CHAPTER
2, 3
BASIC CHEMISTRY & MOLECULES OF LIFE
I. Basic Chemistry
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.
3. All matter (both living and non-living) is composed of 92 naturally-occurring elements.
4. Six elements (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur—acronym CHNOPS) make
up 98% of the body weight of organisms.
A. Atomic Structure
1. Atoms contain specific numbers of protons, neutrons, and electrons.
2. Protons and neutrons are in the nucleus of an atom; electrons move around the nucleus.
3. Protons are positively charged particles; neutrons have no charge; both have 1 atomic mass unit (amu)
of weight.
4. Electrons are negatively charged particles located in orbitals outside the nucleus.
5. All atoms of an element have the same number of protons, called the atomic number of the element.
B. The Periodic Table
C. Isotopes
1. 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.
2 Elements and Compounds
A. Ionic Bonding
1. An ionic bond forms when electrons are transferred from one atom to another atom.
2. A salt (e.g., NaCl) is an example of an ionically-bonded compound.
B. Covalent Bonding
1. 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. The three-dimensional shapes of molecules are not represented by structural formulas, but shape is
critical in understanding the biological action of molecules.
3.
Nonpolar and Polar Covalent Bonds: In nonpolar covalent bonds, sharing of electrons is equal, i.e.,
the electrons are not attracted to either atom to a greater degree. With polar covalent bonds, the
sharing of electrons is unequal.
C. 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). Hydrogen bonds
between and within complex biological molecules (e.g., DNA, proteins) help maintain their proper
structure and function.
3. Chemistry of Water
1. All living things are 70–90% water.
2. Because water is a polar molecule, water molecules are hydrogen bonded to one other.
Because of hydrogen bonding, water is liquid between 0º C and 100 o C which is essential for the
existence of life.
Properties of Water
1. Water has a high heat capacity
2. Water is a good solvent.
a. Ionized or polar molecules attracted to water are hydrophilic (“water loving”).
b. Nonionized and nonpolar molecules that cannot attract water are hydrophobic (“water fearing”).
3. Water has a high surface tension.
3.
4
Acids and Bases
1. 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-.
2. The pH scale indicates acidity and basicity (alkalinity) of a solution.
a. pH is the measurement of free hydrogen ions, expressed as a negative logarithm of the H +
concentration (-log [H+]).
b. pH values range from 0 ([H+]=100 moles/liter; most acidic) to 14 ([H+]=10-14 moles/liter; most
basic).
3. Buffers keep pH steady and within limits in living organisms. E. g. Carbonic acid helps keep blood pH
within normal limits: H2CO3 → H+ + HCO3-.
II Carbohydrates
A. Monosaccharides: Ready Energy
1. Monosaccharides are simple sugars with a backbone of 3 to 7 carbon atoms.
Glucose is found in the blood of animals; it is the source of biochemical energy (ATP) in nearly all
organisms.
2. Ribose and deoxyribose are five-carbon sugars (pentoses); they contribute to the backbones of RNA
and DNA, respectively.
B. Disaccharides contain two monosaccharides joined by a dehydration reaction. Sucrose (table sugar) is
composed of glucose and fructose.
C. Polysaccharides as Energy Storage Molecules
1. Starch, found in many plants, is a straight chain of glucose molecules with relatively few side
branches. Amylose and amylopectin are the two forms of starch found in plants.
2. Glycogen is a highly branched polymer of glucose with many side branches. It is the storage form of
glucose in animals.
3. Cellulose is a polymer of glucose which forms microfibrils, the primary constituent of plant cell walls.
4. Chitin is a polymer of glucose with an amino group attached to each glucose.
III Lipids
Fat provides insulation and energy storage in animals.
Phospholipids form plasma membranes and steroids are important cell messengers.
Waxes have protective functions in many organisms.
Triglycerides: Long-Term Energy Storage
1. Fats and oils contain two molecular units: glycerol and fatty acids.
2. Triglycerides are glycerol joined to three fatty acids by dehydration reactions.
3. A fatty acid is a long hydrocarbon chain with a carboxyl (acid) group at one end.
a. Most fatty acids in cells contain 16 to 18 carbon atoms per molecule.
b. Saturated fatty acids have no double bonds between their carbon atoms.
c. Unsaturated fatty acids have double bonds in the carbon chain where there are less than two
hydrogens per carbon atom.
4. Fats contain saturated fatty acids and are solid at room temperature (e.g., butter).
5. Oils contain unsaturated fatty acids and are liquid at room temperature.
6. Animals use fat rather than glycogen for long-term energy storage; fat stores more energy.
IV Proteins
A. Protein Functions
1. Support proteins include keratin, which makes up hair and nails, and collagen fibers, which support
many of the body’s structures (e.g., ligaments, tendons, skin).
2. Enzymes are proteins that act as organic catalysts to accelerate chemical reactions within cells.
3. Transport functions include channel and carrier proteins in the plasma membrane, and hemoglobin
that transports oxygen in red blood cells.
4. Defense functions include antibodies that prevent infection.
5. Hormones are regulatory proteins that influence the metabolism of cells. For example, insulin
regulates glucose content of blood and within cells.
6. Motion within cells and by muscle contraction is provided by the proteins myosin and actin.
B. Amino Acids: Building Blocks of Proteins
C. Shape of Proteins – determining function
1. The primary structure is the sequence of amino acids;
2. The secondary structure: The  (alpha) helix and the  (beta) sheet;
4. Tertiary structure results from further folding;
5. Quaternary structure results when two or more polypeptides subunits combine.
V Nucleic Acids
DNA (deoxyribonucleic acid): The genetic material
RNA (ribonucleic acid): Messengers and part of protein thynthesis machinary
ATP (adenosine triphosphate) is the only energy form the cell is able to use.
1. Smallest unit of matter that retains the property? Atomic number = ____________?
Mass
Charge
Proton
Neutron
Electron
2. What are the common elements in living organisms? Three most common ones?
3. What is ionic bond? Covalent bond? Polar / non-polar covalent bonds?
4. What does pH value represent? ph = 1 represents  [H+] = __________? Definitions of acidic, neutral and
alkalinic solutions?
5. Polar / non-polar compounds dissolve in polar / non-polar solvent. Water is polar / non-polar. Ion is polar / nonpolar.
6. Isotopes have similar atomic number / number of protons / number of electrons / number of neutrons. Isotopes
have different atomic number / number of protons / number of electrons / number of neutrons.
7. Four bio-molecular polymers? What are their monomers? Their functions? Cell membrane is mostly composed of
__________.
8. What molecules do animal use for short term and long term energy storage?
9. The four levels of protein structure? (Descriptions and figures)
10. What are the reactions of polymer synthesis and degradation?
11. Hydro-carbon compounds are mostly polar / non-polar; or hydrophilic / hydrophobic. This property can change
due to addition of _________________ such as _________________________.
12. Function of a protein depends on its _________________________. Denature is the loss of protein’s
_____________; while renature can happen by slowly removing the denaturing reagents, resulting in the recover of
protein’s _____________________. What factors can cause denature?