SBI 3U7
The Chemical Basis of Life
Chemical Fundamentals
~ Grade 12, Section: 1.1~
Atoms
 Can be highly reactive
 Don’t have a stable structure  uncharged(neutral)
 To attain a stable structure they:
o Transfer electrons b/w a metal atom and a nonmetal atom to form ionic
compounds (E.g. _________)
o Share electrons b/w two nonmetals to form molecular compounds
(E.g.________)
 As individual entities they play virtually no role in living systems
 Atomic number Number of protons = number of
 Mass number
Number of
+ number of neutrons
(generally close to twice the atomic number,
measured in atomic mass units: a.m.u.
1a.m.u. = 1.6606 x 10-24 Kg)
 Standard Atomic Notation
o Oxygen
16
Atomic mass = # n0 + # p+
O
Element symbol
8
Atomic number = # p+ = # eIsotopes
 The number of neutrons can be different for the same element (atom)
 Are atoms of the same element with the same atomic number but a different mass
number
 Isotopes of Hydrogen(see isotopes of Carbon pg. 8 –Table 1)
Name/Symbol
Atomic
Mass
Protons
Neutrons
Relative
Structural
number
Number
abundance
stability
(Z)
(A)
Hydrogen-1, H
1
1
1
0
99.8%
Stable
(Protium)
Hydrogen-2, H
1
2
1
1
o.2 %
Stable
(Deuterium)
Hydrogen-3, H
1
3
1
2
trace
radioactive
(Tritium)
Radioisotopes
 Are isotopes in which their nucleus spontaneously decays
 E.g. C-14 decays in N-14
 Types of radioisotopes
1
SBI 3U7
The Chemical Basis of Life
Radioisotopes
Useful
Radiometric dating
(E.g. carbon-14 dating)
Dangerous
Radioactive tracers
(radioisotopes that
are used to follow
chemicals through
chemical reactions
and trace their path)
Biological
-Melvin Calvin used C-14 labeled
molecules to determine the sequence
of reactions in photosynthesis
-biochemical reactions
-DNA sequence producers
Research
-C-14 and H-3 used as tracers
Medical
- nuclear medicine for diagnosis and
 Radioactivity
results2 in:
treatment
(see table
pg. 10)
-High energy radiation
penetrates and damages cell
molecules
-Regular exposure can lead to
radiation sickness
-Genetic mutations
-Cell death (high enough doses)
o The formation of different elements
o Release radiation
o Release a number of subatomic particles
 Half life:
o the time it takes for one half of the nuclei in a radioactive sample to decay
o varies considerably for different isotopes
o the rate of decay of a particular isotope is CONSTANT
{ANSWER ON p. 10, QUESTIONS #1-6}
Lewis Theory of Bonding
 Atoms and ions are stable if their electrons structures resemble that of a noble gas
(outer shell is full)
 Electrons are most stable when located in a stable octet (a valence shell which
contains 8 electrons)
 Atoms form bonds to achieve a stable outer shell of electrons
2
SBI 3U7
The Chemical Basis of Life
In the1920's it was first recognized that electrons should show wavelength properties and
Schordinger then defined, in a mathematical equation, the properties of the electron waves in
atoms. The solutions to this equation are the orbitals that express the probability of finding
an electon in a given locale in space.
The first orbital can be represented by a sphere, the radius of which would correspond to the
distance at which there is the greatest probability of finding the electron.
Each energy level consists of n2 orbitals where n is the number of the level and each orbital
can contain 2 electrons.
