Chemical Basis of Life

Introduction

A knowledge of chemistry is essential for understanding

organisms

Important to biology are inorganic compounds,

including water, simple acids and bases and simple salts
 Element
Substances that cannot be broken down into simpler substances by ordinary
chemical reactions

Each has a chemical symbol

Four elements comprise the mass of most organisms

• Oxygen, carbon, hydrogen and nitrogen

In addition, other elements such as calcium and trace elements are present
Elements in the Human Body
 Elements in the Human Body

Essential Elements Variable Elements Trace Elements

S H O P C N Na K Ca Mg Fe Cl Cu Zn Mn Se Si F I
Invariably found in variably found in living found in trace amounts in
all living organisms organisms some, but not all, organisms
Functions of elements
 Atom Overview
ATOM- is the smallest particle of an element that maintains the
characteristics of that element

Atom is made up:

• Nucleus
• Electron cloud or shells

Nucleus and electron cloud consists of 3 sub-atomic particles:

• Protons
• Neutrons
• Electrons
 Atom Composition
The Nucleus
• Protons
• Positively charged particles in the nucleus
• Neutrons
• Particles of the nucleus that have no electrical charge
Electron cloud/ shells
• Electrons
• Negatively charged particles in atoms
• Found around the nucleus within electron clouds
 Sub-atomic Particles
Particle Charge Mass (g) Location

Electron
(e-) -1 9.11 x 10-28 Electron
cloud
Proton
(p+) +1 1.67 x 10-24 Nucleus
Neutron
(no) 0 1.67 x 10-24 Nucleus
 Atomic Number
Atoms are composed of identical protons, neutrons, and electrons
• How then are atoms of one element different from another
element?

Elements are different because they contain different numbers of

PROTONS

The atomic number of an element is the number of protons in the

nucleus

# protons in an atom = # electrons

 Atomic Number

Atomic number (Z) of an element is the number of protons in

the nucleus of each atom of that element.

Element # of protons Atomic # (Z)

Carbon 6 6

Phosphorus 15 15

Gold 79 79
 Mass Number
Mass number (A) is the number of protons and neutrons in the
nucleus of an element:
Mass # = p+ + n0

Nucleus p+ n0 e- Mass #
Oxygen - 16 8 8 8 16

Arsenic - 75 33 42 33 75

Phosphorus - 31 15 16 15 31
 Complete Symbols
Contain the symbol of the element, the mass number and the
atomic number.

Superscript → Mass
number

Subscript →
Atomic
number
X
 Symbol Form
 written in symbol form
Mass
number 35
symbol of
Atomic 17 Cl the element
number

 symbol tells us that the atom

 is of element chlorine
 has atomic number 17 (so it contains 17 protons)
 has 17 electrons (number of protons = number of electrons)
 it must contain 35 – 17 = 18 neutrons
 has mass number 35 (so number of protons + number of neutrons = 35)
 Exercise I

 Find each of these:

a) number of protons
b) number of neutrons 80
c) number of electrons 35 Br
d) Atomic number
e) Mass Number
 Answer Exercise I

 Find each of these:

a) number of protons = 35
b) number of neutrons =80-35=45 80
c) number of electrons = 35 35 Br
d) Atomic number = 35
e) Mass Number = 80
 Exercise II
 If an element has an atomic number of 34 and a mass number of
78, what is the:

a) number of protons
b) number of neutrons
c) number of electrons
d) complete symbol
 Answer Exercise II
 If an element has an atomic number of 34 and a mass number of
79, what is the:

a) number of protons = 34
b) number of neutrons =78-34 = 44 79
c) number of electrons = 34 34 Se
d) complete symbol = Selenium (Se)
 Isotopes
• Atoms of an element that have the same number of protons and electrons ,but
different numbers of neutrons.

