The mass of subatomic particles is too small to be conveniently measured in grams so atomic mass units (amu) are used instead. Atomic mass units are also called daltons. One amu (or dalton) is approximately 1.7 X 10-24g.
Protons and neutrons have a mass of approximately 1 amu. The mass of an electron is much less. The total mass of an atom is due mostly to the mass of protons and neutrons.
approx. 1 amu
approx. 1 amu
Charge is a state in which particles are either attracted to each other or they repel each other. Two particles that are attracted to each other have opposite charges (positive and negative). Particles that repel each other have the same charge; they are both either positive or they are both negative.
Protons have a positive charge and electrons have a negative charge. Particles with positive charges are attracted to particles with negative charges. Two particles with the same charge (both positive or both negative) will repel each other.Atoms are neutral. The number of electrons (negatively charged) is equal to the number of protons (positively charged), therefore the overall charge is zero.
The atomic mass is calculated as the sum of the mass of protons, electrons, and neutrons.
The mass of electrons is small enough that we can generally disregard it in our calculations of atomic mass. The mass number is the number of protons and neutrons.
Most of an atom is empty space.
The atomic number is the number of protons.
All atoms of an element have the same atomic number.
The number of protons contributes to the physical properties of an element.
Atoms are neutral, therefore the number of electrons is equal to the number of protons.
Isotopes are atoms that have the same number of protons and differ only in the number of neutrons. Three different forms of hydrogen are shown below.
Most isotopes are stable but radioactive isotopes are unstable and break down into more stable forms by emitting particles and energy (radiation).
Radiation can be detected, so radioactive isotopes are useful as labels in scientific research and medical diagnostic procedures.
Energy is the capacity to produce change. For example, energy is needed to move Matter.
Potential energy is energy that is stored in matter. For example, a ball located at the top of a hill will roll down the hill. Due to it's position, it has more potential than an identical ball located at the bottom of the hill.
Electrons at greater distances from the nucleus contain more potential (stored) energy.
Example - Many of the chemical reactions that are associated with energy (ex: photosynthesis) involve electrons moving to higher or lower energy levels.
Distribution of Electrons
The different energy levels are also called electron shells. The first shell is the K shell, the next is the L, followed by M, N, etc.
Electrons in the K shell have the least energy. Electrons that are further from the nucleus have more potential energy.
The maximum number of electrons in each shell is given by the formula 2N2 where N is the shell number. From this formula, the maximum number in each shell is 2, 8, 18, 32, etc. The maximum number of electrons in the last (outer) shell is 8.
It is convenient to draw electrons as occupying a circular space around the nucleus. In reality, electrons do not move around the nucleus in circles.
Pairs of electrons occupy spaces called orbitals. An orbital can hold 2 electrons.
The first shell has one spherical orbital called the 1s orbital. The second shell has 4 orbitals. One is spherical (called 2s) and the other three are dumbbell-shaped and at right angles to each other. These are referred to as 2p orbitals. The arrangement of three dumbbell-shaped orbitals can be in the model shown below.
The third and higher shells have s and p orbitals as well as other kinds of orbitals.
The inner shells of atoms are filled with the maximum number of electrons but the outer shells may or may not be filled..
An atom with only one shell requires two electrons to complete its outer shell. Atoms with more than one shell require 8 electrons to complete their outer shells.
The periodic table (below) is a table showing the atomic symbol, atomic mass, and atomic number of all of the elements. The elements are arranged from left to right according to their atomic number. Elements in the first seven rows are also arranged by the number of electron shells. Elements in the first row have one shell, those in the second row have two shells etc.
A more detailed, interactive periodic table can be seen by clicking the link below.
Bonding and the Outer Shell
Atoms with incomplete shells react with others in a way that allows it to complete the outer shell. Atoms react to give up, receive, or share electrons to produce a completed outer shell.
Atoms with a complete outer shell do not react with other atoms.
The outer shell is called the valence shell. Its electrons are valence electrons.
Chemical bonds form when two or more atoms react to fill their outer shells with electrons.
A compound is two or more elements joined together by chemical bonds.