Element
Atomic 1S 2S 2px 2py 2pz 3s
3px 3py 3pz
Number
Hydrogen 1
1
Helium
2
2
Lithium
3
2 1
Carbon
6
2 1 1 1 1 Excited
2 2 1 1
Ground
Nitrogen
7
2 2 1 1 1
Oxygen
8
2 2 2 1 1
Fluorine
9
2 2 2 2 1
Neon
10
2 2 2 2 2
Sodium
11
2 2 2 2 2 1
Magnesium 12
2 2 2 2 2 1
1
Phosphorus 15
2 2 2 2 2 2
1 1 1
Sulfur
16
2 2 2 2 2 2
2 1 1
Argon
18
2 2 2 2 2 2
2 2 2
Valence Electrons:
3
SBI 3U7
The Chemical Basis of Life
 electrons found on the outermost orbital
 the number of valence electrons is given by the group number
 E.g. S is found in group 6 6 valence electrons
Ca is found in group 2 2 valence electrons
 the chemical behaviour of an atom is determined by the number and arrangement of
its valence electrons
Electronegativity
 A measure of the attraction an atom has for electrons in a chemical bond
 All atoms in the periodic table have been assigned an electronegativity number (En)
;see fig 7 pg. 14 and read pg. 14. See below.
 When two atoms form a chemical bond they are both attracted to their own valence
electrons as well as to the valence electrons of the other atom
 If two atoms which are bonding are identical, then they will both be equally attracted
to the electrons [The Electronegativity difference (En) is 0]
 If the bond is forming b/w two different atoms , then there may be a significant
difference in their attraction for the electrons [En is greater than 0 (See below)]
 + and - are used to identify partial negative charge and positive charge respectively.
 The type of chemical bond which forms b/w two atoms will be a function of their
respective electronegativities.
 As you move up, or to the right on the periodic table the electronegativity values tend
to increase
Types of Bonds
Ionic Bond
4
vs.
Covalent Bond
SBI 3U7
The Chemical Basis of Life
• Are bonds between metals and nonmetals
• Transfer of electrons
• E.g.
•
•
•
•
-
Are bonds between two nonmetals
Share of electrons
E.g. ____________________
Types of covalent bonds
Simple _________, double
__________, triple _______
- polar
- non-polar
Polar Covalent Bonds
Is there a correlation between electron affinity and electronegativity?
 Yes! The greater the electron affinity, the greater its electronegativity will be.
Each nucleus pulls on the
shared pair of electrons
Ex. H and O
O pulls more b/c it has a
higher electronegativity
the shared pair of e- is
pulled more to H
The covalent bond is
polarized
There is uneven distribution
of charges
 Ex. Try N and H
Non-Polar Covalent Bonds (Pure Covalent Bonds)
 When both atoms pull EQUALLY on the shared
pair of electrons, so there is no NET CHARGE
created, so NO POLES.
 These are PURE covalent bonds
 E.g.
Molecular Shape
The shape of molecules will change when covalent bonds are formed. This process is
known as Hybridization.
The Valence Shell Electron Pair Repulsion (VSEPR) theory assists in predicting the shape
of the molecule. The electron pairs in the molecule will repel each other forcing them to
move as far as possible.
5
SBI 3U7
The Chemical Basis of Life
Molecular Polarity
 The polarity of a molecule as a whole is dependent on bond polarity and molecular
shape
Nonpolar Molecule
 Nonpolar molecules are said to be hydrophobic (“water fearing”) DO NOT
dissolve in water but they DO dissolve in other nonpolar molecules
 Symmetrical molecular structures produce non-polar molecules (whether the bonds
are polar or not)
 E.g.
