The Chemical Basis of Life
• Why are we studying chemistry in a biology
course???
• At the base of the
hierarchy of life are
atoms and molecules!
• Many biological processes
take place on a molecular
level
Biosphere
Ecosystem
Florida coast
Community
All organisms on
the Florida coast
Population
Group of brown
pelicans
Organism
Brown pelican
Spinal cord
Nerve
Organ system
Nervous system
Brain
Organ
Brain
Tissue
Nervous tissue
Cell
Nerve cell
Atom
Nucleus
Organelle
Nucleus
Molecule
DNA
• The food we eat is made up
of chemical elements, many
of which are essential to life
Elements, Atoms and Molecules
• Living organisms are made up of 25 chemical
elements
• An element is a ‘substance’ that cannot be broken
down to any other substance by ordinary chemical
means
– Remember your Periodic Table of Elements?
– Oxygen (O), Carbon (C), Nitrogen (N), Hydrogen
(H) = ~96% of the weight of the human body
• Main ingredients of proteins, sugars and fats
Elements, Atoms and Molecules
• The next 3.99% is made up of
– Calcium (Ca)  bone formation
– Phosphorus (P)  DNA synthesis
– Potassium (K)  cell signaling, nervous system
– Sulfur (S)
– Sodium (Na)
– Chlorine (Na)
– Magnesium (Mg)
Elements, Atoms and Molecules
• The remaining 0.01% are represented as trace
elements
– very small quantities, but extremely important
• Examples of trace elements include:
– Iron (Fe) – hemoglobin, binds oxygen
– Copper (Cu) – enzyme function
– Fluorine (F) – prevents tooth decay
– Iodine (I) – thyroid hormones
Elements, Atoms, and Molecules
• An element is a unique substance that cannot be
broken down to into smaller substances
• An atom is the smallest unit of matter (stuff that the
universe is made of) that still retains the properties of
an element
• A molecule is a substance consisting of 2 or more
elements (either the same or different)
– Sodium chloride (NaCl; “table salt”)
– Water (H2O)
– O2 (oxygen)
The Periodic Table of Elements lists all of the
known elements and their atomic numbers
Atoms
• An atom is made up of:
− Proton: (+) charge
− Electron: (-) charge
− Neutron: neutral, no charge
• Each elements differs by the number of protons,
neutrons and electrons found in their respective atoms
Elements
• An element is an atom with a specific number of
protons in its nucleus
• Every element has an atomic number. The atomic
number is the number of protons in the nucleus of the
atom
Structure of an Atom
proton
neutron
+ = +
= = + =
+ + =
= +
nucleus
electron
An atom is made up
of a nucleus which
contains protons
(positive charge) and
neutrons (no charge)
and is surrounded by
a cloud of electrons
(negative charge)
An Introduction to Chemistry
ATOM
proton
neutron
+ = +
= = + =
+ + =
= +
nucleus
electron
• The electrons are
much, much smaller
than the nucleus and
circle around the
atom at the speed of
light in energy layers,
or shells
ATOM
8
7
1
2
+ = +
= = + =
+ + =
= +
6
5
electron
3
4
• The first shell of an
atom always contains
up to two electrons
• The outer shells
always contain up to
eight electrons.
• An atom is stable
when the outermost
shell of electrons is
complete
• Let’s take a look at Oxygen
• Oxygen has an atomic number
of 8 so it has:
O
– 8 protons
– 8 neutrons
– 8 electrons
• 2 of the 8 electrons are in the first electron shell,
leaving 6 for the outermost electron shell (8-2 =
6)
• Its outermost electron shell is not complete; it
wants 8 electrons and only has 6 ( so it needs 2
more)
• Now let’s look at Hydrogen
• Hydrogen has an atomic number of 1
so it has only 1 proton and 1 electron
• With only 1 electron, it has only 1
electron in its first electron shell
• Like oxygen, is outermost electron
shell is not complete; it wants 2
electrons and only has 1 ( so it needs
1 more)
H
• But what if oxygen – which needs 2 more
electrons – could share an electron with 2
hydrogen atoms? The shared electrons would
orbit around the atoms completing the
outermost electron shells for all 3 atoms
O
H
H
• This is exactly what happens….when oxygen shares
its electrons with 2 hydrogen atoms, theresulting
molecule is water, or H2O
O
WATER
Covalent Bonds
• The sharing of outer shell electrons is called a
covalent bond. The resulting bonding of atoms to one
another forms a molecule.
