2.1 Chemical Elements
1. Matter is defined as anything that takes up space and has mass.
2. Matter exists in three states: solid, liquid, and gas.
1. All matter (both living and non-living) is composed of 92 naturally-occurring elements.
2. Elements, by definition, cannot be broken down to simpler substances with different chemical or physical properties.
3. Six elements (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur—acronym CHNOPS) make up 95% of the body weight of organisms.
1. Elements consist of tiny particles called atoms.
2. An atom is the smallest unit of an element that displays the properties of the element.
3. One or two letters (e.g., H, Na) create the atomic symbol of the element.
4. Atoms contain specific numbers of protons, neutrons, and electrons.
5. Protons are positively charged particles; neutrons have no charge; electrons are negatively charged particles.
6. Protons and neutrons are in the nucleus of an atom; electrons move in orbitals around the nucleus in an electron shell.
C. Atomic Number and Mass Number
The atomic number equals the number of protons of an element.
Each element has a different atomic number.
The mass number is the sum of protons and neutrons in the nucleus.
Protons and neutrons have one atomic mass unit (amu) of weight; electrons have zero.
D. The Periodic Table
The periodic table groups elements according to certain chemical and physical characteristics.
The atomic mass is the average of the AMU for all the isotopes of that atom.
Groups are the vertical columns in the table and periods are the horizontal rows. Atomic mass increases as you move down a group or across a period.
Isotopes are atoms of the same element that differ in the number of neutrons (and therefore have different atomic masses). For example, carbon-12 has 6 protons and 6 neutrons; carbon-14 has 6 protons and 8 neutrons.
2. A carbon atom with 8 rather than 6 neutrons is unstable; it releases energy and subatomic particles and is thus a radioactive isotope.
3. Because the chemical behavior of a radioactive isotope is the same as a stable isotope of a particular element, low levels of the radioactive isotope (e.g., radioactive iodine or glucose) allow researchers to trace the location and activity of the element in living tissues; these isotopes are called tracers.
4. High levels of radiation can destroy cells and cause cancer; careful use of radiation can sterilize products and kill cancer cells.
F. Electrons and Energy
In an electrically neutral atom, the positively charged protons are balanced by the negatively charged electrons (remember that neutrons are electrically neutral).
Since electrons are found outside the nucleus and occupy orbitals around the nucleus, many scientists have tried to create models to show the exact location of the electrons.
The Bohr model (named after physicist Niels Bohr) is a helpful way to visualize electron location in an element.
According to the Bohr model, electrons occupy orbitals within various energy levels (or electron shells) near or distant from the nucleus of the atom. The farther the orbital from the nucleus, the higher the energy level.
5. When atoms absorb energy during photosynthesis, electrons are boosted to higher energy levels. When the electrons return to their original energy level, the released energy is converted into chemical energy. This chemical energy supports all life on Earth.
6. The innermost shell of an atom is complete with 2 electrons; all other shells are complete with
8 electrons. This is called the octet rule.
7. The outermost electron shell is called the valence shell, and determines the atom’s chemical properties; atoms will give up, accept, or share electrons in order to have 8 electrons in its valence shell.
2.2 Molecules and Compounds
When atoms of two or more elements bond together, they form a molecule, which is the smallest part of a compound that has the properties of the compound.
A compound is a molecule that contains at least two different elements (ex. H2O).
3. A formula tells you the number of each kind of atom in a molecule (ex. Glucose, C6H12O6).
4. Electrons possess energy, therefore bonds that exist between atoms in molecules contain energy.
A. Ionic Bonding
An ionic bond forms when electrons are transferred from one atom to another atom.
2. By losing or gaining electrons, atoms fill outer shells, and are more stable (the octet rule).
3. Example: sodium loses an electron and therefore has a positive charge; chlorine gains an electron to give it a negative charge. Such charged particles are called ions.
4. Attraction of oppositely charged ions holds the two atoms together in an ionic bond.
5. A salt (e.g., NaCl) is an example of an ionically-bonded compound.
B. Covalent Bonding
Covalent bonds result when two atoms share electrons so each atom has an octet of electrons in the outer shell (or, in the case of hydrogen, 2 electrons).
2. Hydrogen can give up an electron to become a hydrogen ion (H+) or share an electron with another atom to complete its shell with 2 electrons.
3. The structural formula of a compound indicates a shared pair of electrons by a line between the two atoms; e.g., single covalent bond (H–H), double covalent bond (O=O), and triple covalent bond (N ≡ N). Each line between the atoms represents a pair of electrons.
4. There are two types of covalent bonds: nonpolar covalent bonds and polar covalent bonds.
5. In nonpolar covalent bonds, sharing of electrons is equal, i.e., the electrons are not attracted to either atom to a greater degree.
6. With polar covalent bonds, the sharing of electrons is unequal.
In a water molecule (H2O), sharing of electrons by oxygen and hydrogen is not equal; O with more protons attracts the electrons closer to it.
Attraction of an atom for electrons in a covalent bond is called the electronegativity of the atom; an oxygen atom is more electronegative than a hydrogen atom.