• Hydrogen isotopes
• Hydrogen has 1 proton, 1 electron and 0 neutrons
• Deuterium has 1 proton, 1 electron and 1 neutron
• Therefore, it is heavier than hydrogen but has similar chemical properties and slightly different physical
properties
• Tritium has 1 proton, 1 electron and 2 neutrons

Isotopes 23Na 24 Na
11
number of protons 11 11
number of electrons 11 11
number of neutrons 23 - 11 = 12 24 – 11 = 13
 Ions
• Ion – electrically charged particle
• Thus, atoms whose # of electrons does NOT EQUAL the # of protons
• Either positively or negatively charged
• Positively charged = loses one or more electrons
• Negatively charged = gains one or more electrons

• Determining the charge of an ion:

Overall charge = # of protons - # of electrons
 Symbol for Ions
• Includes:
• Atomic number
• Mass number
• Element symbol
• Charge
• Example:
• 35 protons, 45 neutrons, 36 electrons
80 -1
Br 35
• 12 protons, 12 neutrons, 10 electrons
24 +2
Mg 12
Exercise: For each of the following species determine number of
protons, neutrons and electrons
Protons Electrons Neutrons
70Ga 31 31 70-31 = 39
70Ga3+ 31 31 - 3 = 28 70-31 = 39
79Se2- 34 34 + 2 = 36 79-34 = 45
73Ge4+

65Zn2+

75As3-

40Ar

84Kr+

40Ca2+

32S2-

35Cl-

37Cl-
 The Periodic Table
In 1869,Dmitri Ivanovitch Mendeléev
created the first accepted version of the
periodic table.

He grouped elements according to their

atomic mass, and as he did, he found that
the groups had similar chemical properties.

Blank spaces were left open to add the new

elements he predicted would occur.
 Cont’
• Periodic Law - When the elements are arranged in order of increasing atomic
number, there is a periodic repetition of their physical and chemical properties

• Modern Periodic table consists of:

 Periods - Horizontal rows of the periodic table (side to side)
Groups or families - – vertical (up and down) column of elements in the
periodic table
 Cont’
Groups – Arranged by the # of valence electrons i.e. # of electrons in the
outer shell
• Elements in the same group has same # of valence electrons
• Each group has similar chemical and bonding properties
• 8 groups

Periods – Arranged by increasing atomic number

• Elements in a period have the same number of electronic shells
• 7 periods
 Groups
1 8
2 345 67
Groups go down
on the periodic
table

Elements in the
same group, have
the same number
of valence
electrons
 Periods
1
2
Periods go
3
across on the
4 periodic table
5
6 Periods have the
7 same number of
“shells”
 Arrangement of electrons in the atom
• Electrons are arranged in energy levels i.e. Electron shells, around the
nucleus
• Each energy level can only hold a certain # of electrons
 Cont’
Main rule – electrons always go into the shell nearest to the nucleus, if
there is room. Once the shell is filled up, the electrons go into the next
available shell.

Outermost shell of an atom is called the valence shell

This shell should have electrons before it can be called a valence shell

The electrons in the valence shell are called the valence electrons
The Electronic Configuration of Atoms

Mass number
16 (Nucleon)

8
O O

Atomic
number
(Proton)
The Electronic Configuration of Atoms

Mg
 Periodic Table Trends

 Atomic radius/size
 Ionisation energy
 Electron negativity
 Electron affinity
 Metallic Character
 Ionic radius
 Atomic Radius

Atomic radius is the distance

from the center of an atom’s
Radius nucleus to its outermost
electron.
 Atomic Radius
Atomic Radius decreases

H
Li F
Na
K

At
Fr

From left to right the atomic radius decreases because the number of protons
increases. Thus our effective nuclear charge also increases and our radius
decreases.
As we move down the group the atomic radius increases because with each atom
we add a new energy shell
Atomic Radii of Representative Elements (nm)
1A 2A 3A 4A 5A 6A 7A