Atoms with unfilled outer shells may transfer electrons from one to another. The transfer enables the atoms to have complete outer shells.
A sodium atom (Na) and a chlorine atom (Cl) are shown below. A single circle represents the nucleus (protons and neutrons) of the atoms. Dots represent the electrons. The sodium atom has a total of 11 electrons and one electron in its outer shell. Chlorine has a total of 17 electrons with seven in its outer shell.
From this, we can see that the atomic number (number of protons) of sodium is 11 because the number of protons is the same as the number of electrons. Refer to the periodic table to verify that the atomic number of sodium is 11.
When sodium chloride (NaCl) is formed, one electron from sodium is transferred to chlorine.
Atoms are neutral. When an atom transfers electrons to another, the atom that loses one or more electrons becomes positively charged and the atom that gains one or more electrons becomes negatively charged. These charged particles are called ions. Positively charged ions are cations. Negatively charged ions are anions.
Ions have a charge and are written with a plus (+) or a minus (-) sign. For example, calcium loses two electrons to form a calcium ion. The chemical symbol for a calcium ion is therefore Ca++ or Ca+2.
The ions in a compound are attracted to each other due to opposite charges. The attraction, called an ionic bond, holds the ions together.
A compound formed by ionic bonds is called an ionic compound or salt.
A large number of sodium and chloride ions form a crystal as seen below in the photograph of table salt (sodium chloride).
Ionic bonds are weak and the ions can be separated in water (discussed later).
Draw a calcium atom. Draw a chlorine atom. Use circles to represent electrons and tell how many protons and neutrons are in the nucleus. Draw calcium chloride. Click here to view the answer.
Covalent bonds form when atoms share electrons.
Hydrogen atoms contain one electron and one proton.
In the diagram below, two hydrogen atoms are bonded by a single covalent bond. The two atoms each share a pair of electrons.
are two or more atoms that are held together by chemical bonds.
They may be composed of atoms of the same element or of different
elements. In the example above, two hydrogen atoms are held together to
form one molecule of hydrogen. A molecule of hydrogen can be written as
Molecules have a fixed number of atoms. The subscripts in
the formula of a molecule indicate the number of atoms in the molecule.
For example one molecule of CH4 has one carbon atom and four huydrogen atoms.
The number of ions in an ionic compound (discussed
earlier) is not fixed. For example a large crystal of table salt (NaCl)
will have more ions than a small crystal. The subscripts in the
chemical formula of an ionic compound indicate the ratio of ions. For
example CaCl2 has twice as many chloride ions as calcium ions.
Carbon has four electrons in its outer shell. It needs four more electrons. Hydrogen needs one.
The shorthand method for writing one molecule of methane is CH4. It may also be written as shown on the right side of the diagram above.
The model of a methane molecule below shows that each hydrogen atom (white) is an equal distance apart. The black sphere represents a carbon atom.
The outer shells of oxygen atoms have six electrons. They need two additional electrons to become stable. This can be accomplished by sharing two pairs of electrons.
In a double bond, two atoms share two pairs of electrons (4 electrons).
In a triple bond, 2 atoms share 3 pairs of electrons (6 electrons).
Valence and Valence Electrons (BIO 101 only)
Straight lines can be used to represent a covalent bond between two atoms. A single line is used to represent a single bond, two lines are used to represent a double bond and three lines represent a triple bond. Some single, double, and triple bonds are shown below.
Valence electrons are those in the outer shell (valence shell).
The number of bonds that an atom can form is determined by the number of electrons in its valence shell. This number is often called its valence. Hydrogen forms 1 bond, oxygen forms 2 bonds, and carbon forms four. Some elements may form different numbers of bonds. For example, phosphorous may form 3 bonds with some atoms but 5 with others.
Atoms vary in their attraction for electrons. The strength of this attraction is an atom's electronegativity.
Two covalently-bonded atoms that differ in their electronegativity will not share electrons equally and the molecule will be polar. The atom that is more electronegative will exert a stronger attraction for the electrons and will therefore have a partial negative charge. The atom that is less electronegative will have a partial positive charge.
