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Self-Instructional on Basic Chemistry for Biology
Atoms and Elements
All things are made of a substance called matter. You can think of matter as everything that is not empty space. Many people believe that the space around them is empty space. While this may be true for an astronaut on a space walk, it is not true for us here on earth.
So what kind of matter surrounds you in this "empty" space? Well, one would hope that air would be in the vicinity. Although we can not see the air, it is all around us. Air is made of tiny units of matter, moving rapidly and bouncing off one another and other things. What can make up substances that are so important but invisible?
All matter (including the air we breathe) is composed of very tiny, basic units called atoms. First let us find out what particles make up the atom. An atom is composed of three types of subatomic particles:
If everything is made up of atoms, then how can all matter be so different? Atoms can have different numbers of protons, electrons, and neutrons. These different numbers of subatomic particles define the different elements. An element is a pure substance made up of only one kind of atom. Examples of different elements include Hydrogen, Carbon, Sulfur, Oxygen, Nitrogen and Phosphorus. There are many more elements such as Gold, Silver, Mercury or Uranium, but the elements listed first are the ones that generally compose organic matter.
Different elements have very different physical properties or characteristics. Atoms of the same element have the same number of protons, electrons, and neutrons. However, atoms of different elements have different numbers of protons, electrons, and neutrons. All protons are identical to one another, as are all electrons and all neutrons. It is only the number of these subatomic particles that creates the different properties found among the elements.
Take Hydrogen and Helium as an example. Hydrogen has one proton and one electron. Helium has two protons, two electrons, and two neutrons. How different are Hydrogen and Helium from each other? They are both gases and they are both lighter than air. However, the Hindenberg blimp that burned in a matter of minutes was filled with Hydrogen, which is extremely flammable. The Goodyear blimp is filled with Helium, which is non-flammable and called an inert, or non-reactive gas. Although the difference in the numbers of protons and electrons is not great between Hydrogen and Helium, these two elements have very different properties.
Practice Round One
1. Define the following terms in your own words: matter, element, inert.
2. Are all of the subatomic particles in one element exactly like all of the subatomic particles in a different element?
3. What makes elements so different from one another?
4. What subatomic particles make up atoms?
Atomic mass and Atomic number
All elements can be identified by their atomic mass and atomic number. These two values can tell you how many protons, electrons, and neutrons are in any element. The following are examples of the atomic mass and atomic number for the atoms found in several different elements.
Do you see a pattern forming? Electrons are very light compared to the mass of neutrons and protons. Neutrons and protons have approximately the same mass.
Practice Round Two
1. What does the atomic number of an element represent: the number of protons, electrons or neutrons?
2. How can the atomic weight of an element be calculated?
3. How do the concepts of mass and weight differ?
Remember, the most important skill in science is the ability to make an educated guess and draw conclusions about the information. Getting the right answer is secondary to perfecting this skill. If you are able to draw a few reasonable conclusions based on the information available, you should consider yourself successful.
Structure of the Atom
Because the number of protons and electrons must be equal in all neutral atoms, the atomic number could represent either the number of protons or electrons. Scientists have decided that the number of protons represents the atomic number, because the number of electrons may vary when atoms participate in chemical reactions.
The element Hydrogen is unique in that it has no neutrons. Therefore, most of the mass of a Hydrogen atom must come from the proton, because electrons have a tiny mass when compared with protons and neutrons.
The actual atomic mass of each subatomic particle is as follows:
In practice, we round off the numbers and count the mass of the electron as zero. Atomic weight is equal to the number of protons plus the number of neutrons.
You do not have to memorize all the atomic numbers and atomic weights. They are all on a handy table called the Periodic Table of the Elements, which we will learn to use in this unit. Before going on to the periodic table let's learn more about the parts of the atom.
The Bohr Model
A physicist, Neils Bohr, designed a model for atomic structure. It is called the Bohr model (of course) and is a simple but excellent way to visualize the structure of atoms. The Bohr Model describes the protons and neutrons located at the center of the atom, in what we term as the nucleus. The electrons exist around the nucleus in what we call electron shells.
Figure 1. Bohr Model of the atom.
In addition to mass, subatomic particles also have charges. Electrons have a charge of negative one, and protons have a charge of positive one. These positive and negative charges are opposite and exactly equal in strength. For this reason, an atom with one electron and one proton has no net charge. The +1 charge of the proton and the -1 charge of the electron cancel each other out. Neutrons, as their name suggests, are neutral, or uncharged particles. Neutrons contribute mass, but no charge to an atom.
