2-1 Chemistry - the study of matter
Atom - the smallest unit of matter
- contains 3 subatomic particles:
1.proton - positive charge
2.neutron - no charge
- both are found in the center of the atom
(nucleus)
3. electron - negative charge
- constantly moving in space around the nucleus
- atom has equal number of protons and electrons,
therefore atom is neutral
Element
- consists of only 1 kind of atom
- about 100 elements known
- have a universal name represented by a symbol of
1-2 letters Ex.: H hydrogen
C carbon
Na sodium
Atomic number
- the same as the number of protons and will also
be equal to the number of electrons
****some atoms have different numbers of neutrons in
nucleus and their atoms are called isotopes
mass number
- the number of protons and neutrons
- identifies isotopes
atomic mass
- the weighted average of the masses of an
element's isotopes
****isotopes of the same element have the same
chemical properties
Radioactive isotopes
- nuclei are unstable; break down over time
releasing radiation
- radiation may be harmful but also useful
Ex. treat cancer
Detect age of fossils
Kill bacteria that can spoil food
Chemical Compounds
- substances formed by combining 2 or more
elements
- chemical formula - shorthand that shows us the
chemical composition: H2O 2:1
NaCl 1:1
- the properties of the compound is usually
different from the elements from which it was formed
Chemical Bonds
- hold atoms together in compounds
- involve electrons
- valence electron is the electron available to form
bonds
Types of bonds
1. Ionic
- formed when one or more electrons are transferred
to another atom
- atoms that lose electrons positive charge
- atoms that gain electrons  negative charge
See Fig 2-3 NaCl - the attraction
between the Na+ and Cl-
2. Covalent
- sharing of electrons between atoms forming a
molecule
- the smallest unit of most compounds (Ex. H2O)
There are two types of covalent bonds:
nonpolar – equal sharing of electrons
polar – unequal sharing of electrons
single covalent bond - shares 2 electrons
double covalent bond - shares 4 electrons
triple covalent bond - shares 6 electrons
Van der Waals Forces
- occurs when the sharing of electrons between 2
atoms is not equal
- a slight attraction can develop between oppositely
charged regions of nearby molecules thereby
holding molecules together
 See example: Gecko toes have the ability to stick to
most surfaces due to Van der Waals forces
Gecko
2-2 Properties of Water
A.
Water is neutral
- 10 protons balance out 10 electrons
B. Exhibits polarity
- there is uneven distribution of electrons between the
oxygen and hydrogen atoms
- more negative near the oxygen and more positive
between the hydrogen atoms
- because of polarity, H2O molecules attract each
other forming a hydrogen bond
- not very strong
- weaker than covalent or ionic bonds
C. Exhibits cohesion
- attraction between molecules of the same
substance (water molecules stick together)
- allows small insects to walk across surfaces
D. Exhibits adhesion
- Water is attracted to molecules of different
substances
Ex. H2O sticks to sides of glass cylinder
dipping slightly in the center
Solutions and Suspensions
H2O is not pure and is sometimes mixed with
other substances
Mixture
- composed of 2 or more elements or compounds;
they are not chemically combined
Ex. salt and pepper
Types of Mixtures
1. solution
- all of the components are evenly distributed
solute - substance dissolved
solvent - liquid in which the solute is dissolved
***** water is the greatest solvent in the world
2. suspension
- mixture of water and undissolved material
- occurs when some materials do not dissolve
when placed in water
- they separate into pieces that do not settle out
because movement of water molecules keeps them
suspended.
Ex. Blood; both a solution and a suspension.
Acids, bases, and pH
Water molecules react to form ions

H2O 
H+ + OHWater hydrogen ion hydroxide ion
The reaction can occur in either direction (a reversible
reaction)
pH scale
- measurement of the H+ concentration in a
solution
- it shows the degree of acidity or alkalinity
- scale is from 0-14 Fig 2-10
- solutions with pH below 7 (neutral) are acidic
and contain more hydrogen ions
- solutions with pH above 7 are basic and contain
more hydroxide ions
- each step represents a factor of 10
pH of 8 is 10 times more basic than pH 7
Acids
- any compound that forms hydrogen ions in
solution (H+)
- strong acids have pH of 1-3
Ex. HCL - stomach acid has pH of 1.0
Base
- a compound that produces hydroxide ions in
solution ( OH- )
- strong bases have pH 11-14 (lye)
Buffers
- weak acids or weak bases that react with strong
acids or bases to keep pH of body fluids from
changing suddenly
- pH must stay in the range of 6.5-7.5 and may
effect cellular chemical reactions if it does not.