In the drawing below, hydrogen shares one pair of electrons with chlorine by a single covalent bond. The electrons are not shared equally because chlorine is more electronegative; it has a stronger attraction for electrons and thus a partial negative charge. The hydrogen has a partial positive charge because it has less access to the shared electrons.
The diagram below shows that water is composed of two hydrogen atoms bonded to an oxygen atom by two covalent bonds. Each hydrogen atom shares one pair of electrons with the oxygen atom.
Oxygen is much more electronegative than hydrogen and the shared electrons spend more time closer to the oxygen part of the molecule than to the hydrogen part. Unequal sharing of electrons results in the oxygen having a partial negative charge and the hydrogen atoms having a partial positive charge.
A hydrogen bond is an attraction between a molecule containing hydrogen and another molecule or particle. The attraction occurs because the molecule containing hydrogen is polar and the other particle is also charged or polar. Molecules containing hydrogen are often polar because of unequal sharing of electrons.
When hydrogen is covalently bonded to a more electronegative atom such as oxygen or nitrogen, a partial positive charge develops on the hydrogen due to unequal sharing of electrons. The partial positive charge on the hydrogen atom will be attracted to other particles with a negative charge. The attraction between the hydrogen and another particle is called a hydrogen bond. It is not a true bond because electrons are not shared. It is simply an attraction. For example, water molecules are polar and therefore attracted to each other by hydroen bonds.
Hydrogen bonds are weak.
The drawing below shows hydrogen bonds between water molecules. The hydrogen bond forms between the hydrogen of one molecule (partial positive charge) and the oxygen of another molecule (partial negative charge).
Draw two atoms that are bonded by a single covalent bond. Draw 2 atoms bonded by a double covalent bond and 2 bonded by a triple covalent bond. Finally, draw two atoms that are bonded by a polar covalent bond. Use any hypothetical atoms. After your diagrams are complete, identify the atom. Use the periodic table if necessary.
When an atom forms covalent bonds, the s orbital and the p orbitals of the valence shell may become rearranged to form four new hybrid orbitals. The red structures in the model below represent the hybridized orbitals.
The arrangement of the new orbitals of the outer shell determine the shape of the molecule. Each hybrid orbital in a the carbon atom shown below shares one pair of electrons with a hydrogen atom to form methane (CH4). The molecule shaped like a tetrahedron with the carbon atom in the center and a hydrogen atom at each apex. The white structures in the model of methane below represent hydrogen atoms and the black structure is a carbon atom.
The two hydrogen atoms in a water molecule share electrons with two of the hybrid orbitals. The angle between the two hydrogen atoms is 104.5 degrees. The white structures in the drawing below represent hydrogen atoms and the red structure represents an oxygen atom.
The chemical equation for producing water from hydrogen and oxygen is:
2H2 + O2 → 2H2O
Notice that the reactants are written on the left and products on the right. In the equation above, hydrogen (H2) and oxygen (O2) are reactants; water (H2O) is the product.
The equation below (bottom of diagram) is not balanced because the number of atoms on the left side of the arrow is not equal to the number on the right side. Matter cannot be created or destroyed as a result of a chemical reaction.
In a balanced chemical equation, the number of atoms of each element on the left side of the equation is the same as the number on the right.
Most chemical reactions are reversible. The arrow below indicates that the reaction is reversible.
CO2 + H2O → H2CO3
In the reaction above, carbonic acid (H2CO3) accumulates when the concentration of CO2 is high. A higher concentration of CO2 produces a faster reaction due to more frequent molecular collisions. At low CO2 concentration, the reaction moves toward the left, causing carbonic acid to break down and form CO2 + H2O.
An equilibrium occurs when the rate of the forward reaction is equal to the rate of the reverse reaction.
Important Concepts Regarding Covalent Bonds
Energy is often defined as the ability to cause change. For example, movement requires energy.
Energy is required to form a covalent bond and energy is released when a Covalent bond is broken. Covalent bonds can therefore be used by organisms to store energy. The energy that is stored can be used to perform work.