• But covalent bonds are not the only types of bonds
that atoms can form.
• Let’s look at another example; this time with Sodium
and Chlorine
• Sodium (Na) has 11 electrons: 2 in the first shell,
8 in the second shell and 1 in the outermost
shell
• Chlorine (Cl) has 17 electrons: 2 in the first shell,
8 in the second shell and 7 in the outermost
shell
• If Sodium donated its extra electron to Chlorine,
its outermost electron shell would be complete
• When Chlorine accepts this extra electron, it’s
outer electron shell will also be complete
• Since Sodium lost an electron, it has one more
proton than it does electrons (11 protons, only
10 electrons); this gives Sodium a positive (+)
charge
• Since Chlorine gained an electron, it has one
more electron than it does protons (17 protons,
and 18 electrons); this gives Chlorine a negative
(-) charge
• The resulting atoms are now called ions, since
they have an electrical charge. When two atoms
exchange electrons, they form an ionic bond
• Na+ (sodium ion) is attracted to the Cl- ion
(chloride ion) and they bond to one another,
forming NaCl (sodium chloride)
Hydrogen Bonds
• Covalent bonds exist between atoms sharing
electrons
• Ionic bonds exist between ions, atoms that have
exchanged (gained or lost) electrons, and as a result
have a positive or negative charge
• Hydrogen bonds are a type of bond that exist between
molecules, and result from an unequal sharing of
electrons within the molecule
• Recall that in a water molecule, two hydrogen
atoms share electrons with an oxygen atom,
completing the outer shell of all 3 atoms
O
H
H
• But the electrons do not spend an equal amount
of time with hydrogen as they do oxygen
++
+
+
O
+ +
++
+
H
+
H
• This is because oxygen has 8 protons in its
nucleus, while hydrogen only has 1
• Remember that opposites attract. The difference
in positive charges pulls the
shared electrons
toward oxygen, and
away from the two
hydrogen atoms
+++
++
++O
+
+
H
+
H
• The abundance of electrons near oxygen makes
the oxygen atom in a water molecule slightly
negative
(-)
• Likewise, the 2
hydrogen atoms
become slightly
positive since their
shared electrons
spend so little
time near them
++
+
+
++ +
+
+
(+)
+
(+)
• A water molecule is said to be polar in that it has
two ends of opposing charges: a slightly positive
charge near the hydrogen atoms, and a slightly
negative charge near the oxygen atom
(-)
O
H
(+)
H
(+)
• The bonds
that form
between the
positive and
the negative
ends of two or
more polar
molecules are
called
hydrogen
bonds
Water is the solvent of life
• Because of its polar properties, water is an incredible
solvent
• A solvent is an agent that dissolves substances or
solutes, together making up a solution
Na+ ions in
solution
Cl- ions in
solution
Table salt, NaCl
• The positive and
negative ends of a
water molecule attract
ions, even those once
joined by ionic bonds
• For example,
table salt, NaCl
is readily
separated back
into Na+ and Clions in water
Water is essential to life
• Because of its polar properties, water is also
cohesive, or “sticky”
• Cohesion exists because the positive (hydrogen) end
of one water molecule is drawn
towards the negative (oxygen) end of another
water molecule
Water: Heat Capacity
• Because of its hydrogen bonds, water is said to have
a high heat capacity, or ability to absorb a large
amount of heat energy without an increase in its own
temperature
– To increase the temperature of water, heat energy
must first disrupt the hydrogen bonds that have
formed between water molecules
Water: Heat Capacity
• We experience the benefits of water’s high heat
capacity every time we sweat.
• Our body provides the heat to evaporate water from a
liquid to a gas (water vapor), keeping us cool
• This is the same reason why dogs pant and pigs
wallow in the mud!
Water’s amazing properties
• Water is unique in that it naturally exists in all phases
(gas, liquid, solid) on Earth
• Water is also unique in that its solid phase (ice) is less
dense than its liquid phase (water)
Water’s amazing properties
• At low temperatures, the hydrogen bonds between
water molecules stabilize
• This creates a 3-dimensional shape, or crystal that
traps air between the water molecules
• The trapped air causes ice to take up more space than
liquid water, making it less dense and
causing ice to float