The Chemical Basis of

Life I
Atoms, Molecules &
Water

Definitions you should know

Matter: anything that contains mass
and occupies space, composed of atoms
Atoms: the smallest functional units of
matter, cannot be broken down further
by ordinary chemical or physical means
Molecules: two or more atoms bonded
together
Element: pure substance of only one
kind of atom
Subatomic particles: found within
atoms
Protons: positive charge, in nucleus

2.1 Atoms
Learning Objective
1. Describe the general structure of
atoms and their subatomic particles.

Definitions you should know

1.Orbitals: the region around the
nucleus of the atom where electrons
are found
2.Electron shells or energy levels: a
grouping of electrons surrounding the
nucleus of an atom; the chemical
properties of an atom are determined
by the outermost electron shell
3.Valance electrons: electrons in the
outermost shell of an atom
4.Dalton: also known as atomic mass
unit (amu) equals 1/12 the mass of a

2.1 Atoms
Learning Objective
2. Discuss the way electrons orbit the nucleus
of an atom within discrete energy levels.

2.1 Atoms Learning Objectives

3. Relate atomic structure to the periodic table
of the elements.
Atomic number: number of protons in a
specific element
Atomic mass: number of protons plus the
number of electrons

2.1 Atoms
Learning Objective
5. Explain how a single element may exist in
more than one form, called isotopes, and how
certain isotopes have importance in human
medicine.
Isotope: element with the same number of
protons but different number of neutrons
Similar chemical properties can have
different physical properties
12
C and 14C
Half-life: time it takes for 50% of the isotope to
decay
Radioisotopes: lose energy by emitting

2.1 Atoms
Learning Objective
6. List the elements that make up most of the
mass of all living organisms.

2.2 Chemical bonds and molecules

Learning Objective
1. Compare and contrast the types of atomic
interactions that lead to the formation of
molecules.
2. Explain the concept of electronegativity and
how it contributes to the formation of polar
and nonpolar covalent bonds.
3. Describe how a molecules shape is
important for its ability to interact with
other molecules.
4. Relate the concepts of a chemical reaction
and chemical equilibrium.

Definitions you should know

Molecule: two or more different atoms
bonded together
Molecular formula: types and number of
atoms in a molecule
Compound: a molecule composed of two or
more different elements
Covalent bond: atoms share a pair of
electrons
Ionic bond: gain and loss of an electron
between two atoms, resulting in positive and
negative charges the hold the two atoms close
together
Hydrogen bond: A hydrogen bond forms
when a hydrogen atom from one polar

Covalent bonding: Inner shell holds 2

electrons, outer holds 8 electrons=octet rule

 The octet rule states than many atoms are

most stable when they have 8 electrons in
their outermost electron shell
Exceptions are hydrogen and helium-their
outermost shell can only hold 2 electrons

 Single covalent bond: sharing of 2 electrons

between atoms; H-F
Double covalent bond: sharing of 4
electrons (2 pairs) between 2 atoms; O=O
Why does the O2 molecule obey the octet rule ?

 Polar covalent bonds occur because of

electronegativity
Electronegativity of an atom is a measure of
its ability to attract electrons in a bond with
another atom
Shared electrons are more likely to be
closer to the nucleus of the atom of higher
electronegativity
Water is an example of a molecule that has
polar covalent bonds

Hydrogen bonds: allow interactions

between and within molecules

Ionic Bonds: involve an attraction

between positive and negative ions

Definitions you should know

Ion: a charged atom, resulting from gaining
or losing and electron
Cation: a positively charged ion
Anion: a negatively charged ion

Shapes of molecules: depends on the types

of bonds between their atoms, temperature of
their environment, pH of the solution

Enzymes
Substrates
Noncovalent
interactions

Free Radicals are a special class of highly

reactive molecules
What is a free radical ?
A molecule containing an atom with a single,
unpaired electron in its outer shell
Formed by Exposure of cells to radiation or
toxins
Harmful: causing a cell to rupture, damage
DNA,
Helpful: used to kill invading cells (bacteria)
Vitamines C & E are antioxidants which
destroy the free radical
Free radicals can either by charged or
neutral

Chemical Reactions change elements or

compounds into different compounds
Chemical Reaction: when one or more
substances are changed into other substances
by the making or breaking of chemical bonds
Catalyst: substance that speeds up the rate
of a chemical reaction
Chemical equilibrium: the rate of the
formation of products equals the rate of the
formation of reactants
CH4 + 2O2
(methane) (oxygen)
dioxide) (water)

CO2

+
2H2O
(carbon

2.3 Properties of WaterLearning

Objectives
1. Describe how hydrogen bonding determines
many properties of water.
2. List the properties of water that make it a
valuable solvent, and distinguish between
hydrophilic and hydrophobic substances.
3. Explain how the molarity of a solutionthe
number of moles of a solute per liter of solution
is used to measure the concentration of solutes in
solution.
4. Discuss the properties of water that are critical
for the survival of living organisms
5. Explain how water has the ability to ionize into
hydroxide ions (OH) and into hydrogen ions (H+),
and how the H+ concentration is expressed as a
solutions pH.

Definitions you should know

Solution: solute dissolved in a solvent
Hydrophilic: water loving
Hydrophobic: water hating
Amphipathic: part of the molecule is polar
and a second part is nonpolar
Micelle: a sphere of amphipathic molecules in
solution (water)
Concentration: the amount of a dissolved
solute per unit volume of liquid (solvent)
Molecular mass: is equal to the sum of the
atomic masses of all the atoms in the
molecule. Ie. Glucose has a molecular mass
of 180
Molarity: the number of moles of a solute

Water exists in three states

Temperature and the state of water

Solid (ice) 0C, liquid , gas (100C)
Heat of Vaporization-the amount of heat
required to convert unit mass of a liquid into
the vapor without a change in temperature.
For water at its normal boiling point of 100 C,
the heat of vaporization is 2260 J g-1.
This means that to convert 1 g of water
at 100 C to 1 g of steam at 100 C,
2260 J of heat must be absorbed by the
water.
Conversely, when 1 g of steam at 100 C
condenses to give 1 g of water at 100
C, 2260 J of heat will be released to the

Heat of Fusion-the amount of heat required

to convert unit mass of a solid into the liquid
without a change in temperature. (or released
for freezing)
For water at its normal freezing point of 0 C,
the specific heat of Fusion is 334 J g-1. This
means that to convert 1 g of ice at 0 C to 1 g
of water at 0 C, 334 J of heat must be
absorbed by the water. Conversely, when 1 g
of water at 0C freezes to give 1 g of ice at
0C, 334 J of heat will be released to the
surroundings.
Water is most dense at 4C, does ice float or

Cohesion
Adhesion
Surface tension
Evaporation/Transporatio
n
Solvent
Hydrolysis reaction
Dehydration reaction

pH=-log10 [H+]

Buffers minimize
fluctuations in the pH
of fluids
CO2 + H2O
H2CO3
H++ HCO3