The Concept of the Mole (BIO 101 only)
Oxidation is the loss of electrons from an atom or molecule. It is also the loss (removal) of hydrogen atoms from a molecule. A loss of energy is associated with the loss of electrons or hydrogen atoms.
Reduction is the gain of electrons or the gain of hydrogen atoms. This process stores energy.
Oxidation and reduction occur together. When a atom or molecule is oxidized, another must be reduced.
Example: Na + Cl → Na+Cl- - The Na is oxidized; the Cl is reduced.
Electrons (or hydrogen atoms) function as energy carriers. An atom or molecule that is reduced (gains electrons or hydrogen atoms) also gains energy as a result of the oxidation. Similarly, oxidation is associated with the loss of energy.
Reactions in which one atom or compound is reduced and another is oxidized are called redox reactions.
One mole of a substance is equal to 6.02 X 1023 (Avogadro's number) particles of the substance. For example, one mole of glucose contains 6.02 X 1023 molecules of glucose.
One mole of a substance has a mass in grams that is equal to the sum of the mass number of each atom in one molecule of the substance. For example, if we sum the mass numbers of each of the atoms in one molecule of glucose (C6H12O6, carbon is 12, hydrogen is 1, and oxygen is 16) we get 72 + 12 + 96 = 180. One mole of glucose (6.02 X 1023 molecules) has a mass of 180 grams. This is convenient for chemical calculations because one mole of any substance has 6.02 X 1023 particles.
The concentration of solutions can be measured as the number of moles of solute dissolved in one liter of solvent. This measurement is called the molarity of the solution.
Water covers approximately 71% of Earth's surface. Life evolved in water. Living things are 70-90% water. In nature, water is a solvent for many kinds of chemical reactions.
Water is a polar molecule because the oxygen atom is much more electronegative than the hydrogen atoms, resulting in unequal sharing of electrons. As a result, it forms hydrogen bonds with other polar or charged particles.
Cohesion and Adhesion of Water Molecules
The hydrogen bonds between adjacent water molecules are very weak. As a result, they form and break rapidly, often lasting only a few trillionths of a second. At any instant in time, a large proportion of water molecules are bonded to nearby water molecules, giving water a cohesive property.
Water molecules are also attracted to other polar substances causing them to adhere to many kinds of materials. The meniscus shown below forms when water adheres to the sides of the glass container.
The photograph below shows water on the roof of a waxed car. The water molecules cling to each other but not to the waxed surface because the wax is nonpolar.
This water strider is able to remain on the surface of water because of hydrogen bonding between the molecules. The insect is light and it's weight is spread over the water so that there is not much weight at any one point.
The partial positive and negative charges on a water molecule produce attractions with ions and other polar molecules. The attraction between water molecules and ions may be strong enough to separate the ions, causing the ions to become suspended (dissolved) in the water.
Below: Note that the orientation of the water molecules is depends on the charge of the ion.
The ability of water to flow freely while hydrogen-bonded to other molecules and ions makes it an excellent transport medium.
In the example above, the salt (NaCl) becomes dissolved in the water, forming a solution. A solution is composed of a substance dissolved in another substance. The substance dissolved is the solute and the substance that dissolves the solute is a solvent. In this example, the solvent is water and the solute is salt. A solution in which water is the solvent is called an aqueous solution.
Temperature Change of Water
A given amount of heat energy will change the temperature of water less than it will change the temperature of most other kinds of substances. It takes a relatively large amount of heat will raise the temperature of water a small amount. This property is due to hydrogen bonding. Normally, adding heat energy to a substance causes increased motion of the molecules. The hydrogen bonds between water molecules, however, cause resistance to increased motion; additional heat energy is needed to break the bonds. Similarly, a large amount of heat is released as water cools.
It takes 1 calorie of heat to raise the temperature of 1 gram of water 1 degree C. To raise the temperature of an equal volume of air 1 degree C takes 0.0003 calories. Water requires 3000 times more energy than air.
This property protects organisms from rapid temperature changes. On a larger scale, ocean currents carry an enormous amount of heat energy and have a major impact on climate.
