic number from the atomic mass.

    A simple way of indicating the mass number of a particular isotope is to list it as a superscript on the left side of an element’s symbol. Atomic numbers are often listed as a subscript on the left side of an element’s symbol. Thus, we might see

    which indicates a particular isotope of copper. The 29 is the atomic number, Z, (which is the same for all copper atoms), while the 63 is the atomic mass (A) of the isotope. To determine the number of neutrons in this isotope, we subtract 29 from 63: 63 − 29 = 34, so there are 34 neutrons in this atom.

    Allotropes of an element are different and separate from the term isotope and should not be confused. Some chemical elements can form more than one type of structural lattice, these different structural lattices are known as allotropes. This is the case for phosphorus as shown in Figure 2.2. White or yellow phosphorus forms when four phosphorus atoms align in a tetrahedral conformation (Fig 2.8). The other crystal lattices of phosphorus are more complex and can be formed by exposing phosphorus to different temperatures and pressures. For example, the cage-like lattice of red phosphorus can be formed by heating white phosphorus over 280 o C (Fig 2.8). Note that allotropic changes affect how the atoms of the element interact with one another to form a 3-dimensional structure. They do not alter the sample with regard to the atomic isotope forms that are present, and DO NOT alter or affect the atomic mass (A) of the element.

    Different allotropes of different elements can have different physical and chemical properties and are thus, still important to consider. For example, oxygen has two different allotropes with the dominant allotrope being the diatomic form of oxygen, O2. However, oxygen can also exist as O3, ozone. In the lower atmosphere, ozone is produced as a by-product in automobile exhaust, and other industrial processes where it contributes to pollution. It has a very pungent smell and is a very powerful oxidant. It can cause damage to mucous membranes and respiratory tissues in animals. Exposure to ozone has been linked to premature death, asthma, bronchitis, heart attacks and other cardiopulmonary diseases. In the upper atmosphere, it is created by natural electrical discharges and exists at very low concentrations. The presence of ozone in the upper atmosphere is critically important as it intercepts very damaging ultraviolet radiation from the sun, preventing it from reaching the Earth’s surface.

    Figure 2.8 Allotropes of Phosphorus. (A) White phosphorus exists as a (B) tetrahedral form of phosphorus, whereas (C) red phosphorus has a more (D) cage-like crystal lattice. (E) The different elemental forms of phosphorus can be created by treating samples of white phosphorus with increasing temperature and pressure.

    Electrons and the Periodic Table of the Elements

    Remember that electrons are 2000 times smaller than protons and yet each one contains an equal, but opposing charge. Electrons have a negative charge while protons have a positive charge. Interestingly, when elements exist in their elemental form, as shown on the periodic table, the number of electrons housed in an atom is equal to the number protons. Therefore, the electric charge of an element cancels itself out and the overall charge of the atom is zero.

    Electrons are the mobile part of the atom. They move and orbit the nucleus of the atom in the electron cloud, the term used for the space around the nucleus. However, they do not move around in random patterns. Electrons have addresses, or defined orbital spins, within the electron cloud, much the same way our apartment buildings have addresses within our cities. To find the address of an electron, you need to know a little bit about the organization of the electron cloud (…or the city that the electron lives in).

    The electron cloud of an atom is divided into layers, called shells, much the way an onion has layers when you peel it. However, it is incorrect to think of a shell as a single layer without thickness and depth to it. A shell has 3-dimensional space within it that contains a wide variety of ‘apartments’ or spaces for the electrons to occupy. Thus, the shell, or n number, is only the first part of an electron’s address within an atom. It would be similar to only knowing the neighborhood where your friend lives. If you only know the neighborhood, it will be difficult to find your friend if you want to take them to dinner.

    There are a total of 7 shells (or layers) that an atom can have to house it’s electrons. If an atom is small, it may only have 1 or 2 shells. Only very large atoms have all 7 layers. After this point, adding an 8th shell appears to make the atom too unstable to exist…at least we have never found atoms containing an 8th shell! In the periodic table (Fig. 2.9), you will notice that there are a total of 7 rows on the periodic table (note that the Lanthanide and Actinide rows of elements are generally shown below the main table to make them fit onto one page, but they really belong in the middle of rows 6 and 7 on the periodic table, according to their atomic numbers). Each of these rows represents an electron shell. Thus, as atoms get larger and house more electrons, they acquire additional shells, up to 7.