 Asymmetrical molecular shapes produce nonpolar molecules if the bonds are NOT
polar
o E.g. __________________
Polar Molecules
 asymmetrical molecular shapes produce polar molecules if the bonds ARE polar
 E.g._______________________
 Polar molecules are said to be hydrophilic (“water loving”) they do dissolve in
water (whether the bonds are polar or not)
 Other example: ________________________
{ANSWER ON P. 16, Practice questions: #8-9}
6
SBI 3U7
The Chemical Basis of Life
Intermolecular Bonds
 Are weaker than the intramolecular covalent and
ionic bonds
 Determine the physical state of molecular
substances at a given pressure and temperature
and are broken when:
 Types of bonds
Van der Waals Forces
Types of van der Waals Forces
London dispersion forces
Dipole-dipole forces
7
Description
-are the only forces that exist
b/w noble gases and nonpolar
molecules
-are formed by the temporary
unequal distribution of
electrons
-hold polar molecules to one
another
-the partially positive side of
one polar molecule attracts
the partially negative side of
the other polar molecule
Kind of Bonds
The weakest
forces
Stronger than
London forces
SBI 3U7
The Chemical Basis of Life
Hydrogen bonds
-are strong dipole-dipole
The strongest
forces that only form b/w an forces
electropositive H of one polar
molecule and an
electronegative N,O, or F of
a neighboring polar molecule
Types of Substances
Substances
Solids
Substance
Solid
Liquid
Gases
Classification
Soluble
Description
Solids that dissolve in water
Examples
NaCl (H2O)
Insoluble
Solids that dissolve very little
in water
Two liquids that dissolve in
each other
Iron
Chalk
Ethanol(H2O)
Ethylene glycol(H2O)
Gasoline (oil)
Gasoline (H2O)
Oil(H2O)
Miscible
Immiscible
8
Liquids
Two liquids that do not
dissolve in each other
SBI 3U7
Gas
The Chemical Basis of Life
Slightly Soluble
Small nonpolar molecules that Oxygen
cannot form hydrogen bonds
Carbon dioxide
with water
Water: The Versatile Solvent
 Water is called universal solvent b/c so many different substances dissolve in it.
The Unique Properties of Water
1. High Polarity (Good Solvent)
 Water has an excellent dissolving ability due to its polarity – water molecules
provide partial positive and negative charges to which other polar molecules or
ions can attach
 Example: The dissolving of NaCl in water
 Since many of the most important biological molecules are either charged or
highly polar, they are soluble in water water a good transport medium.
E.g.
o blood is ≈50% water
o plants transport minerals dissolved in water from the soil to the leaves and
disaccharides dissolved in water from leaves to other areas (roots, stem,
flowers etc.)
o Water is a major constituent in lungs (90%) and brain (70 %)
o Water is part of the fat tissue (25%) and bones (20%)
2. High Specific Heat (specific heat of fusion and vaporization)
 Heat capacity: the amount of energy to raise the temperature of a standard amount
of substance by 1oC
 Hydrogen bonds absorb heat when they break and release heat when they form,
minimizing temperature changes
 Water stabilizes body temperature as well as that of the environment
o Freezing (releases heat) and thawing (absorbs heat) does a great deal to
moderate the environment
 It takes a great deal of energy to heat 1 mol of water 10C
o The large amount of water in an organism absorbs or releases heat without
radically changing the temperature of the organisms
 Water readily transmits heat from one region to another
o Large temperature changes are unlikely
3. High Boiling and Freezing Point
 There is a large (100 0C) difference between the melting and the boiling points
o A vast array of living organisms are found living between those two extremes
 All H bonds must break to change from liquid to gas
9
SBI 3U7
The Chemical Basis of Life
o In natural habits on Earth, water rarely boils
 Water is less dense as it cools to freezing point, ice forms at surface
o Ice that forms on surface of lakes and seas insulates the water
underneathliving organisms can survive there.
4. High Heat of Evaporation (Water as a Coolant)
 Many hydrogen bonds must be broken for water to evaporate; because of
remarkable strong intermolecular attractions b/w water molecules, it requires a
great deal of energy (in the form of heat) to evaporate water
o The evaporation of water cools body surfaces
o E.g. transpiration in plants and perspiration in animals and humans
5. Water is Transparent
 Light penetrates water
plants can live in water b/c can receive light for photosynthesis process.
light can reach structures inside living organisms such as chloroplast in plant cells
and the retina in the human eye.