Freezing and Evaporation of Water
Water has kinetic energy because the molecules are constantly in motion. The molecules of hot water have greater movement than those of cold water, thus, hot water has more energy. As the temperature of water decreases, there is less energy for breaking hydrogen bonds. At 0 degrees C, the hydrogen bonds do not break and ice forms. During the freezing process, as the particles are prevented from moving by hydrogen bonds, their kinetic energy is released in the form of heat. When zero degree water changes to ice, 80 calories/gram are released from the water. Thus, in order to convert 1 gram of water at 0 degrees C to ice at 0 degrees C, 80 calories must be removed.
Similarly, 536 calories/gram must be added to change 100 degree water to water vapor without changing the temperature. Once vaporized, additional calories will raise the temperature of the vapor. At 0 degrees C, water requires 597 calories/gram to evaporate. The high heat of vaporization occurs because hydrogen bonds must be broken before water molecules can escape the liquid and it takes energy to break the bonds. Even at low temperatures, only the most energetic (hottest) molecules are able to leave the liquid and become vapor. The result of removing the most energetic molecules is that the average amount of energy of those that remain behind is less.
A large amount of energy is also needed to evaporate water as is indicated by the broken line in the diagram above. The high heat of vaporization enables organisms to use evaporation as a cooling mechanism because each gram of water that evaporates from the surface of an organism at 25 degrees C removes 580 calories of heat.
Water is most dense at 4 degrees and as it warms, it becomes less dense due to increased molecular motion associated with temperature increases.
Hydrogen bonds hold water molecules farther apart than they would be without the bonds. The normal motion of liquid water molecules causes some of the hydrogen bonds between water molecules to break, enabling them to become packed closer together. As water gets colder than 4 degrees C, there is less movement of the molecules and therefore less breaking of hydrogen bonds. Increased hydrogen bonding results in a greater average distance between water molecules. The water becomes less dense because a given volume contains fewer molecules. As ice forms, the number of hydrogen bonds becomes maximal (4 per water molecule) causing ice to be less dense than water.
Ice floats on water because it is less dense than water. Other compounds are more dense at lower temperatures and the solid form does not float on the liquid form.
We learned earlier that atoms that gain or lose electrons become ions. Hydrogen is the smallest atom, composed of one electron and one proton. It can lose its electron to become an ion. A hydrogen ion, however, is a proton because there are no remaining electrons. The words "proton" and "hydrogen ion" are often used interchangeably in discussion of biological topics.
Water molecules can ionize. When two water molecules form a hydrogen bond, the proton (H+) of one water molecule may be removed and transferred to the other molecule forming H3O+ (a hydronium ion). The molecule that lost the proton becomes OH-.
H2O → H3O+ + OH-
The ionization of water therefore produces equal numbers of hydrogen ions (H+) and hydroxide ions (OH-) and the hydrogen ions are attached to nearby water molecules forming hydronium ions (H3O+).
The process is reversible; the hydrogen ion (H+) and hydroxide ioni (OH-) can combine to form water.
pH (BIO 101 only)
Some molecules form ions when they are dissolved in water. For example, the HCl molecule comes apart (it dissociates) and produces H+ and Cl-. The electron that was normally with the H remains with the Cl. The H now has a positive charge because it no longer has an electron. Similarly, the Cl has a negative charge because it has the electron from the H atom.
HCl → H+ + Cl-
Acids are substances that dissociate to produce hydrogen ions and a negative ion (anion). HCl is therefore an acid.
Bases are substances that combine with hydrogen ions, thus lowering the concentration of hydrogen ions. Substances that produce hydroxide ions ( OH-) are bases because hydroxide ions are capable of combining with hydrogen ions to form water, thus lowering the concentration of hydrogen ions. Bases are therefore proton acceptors.
OH- + H+ → H2O
When NaOH is dissolved in water, an electron from the sodium atom remains with the OH. This produces a sodium ion (Na+) and a hydroxide ion (OH-). NaOH is therefore a base.
NaOH → Na+ + OH-
Most bases produce hydroxide ions and a cation when dissolved in water.