    Fig 2.9 Structure of the Periodic Table. Each element on the periodic table is represented by the atomic symbol (Cu for Copper), the Atomic Number in the upper lefthand corner, and the Atomic Mass in the righthand corner.

    Source: Robson, G.(2006) Wikipedia.

    Within this textbook, we are not concerned with learning the addresses of all the electrons, but we are very interested about the electrons that are nearest to the surface of the atom, or the ones that are in the outer shell of the atom. The electrons that are closest to the surface of the atom are the most reactive and are integral in forming bonds between the atoms. These electrons are said to be housed in the atom’s, valence shell, or the electron shell that is the farthest away from the nucleus of the atom. (or nearest to the surface of the atom).

    Features of the Periodic Table

    Elements that have similar chemical properties are grouped in columns called groups (or families). As well as being numbered, some of these groups have names—for example, alkali metals (the first column of elements), alkaline earth metals (the second column of elements), halogens (the next-to-last column of elements), and noble gases (the last column of elements).

    Each row of elements on the periodic table is called a period. Periods have different lengths the first period has only 2 elements (hydrogen and helium), while the second and third periods have 8 elements each. The fourth and fifth periods have 18 elements each, and later periods are so long that a segment from each is removed and placed beneath the main body of the table.

    Certain elemental properties become apparent in a survey of the periodic table as a whole. Every element can be classified as either a metal, a nonmetal, or a semimetal, as shown in Figure 2.10 “Types of Elements”. A metal is a substance that is shiny, typically (but not always) silvery in color, and an excellent conductor of electricity and heat. Metals are also malleable (they can be beaten into thin sheets) and ductile (they can be drawn into thin wires). A nonmetal is typically dull and a poor conductor of electricity and heat. Solid nonmetals are also very brittle. As shown in Figure 2.7 “Types of Elements”, metals occupy the left three-fourths of the periodic table, while nonmetals (except for hydrogen) are clustered in the upper right-hand corner of the periodic table. The elements with properties intermediate between those of Another way to categorize the elements of the periodic table is shown in Figure 2.11 “Special Names for Sections of the Periodic Table”. The first two columns on the left and the last six columns on the right are called the main group elements. The ten-column block between these columns contains the transition metals. The two rows beneath the main body of the periodic table contain the inner transition metals. The elements in these two rows are also referred to as, respectively, the lanthanide metals and the actinide metals (Fig 2.11).

    Fig 2.10. Types of Elements. Elements are either metals, nonmetals, or semimetals. Each group is located in a different part of the periodic table.

    Fig 2.11. Special Names for Sections of the Periodic Table. Some sections of the periodic table have special names. For example, the elements lithium, sodium, potassium, rubidium, cesium, and francium are collectively known as alkali metals. Note that the main group elements do not include the transition metals.

    The periodic table is organized on the basis of similarities in elemental properties, but what explains these similarities? It turns out that the arrangement of the columns or families in the Periodic Table reflects how subshells are filled with electrons. Of note, elements in the same column share the same valence shell electron configuration. For example, all elements in the first column have a single electron in their valence shells. This last observation is crucial. Chemistry is largely the result of interactions between the valence electrons of different atoms. Thus, atoms that have the same valence shell electron configuration will have similar chemistry (Fig 2.12).

    Fig 2.12. Number of Valence Shell Electrons. The placement of elements on the periodic table corresponds with the number of valence electrons housed in that element. Families (columns) on the periodic table all contain the same number of valence shell electrons, which gives them similar chemical properties and reactivities. You can easily count across the main group elements to see the increasing number of electrons in the valence shell. All of the transition metals have 2 e- in their valence shell, although they also contain an inner orbital subshell that is very close to the valence shell. This gives some of these metals different levels of reactivity. Note that the maximum number of valence shell electrons possible is 8, and that is obtained only by the Noble Gases.