6 Lower Density of Ice (Ice Floats)
 Lakes do not freeze because ice is less dense than waterit floats
 Water is an anomaly in that it is less dense in its solid form
o While most liquids become solids when compressed, water does not (if you put
pressure on ice, it melts)
o The pressure increases as depth increases in the ocean; if water were like most
other substances solidification would occur at a certain depth
 The fact that ice melts as pressure is applied means that will stay liquid even at
temperature below freezing
o This property allows sea life to exist, otherwise ice would sink
7. Cohesion: (hydrogen bonds hold molecules together)
 Molecules are cohesive because of the remarkable strong intermolecular attractions
b/w water moleculeshigh surface tension (the force b/w the molecules of water
at the surface)
o E.g. A water strider walks on the surface of a pond
 Molecules are adhesive because water forms strong hydrogen bonds with other
polar or charged substances
o E.g.
-leaves pull water upward from the roots
-seeds swell and germinate (capillary action)
Chemical Transformation of Molecules
10
SBI 3U7
The Chemical Basis of Life
 Chemical Reactions are processes in which the structure or bonding of molecules
changes. These may occur in three ways:
o By the transfer of electrons in redox reaction
o By the transfer of protons in acid-base reactions
o By the transfer of atoms b/w molecules in breaking and making chemical bonds
 Chemical reactions do not create or destroy energy, but “changes” in energy
usually accompany chemical reactions. The energy associated with chemical
reactions can be measured by using the unit called calorie or joule (1cal= 4.134 J
and 1J= 0.239 cal)
Redox Reactions (Reduction Oxidation Reactions)
 Are chemical reactions which involve the transfer of electrons from an atom to
another
o Oxidation is loss of electrons
o Reduction is gain of electrons
Memory aid:
OIL - oxidation is loss
RIG – reduction is gain
 Oxidation and reduction always occur together (if one atom is oxidized during a
reaction then another must be reduced)
 A neutral element by itself has an oxidation number “0”
 When an atom loses electrons its oxidation number becomes more positive
o E.g.
H22H+ + 2eNa  Na+ + e When an atom gains electrons its oxidation number becomes more negative
o E.g.
Cl2+ 2e-  2ClO2+4H+ + 4e-  2 H2O

E.g. of a redox reaction
CuO + Mg  Cu + MgO
ionic compound
ionic compound
o If you rewrite this as an ionic equation, it turns out that the oxide ions are
spectator ions and you are left with:
Reduction by gain of eCu 2++ Mg Cu
+ Mg2+
Oxidation by loss of e-
11
SBI 3U7
The Chemical Basis of Life
o If you look at the equation above, the magnesium is reducing the copper (II)
ions by giving them e- from the magnesium to create the magnesium ions 
magnesium is a reducing agent
o Looking at it the other way around, the copper (II) ions are removing e- from
the magnesium to create magnesium ions the copper (II) ions are acting as an
oxidizing agent
DO NOT MIX THEM UP!




o Two ways to identify oxidizing and reducing agents in redox reactions
The First Way
The Second Way
An oxidizing agent oxidizes
 An oxidizing agent oxidizes
something else
something else
Oxidation is loss of e
 That means that the oxidizing agent
must be being reduced
That means that an oxidizing agent
takes e from the other substance
 Reduction is gain of eSo an oxidizing agent must gain e So an oxidizing agent must gain e
Redox reactions are involved in cellular respiration and photosynthesis
o In cells , sugars are oxidized in a series of controlled redox reactions in which
the energy is harnessed and stored in the chemical bonds of special molecules
o The metabolic processes (glycolysis, Kreb’s cycle and electron transport
phosphorilation, involve the transfer of electrons (at varying energy stages) by
redox reaction
AH2
AH2 is oxidized
NAD+
NAD+ is reduced
BH2
B is
reduced
NADH +H+ is oxidized
A
NADH + H+
B
Acids-Bases Reactions
An ACID
 Is a substance that adds HYDROGEN IONS to a solution and are sometimes
referred to as hydrogen ion donors
HCl(g)+H2O (l) H3O+(aq)+Cl- (aq)
 Acidic solutions have
12
SBI 3U7
The Chemical Basis of Life
o
o
o
o
+
-
more H ions than OH
sour taste
the ability to conduct electricity
the ability to turn blue litmus red
A BASE
o Is a substance that reduces HYDROGEN ION concentration in a solution
NaOH(s)  Na+(aq) + OH-(aq)
o Some bases such as ammonia (NH3), a product of decomposed plant an animal matter
acts as a base by biding a hydrogen ion from the solution resulting in the formation of
an ammonium ion.
