Chapter 2

THE CHEMISTRY OF LIFE

EB 2005-INTRODUCTORY
BIOLOGY
 Learning Objectives:
1. Define matter, mixture, substance, compound and element.
2. Name the essential elements of life.
3. Define proton, electron and neutron by describing the location in the
atom, mass, and charge.
4. Define isotope and describe its use in biology.
5. Describe covalent bonding; ionic bonding; hydrogen bonding.
6. Define ion.
7. Describe the structure of water.
8. List the properties of water.
9. Define acid and base.
10.Name and describe the major classes of biomolecules.

2
Overview: Chemical Foundations
of Biology

The bombardier beetle uses chemistry to defend itself.

3
Organisms are composed of matter, which is
anything that takes up SPACE and has MASS

Volume is the size of something, in other words the amount

of space something takes up.

4
Elements and Compounds
• Elements are the basic building
blocks of all matter. • A compound is
• They could not be broken a substance
down into anything else. consisting of two
• Today there are 110 known or more
elements: 25 are essential to elements
life. combined in a
fixed ratio.

• A compound has its own properties but

which can be broken down into other
substances.

• Chemists break down compounds using

special chemical methods which may
include heat, electricity, and adding
other substances to the compounds.

5
Essential Elements of Life
 Essential
elements include
carbon, hydrogen,
oxygen, and
nitrogen.

 Make up 96% of
living matter.

 A few other
elements make up
the remaining 4%
of living matter.

6
Periodic Table of Elements
 Compounds

Sodium Chloride Sodium Chloride

Na + Cl =
NaCl
8
Effects of Essential Element Deficiencies

(a) Nitrogen deficiency (b) Iodine deficiency

9
 Atoms
 An element’s properties
depend on the structure of its
atoms.
 Each element consists of a
certain kind of atom that is
different from those of other
elements.
 An atom is the smallest unit
of matter that still retains the
properties of an element.
 Anything smaller than an atom
is just energy, not matter.

10
 Subatomic Particles
 Atoms of each element are
composed of even smaller parts
called subatomic particles.

 Relevant subatomic particles

include
 Neutrons, which have no

electrical charge (neutral)

 Protons, which are positively

charged (+)
 Electrons, which are

negatively charged (-)

 Protons and neutrons are found in the atomic nucleus.

 Electrons surround the nucleus in a “cloud”.

11
Simplified models of an atom

12
Atomic Number and Atomic Mass
 Atoms of the various elements differ in their number of subatomic
particles.

 The atomic number of an element

 Is the number of protons

 Is unique to each element

 The atomic mass of an element

 Is the sum of protons plus neutrons in the nucleus of an atom

 Is an approximation of the atomic mass of an atom

Atomic number
= no. of electrons = no. of protons
Symbol/Name
Atomic Mass
= no. of protons + no. of neutrons
= mass of a particular atom in dalton

13
 Exercise

1. A lithium atom has 3 protons and 4 neutrons. What is

the atomic mass in daltons?

2. A nitrogen atom has 7 protons. A rarer isotope of

nitrogen has 8 neutrons. What is the atomic number
and atomic mass of the rarer isotope? Give the
chemical symbol of the rarer isotope.

14
Isotopes

• Elements with the same

number of protons and
electrons but different
number of neutrons
• Hence, have different
atomic mass.

15
Carbon Isotopes
Carbon-12 makes up
about 99% of all naturally
occurring carbon.

Both carbon-12 and

carbon-13 are stable (their
nuclei remain intact
forever)

Carbon-14 is unstable and

radioactive. A radioactive
isotope is one that gives
off particles and energy
when the nucleur decays.

16
Radioisotopes can be used to
locate cancerous tissues

Cancerous
throat tissue

17
Electron Configuration & Chemical Properties

 The chemical behavior of an atom is defined by its electron

configuration and distribution.

 The periodic table of the elements shows the electron distribution

for all the elements.

18
Examples
Has 1 electron

Has 8 electrons

Has 11
electrons
 Energy Levels of Electrons
 Electrons vary in the amount of energy – the further an electron
is from the nucleus, the greater the energy. (kinetic energy)

 Energy is defined as the ability to do

work.

20
Valence Electrons and Electron Orbitals
 Valence electrons are those in the outermost, or valence shell. They determine the
chemical behavior of an atom.
 An orbital is the three-dimensional space where an electron is found 90% of the time.
 Each electron shell consists of a specific number of orbitals.

