1. Philosophical considerations aside, organisms are basically ordered
aggregations of chemicals and biological processes are merely
biochemical reactions. Therefore an understanding of basic biochemistry
is necessary in order to understand biology.
I. Matter is composed of elements
A. Matter
1. Matter refers to anything that takes up space and has mass
2. All matter (living and nonliving) is composed of basic elements
a. Elements = fundamental forms of matter that occupy space and have
mass, cannot be broken down to substances with different chemical or
physical properties
b. There are 92 naturally occurring elements
b. Six elements (C, H, N, O, P, S) make up 98% of most organisms
II. Atoms form compounds and molecules
A. Molecules = two or more atoms of same element bonded together (e.g.,
O2)
B. Compound = two or more different elements bonded together (e.g., H2O)
C. Bonds are not physical links, they are links of pure energy. Types
of bonds:
1. Covalent bond - involves sharing of electron(s). Electrons possess
energy; bonds that exist between atoms in molecules contain energy.
a. Sharing of a pair of electrons creates a single bond represented
by single dash, e.g. water H2O is made of two single bonds H-O-H.
Sharing two pairs of electrons is represented by two dashes, C=C
b. Know the number of covalent bonds each of the six most important
elements can form.
Element
# of covalent bonds
Hydrogen (H) 1
Oxygen (O) 2
Nitrogen (N) 3
Carbon (C) 4
Phosphorous (P) 5
Sulfur (S) 2
2. Ionic bond - electrons are transferred from one atom to another,
e.g. salt NaCl
3. Hydrogen bond - weak attractive force between slightly positive
hydrogen atom of one molecule and slightly negative atom in another or
the same molecule

2. a. E.g. in a water molecule the electrons spend more time orbiting
the oxygen than the hydrogens, therefore the oxygen becomes slightly
negative and the two hydrogens become slightly positive
b. Such polar molecules attract each other like magnets
BASIC ORGANIC CHEMISTRY
Because carbon needs four electrons to fill its outer shell it can form
millions of different combinations with other atoms - ten times more
than all other atoms put together.
I. Organic molecules
A. Life as we know it is based on carbon
1. Carbon has four electrons in outer shell; bonds with up to four
other atoms (usually H, O, N, or another C)
2. Ability of carbon to bond to itself makes possible carbon chains and
rings which serve as the backbones of organic molecules
3. Organic molecules - contain carbon and hydrogen, most also contain
nitrogen, and oxygen
4. Functional groups - clusters of atoms with characteristic
structure and functions
B. Monomers and polymers
1. Most important biological compounds are polymers
a. Polymers - large compounds made of identical or nearly
identical repeating subunits
b. Monomers - the subunits of polymers
2. Making and breaking polymers
a. Condensation - making polymers by lining up monomers and
eliminating a water molecule, a hydroxyl (OH) group is removed from one
monomer and a hydrogen (H) is removed from the other
b. Hydrolysis - breaking polymers apart by introducing a water
molecule
c. Condensation/hydrolysis movie of sucrose (table sugar)
PRINCIPLE ORGANIC POLYMERS
I. Carbohydrates- contain C, H and O in the proportion 1:2:1 (CH2O).
A. Most abundant organic compounds in nature
B. Serve both as structural compounds and as energy reserves to
fuel life processes

3. C. Carbohydrate monomers are called monosaccharides
1. Alpha Glucose, a six carbon sugar (C6H12O6) is the immediate
energy source to cells. You should know its structure
D. Carbohydrate polymers are called polysaccharides
1. Starch is straight chain of alpha glucose molecules with few
side branches, mostly from plant sources
2. Glycogen is highly branched polymer of alpha glucose with
many side branches; called "animal starch," it is storage carbohydrate
of animals
3. Cellulose is a polymer of beta glucose molecules, it is
primary constituent of plant cell walls
E. Disaccharides - 2 monosaccharides linked together
1. Sucrose (table sugar ) - glucose and fructose linked
together, transported throughout plants
2. Lactose (milk sugar) is glucose + galactose
F. Virtually all carbohydrates come from plants which use the sun's
energy to make alpha and beta glucose.
II. Lipids - fats, oils, fatlike substances, some vitamins and steroids
A. Primarily energy sources and structural compounds
B. Two principle characteristics:
1. Hydrophobic - insoluble in water
2. Large number of bonded hydrogens - therefore release a
larger amount of energy than other organic compounds. Fats yield 9 cal/
gm, carbohydrates 4 cal/gm
C. Major lipids:
1. Triglycerides (fats and oils) - three fatty acids joined to
a glycerol molecule:
a. Fatty acid - long hydrocarbon chains with terminal
carboxyl (COOH) group
Saturated fatty acids have no double bonds between
their carbon atoms
Unsaturated fatty acids have double bonds in the carbon
chain
% saturated/unsaturated fat in some common foods
Unsaturated