Li Be B C N

O F

Na Mg Al Si P S Cl

K Ca Ga Ge As Se Br

Rb
Sr In Sn Sb Te I

Cs Ba Tl Pb Bi Po At
 Ionization Energy
Energy needed to remove one of atom’s electrons from its outermost shell

decreases
Ionization energy
H
Li F
Na
K

At
Fr

Ionization energy
increases
 From left to right the IE increases because we have a higher effective nuclear charge, which means we have a
greater force. As we go down the group the atomic radius increases thus our force becomes less .i.e IE
decreases. Thus the higher the IE the less likely you are to give-up e- . This translates to electronegativity
 Electronegativity
Electronegativity (E.N.): Ability of an atom to attract electrons to
an element.

 From left to right the EN increases because the number of protons increases. Because we have a higher
effective nuclear charge the force used to pull the e- will be much higher..
 As we move down the group the EN decreases because with each atom we add a new energy shell
 Electron Affinity
Energy released when an atom gains an electron to form a
negative ion/anion.

Electron Affinity decreases

H
Li F
Na
K

At
Fr

Electron Affinity increases

 From left to right the EA increases because when an atom gains an e- it loses energy and becomes stable –
Exothermic rxn (Decrease in atomic radius). As we move down the group the EA decreases because the atomic
radius increases thus we go from exothermic rxn to endothermic rxn
 Metallic Character
Defined as how readily an atom can lose an electron
TREND:
Metallic characteristics decrease from left to right across a period. This is
caused by the decrease in radius of the atom that allows the outer electrons
to ionize more readily.

Metallic characteristics increase down a group. Electron shielding causes the

atomic radius to increase thus the outer electrons ionizes more readily than
electrons in smaller atoms.

Metallic character relates to the ability to lose electrons, and nonmetallic

character relates to the ability to gain electrons.
Metallic character decreases
 Ionic Radius
 Anion (negative ion), its size increases, since the nuclear charge remains the same but
the repulsion resulting from the additional electron(s) enlarges the domain of the
electron cloud.
 Cation (positive ion) smaller than neutral atom, since removing one or more
electrons reduces electron-electron repulsion but the nuclear charge remains the
same, so the electron cloud shrinks.
 From top to bottom of a periodic group both the atomic radius and the ionic radius
increases.

+
Li F Li+ F--

Changes in size when Li reacts with F to form LiF

Summary of Periodic Trends
Metallicity inreases
Atomic Radius increases/ Ionic size

Ionization energy increases

Electronegativity increases
Electron affinity increases
H
Li F
Na
K

At
Fr

Electronegativity increases

Ionization energy increases

Electron Affinity increases https://www.youtube.com/watch?v=hePb00CqvP0
 Mixtures
The slight charge of water molecules make them especially good at forming
mixtures

• Substance composed of two or more elements or compounds that are

mixed together but not chemically combined
• The mixtures that are made with water can be of two types
• Solutions
• Suspensions
 Solutions

A solution is a mixture in which one substance is dissolved in another

• Substances undergo a physical but not a chemical change
• Most common are solutions of water and many other substances, such as
sugar, salt, tea, and cocoa
• In these solutions, water is the solvent, or substance that does the
dissolving
• The substance that is dissolved is the solute
• Water is known as the universal solvent
 Acids
Compounds that release hydrogen
ions into solution are known as
acids

Acids are found in many of the

foods we eat
• Apples and pears contain malic
acid
• Oranges, grapefruits, and
lemons taste sour because they
contain citric acid
 Bases
Bases are compounds that release
hydroxide ions into solution

Strong acids and bases are highly

reactive chemical compounds

They can attack and break a

variety of chemical bonds, thus
making them potentially
dangerous to living tissue
Strong acids and bases can cause severe chemical
burns
e.g. battery acid (pH ~ 1.0)

In high concentrations, can kill organisms in an

ecosystem
 Buffers
Weak acids or bases that react with strong acids or bases to prevent
sharp, sudden changes in pH (neutralization).