21
 Exercise

i) Atomic number :
1.
ii) Protons and electrons :
iii) Electron shell:
iv) Valence electrons in the valence shell:

2. In which shell do electrons have most potential

energy and least potential energy?

22
23
 Forming Ionic Compounds (Salts)

• Ionic bonds form

between METALS
and NONMETALS
when Electrons are
transferred (lost or
received).

• Columns 1,2,13 may

transfer with columns
15,16,17.
 Forming Ionic Compounds
• Electrons get
transferred as a Atom gained one
result of energy input. electron. It now has
This may also occur a negative charge.

when materials are

placed in solution.

• A variety of
combinations are
possible depending This atom lost one
electron and now has
on the valence a positive charge.
electron number.
 Ionic Bonds
• An ionic bond is the attraction between a
positively charged cation and a negatively
charged anion.
Atoms Combine by Chemical Bonding
to Form Molecules
 Atoms with incomplete valence shells interact with other atoms in
order to complete the valence shell of each partner.
 Atoms complete their valence shell either by sharing or transferring
their valence electrons.
 These interactions results in atoms staying together, held by attractions
called chemical bonds.

Strong Chemical Bonds Weak Chemical Bonds

Van der Waals

Ionic Bonds Covalent Bonds Hydrogen Bonds
Interactions
Strong chemical bonds connect Weak chemical bonds connect
between the atoms to form between molecules to form
molecules compounds

27
FORMATION OF
COVALENT BONDS
-Water

28
 Molecules
 A molecule consists of two or more atoms held together by covalent
bonds.
 A single bond is the sharing of one pair of valence electrons.
 A double bond is the sharing of two pairs of valence electrons.

29
Covalent bonding in compounds

30
 Electronegativity
 Electronegativity is the attraction of a particular kind of atom for
the electrons in a covalent bond. The higher the electronegativity of
an atom, the stronger it pulls the shared electrons toward itself.

Covalent Bonds

Polar Covalent Bonds Non-Polar Covalent Bonds

• There is different • There is similar electronegativities.

electronegativities.
• unequal distribution and sharing • Two atoms of the same element share
of electrons the electrons equally

31
Non-polar Covalent Bonds
> Cl-Cl (Cl atom has an electronegativity value of 3.0)

Polar Covalent Bonds

• 2 nonmetal atoms that have different electronegativities
•Eg: H-Cl, the electronegativity of the Cl (3.0) and H atom (2.1)
•Positively charged H bonded to negatively charged Cl

32
33
Structure of Water
• The two hydrogen atoms are joined to
one oxygen atom by single covalent
bond.
δ+ • But the electrons of the covalent
bonds are not shared equally
between the oxygen and the hydrogen.
• Oxygen attracts the electrons of the
covalent bonds stronger than does
δ- hydrogen. This results in the
creation of positive and negative
δ+ poles (δ+ and δ-)
• Therefore, water is a polar molecule.
• In water, the oxygen end of the
molecule has a slight negative charge,
while the two hydrogen atoms are
slightly positive.

34
 In some cases, atoms
Ionic Bonds
take electrons away from
their bonding partners.
 Electron transfer
between two atoms
creates ions.
 Ionic bonds form
between METALS and
NONMETALS when
Electrons are transferred
(lost or received).

 Ions are atoms with more or fewer electrons than usual. Ions are charged
atoms.
 An anion is negatively charged ions.

 A cation is positively charged ions.

An ionic bond is an attraction between anions and cations.

35
 Forming Ionic Compounds (Salts)

• Ionic bonds form

between METALS
and NONMETALS
when Electrons are
transferred (lost or
received).

• Columns 1,2,13 may

transfer with columns
15,16,17.
 Forming Ionic Compounds
• Electrons get
transferred as a Atom gained one
result of energy input. electron. It now has
This may also occur a negative charge.

when materials are

placed in solution.

• A variety of
combinations are
possible depending This atom lost one
electron and now has
on the valence a positive charge.
electron number.
 Ionic Bonds
• An ionic bond is the attraction between a
positively charged cation and a negatively
charged anion.
39
 Ionic Compounds

 Ionic compounds are often called salts, which may form crystals.

40
 Weak Chemical Bonds
 Advantage of weak bonding is the contact between molecules can be
brief; the molecules come together, respond to one another and
then separate
 Weak chemical bonds
 reinforce the shapes of large molecules.
 help molecules adhere to each other.

