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CHAPTER 2
CHEMISTRY AND BIOCHEMISTRY
TOPIC 2: BASIC CHEMISTRY FOR BIOLOGY
1. Matter consists of chemical elements in pure
form and in combinations called compounds
2. An element’s properties depend on the
structure of its atoms
3. The formation and function of molecules
depend on chemical bonding between atoms
4. Chemical reactions make and break chemical
bonds
Chemistry is the science dealing with the properties &
the transformations (chemical reactions) of all forms
of matter
Matter is ….anything that takes up
space (volume) or has mass.
Matter is made of elements.
Concept 1 Matter consists of
chemical elements in pure form
and in combinations called
compounds
Matter: Anything that takes up space
and has mass
States of Matter
 ELEMENT = A substance that cannot be broken
down into other substances by chemical
reactions.  TRACE ELEMENT = Element required by an
organism in extremely minute quantities.
Example: Fe (Iron)  COMPOUND = A pure substance composed of
two or more elements combined in a fixed
ratio. Example: NaCI (sodium chloride)
All Matter is composed of :
Atom – Means “unable to be cut” (Greek:
atomos)
Smallest possible unit of matter that
retains the physical and chemical
properties of its element.
Elements
 Substances that can’t be
broken down into simpler
substances
 92 naturally occurring
elements
 25 - 36 chemical elements
are essential to life.
 96% of human mass is
made up of C, H, O, N
Structure of Atoms
C
H
N
O
P
S
Structure of Atoms
Chemistry is the science dealing with the properties
& the transformations (chemical reactions) of all
forms of matter
Matter is ….anything that takes up space
or has mass.
Matter is made of elements.
Structure of Atoms
Atoms contain protons, neutrons, and electrons.
Protons - positive charge – 1 atomic mass unit
Neutrons – no charge – 1 atomic mass unit
Electrons – negative charge – almost no mass
Structure of Atoms
Structure of Atoms
Atomic Number
= number of protons
In atom
Atomic Mass
= mass of protons,
neutrons and
electrons in atom
Structure of Atoms
C
H
N
O
P
S
Isotopes
Structure of Atoms
Isotopes – alternative forms of an atom that differ in their number
of neutrons (same atomic number, different MASS number)
How are these atoms different from each other?
What can isotopes be used for?
Isotopes
ISOTOPES
Atoms of an element that
have the same atomic
number but different
mass number.
They have the
same number of protons,
but a different number of
neutrons.
RADIOACTIVE ISOTOPE
Unstable isotope in which
the nucleus spontaneously
decays, emitting
subatomic particles
and/or energy as
radioactivity. Loss of
nuclear particles may
transform one element to
another A radioactive
isotope has a fixed half-life:
HALF LIFE = Time for 50%
of radioactive atoms in a
sample to decay.
Differing
Numbers of
Neutrons
1
Hydrogen:
Deuterium:
H
1
1
H
2
1
Tritium
H
3
Applications of isotopes:
Carbon Dating
Applications of isotopes:
Carbon Dating
 99% of carbon atoms have 6 neutrons (12C).
Most of the remaining 1% of carbon atoms have
7 neutrons (13C) while the rarest carbon isotope,
with 8 neutrons, is 14C.
 Both 12C and 13C are stable isotopes while 14C
is radioactive
 When 14C decays, one of its neutrons is
converted to a proton and an electron.
 This converts 14C to 14N, transforming the
atom to a different element.

Applications of isotopes:
Carbon Dating
By comparing the ratio of
radioactive (14C) and
stable (12C) isotopes in
a fossil with the ratio
of isotopes in living
organisms, one can
estimate the age of a
fossil less than 50,000
years old.
Application of isotopes:
Nuclear scintigraphy
Diagnostic radiopharmaceuticals –
Technetium 99
Iodine 131: diagnosis and treatment of
thyroid tumours
PET scanning (positron Emmision
Tomography)
CT scanning (computer tomography)
Generally short-lived isotopes linked to
chemical compounds to be traced.
Structure of Atoms: Electron Orbitals
There are certain spaces around the nucleus where
electrons are likely to be found. The electron is
found a certain distance from the nucleus called a
shell. Within a shell is an orbital that holds 2
electrons.
Structure of Atoms: electron
Orbitals
The outermost electron shell is referred to
as the valence shell.
Structure of Atoms: Electron Orbitals
RULES
1. First energy shell can
ABOUT
contain a maximum of 2
ELECTRONS!
electrons
2. All other shells can
contain a maximum of 8
electrons (there are
exceptions)
An atom is most stable when
the valence shell contains
a full 8 electrons =
OCTET RULE
Structure of Atoms
RULES
Electrons determine
ABOUT
chemical reactivity.
ELECTRONS!
Atoms are reactive
unless they have a full
valence shell of
electrons!
Chapter 2 Chemical Principles
Structure of Atoms
Chapter 2 Chemical Principles
Structure of Atoms
Which atoms on the periodic table have a
full valence shell?
Which atoms on the periodic table have
only one electron in the valence shell?
Which atoms on the periodic table have
seven electrons in the valence shell?
A Brief Review: Types of
Bonding
INTRAMOLECULAR
FORCES
Ionic Bonding
Covalent Bonding
(Polar Covalent
bonding)
INTER-MOLECULAR
FORCES
Dipole-dipole
interactions
(Van
Der Waals Forces)
Hydrogen Bonds
Bonding between elements (in
compounds and molecules)
BONDING
IONIC BONDING
COVALENT BONDING
non-polar
covalent
and
polar covalent
Bonding and electronegativity
Electronegativity is the tendency of an atom
to attract electrons.
If the electronegativity of an atom is high,
then it attracts and holds on to electrons.
If the electronegativity of an atom is low, then
it tends to give electrons away.
Bonding and electronegativity
Where on the Periodic Table do you find the
atoms with high electronegativity?
Where do you find those atoms with low
electronegativity?
Which atom has the highest
electronegativity?
Ionic Bonding
Ionic bonding – Atoms transfer or accept electrons
from one another
Look at the following diagram with regards to
sodium (Na) and chloride (Cl)
What must each do to fulfill the octet rule?
Ionic
Bonding
Ionic bonding
The sodium ion and the chloride ion will be attracted
to each other and form an ionic bond.
Na +
Cl -
The ionic bond is due to the attractive forces
between the now positively charged sodium & the
negatively charged chloride.
By looking at the periodic table, can you
predict which atoms may form ionic bonds?
Bonding: Covalent Bonding
Non-polar covalent bond – equal sharing of
electrons
Polar covalent bond – unequal sharing of
electrons
What does the word polar mean?
Covalent bonding
Bonding: Covalent Bonding
C
How many electrons are
needed to fill the valence
shell of carbon?
H
How many electrons are
needed to fill the valence
shell of hydrogen?
In the molecule of methane (CH4), the electrons
are shared equally between the carbon and
hydrogens.
Bonding
Covalent bonding
Covalent Bonding
Polar Covalent Bonding
Polar covalent bond – unequal sharing of
electrons
A great example of a molecule with polar
covalent bonds is water. Why is water
considered polar?
What is a partial positive and partial
negative charge?
Polar covalent bond
Chapter 2 Chemical Principles
Bonding
Covalent bonding
Polar covalent bond
Inter-molecular forces: dipoledipole interactions and
hydrogen bonding
Van Der Waals Forces – Dipole
Dipole interactions
Hydrogen Bonding