Chapter 2: The Chemistry of Life
I.
II.
The Nature of Matter
a. Atoms are the smallest, indivisible particles of matter
i. First theorized by Democritus about 2500 years ago (ya)
ii. Atoms made of two parts that consist of a combination of three different subatomic
particles
1. Nucleus is the “core” of an atom
a. Protons have a positive charge
b. Neutrons have a neutral charge
2. Electron cloud
a. Divided into orbitals (layers)
b. First layer is smallest and contains maximum of 2 electrons
c. Second layer contains maximum of 8 electrons
d. Third layer maximum of 8 electron
b. Elements and Isotopes
i. Element is a pure substance consisting of a single type of atom
ii. Isotopes are atoms of the same element with different numbers of neutrons
iii. Radioactive isotopes have an unstable nucleus that bread down at a constant rate
over time and radiation
c. Chemical Compounds
i. Substance formed when two or more elements are chemically combined in a fixed
ratio
ii. Properties of compounds are typically different then their constituent elements
d. Chemical Bonds
i. Atoms are stable when they have 8 electrons in the outermost layer of the electron
cloud. This is the valence shell.
ii. Electrons found in the valence shell are called valence (bonding) electrons
iii. Atoms will form bonds in order to obtain a total of 8 electrons in order to become
more stable
iv. Two main types of bonds
1. Ionic bonds form when electrons are transferred from a metal to a nonmetal
and form ions
a. Ions are atoms that have gained or lost electrons
b. Cations have lost electron(s) and have a positive charge
c. Anions have gained electron(s) and have a negative charge
2. Covalent bonds from when electrons are shared between two, or more,
nonmetals to form a molecule
a. Single bonds are formed when a single electron is shared between
two nonmetals
b. Double bonds from when two electrons are shared, triple bonds share
three electrons
c. A molecule is the smallest unit of a compound (H2O)
d. Some elements also form molecules of pure substances (O2, N2)
3. Van der Waals Forces
Properties of Water
a. The Water Molecule
i. Polarity—water is a polar molecule because electrons are shared unevenly within
the molecule making one side slightly negative, and the other slightly positive
III.
ii. Hydrogen bonding—the partial negative charge on the oxygen of
one water molecule can attract to the partial positive charge on
the hydrogens of another molecule
1. Cohesion—water molecules stick together because of
hydrogen bonding
2. Adhesion—water molecules stick to other substances, this
can be seen when a meniscus forms in a graduated cylinder
3. Heat capacity—up to four hydrogen bonds can form in each water molecule
making it resistant to changes in temperature; this is a high heat capacity or
high specific heat
iii. Solutions and suspensions
1. Water is not always pure and exists as a mixture with other substances. A
mixture is physically combined, but not chemically combined
2. Types of mixtures
a. Homogeneous mixtures are consistent throughout.
b. Heterogeneous mixtures are not distributed consistently
c. Solutions are homogenous mixtures in which a solute is dissolved in a
solvent
d. Suspensions are mixtures with nondissolved materials that do not
settle out
iv. Acids, Bases, and pH
1. Sometimes water molecules dissociate and split to form ions of hydrogen
(H+) and hydroxide (-OH)
2. The concentration of hydrogen (H+) is measured on the pH scale
a. pH scale ranges 0-14
b. 0 is most acidic with highest concentration of hydrogen ion (H+)
c. 14 most basic with highest concentration of hydroxide ion (-OH)
d. Pure water has pH 7 and equal concentrations of hydrogen ions (H+)
and hydroxide ion (-OH)
3. Buffers are weak acids or bases that can prevent sharp or sudden changes in
pH
Carbon Compounds
a. Organic compounds have carbon-carbon bonds
b. The Chemistry of Carbon
i. Carbon is versatile due to its ability to form up to four covalent bonds
1. Bonds with hydrogen, oxygen, phosphorus, sulfur, and nitrogen to form the
molecules of life
2. Carbon can form
a. Chains
b. Branching chains
c. Rings
d. Single, double, or triple bonds
c. Macromolecules—large molecules
i. Most are formed during polymerization in which larger molecules are formed by
joining smaller molecules
ii. Monomers are small units joined together to make long chain polymers
iii. Carbohydrates are sugars and starches composed of carbon, hydrogen, and oxygen
1. Monosaccharides are simple sugars
a. Glucose (C6H12O6)
b. Galactose (C6H12O6)
c. Fructose (C6H12O6)
d. Glucose, galactose, and fructose are structural isomers and have same
chemical formula, but different structural formula
2. Disaccharides are formed by joining two monosaccharides in a dehydration
synthesis (condensation) reaction
a. Maltose=glucose+glucose (C12H22O11)
b. Lactose=glucose+galactose (C12H22O11)
c. Sucrose=glucose+fructose (C12H22O11)
3. Polysaccharides are formed by joining three or more monosaccharides in a
dehydration synthesis reaction.