The protons in the oxygen in a water molecule attracts the electrons, giving that side of the molecule a more negative charge and the side of the molecule with the two hydrogen atoms a more positive charge.
The polarity of molecules affects how they interact with other molecules.
2.3 Chemistry of Water
The shape of water and of all organic molecules is necessary to the structural and functional roles they play in living things.
A hydrogen bond is the attraction of a slightly positive hydrogen atom to a slightly negative atom in the vicinity.
A. Hydrogen Bonding
A hydrogen bond is a weak attractive force between the slightly positive charge of the hydrogen atom of one molecule and slightly negative charge of another atom (e.g., oxygen, nitrogen) in another or the same molecule.
Many hydrogen bonds together are relatively strong.
Hydrogen bonds between and within complex biological molecules (e.g., DNA, proteins) help maintain their proper structure and function.
B. Properties of Water
Water has a high heat capacity
a. The temperature of liquid water rises and falls more slowly than that of most other liquids.
b. A calorie is the amount of heat energy required to raise the temperature of one gram of water 1°C.
c. Because the hydrogen bonds between water molecules hold more heat, water temperature falls
more slowly than other liquids; this protects organisms from rapid temperature changes and helps them maintain homeostatic temperature.
2. Water has a high heat of evaporation
a. When water boils, it evaporates, or vaporizes into the environment.
b. Hydrogen bonds between water molecules require a relatively large amount of heat to break.
This property moderates Earth’s surface temperature and permits living systems to exist.
When animals sweat, evaporation of the sweat removes body heat, thus cooling the animal.
Water is a solvent
Water dissolves a great number of substances (e.g., salts, large polar molecules).
A solution contains dissolved substances called solutes.
Ionized or polar molecules attracted to water are hydrophilic (“water loving”).
Nonionized and nonpolar molecules that cannot attract water are hydrophobic (“water fearing”).
Water molecules are cohesive and adhesive
Cohesion allows water to flow freely without molecules separating.
Adhesion is the ability to adhere to polar surfaces; water molecules have positive and negative poles.
Water rises up a tree from roots to leaves through small tubes.
Adhesion of water to walls of vessels prevents the water column from breaking apart.
Cohesion allows evaporation from leaves to pull water column from roots.
Water has a high surface tension and is relatively difficult to break through at its surface.
This property permits a rock to be skipped across a pond surface, and supports insects walking on the surface.
Frozen water (ice) is less dense than liquid water
Unlike most substances, frozen water (ice) is less dense than liquid water.
Below 4°C, hydrogen bonding becomes more rigid but more open, causing expansion.
Because ice is less dense, it floats; therefore, bodies of water freeze from the top down.
If ice was heavier than water, ice would sink and bodies of water would freeze solid.
This property allows ice to act as an insulator on bodies of water, thereby protecting aquatic organisms during the winter.
2.4. Acids and Bases
When water ionizes or dissociates, it releases a small (1 x 10-7 moles/liter) but equal number of hydrogen ions (H+) and hydroxide ions (OH-); H2O → H+ + OH- .
Acid molecules dissociate in water, releasing hydrogen (H+) ions: HCl → H+ + Cl-.
Bases are molecules that take up hydrogen ions or release hydroxide ions. NaOH → Na+ + OH-.
The pH scale indicates acidity and basicity (alkalinity) of a solution.
pH is the measurement of free hydrogen ions, expressed as a negative logarithm of the H+ concentration ( -log [H+]).
pH values range from 0 (1 x 100 moles/liter; most acidic) to 14 (1 x 10-14 moles/liter; most basic).
One mole of water has 1 x 10-7 moles/liter of hydrogen ions; therefore, it has a neutral pH of 7.
An acid is a substance with pH less than 7; a base is a substance with pH greater than 7.
Because it is a logarithmic scale, each lower unit has 10 times the amount of hydrogen ions as the next higher pH unit; moving up the pH scale, each unit has 10 times the basicity of the previous unit.
Buffers keep pH steady and within normal limits in living organisms.
Buffers stabilize the pH of a solution by taking up excess hydrogen (H+) or hydroxide (OH-) ions.
Carbonic acid helps keep blood pH within normal limits.
A. The Interconnectedness of Water, Plants, and People (Biological Systems reading)
Acid deposition is rain or snow with a pH < 5.0, and dry acidic particles that settle on the Earth from the atmosphere.
The burning of fossil fuels increases the amount of acid deposition that falls from the atmosphere to the Earth.
Impact on Lakes
Aluminum may leach from the soil of lakes and acid rain may convert mercury deposits to methyl mercury, which is toxic and accumulates in fish.
Impact on Forests
Acid rain damages plant leaves so they cannot conduct photosynthesis.
Acid rain stresses plants and they are then more susceptible to disease and pests.
When toxins are leached into the soil, the toxins can kill vital soil fungi that help roots absorb nutrients.
Impact on Humans and Structures
Inhaling dry acidic particles can increase the chance of respiratory illnesses such as asthma.
Limestone and marble structures break down from acid rain.
Paint on houses and cars can also degrade from acid rain.