    Fig 2.13. Role of iron in oxygen transportation. The hemoglobin protein makes up about 95% of the dry content of the red blood cell and each hemoglobin protein can bind and carry four molecules of oxygen (O2).

    Adapted from: and

    The octet rule drives the chemical behavior of atoms. Atoms will chemically react and bond to each other form molecules, which are simply two or more atoms chemically bonded together. A compound is a type of molecule that contains two or more different types of atoms. In short, atoms form chemical bonds with other atoms, thereby obtaining the electrons they need to attain a stable electron configuration. The familiar water molecule, H2O, consists of two hydrogen atoms and one oxygen atom bonded together (Figure 2.8). Atoms can form molecules by donating, accepting, or sharing electrons to fill their outer shells.

    Figure 2.8 Two or more atoms may bond with each other to form a molecule. When two hydrogens and an oxygen share electrons via covalent bonds, a water molecule is formed.

    Chemical reactions occur when two or more atoms bond together to form molecules or when bonded atoms are broken apart. The substances used in the beginning of a chemical reaction are called the reactants and the substances found at the end of the reaction are known as the products. An arrow is typically drawn between the reactants and products to indicate the direction of the chemical reaction. Most chemical reactions can go in either direction. For the creation of the water molecule shown above, the chemical equation would be:

    2 H2 + O2 → 2 H2O

    This is an example of a balanced chemical equation, wherein the number of atoms of each element is the same on each side of the equation.

    BIO 140 - Human Biology I - Textbook

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    Chapter 1

    Elements and Atoms: The Building Blocks of Matter

    By the end of this section, you will be able to:

    • Discuss the relationships between matter, mass, elements, compounds, atoms, and subatomic particles
    • Distinguish between atomic number and mass number
    • Identify the key distinction between isotopes of the same element
    • Explain how electrons occupy electron shells and their contribution to an atom&rsquos relative stability


    The substance of the universe&mdashfrom a grain of sand to a star&mdashis called matter . Scientists define matter as anything that occupies space and has mass. An object&rsquos mass and its weight are related concepts, but not quite the same. An object&rsquos mass is the amount of matter contained in the object, and the object&rsquos mass is the same whether that object is on Earth or in the zero-gravity environment of outer space. An object&rsquos weight, on the other hand, is its mass as affected by the pull of gravity. Where gravity strongly pulls on an object&rsquos mass its weight is greater than it is where gravity is less strong. An object of a certain mass weighs less on the moon, for example, than it does on Earth because the gravity of the moon is less than that of Earth. In other words, weight is variable, and is influenced by gravity. A piece of cheese that weighs a pound on Earth weighs only a few ounces on the moon.

    Elements and Compounds

    All matter in the natural world is composed of one or more of the 92 fundamental substances called elements. An element is a pure substance that is distinguished from all other matter by the fact that it cannot be created or broken down by ordinary chemical means. While your body can assemble many of the chemical compounds needed for life from their constituent elements, it cannot make elements. They must come from the environment. A familiar example of an element that you must take in is calcium (Ca ++ ). Calcium is essential to the human body it is absorbed and used for a number of processes, including strengthening bones. When you consume dairy products your digestive system breaks down the food into components small enough to cross into the bloodstream. Among these is calcium, which, because it is an element, cannot be broken down further. The elemental calcium in cheese, therefore, is the same as the calcium that forms your bones. Some other elements you might be familiar with are oxygen, sodium, and iron. The elements in the human body are shown in Figure 1, beginning with the most abundant: oxygen (O), carbon (C), hydrogen (H), and nitrogen (N). Each element&rsquos name can be replaced by a one- or two-letter symbol you will become familiar with some of these during this course. All the elements in your body are derived from the foods you eat and the air you breathe.

    Figure 1: The main elements that compose the human body are shown from most abundant to least abundant.

    In nature, elements rarely occur alone. Instead, they combine to form compounds. A compound is a substance composed of two or more elements joined by chemical bonds. For example, the compound glucose is an important body fuel. It is always composed of the same three elements: carbon, hydrogen, and oxygen. Moreover, the elements that make up any given compound always occur in the same relative amounts. In glucose, there are always six carbon and six oxygen units for every twelve hydrogen units. But what, exactly, are these &ldquounits&rdquo of elements?