2-3 Chemistry of Carbon
- C has 4 valence electrons
- Each can join with an electron from another
atom forming covalent bonds
- Carbon can bond to other carbon atoms giving
them the ability to form long chains of unlimited
length
- Carbon-carbon (C-C) bonds can be single,
double or triple covalent bonds
- carbon chains can close up to form rings
Carbon compounds
Macromolecules
- molecules in living cells that are large
- made through the process of polymerization
- smaller units
(monomers) are joined to form polymers
Four groups of Organic Compounds
1. Carbohydrates
- made of C,H,O in a 1:2:1 ratio
- main source of energy in living things (quick
energy)
- used also in plants and animals for structural
purposes (cell wall of plants [cellulose]); also chiton,
glycogen, and plant starch
- simple (single) sugar molecules are
monosaccharides
Ex. glucose, galactose (milk), and
fructose (fruits)
- large, complex sugar molecules are polysaccharides
Ex. glycogen (animal starch) stored in
liver and muscle, and cellulose (plant cell wall)
2. Lipids (fats, oils, waxes)
- large molecules; not soluble in water
- contain C,H,O but not in the same ratio as
carbohydrates
- store energy, part of cell membrane, some act as
hormones
- made of glycerol and fatty acids
- if saturated, fatty acids contain maximum number of
H atoms
- if unsaturated, fatty acid chain contains a double or
triple bond
- if polyunsaturated, contains more than one double
bond
Lipids
3. Nucleic Acids
- macromolecules containing H,O,N,C,P
- polymers made up of monomers of
nucleotides
- made up of: 5-carbon sugar
- phosphate group
- nitrogenous base Fig 2-15
- store and transmit hereditary information
- Two types: 1. RNA - ribonucleic acid
- contains ribose (sugar)
2. DNA - deoxyribonucleic acid
- contains deoxyribose (sugar)
4. Proteins
- macromolecules containing N,C,H,O, S,P
- made of amino acids Fig 2-16
- more than 20 different amino acids in nature
- side group (R chain) determines each amino acid
- instructions for bringing together different amino
acids to form proteins is found in DNA
- proteins have specific functions which depend on its
shape:
a. control rates of reactions and regulate cell
processes
(enzymes)
b. some are found in bones and muscles (structural
proteins)
c. some are involved in transporting substances
in/out of cell (carrier proteins)
d. some fight disease (antibodies)
- proteins have 4 levels of organization:
a. chain
b. twisted or folded
c. a folded chain
d. more than one chain
in a specialized
arrangement
2-4 Chemical Reactions and
Enzymes
A. Chemical Reaction
- a process that changes one set of chemicals into
another set
- may occur slowly or quickly
- reactants - chemicals or compounds that enter
the reaction (also known as substrate)
- products- chemicals or compounds produced by
the reaction
- always involve breaking bonds of reactants and
forming new bonds in the products
Typical Chemical Reaction
CO2 + H2O  H2CO3 (carried in blood to
Carbonic acid
lungs)
H2CO3  CO2 + H2O
Exhaled
B. Energy in Reactions
- released or absorbed whenever chemicals bonds
break or are formed
- when bonds break energy is released (exergonic
reaction)
- when bonds are formed energy is absorbed
(endergonic reaction)
- involves changes in energy
Energy changes:
- important factors in determining whether a
chemical reaction will occur
- reactions that release energy occur spontaneously
- reactions that absorb energy will not take place
without a source of energy
- organisms need to carry out reactions that require
energy to stay alive
Therefore: every organism must have a source energy
to carry out chemical reactions
Activation Energy
- the amount of energy needed to get a reaction
started
- a factor in whether an organism releases or
absorbs energy
C. Enzymes
- a biological catalyst
- substance that speeds up the rate of a reaction by
lowering the activation energy
- used by cells to speed up chemical reactions that
take place in the cell
- enzymes are specific; they work only on one
type of reaction
Ex. lipase works on lipids
 1. Enzyme-substrate complex
- substrates - the reactants of an enzymecatalyzed reaction (what the enzyme works on)
- the complex reduces the amount of energy
needed for the reaction
 See Fig 2-21
2. Regulation of enzymes
- changes in pH
- changes in temperature; in the body, enzymes
work best at 37 degrees Celsius
- cells regulate enzyme activity by containing
proteins that can turn enzymes on/off at specific
times in the life of the cell