41
 Hydrogen Bonds

 A hydrogen bond
forms when a
hydrogen atom
covalently bonded to
one electronegative
atom is also attracted
to another
electronegative atom.
Hydrogen Bonding Between Water Molecules
The unique properties
that result from
hydrogen bonding are:

1. Cohesion
2. Surface tension
3. Ability to absorb and
store large amount of
heat
4. High boiling point
5. Solid form (ice) that is
less dense than liquid
6. Solvent properties

Water molecules form hydrogen bonds because they are polar. The
positively charged hydrogen of one water molecule is attracted with the
negatively charged oxygen of another water molecule.

43
 Cohesion
Water molecules
exhibit cohesion.

Cohesion is the
bonding of a
high percentage
of the molecules
to neighboring
molecules. This
is due to hydrogen
bonding.

Water is primarily "pulled" upward due to the cohesion of water

molecules within the xylem tracheids and vessels. Like a steel wire,
the chain of water molecules is literally pulled through the plant's
vascular system, from the roots to the leaves.

44
 Surface Tension
Water tension is a
measure of how difficult
to break or stretch the
surface of a liquid. Water
has a greater surface
tension than most other
liquids.

45
 Heat Capacity
• Heat is the amount of energy produced with the movement of atoms and molecules in a
body of water.

• Temperature measures the intensity of heat or the average speed of molecules

• When water is heated, large amount of heat is absorbed to first disrupt the hydrogen
bonds and then makes the molecules move faster. Once the molecules start moving
fast, the temperature rises. (increases boiling point)

• When the water cools down, hydrogen bonds reform, a process that releases heat
energy. Thus water can release a relatively large amount of heat energy while the
temperature drops only slightly.

46
 Moderation of Temperature
• The heat capacity of water is high
compared to other common
materials.
• This means that it can absorb or can
lose a lot of heat energy without
changing its temperature very much.
• This buffers the environment
against large and rapid temperature
changes.
• The temperature change of the
surface waters of the oceans (or lakes,
or even a swimming pool) is small
compared to the temperature change Perspiration is your body's
of the surrounding air. This is due to natural mechanism to
the high heat capacity of water. control body temperature.

47
 Solid form is less dense compared to liquid
liquiod form

• The hydrogen bonds in ice are more “ordered” than in liquid water, making ice less
dense.

• Since ice floats in water, life can exist under the frozen surfaces of lakes and polar
seas. Also during summer, floating ice insulates the liquid water below, allowing life to
persist under the frozen surface.

48
 Versatile Solvent
• A SOLUTION is a liquid
consisting of a
homogeneous mixture of
two or more substances.
The dissolving agent is
called the SOLVENT, and
a substance that is
dissolved is a SOLUTE.

• An AQUEOUS SOLUTION is a solution in which the solvent is water.

• As the solvent inside all cells, in blood, and in plant cell, water dissolves
an enormous variety of solutes necessary for life.

49
Water can also interact with polar
molecules such as proteins

50
 Dissociation of water molecules
leads to acidic and basic conditions
that affect living organisms

Water can dissociate into hydronium ions and hydroxide ions.

Changes in the concentration of these ions can have a great affect on
living organisms.

51
The chemistry of life is sensitive to
acidic and basic conditions

52
 The Threat of Acid Precipitation

• Acid precipitation refers to rain, snow, or fog with a pH lower than pH 5.6.
• It is caused primarily by the mixing of different pollutants with water in the air.
• It can damage life in Earth’s ecosystems.

53
 Van der Waals Interactions
• Molecules with non-polar covalent bonds may have positively and
negatively charged regions.

• This is because electrons are moving and may results in temporary

polarity (positive and negative charge).

• This temporary positive and negative charge enables molecules to

stick to each other.

• This Van der Waals interaction only occur when atoms and
molecules are very close to each other.

Attractive interactions resulting from dipole-

dipole interaction of two H-Cl molecules
 Chemical reactions make and break
chemical bonds
A chemical reaction is the making and breaking of chemical bonds. It
leads to changes in the composition of matter.

Chemical reactions convert reactants to products.

55
 Chemical Reactions Rearrange Matter
There are thousands of chemical reactions routinely carried out in living
cells. These chemical reactions do not create or destroy matter; they
only rearrange it in various ways. Chemical reactions involve the making
and breaking of chemical bonds.

