Chemical Basis of Life: Atoms and Molecules

Lesson 2

Describe interactions among atoms,

including covalent, ionic, hydrogen
bonding and non-polar interactions.

Discuss the behaviour of water due to

hydrogen bonding and the benefits of
water to living organisms.

To understand biology the

knowledge of basic chemistry is
necessary

Living things are complex

structures of atoms and
molecules

The chemistry of life is what

allows living things to function
and interact

1. Living things are living matter

comprised of combinations of
several elements.
2. Elements are substances that
cannot be changed in normal
chemical reactions
A. there are 92 naturally occurring
elements
ranging from hydrogen to uranium
B. Each element has a unique chemical
symbol
C. Four elements (C,H,O,N) make up
96% of
most living organisms

Most common
elements:
Oxygen (O)
Carbon (C)
Hydrogen (H)
Nitrogen (N)

Minor elements:
Calcium (Ca)
Phosphorous (P)
Potassium (K)
Sulfur (S)
Sodium (Na)
Magnesium (Mg)
Chlorine (Cl)
Iron (Fe)

Atoms
Atoms are the fundamental particles of
elements
- Atoms are the smallest components of an element
that retains the chemical properties of the
element
- Components of atoms include protons,
neutrons, and
electrons
Typical Structure
of an atom

An atom is uniquely identified by its

number of protons (its atomic number)
- A proton is a subatomic particle (tiny
particles of matter) with one unit of positive
charge found in the nucleus of an atom
- The periodic table depicts the elements in
order of their atomic number the number
of protons in the nucleus

The atomic mass or mass number indicates

the number of protons and neutrons (protons plus
neutrons) in an atom

Neutrons are uncharged or neutrally charged

subatomic particles found also in the nucleus of
atoms

The atomic mass of an atom indicates

approximately how much matter that atom
contains compared to others

- expressed in Atomic mass units (amus) or

Daltons

An element has 6 protons and 6 neutrons.

What is its atomic mass? What is its mass
number?

Some atoms are called isotopes

- Isotopes have the same atomic number, but differ
in number of neutrons. (same atomic number, but
different mass numbers)
-

Radioisotopes are unstable isotopses due to

excess neutrons; they tend to break down (decay)
emiting radiation (Many are important in
scientific research and medicine

Electrons

are negatively charged

subatomic particles that occupy orbitals
-

Orbitals are regions of 3D space that correspond to

energy levels.

An electrons energy depends on the orbit it occupies

(less energy closer to the nucleus, more energy
away from nucleus)

The outermost electron(s) are known as the valence

electron(s) and they contain the most energy

These outer electron(s) occupy what is called the valence

shell
(most outer orbital)

Electrons can gain energy and move to farther orbitals or

lose energy and move to lower orbitals (closer to nucleus).

Valence electrons determine the

chemical behaviour of atoms

Atoms can undergo chemical reactions

-

The number and arrangement of valence electrons

determines the chemical behaviour of the atom

Most atoms are unstable and aim to fill their valence shell
to become stable

Stable atoms are very unreactive

- max of 2 electrons needed to fill first orbital
- max of 8 electrons needed to fill all other orbitals

Unstable atoms are reactive and may gain, lose or share

valence electrons to become stable.

 What determines the chemical behaviour

of a particular element?
Oxygen (O) has six valence electrons. It
needs how many more electrons to fill its
other shell and become stable.

Atoms when they react can chemically combine

and form molecules and compounds
-

When two or more atoms join and form stable particles they
are called Molecules
- Molecules may be composed of different or similar atoms
- Eg. H2O, O2, H2, N2 CO2, NH3

Compounds result when two or more different elements

combine
- Eg. C6H12O6, H20

Note: All compounds are molecules but not all molecules

are
compounds.

A substance (compound and

molecules) can be described
by a chemical formula
-

Chemical formulas indicate the types

of atoms in a substance and their ratio
-

Examples: H2o,

C6H12O6

Subscripts indicate the number of

atoms of a particular element in the
chemical. No subscript indicates 1
atom of an element
Chemical formulas may be shown as
emperical (simplest formula),
molecular formulas or structural
formulas

Types of
Chemical Formulas
Emperical
CH2O
NH2
Molecular
H2O
C6H12O6
N2H2
Structural

D.

Chemical equations describe chemical reactions

1. Reactants- substances that participate in the reaction (generally

written on the left side of the equation)

2. Products substances that are made ( written on the right side of

the equation

3. Reversible reactions are indicated by double arrows between

reactants and products

Samples
N2 + 3 H2 2 NH3

2 H2O 2 H2 + O2

2 Na(s) + 2 HCl(aq) 2 NaCl(aq) + H2(g)

2 H2 + O 2

2 H2O

Atoms are joined by chemical bonds

- Chemical bonds are forces of attraction between
atoms
- They represent a certain amount of energy;
- That amount of energy would be required to break
that bond (activation energy)
- Important Bonds to note
- Covalent Bonds
- Ionic Bonds
- Hydrogen bonds

In covalent bonds electrons are shared to fill the

valence shells of all the atoms involved

Each atom shares one(1) electron to make a shared pair

of electrons

Covalent bonds are strong chemical bonds

Single, double or triple covalent bonds can exist

Electronegativity
A large nucleus with many protons
attracts electrons more strongly
than a small nucleus with few
protons