Produced naturally by the body to maintain homeostasis

Weak Acid Weak Base

 Buffer Systems

It is imperative for cells to respond to changes in

pH

Changes disrupt cellular processes & functioning

of biological molecules

Buffer systems help resist large and abrupt

swings in pH
Bicarbonate Buffer System

Maintains blood pH (7.3 - 7.5)

If pH increases, carbonic acid releases H+ to

neutralize excess OH-

H+ combines with OH- to form water

OH- + H2CO3 → HCO3- + H2O

 Cont’

When pH begins to drop, bicarbonate consumes

excess H+ to shift reaction back towards acid

HCO3- + H+ → H2CO3

System is constantly buffering pH changes

 Cont’

Buffer systems work within narrow range

When range is exceeded, extremely severe effects

If blood pH drops to 7.0:

= respiratory acidosis, coma

If blood pH rises to 7.8:

= alkalosis, tetany
 Neutralization and pH
• Mixing a strong acid and a strong base results in the reaction in which
hydrogen ions and hydroxide ions react to form water
• This type of reaction is called a neutralization reaction
• A measurement system known as the pH scale indicates the relative
concentrations of acids and bases
• The pH scale ranges from 0 – 14
• Pure water has a pH value of 7.0
• Acids have pH values of less than 7.0
• Bases have pH values of more than 7.0
 Suspensions
Some materials do not break into individual molecules when placed
in water but still form pieces so small that they will not settle to the
bottom of a container

The movement of water keeps these particles suspended

Suspensions
 Chemical Compounds in Living Things
Although the earth’s crust contains 90 naturally occurring chemical elements, only 11 of
these elements are common in living organisms

Another 20 are found in trace amounts

Just four elements – carbon, nitrogen, oxygen, and hydrogen – make up 96.3% of the total
weight of the human body

In varying combinations, the elements carbon, hydrogen, oxygen, and nitrogen make up
practically all the chemical compounds in living things

Divided into two groups

• Organic compounds – contain carbon
• Inorganic compounds – do not contain carbon
 Inorganic Compounds

The natural world is dominated by inorganic compounds

Primarily those compounds that do not contain carbon

Water is inorganic, as are the minerals that make up most

of the sand, soil, and stone of the Earth’s landmasses
 Organic Compounds
Contain carbon

Carbon is a unique element because of its remarkable ability to form

covalent bonds that are strong and stable

Carbon can form 4 single covalent bonds

Carbon can also form chains or rings of almost unlimited length by bonding
to other carbon atoms
• Single, double, or triple
 Questions (Choose the right answer)
1) All of the following are organic compound EXECPT:
a) DNA b) Protein c) Water
d) Fat e) Phospholipids

2) ____________have the same numbers of protons and electrons but different numbers of neutrons.
a) Compounds b) Neutrons c) Elements
d) Electrons e) Isotopes

3) What is the atomic mass of an atom that has 6 protons, 6 neutrons, and 6 electrons?
a) 6 b) 12 c) 18
d) 24 e) None of the above

4) Cohesion is strongest in:

a) Water b) Methyl Alcohol c) Ethyl Alcohol
d) Benzene e) Ether

5) A/an _________ result from gain or loss of electrons.

a) Element b) Electron c) Ion
d) Neutron e) Proton
 Answers
1) All of the following are organic compound EXECPT:
a) DNA b) Protein c) Water
d) Fat e) Phospholipids

2) ____________have the same numbers of protons and electrons but different numbers of neutrons.
a) Compounds b) Neutrons c) Elements
d) Electrons e) Isotopes

3) What is the atomic mass of an atom that has 6 protons, 6 neutrons, and 6 electrons?
a) 6 b) 12 c) 18
d) 24 e) None of the above

4) Cohesion is strongest in:

a) Water b) Methyl Alcohol c) Ethyl Alcohol
d) Benzene e) Ether

5) A/an _________ result from gain or loss of electrons.

a) Element b) Electron c) Ion
d) Neutron e) Proton
END