Just like the poles of magnets, the opposite charges on protons and electrons attract one another. This weak nuclear force helps hold the electrons near the nucleus of the atom. You may wonder how all the positively charged protons could possibly exist close together in the nucleus. The protons are of like charge, so why don't the positive charges repel each other? The answer lies in a second fundamental force, called the strong nuclear force.
Atoms of elements must always have the same number of electrons and protons or the elements would be highly reactive and very unstable. If an atom has an unequal number of electrons or protons, it is an ion. Ions can exist only when surrounded by other ions of opposite charge.
Practice Round Three
1. If the element Sodium has an atomic number of eleven, how many electrons does it have?
2. If an atom of Sodium has eleven negatively charged electrons, it also must have eleven positive charges from which subatomic particle? What would its net charge be?
3. Boron has four electrons, four neutrons, and four protons. What is the atomic number of Boron? What is its atomic weight? What is its overall charge?
4. A hypothetical element has an atomic number of 121 and an atomic weight of 249. How many electrons does it have? How many protons does it have? How many neutrons does it have? What is its overall charge?
The Periodic Table
The periodic table of the elements not only supplies information about the numbers of protons, electrons, and neutrons, but also predicts the reactivity of the atoms of each element. This allows us to predict how different elements will combine to form compounds. The electrons in atoms interact and form chemical bonds to make different compounds with unique properties. Compounds are formed when the atoms of different elements combine through the sharing of their electrons or the interaction of their charges.
Compounds are represented by a molecular formula. A molecule is the smallest unit of a compound that exhibits the defining characteristics of that compound. The molecular formula uses the abbreviation for each element and represents the proportions of each type of atom in a compound. To start, let us review the molecular formulas of a few common compounds that are probably familiar to you.
H2O - water
NaCl - Sodium chloride (table salt)
The periodic table supplies the information we will need to decipher what the molecular formula of a compound represents, and also how to predict the proportions of elements in a compound. The periodic table contains the following information:
What does the molecular formula of H2O represent? "H" is the abbreviation for hydrogen, and "O" is the abbreviation for oxygen. The compound water contains two atoms of hydrogen for every one atom of oxygen. When the atoms of hydrogen and oxygen combine in the above proportions, water is formed. Consider the following molecular formula: H2O2. What does this molecular formula represent? This compound has two hydrogens for every two oxygens. Is this compound water?
No! It is a very common disinfectant called Hydrogen Peroxide that can be found at any drug store. Even though the molecular formula is very similar to water the addition of one oxygen gives hydrogen peroxide very different properties when compared to water.
How small are molecules? Can they ever be seen? The most convincing way to demonstrate the relative size of a molecule of water is to find out how many molecules are in about 1 teaspoon of water. To determine this we need to learn two new concepts. How to calculate the weight of one molecule, and how to use a constant numerical value called Avogadro's number... named after Avogadro of course!
Using the periodic table, let us calculate the molecular weight of water, or the weight of one molecule of H2O.
Step One: What is the atomic weight of two hydrogens?
Step Two: What is the atomic weight of oxygen?
Step Three: What is the combined weight of two hydrogens and one oxygen? This answer will tell us the molecular weight of H2O.
Avogadro's number is approximately equal to 6.02 x 1023. This number tells us how many molecules there are of a substance in a number of grams equal to the molecular weight of that substance. For example, the molecular weight of water is 18, and if you weigh out 18 grams of water in a cup, the cup will contain 6.02 x 1023 molecules of water. If you weigh out the molecular weight of any compound in grams, you will have 6.02 x 1023 molecules of that compound.
Here are some more examples:
The molecular weight of NaCl is 58. Fifty-eight grams of NaCl contains 6.02 x 1023 molecules of NaCl.
The molecular weight of sucrose C12H24012 (table sugar) is 360, and 360 grams of sucrose contains 6.02 x 1023 molecules.
No matter what compound you use, if you weigh out its molecular weight in grams you have 6.02 x 1023 molecules in that amount.
How big is Avogadro's number? Let's put it into perspective. Avogadro's number is approximately 6 x 1023. One million is a mere 1 x 106. Our conclusion? If you had 6 x 1023 dollars you would be MUCH richer than Bill Gates. There are a phenomenal number of molecules in 18 grams of water. Since there are exactly 5 grams of water in a teaspoon, there are 1.673 x 1023 molecules per teaspoon of water. You can see how tiny a molecule must be for so many of them to fit in a teaspoon. There is not a microscope powerful enough to even come close to seeing atoms or molecules.