Nonpolar covalent
bonds forms when electrons
are shared equally
Eg. O2, CO2, CO, CH4, H2

Polar covalent

forms
when one atom is more
electronegative than the other
(creates positive and negative
ends)
Eg. H2O, water

B. Ionic bonds form between cations and

anions
1. An atom becomes an ion when it gains or
loses one or more electrons and thus
becomes charged
2. Cations are positively charged ions (loses
electron(s))
3. Anions are negatively charged ions
(gains electrons(s)), and are named with the

Anions and Cations

Common Cations

Common Anions

hydrogen H+

hydroxide OH-

sodium Na+

chloride Cl-

potassium K+

sulfide S-2

calcium Ca+2

bicarbonate HCO3-

magnesium Mg+2

carbonate CO3-2

ferrous Fe+2

sulfate SO4-2

ferric Fe+3

phosphate PO4-3

Example: a. Sodium (Na+ ) and chloride (Cl-)

ions form sodium chloride
(NaCl)

- Hydrogen bonds

In other words a hydrogen

atom covalently bonded to
an electronegative atom is
attracted to another
electronegative atom
(oxygen or nitrogen)

Example: Water

are weak
attractions
involving partially
charged hydrogen
atoms
-

Hydrogen bonds
individually are weak,
but collectively are
very strong

Ionic bonds form when oppositely charged

atoms are attracted to each other

Polar molecules have no charged ends

Covalent bonds occur when valence

electrons are shared

Chemical formation- H2O

Covalently bonded molecule
Essential component of living forms
Important medium for living things to exist

Polar
Easily dissociates
Universal Solvent
High Specific Heat
High heat of vaporization
Important in Metabolism
Lubricant
Supporting Substance
Habitat
Etc.

Water molecules are

polar covalent
Its Oxygen attracts
electrons more
strongly than its
hydrogens

This creates a dipolar

structure
Allows for hydrogen
bonding

Waters ability to hydrogen bond

is responsible for several of its
properties

Cohesive nature droplet

formation, cling to each other
Capillary Action

Adhesive nature
cling to other surfaces

Crystal structure of ice

Water molecules are
spaced out by H-bonds
Ice is less dense than
liquid water
Water is most dense at
4o C
Ice floats on water

Surface ice insulates the liquid water below

This allows fish, frogs and other aquatic
organisms to survive winters in frozen lakes

Water has the tendency to ionize

Hydroxyl ion -OHHydronium ion - H+ (or oxonium ion H3O+ )

pH is the measure of the concentration of

hydrogen ions (H+) in a substance

At neutral pH, H+ = OH- = 7.0

pH greater than 7.0 is alkaline
pH lower than 7.0 is acidic

Acid (pH < 7)

Protons donors
Large concentration of hydrogen ions (H+)
Releases H+ in solution

Buffers are
substances that
resists (prevents)
changes in pH
when an acid or
base is added.

Base (pH > 7)

Protons acceptors
Low concentration of H+
Releases OH- in solution

Neutral pH is 7.0
Concentration of H+ and OH- are equal

Water readily dissolves other polar

molecules (and also ionic substances)
(hydrophilic molecules)

It does not dissolve non-polar molecules

(hydrophobic molecules)

This property is very important in

Transport blood, sap etc.
Removal of waste urine
Secretions

Specific heat can be defined as the amount of heat energy

required to raise the temperature of 1gm of something by 1
degree Celsius. (It is expressed in calories)

It is how well a substance resists changing its

temperature

The amount of heat energy required to raise the

temperature of water is quite large;

Its takes a lot of heat to increase the kinetic energy of water

molecules and thus break bonds between water molecules
Thus water is fairly stable with changing temperatures; this
helps stabilize the Earths surface
This is essential for reactions involving enzymes

Much heat energy is required to change

liquid water to vapour.

This means that water can absorb or can lose a

lot of heat energy without changing its
temperature very much.

This buffers the environment against large, rapid

temperature changes.

Temperature Control (Cooling)

Evaporation
Transpiration

Property

Benefit to life

a liquid at room temperature, water dissolves more

substances than any other common liquid

liquid medium for living things and for the chemistry of life

much heat energy needed to raise the temperature of water aquatic environment slow to change temperature; bulky
organisms have stable temperatures
evaporation of water requires a great deal of heat

evaporation causes marked cooling; much heat is lost by

evaporation of a small quantity of water

much heat has to be removed before water freezes

cell contents and water in aquatic environments are slow to

freeze in cold weather

ice is at maximum density at 4 C

ice forms on the surface of water, insulating the water

below, and allowing much aquatic life to survive freezing

surface water molecules orientate with hydrogen bonds

formed inwards

certain animals exploit surface tension to move over water

surfaces

water molecules slide past each other easily

water flows easily through narrow capillaries (low

viscosity)

water molecules adhere to surfaces

water adheres to walls of xylem vessels as it is drawn up

the stem to the leaves, from the roots

water column does not easily break or pull apart under

tension

water can be lifted by forces applied at the top, and so can

be drawn up xylem vessels in tree trunks by force generated
in transpiration from leaves

water is transparent

aquatic plants can photosynthesise at some depth in water

On a scrap piece of paper

List two (2) things you understood well from
todays lesson.

List two (2) things that were confusion.

Submit your paper before leaving