    Atoms and Subatomic Particles

    An atom is the smallest quantity of an element that retains the unique properties of that element. In other words, an atom of hydrogen is a unit of hydrogen&mdashthe smallest amount of hydrogen that can exist. As you might guess, atoms are almost unfathomably small. The period at the end of this sentence is millions of atoms wide.

    Atomic Structure and Energy

    Atoms are made up of even smaller subatomic particles, three types of which are important: the proton , neutron , and electron . The number of positively-charged protons and non-charged (&ldquoneutral&rdquo) neutrons, gives mass to the atom, and the number of each in the nucleus of the atom determine the element. The number of negatively-charged electrons that &ldquospin&rdquo around the nucleus at close to the speed of light equals the number of protons. An electron has about 1/2000th the mass of a proton or neutron.

    Figure 2 shows two models that can help you imagine the structure of an atom&mdashin this case, helium (He). In the planetary model, helium&rsquos two electrons are shown circling the nucleus in a fixed orbit depicted as a ring. Although this model is helpful in visualizing atomic structure, in reality, electrons do not travel in fixed orbits, but whiz around the nucleus erratically in a so-called electron cloud.

    Figure 2: (a) In the planetary model, the electrons of helium are shown in fixed orbits, depicted as rings, at a precise distance from the nucleus, somewhat like planets orbiting the sun. (b) In the electron cloud model, the electrons of carbon are shown in the variety of locations they would have at different distances from the nucleus over time.

    An atom&rsquos protons and electrons carry electrical charges. Protons, with their positive charge, are designated p + . Electrons, which have a negative charge, are designated e &ndash . An atom&rsquos neutrons have no charge: they are electrically neutral. Just as a magnet sticks to a steel refrigerator because their opposite charges attract, the positively charged protons attract the negatively charged electrons. This mutual attraction gives the atom some structural stability. The attraction by the positively charged nucleus helps keep electrons from straying far. The number of protons and electrons within a neutral atom are equal, thus, the atom&rsquos overall charge is balanced.

    Atomic Number and Mass Number

    An atom of carbon is unique to carbon, but a proton of carbon is not. One proton is the same as another, whether it is found in an atom of carbon, sodium (Na), or iron (Fe). The same is true for neutrons and electrons. So, what gives an element its distinctive properties&mdashwhat makes carbon so different from sodium or iron? The answer is the unique quantity of protons each contains. Carbon by definition is an element whose atoms contain six protons. No other element has exactly six protons in its atoms. Moreover, all atoms of carbon, whether found in your liver or in a lump of coal, contain six protons. Thus, the atomic number , which is the number of protons in the nucleus of the atom, identifies the element. Because an atom usually has the same number of electrons as protons, the atomic number identifies the usual number of electrons as well.

    In their most common form, many elements also contain the same number of neutrons as protons. The most common form of carbon, for example, has six neutrons as well as six protons, for a total of 12 subatomic particles in its nucleus. An element&rsquos mass number is the sum of the number of protons and neutrons in its nucleus. So the most common form of carbon&rsquos mass number is 12. (Electrons have so little mass that they do not appreciably contribute to the mass of an atom.) Carbon is a relatively light element. Uranium (U), in contrast, has a mass number of 238 and is referred to as a heavy metal. Its atomic number is 92 (it has 92 protons) but it contains 146 neutrons it has the most mass of all the naturally occurring elements.

    The periodic table of the elements , shown in Figure 3, is a chart identifying the 92 elements found in nature, as well as several larger, unstable elements discovered experimentally. The elements are arranged in order of their atomic number, with hydrogen and helium at the top of the table, and the more massive elements below. The periodic table is a useful device because for each element, it identifies the chemical symbol, the atomic number, and the mass number, while organizing elements according to their propensity to react with other elements. The number of protons and electrons in an element are equal. The number of protons and neutrons may be equal for some elements, but are not equal for all.