Practice Round Four
1. Label the following diagram taken from the periodic table for the element carbon:
2. Define the following terms: compound, molecule, molecular weight, and what Avogadro's number represents.
3. Using the periodic table, calculate the molecular weight for the following compounds: NaCl - sodium chloride, NaOH - sodium hydroxide, and C6H12O6 - glucose.
4. How many grams of the above compounds would you need to have 6.02 x 1023 molecules of each compound?
How Compounds Form
We have already touched on the formation of ionic compounds and the sharing of electrons, but now we should discuss this more fully. Atoms of different elements form chemical bonds with one another to produce compounds such as H2O and NaCl. Electrons present in the atoms of each element are responsible for chemical bond formation. To understand the basics of this process we will reintroduce the Bohr model of the atom in greater detail.
Electrons are constantly on-the-move. They travel so fast and erratically that it is impossible to predict their exact location. This is due to what physicists call the Heisenberg Uncertainty Principle. However, we can say that an electron has a high probability of being found in a certain region around the atom, and this region is what we name the orbital. Electrons do NOT orbit the atom in nice regular circles, like planets orbit the sun. They zip around in random paths around the nucleus like a moth flitting around a light bulb. Electron particles have such a small mass that they behave much like light waves. This may be hard to understand, but don't worry; even the best physicists and chemists have a difficult time understanding the wave-particle nature of electrons.
Electrons with different amounts of energy inhabit orbitals in different electron shells. Physicists have calculated how far each electron shell is from the nucleus of the atom. They have also discovered that the greater the number of electrons in an atom, the more electron shells are necessary to accommodate the electrons.
For example, one atom of Hydrogen can be represented by the following Bohr diagram at right. Protons are represented by 1p+, 2p+, 3p+ etc. Electrons are represented by e-.
The dark center region represents the nucleus that contains the protons and neutrons. The nucleus is responsible for nearly the entire mass of the atom. The area around the nucleus represents the probable location of the one electron in hydrogen. The electron of hydrogen spends most of its time in the first, low energy, electron shell. There is only one orbital in this first electron shell. The orbital is spherically shaped and can hold up to two electrons.
Why is more than one electron shell necessary for atoms with several electrons? Electrons are full of energy, and always trying to stay as far apart from each other as possible. Electrons repel each other because they all have a negative charge. The electron shells closer to the nucleus cover a smaller area and therefore can hold only a certain number of electrons. As electron shells get further from the nucleus of the atom they circumscribe a larger region and can accommodate a larger number of electrons. Each electron orbital has a specified number of electrons it can hold.
What element is represented by the Bohr Model below?
The first electron shell is closest to the nucleus. It can hold up to two electrons. The second electron shell can hold up to eight electrons and the third electron shell can hold anywhere from eight to 18 electrons and so on. Electrons fill the electron shells closest to the nucleus first, and then fill the outer shells accordingly. For example, an atom of Hydrogen (H) with one electron has its electron in the first electron shell. An atom of Helium (He) has two electrons that are both found in the first electron shell. An atom of Lithium (Li) has three electrons, two of which are in the first shell, and the third going into the second electron shell.
The electron orbital configurations quickly become very complex after eight electrons fill the third electron shell. A good general chemistry text can explain the more complicated electron shells, but for our purposes we will examine how electrons are distributed in the first 18 elements of the periodic table. The first three electron shells are filled with two, eight and 18 electrons, respectively. Even though the third shell can hold up to 18 electrons, it can be considered full when it contains eight electrons.
What is the significance of an electron shell being filled? When an electron shell is filled the atom is stable or non-reactive. Let's consider atoms of the elements Hydrogen and Helium once again. Hydrogen, with only one electron in the first shell, is very reactive. It is highly flammable. However, Helium, with two electrons in the first electron shell, is non-reactive. It is called an inert gas.
While all of this is interesting, you may wonder what this has to do with forming compounds. The answer lies in the stability of the outermost electron shell. Filling the outermost electron shell with electrons makes an atom stable. Atoms combine with other atoms in order to borrow or share electrons. This allows them to fill their outermost electron shell and become stable. A favorite example of many introductory biology textbooks is the compound sodium chloride.
Sodium (Na), atomic number eleven, has eleven electrons. Two are in the first electron shell, eight are in the second electron shell, and one is in the third electron shell. Is the outermost shell filled? How many electrons will it take to fill the third shell?
Bohr model of Sodium:
Chloride (Cl), atomic number 17, has 17 electrons. Two are in the first electron shell, eight are in the second electron shell, and seven are in the third electron shell. Is the outermost shell filled? How many electrons will it take to fill the third shell?