Water molecules have a slight tendency to dissociate, forming both H+ and OH- as shown below. Water is neutral when it ionizes because the number of H+ equals the number of OH-.
H2O → H+ + OH-
The measure of the strength of an acid or base is called the pH. It is a measure of the concentration of hydrogen ions (H+).
The pH scale is a logarithmic scale; each decrease of 1 pH unit corresponds to a 10-fold increase in the concentration in hydrogen ions.
The pH can be calculated using the equation below. It is the negative log (base 10) of the hydrogen ion concentration.
pH = -log10[H+]
The brackets above are used to indicate concentration. It is measured in moles per liter.
Water has a hydrogen ion concentration of 0.0000001 X 10-7 moles per liter. The pH of pure water is therefore 7.
The product of hydrogen ion concentration and hydroxide ion concentration is always 1 X 10-14, so if the number of one kind of ion is known, the other can be calculated. For example, a solution with a pH of 4 (or 1 X 10-4 hydrogen ions) will have 1 X 10-10 hydroxide ions because 10-4 X 10-10 = 10-14. The table below shows the concentration of hydrogen and hydroxide ions at different pH levels.
| pH || [H+] || [OH-] || [H+] X [OH-] |
|0||1 X 10-0 ||1 X 10-14 ||1 X 10-14 |
|1||1 X 10-1 ||1 X 10-13 ||1 X 10-14 |
|2||1 X 10-2 ||1 X 10-12 ||1 X 10-14 |
|3||1 X 10-3 ||1 X 10-11 ||1 X 10-14 |
|4||1 X 10-4 ||1 X 10-10 ||1 X 10-14 |
|5||1 X 10-5 ||1 X 10-9 ||1 X 10-14 |
|6||1 X 10-6 ||1 X 10-8 ||1 X 10-14 ||acid|
|7|| 1 X 10-7 ||1 X 10-7 ||1 X 10-14 ||neutral|
|8||1 X 10-8 ||1 X 10-6 ||1 X 10-14 ||base|
|9||1 X 10-9 ||1 X 10-5 ||1 X 10-14 |
|10||1 X 10-10 ||1 X 10-4 ||1 X 10-14 |
|11||1 X 10-11 ||1 X 10-3 ||1 X 10-14 |
|12||1 X 10-12 ||1 X 10-2 ||1 X 10-14 |
|13||1 X 10-13 ||1 X 10-1 ||1 X 10-14 |
|14||1 X 10-14 ||1 X 10-0 ||1 X 10-14 |
The pH scale ranges from 0 to 14. An acid has a pH less than 7. A base has a pH greater than 7. A pH of 7 is neutral. A substance that has the same number of hydrogen ions and hydroxide ions is neutral.
The equation below shows that when water ionizes, it produces one hydrogen ion and one hydroxide ion. Water is therefore neutral. The table above shows that it has the same concentration of hydroxide ions as hydrogen ions.
H2O → H+ + OH-
This equation can also be writen as shown below because the hydrogen ion becomes attached to another water molecule producing H3O+.
2H2O → H3O+ + OH-
Buffers are substances that prevent the pH of a solution from changing. They do this by either accepting hydrogen ions if the solution becomes acidic or by releasing hydrogen ions if the solution becomes basic.
Carbonic acid is an important buffer in biological systems. The equation below shows that carbon dioxide dissolved in water produces carbonic acid and carbonic acid further dissociates to produce hydrogen ions and bicarbonate ions.
| CO2 || + || H2O|| ↔ ||H2CO3 || ↔ ||H+ || + ||HCO3- |
Carbonic acid is a weak acid; at any point in time there are some molecules that are not dissociated and others have dissociated to form hydrogen ions and bicarbonate ions. If the solution becomes acidic, the reaction shown above will move toward the left, that is, hydrogen ions combine with bicarbonate ions to form carbonic acid. The concentration of hydrogen ions therefore does not change as much as it would change without the presence of bicarbonate ions.
H2CO3 ← H+ + HCO3-
If the solution becomes more basic, the equation moves toward the right. Carbonic acid dissociates to release hydrogen ions and bicarbonate ions.
H2CO3 → H+ + HCO3-