a. Structural polysaccharide
i. Cellulose (in plants) is a chain of glucose molecules
ii. Chitin (in animals) is a chain of glucose molecules with a
nitrogen
b. Storage polysaccharide
i. Starch (in plants) is a spiral chain of glucose molecules
ii. Glycogen (in animals) is a branching chain of glucose
molecules
iv. Lipids are fats, waxes, oils, and steroids
1. Hydrophobic and generally insoluble in water
2. Made mostly of hydrogen and carbon (hydrocarbons)
3. Steroids, such as hormones, serve as chemical messengers
4. Formed by joining fatty acid to a glycerol
a. Saturated fats have only carbon to carbon single bonds
i. Unhealthy b/c can stack together and form multiple hydrogen
bonds
ii. Form plaque in your arteries
iii. Solid at room temperature, e.g. butter, lard,
b. Monounsaturated (unsaturated) fats have a single double bond
i. Healthier b/c double bends molecule making it more difficult
to stack
ii. Liquid at room temperature, e.g. olive oil, corn oil, sesame oil,
canola oil, peanut oil
c. Polyunsaturated fats have at least two double bonds
i. Healthiest b/c numerous double bonds make it difficult to
stack
ii. e.g. linseed oil
v. Nucleic acids
1. Contain hydrogen, oxygen, nitrogen, carbon, and phosphorus
2. Polymers of nucelotides
a. Five carbon sugar (ribose or deoxyribose)
b. Phosphate
c. Nitrogenous base (adenine, guanine, cytosine, thymine, or uracil)
3. ATP is a nucleotide used to transfer chemical energy in the cell
4. DNA and RNA transmit hereditary (genetic) information
vi. Proteins
1. Contain nitrogen, carbon, hydrogen, and oxygen
2. Polymers (chains) of amino acids
a. 20 amino acids used to form a polypeptide (amino acid chain)
b. Amino acid have same basic structure and contain
i. amino group (-NH2)
ii. carboxyl group (-COOH)
IV.
iii. R group—unique for each amino acid
c. Amino acids are joined by covalent bonds called peptide bonds
3. Four levels of organization in proteins
a. Primary structure is the order of amino acids forming the polypeptide
chain
b. Secondary folding or coiling of the polypeptide chain (α helix, β
pleated sheet, or random coil)
c. Tertiary structure is the three dimensional arrangement (e.g. folding
of α helix to form a bow)
d. Quaternary structure is formed when multiple tertiary level
polypeptides are joined together
Chemical Reactions and Enzymes
a. Chemical Reactions change one set of chemical compounds into another
i. Reactants are changed into products
ii. C6H12O6 + O2  H2O + CO2
glucose + oxygen  water + carbon dioxide
REACTANTS 
PRODUCTS
b. Energy in Reactions
i. Energy changes—energy is converted in chemical reaction
1. Energy is released when bonds are broken
a. Heat—most common release
b. Light—sometimes if material combusts
c. Sound—only if an explosion occurs
2. Energy is absorbed when bonds are formed and usually requires an input of
energy
a. Heat
b. Light
c. Electricity
ii. Energy Sources—all living organisms need energy in order to stay alive
1. Plants absorb energy from the sunlight—they are autotrophs
2. Animals obtain their energy from the food they eat—they are heterotrophs
iii. Activation Energy
1. Few chemical reactions occur spontaneously (on their own)
2. Energy that is necessary to initiate a chemical reaction is called activation
energy, e.g. flame used to burn cellulose (paper, wood, or cardboard)
c. Enzymes
i. Catalysts speed up the rate of a reaction by decreasing the necessary amount of
activation energy for a reaction to occur
ii. Nature’s Catalyst
1. Enzymes are proteins that act as biological catalysts
2. Example—carbonic anhydrase
a. Carbon dioxide is a gas and can not travel through our bloodstream
b. Our bodies combine carbon dioxide with the water in our blood to
produce liquid carbonic acid—the enzyme, carbonic anhydrase
regulates this reaction
c. Carbonic anhydrase speeds up this reaction about 10 million times—
without it, carbon dioxide would build up faster than it could be
removed and would poison us
3. The Enzyme-Substrate Complex
a. Reactants must come into contact with one another in order for a
reaction to occur
b. Heating reactants causes molecules to move faster and increases their
chance of “bumping” into another—sometimes this is still not enough
c. Enzymes attach to reactants and “introduce” them to another, and
speed up this process—therefore enzymes catalyze these reactions
d. Enzymes are specific to the reactants they “match up”
i. Reactants attach to an enzyme at the “active site”
ii. Reactants are specific to an active site and work like a lock and
key
4. Regulation of Enzyme Activity
a. Temperature—high temperatures can denature enzymes, by causing
them to fall apart
b. pH—changing pH can also denature enzymes
c. Regulatory molecules—can block enzymes from “introducing”
molecules