4. Saturated
safflower 72 beef 48
soybean 59 butter 55
corn 53 fish 15
coconut oil 86
chocolate 56
b. Glycerol - three carbon molecule
1) Fats - triglycerides containing saturated fatty
acids (e.g. butter is solid at room temperature)
2). Oils - triglycerides with unsaturated fatty acids
(e.g. corn oil is liquid at room temperature)
c. Triglycerides are synthesized via condensation
2. Phospholipids - two fatty acids attached to phosphate group
a. phosphate heads are hydrophilic (water soluble) but
tails are hydrophobic (water insoluble) therefore they spontaneously
line up to form a lipid bilayer
b. very important because they form biological membranes
III. Polypeptides - polymers of nitrogen containing molecules called
amino acids, joined together by peptide bonds
A. Amino acids consist of:
1. Amino group - NH2 (positive charge)
2. Carboxyl group - COOH (negative charge)
3. Central carbon atom
4. R group - different substitution to the molecule, determines
nature of the amino acid
B. About 50,00 different proteins in humans, serve a variety of
functions:
1. Structural - e.g. muscles, hair, fingernails, collagen
2. Enzymes - biological catalysts which regulate biochemical
reactions
C. Proteins - large polypeptides with molecular weights from 10,000 -
1,000,000
D. Enzymes - large globular proteins from 12,000 to 1 million molecular
weights that act as catalysts
1. Catalysts - substances that accelerate chemical reactions but
which remain unchanged or unused in the process

5. 2. Enzymes generally named by adding -ase to root name of substrate
they react upon, e.g. amylase breaks down amylose (starch)
E. Polypeptide structure - due to interactions between adjacent
hydrogen bonds and R groups proteins form complex three dimensional
structures
C. Polypeptides can be denatured
1. Both temperature and pH can change polypeptide shape
a. Examples: heating egg white causes albumin to congeal; adding acid
to milk causes curdling. When such proteins lose their normal
configuration, the protein is denatured
b. Once a protein loses its normal shape, it cannot perform its usual
function
IV. Nucleic Acids - polymers of nucleotides
A. Nucleotides made up of:
1. Phosphate group - PO4
2. Five carbon sugar called ribose (or deoxyribose)
3. Nitrogenous base - ring structure containing C & N
B. Important Nucleic Acids:
1. DNA (deoxyribonucleic acid) - the molecule which stores the genetic
information passed on form parent to offspring
2. RNA (ribonucleic acid) - serves as the translator of the genetic
information contained in DNA
Page 38 in your text summarizes the structure and function of the four
basic organic molecules in living organisms.
SECONDARY METABOLITES
I. Proteins, lipids, carbohydrates and nucleic acids are called primary
metabolites because they occur in all plant cells and they are
necessary for the life of the plant.
II. Secondary metabolites are an assortment of many different compounds
which serve a variety of functions, and that are restricted to
different species of plants. They include:
A. Alkaloids - alkaline, nitrogen containing compounds which affect
the human nervous system. At least 10,000 alkaloids have been isolated
from plants. Many names end in -ine, e.g. morphine, caffeine, cocaine,
nicotine, atropine.
B. Terpenoids - polymers of isoprene (see figure 2-26a, p. 33).
Isoprene is emitted by leaves, causing a haze over forests on hot days.

6. Other terpenoids include essential oils (volatile compounds) such as
mint and menthol, taxol (cancer drug), digitalis (heart medicine) and
rubber.
C. Phenolics - compounds based on an aromatic ring with an attached
OH group. Flavonoids are important pigments, tannins are bitter tasting
compounds which probably act as deterrents to herbivores, lignin is an
important compound secreted into the cells of woody plants to provide
structural support. Salicylic acid is the active ingredient in aspirin.