Bohr Model of Chlorine:
With their outermost electron shells unfilled sodium and chlorine are not as stable as they would like to be. When an atom of sodium and chlorine come in close proximity, the single electron in the sodium's outermost electron shell can be donated to the outermost shell of the chlorine atom. Would the outermost shell of sodium then be filled? Would the outermost shell of chlorine then be filled?
Since the outermost shell of sodium is now the second electron shell, we see that the outermost shell is now stable because it is filled with eight electrons. If a single electron is donated to the 7 electrons in the third electron shell of chlorine, it is now filled with 8 electrons. Both atoms now have filled outermost shells! However, there is one little problem.
Can atoms be stable when the number of protons are not equal to the number of electrons? With 11 protons(+) and 10 electrons(-), what is the overall charge of this sodium atom? With 17 protons(+) and 18 electrons(-) what is the overall charge of this chlorine atom? The sodium atom that has lost one electron has an overall or net charge of +1. The chlorine atom that has gained an extra electron has an overall or net charge of -1.
These charged atoms are called ions. Because these ions have opposite charges they will attract each other, combine together through an ionic bond, and form one molecule of a compound. When one sodium atom and one chlorine atom form an ionic bond they produce sodium chloride, better known as table salt. The ionic bond is of moderate strength when compared to the three major types of chemical bonds that hold atoms together.
This combination allows for a dramatic alteration in the characteristics of the compound when compared to the elements that make it up! If you were to take a tiny chunk of sodium and throw it into water it would explode into flames. Chlorine gas is toxic to all living cells. Chlorine is used to kill tiny organisms in pool water, and chlorine bleach is an excellent disinfectant because it is poisonous to all types of organisms. Since we all eat NaCl everyday and our blood is salty with NaCl you may conclude that compounds are dramatically different from the elements that compose them.
Practice Round Five
1. Choose two elements on the periodic table with an atomic number smaller than Argon that you think will form an ionic bond just as sodium and chlorine do.
2. Write a name for the compound that may be created if atoms of these two elements form an ionic bond.
3. Write the molecular formula for your proposed compound.
4. Where on the periodic table in relationship to sodium can your positively charged element be found? (left, right, up or down.) How many electrons are in its outermost electron shell? Is its outermost electron shell filled?
5. Where on the periodic table in relationship to chlorine can your negatively charged element be found? (left, right, up or down.) How many electrons are in its outermost electron shell? Is its outermost electron shell filled?
6. Do you believe that the periodic table was arranged with a specific order in mind? Why or why not?
Covalent Bonds
We will now discuss another type of chemical bond called the covalent bond. A covalent bond is formed when two or more atoms share electrons. The covalent bond is the strongest chemical bond. These bonds allow for the formation of stable compounds and satisfy the need for atoms to have a filled outer electron shell. When atoms share electrons they actually get close enough that their electron shells overlap. In this way electrons from two or more atoms can share their electrons and form stable molecules. Let's look at a diagram of a well-known compound that is held together by covalent bonds between oxygen and hydrogen.
Oxygen has six electrons in its outermost shell. How many electrons would fill the shell to make it stable?
Hydrogen, as we know, has one electron in its outermost shell. Oxygen needs two electrons to bring the number of electrons in its outermost shell from six to a total of eight. Hydrogen needs one electron to fill its outermost shell. Oxygen will form covalent bonds with two hydrogen atoms in order to access those two needed electrons. One of the electrons from oxygen is shared with each hydrogen, so the hydrogen atoms also have filled their outermost shells.
When one molecule of water is formed, one atom of oxygen combines through overlapping electron shells with two hydrogen atoms. By sharing electrons, all participating atoms that form covalent bonds have filled their outermost electron shells, and therefore make stable compounds.
Post Test on Basic Chemistry for Biology
Define and explain the relationships between the following terms.
1. Matter, atoms, elements, and compounds.
2. Atoms, Molecules and Avogadro's number.
3. Draw a Bohr diagram and label and define the parts of the diagram for the following elements: Aluminum, Neon, and Boron. Are any of these inert? Why or why not?
4. Calculate the molecular weight for the following compounds: MgCl2, C12H22O12, NaH2PO4.
5. Explain in detail how Sodium and Chlorine form an ionic bond using electrons.
6. Draw a Bohr molecule of one molecule of methane CH4 that contains four covalent bonds.
7. Write a short description of the formation of ionic and covalent bonds.
8. Uranium has an atomic number of 92 and an atomic weight of 238. How many neutrons does it have? How did you arrive at your answer?
9. How many molecules are present in the amounts of the following compounds: 10 grams of NaCl, 4 grams of H2O, 100 grams of C6H12O6?
© copyright by Gretchen Kirchner 1996, 2001
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