    Figure 3: (credit: R.A. Dragoset, A. Musgrove, C.W. Clark, W.C. Martin)


    Although each element has a unique number of protons, it can exist as different isotopes. An isotope is one of the different forms of an element, distinguished from one another by different numbers of neutrons. The standard isotope of carbon is 12 C, commonly called carbon twelve. 12 C has six protons and six neutrons, for a mass number of twelve. All of the isotopes of carbon have the same number of protons therefore, 13 C has seven neutrons, and 14 C has eight neutrons. The different isotopes of an element can also be indicated with the mass number hyphenated (for example, C-12 instead of 12 C). Hydrogen has three common isotopes, shown in Figure 4.

    Isotopes of Hydrogen

    Figure 4: Protium, designated 1 H, has one proton and no neutrons. It is by far the most abundant isotope of hydrogen in nature. Deuterium, designated 2 H, has one proton and one neutron. Tritium, designated 3 H, has two neutrons

    An isotope that contains more than the usual number of neutrons is referred to as a heavy isotope. An example is 14 C. Heavy isotopes tend to be unstable, and unstable isotopes are radioactive. A radioactive isotope is an isotope whose nucleus readily decays, giving off subatomic particles and electromagnetic energy. Different radioactive isotopes (also called radioisotopes) differ in their half-life, the time it takes for half of any size sample of an isotope to decay. For example, the half-life of tritium&mdasha radioisotope of hydrogen&mdashis about 12 years, indicating it takes 12 years for half of the tritium nuclei in a sample to decay. Excessive exposure to radioactive isotopes can damage human cells and even cause cancer and birth defects, but when exposure is controlled, some radioactive isotopes can be useful in medicine. For more information, see the Career Connections.

    Career Connection

    Interventional Radiologist

    The controlled use of radioisotopes has advanced medical diagnosis and treatment of disease. Interventional radiologists are physicians who treat disease by using minimally invasive techniques involving radiation. Many conditions that could once only be treated with a lengthy and traumatic operation can now be treated non-surgically, reducing the cost, pain, length of hospital stay, and recovery time for patients. For example, in the past, the only options for a patient with one or more tumors in the liver were surgery and chemotherapy (the administration of drugs to treat cancer). Some liver tumors, however, are difficult to access surgically, and others could require the surgeon to remove too much of the liver. Moreover, chemotherapy is highly toxic to the liver, and certain tumors do not respond well to it anyway. In some such cases, an interventional radiologist can treat the tumors by disrupting their blood supply, which they need if they are to continue to grow. In this procedure, called radioembolization, the radiologist accesses the liver with a fine needle, threaded through one of the patient&rsquos blood vessels. The radiologist then inserts tiny radioactive &ldquoseeds&rdquo into the blood vessels that supply the tumors. In the days and weeks following the procedure, the radiation emitted from the seeds destroys the vessels and directly kills the tumor cells in the vicinity of the treatment.

    Radioisotopes emit subatomic particles that can be detected and tracked by imaging technologies. One of the most advanced uses of radioisotopes in medicine is the positron emission tomography (PET) scanner, which detects the activity in the body of a very small injection of radioactive glucose, the simple sugar that cells use for energy. The PET camera reveals to the medical team which of the patient&rsquos tissues are taking up the most glucose. Thus, the most metabolically active tissues show up as bright &ldquohot spots&rdquo on the images (Figure 5). PET can reveal some cancerous masses because cancer cells consume glucose at a high rate to fuel their rapid reproduction.

    Figure 5: PET highlights areas in the body where there is relatively high glucose use, which is characteristic of cancerous tissue. This PET scan shows sites of the spread of a large primary tumor to other sites.

    The Behavior of Electrons

    In the human body, atoms do not exist as independent entities. Rather, they are constantly reacting with other atoms to form and to break down more complex substances. To fully understand anatomy and physiology you must grasp how atoms participate in such reactions. The key is understanding the behavior of electrons.

    Although electrons do not follow rigid orbits a set distance away from the atom&rsquos nucleus, they do tend to stay within certain regions of space called electron shells. An electron shell is a layer of electrons that encircle the nucleus at a distinct energy level.