56
Photosynthesis is an example of a
chemical reaction.

57
58
Predicting Bond Type; Electronegativity

•metals react with nonmetals to form ions joined by ionic bonds.

•highest degree of ionic character are formed by the reaction of alkali or
alkaline earth metals with the halogens, particularly with fluorine or chlorine.

•Nonmetals react together to form covalent bonds.

•If the bond is between two neighbors in the table, the bond will be less polar
(non polar characteristics)
• For example, carbon and nitrogen are in neighboring columns, and carbon and
fluorine are in Groups 4 and 7
• A carbon-nitrogen bond will be less polar than a carbon-fluorine bond.
Finally, if the two atoms are of the same element, as in a hydrogen molecule or
a chlorine molecule, the bond will be nonpolar.
•The electronegativity (EN) of an element measures its attraction for the
electrons in a chemical bond.

59
 FIGURE 7.3 Electronegativities of some elements (Pauling scale).

Notice that the electronegativity of most metals is close to 1.0 and that the electronegativity of a
nonmetal, although dependent on its location in the table, is always greater than 1.0. In general,
electronegativity increases from bottom to top in a column and from left to right across a period.

60
 Electronegativity useful in predicting the nature of a bond and for
comparing bond types (only an approximation).

atom with the higher electronegativity will be the negative end of the bond
To show partial charges on a polar covalent bond, positive end of the bond marked
with and the negative end of the bond marked with .

61
•Water dissociation (autoionization) occurs due to electric field
fluctuations between neighboring molecules (resulting from
thermal effects)
•effective collisions between two water molecules form
hydroxide and hydronium ions.
•The self-ionization of water (also autoionization of water) is an
ionization reaction in pure water or an aqueous solution, in which
a water molecule, H2O, deprotonates(loses the nucleus of one of
its hydrogen atoms) to become a hydroxide ion, OH−.
The hydrogen nucleus, H+, immediately protonates [gives a
proton (H+)] another water molecule to form hydronium, H3O+.

H2O + H2O <---> H3O1+ + OH1-

62
 Van der Waals Interactions
• Molecules with non-polar covalent bonds may have positively and
negatively charged regions.

• This is because electrons are moving and may results in temporary

polarity (positive and negative charge).

• This temporary positive and negative charge enables molecules to

stick to each other.

• This Van der Waals interaction only occur when atoms and
molecules are very close to each other.

Attractive interactions resulting from dipole-

dipole interaction of two H-Cl molecules
•Attraction forces that cause molecules to attract each
other at moderate distances and repel each other at close
range is called "van der Waals forces". (sum of the
attractive or repulsive forces between molecules (or
between parts of the same molecule)

•Van der Waals forces are much weaker than chemical

bonds

•Two kinds of van der waals forces

64
Dipole-Dipole forces
•occur in polar molecules (molecules that have an unequal sharing of electrons)
•. HCl polar.
•Chlorine atom has an extra electron, which came from the hydrogen atom.
•Because of this, the chlorine part of the molecule is negatively charged, and the hydrogen side of
the molecule is positively charged.
H - Cl
+ -
The positive part of one molecule will move until it is next to the negative part of a neighboring
molecule. These forces between molecules tend to make them 'stick' together.

Dispersion forces
•exist between nonpolar molecules.
•For example, chlorine gas is made up of two chlorine atoms (electrons are equally shared )
Cl - Cl
no overall charge on either side but, since electrons are constantly MOVING. Create temporary
polarity
Cl - Cl
+ -
Temporary charge disappears quickly because the electrons are moving so fast.
•These temporary dipoles allow the temporarily negative side of one molecule to attract the
temporarily positive side of another molecule

65
 Heat Capacity
• Heat is the amount of energy produced with the movement of atoms and molecules in a
body of water.

• Temperature measures the intensity of heat or the average speed of molecules

• When water is heated, large amount of heat is absorbed to first disrupt the hydrogen
bonds and then makes the molecules move faster. Once the molecules start moving
fast, the temperature rises. (increases boiling point)

• When the water cools down, hydrogen bonds reform, a process that releases heat
energy. Thus water can release a relatively large amount of heat energy while the
temperature drops only slightly.

66
67
https://www.chem.wisc.edu/deptfiles/genchem/sstutorial/Text7/Tx71/tx71.html