Chapter 3:
Part I Biochemistry
Matter: Anything that has mass and
takes up space – can be solid, liquid or
gas
Atom: Smallest unit of matter that
cannot be broken down by chemical
means
Parts of an atom:
•Protons (+)
•Electrons (-)
•Neutrons (0)
•Protons and neutrons are found in the
nucleus
•Electrons orbit electron clouds around
the nucleus
•Inner energy level holds two electrons
•Other energy levels holds eight
electrons
•The number of electrons in the outer
energy shell determines the chemical
properties of the atom.
Using the periodic table:
•Atomic number = # of protons
•Atomic mass = # of protons + neutrons
•If number of protons = number of
electrons, atom is neutral (no charge)
•Elements are arranged horizontally in
order of increasing atomic number
•Elements are arranged vertically
according to the number of electrons in
the outer shell
•Isotopes: atoms that differ in their
number of neutrons
•Carbon has 3 isotopes:
•Carbon 12 (most abundant)
•Carbon 13
•Carbon 14 (radioactive - unstable)
•Atom is most stable when the outer shell
is filled
•Number of electrons in outermost shell =
valence electrons
•Ex: Helium – 2 electrons in 1st shell
Neon – 8 electrons in 2nd shell
•Elements in last column of periodic
table have filled outer shells – Noble
gases
•To become stable, atoms form bonds
with other atoms
•Molecules: A group of atoms held
together by covalent bonds
•Ex: O2 or CO2
•Compound: A substance made of
the bonded atoms of two or more
different elements.
•Ex: CO2 or C6H12O6
Chemical/molecular formula: shows
kind and proportion of atoms of
element/molecule
Ex: 5HCl
14Fe
C6H12O6
Na+
8C
6H2O
3CO2
Structural formula: Shows the
arrangement of atoms within the
molecule
Types of bonds: ionic bonds, covalent
bonds & hydrogen bonds
•Ion – an atom that has an electric
charge because it has gained or lost
electrons
•Ions with opposite charges (- or +) are
attracted to each other and form an ionic
bond.
•Ionic bonds – the attractive force
between two oppositely charged ions
Ionic Bonds
•In covalent bonds, atoms share
electrons
•Solution – a mixture in which ions or
molecules are evenly distributed in another
substance
•Some water molecules break apart to form
ions
•Hydronium (H3O+)
•Hydroxide (OH-)
•In water, the balance of these ions is equal
•In solutions such as acids and bases, the
number of hydronium and hydroxide is
unequal
Acids are any compound that increases
the number of hydronium ions when
dissolved in water
HCl  H+ + Cl•H20 and
H+
combine
to form
H3O+
Bases are any compound that increases the
number of hydroxide ions when dissolved
in water (also called alkaline).
NaOH  Na+ + OH-
•pH – a measure of how acidic or basic
a solution is
•Acid – pH 0-6
•Base – pH 8-14
•Neutral - 7
•Buffers: a substance that reacts to
prevent pH changesd in a solution – do
so by taking up excess H+ or OH- ions.
•Help maintain pH in blood, stomach
acid, urine, and intestinal fluid –
example of how your body maintains
homeostasis!!!