    The atoms of the elements found in the human body have from one to five electron shells, and all electron shells hold eight electrons except the first shell, which can only hold two. This configuration of electron shells is the same for all atoms. The precise number of shells depends on the number of electrons in the atom. Hydrogen and helium have just one and two electrons, respectively. If you take a look at the periodic table of the elements, you will notice that hydrogen and helium are placed alone on either sides of the top row they are the only elements that have just one electron shell (Figure 6). A second shell is necessary to hold the electrons in all elements larger than hydrogen and helium.

    Lithium (Li), whose atomic number is 3, has three electrons. Two of these fill the first electron shell, and the third spills over into a second shell. The second electron shell can accommodate as many as eight electrons. Carbon, with its six electrons, entirely fills its first shell, and half-fills its second. With ten electrons, neon (Ne) entirely fills its two electron shells. Again, a look at the periodic table reveals that all of the elements in the second row, from lithium to neon, have just two electron shells. Atoms with more than ten electrons require more than two shells. These elements occupy the third and subsequent rows of the periodic table.

    Electron Shells

    Figure 6: Electrons orbit the atomic nucleus at distinct levels of energy called electron shells. (a) With one electron, hydrogen only half-fills its electron shell. Helium also has a single shell, but its two electrons completely fill it. (b) The electrons of carbon completely fill its first electron shell, but only half-fills its second. (c) Neon, an element that does not occur in the body, has 10 electrons, filling both of its electron shells

    The factor that most strongly governs the tendency of an atom to participate in chemical reactions is the number of electrons in its valence shell. A valence shell is an atom&rsquos outermost electron shell. If the valence shell is full, the atom is stable meaning its electrons are unlikely to be pulled away from the nucleus by the electrical charge of other atoms. If the valence shell is not full, the atom is reactive meaning it will tend to react with other atoms in ways that make the valence shell full. Consider hydrogen, with its one electron only half-filling its valence shell. This single electron is likely to be drawn into relationships with the atoms of other elements, so that hydrogen&rsquos single valence shell can be stabilized.

    All atoms (except hydrogen and helium with their single electron shells) are most stable when there are exactly eight electrons in their valence shell. This principle is referred to as the octet rule, and it states that an atom will give up, gain, or share electrons with another atom so that it ends up with eight electrons in its own valence shell. For example, oxygen, with six electrons in its valence shell, is likely to react with other atoms in a way that results in the addition of two electrons to oxygen&rsquos valence shell, bringing the number to eight. When two hydrogen atoms each share their single electron with oxygen, covalent bonds are formed, resulting in a molecule of water, H2O.

    In nature, atoms of one element tend to join with atoms of other elements in characteristic ways. For example, carbon commonly fills its valence shell by linking up with four atoms of hydrogen. In so doing, the two elements form the simplest of organic molecules, methane, which also is one of the most abundant and stable carbon-containing compounds on Earth. As stated above, another example is water oxygen needs two electrons to fill its valence shell. It commonly interacts with two atoms of hydrogen, forming H2O. Incidentally, the name &ldquohydrogen&rdquo reflects its contribution to water (hydro- = &ldquowater&rdquo -gen = &ldquomaker&rdquo). Thus, hydrogen is the &ldquowater maker.&rdquo

    Chapter Review

    The human body is composed of elements, the most abundant of which are oxygen (O), carbon (C), hydrogen (H) and nitrogen (N). You obtain these elements from the foods you eat and the air you breathe. The smallest unit of an element that retains all of the properties of that element is an atom. But, atoms themselves contain many subatomic particles, the three most important of which are protons, neutrons, and electrons. These particles do not vary in quality from one element to another rather, what gives an element its distinctive identification is the quantity of its protons, called its atomic number. Protons and neutrons contribute nearly all of an atom&rsquos mass the number of protons and neutrons is an element&rsquos mass number. Heavier and lighter versions of the same element can occur in nature because these versions have different numbers of neutrons. Different versions of an element are called isotopes.

    The tendency of an atom to be stable or to react readily with other atoms is largely due to the behavior of the electrons within the atom&rsquos outermost electron shell, called its valence shell. Helium, as well as larger atoms with eight electrons in their valence shell, is unlikely to participate in chemical reactions because they are stable. All other atoms tend to accept, donate, or share electrons in a process that brings the electrons in their valence shell to eight (or in the case of hydrogen, to two).