NH3(g) + H+(aq)  NH4+(aq)
o Bases have
o more OH- ions than H+
o bitter taste and slippery feel
o the ability to conduct electricity
o the ability to turn red litmus blue
Does pure water contain only H2O molecules?
No!
Autoionization of Water
H2O + H2O  H3O+ +
OHHydronium Hydroxide
ion
ion
o Water is capable of being both an acid and a base,
and is unique in this respect
o Reactions in water do not proceed to completion
o Mixtures of weak acids and bases are common in biological systems
 The pH scale
o pH means power of HYDRONIUM ion concentration (H3O+)
o pH is a logarithmic scale ranging from zero (strong acid) to 14 ( strong base)
0
7
14
Very Acidic
Neutral
Very Basic
10-7M
10-14M
(Most biological fluids
E.g. blood 7.35-7.45)
When you add an acid, the pH gets smaller.
When you add a base, the pH gets larger.
o The pH of a solution is defined as the negative logarithm of the hydrogen
ion concentration expressed in moles per liter
1M
13
SBI 3U7
The Chemical Basis of Life
+
pH=-log [H ]
o For a neutral solution [ H+] is 10-7 M giving us :
pH = - log 10-7 = - (-7) =7
*Note: although the pH scale is based on H+ concentration, it also implies OHconcentration.Therefore a solution of pH 10 has a hydrogen ion concentration of 10 -10 M
and a hydroxide concentration of 10-4
o Applications:
How many times more acidic is pH 3 than pH 5?_____________
How many times more basic is pH 13 than pH 8?_____________
Calculate the concentration of H+ when pH=9 ________________
Calculate the pH of a solution when the concentration of hydrogen is 10-5M
 Strong and Weak Acids and Bases
Strong Acids
Ionize completely when dissolved in water
Weak Acids
Ionize partially when dissolved in water
1.3%
+
HCl(g)+H2O (l) H3O (aq)+Cl (aq)
CH3COOH(aq) +H2O(l)
H3O+(aq) +
CH3COO- (aq)
Strong Bases
Weak Bases
Ionize completely when dissolved in water
Ionize partially when dissolved in water
+
NaOH(s)  Na (aq) + OH (aq)
10%
NH3(aq)+H2O(l)
OH-(aq)+ NH4+( (aq)
Equilibrium is a condition in which opposing reactions occur at equal rates.
 Conjugate Acids and Bases
H+
CH3COOH (aq) +H2O (l)
Base
Acid
CH3COO (aq) + H3O+(aq)
Acid
Base
(proton donor) (proton acceptor)
H+
Conclusion:
Acetic acid, acetate, and hydronium ions, and water are conjugate acid-base pairs
14
SBI 3U7
The Chemical Basis of Life
Conjugate base
Conjugate acid
CH3COOH (aq) +H2O (l)
CH3COO- (aq) + H3O+(aq)
Conjugate acid
Conjugate base
 The Neutralization Reaction
o The reaction of an acid and a base to produce water and salt.
HCl(aq) + NaOH  H2O(l) + NaCl(aq)
 Acid-Base Buffers
o The internal pH of most living cells is 7.
o Even a slight change in pH can be very harmful because the structures and
functions of molecules in the cell are very sensitive to the concentration of H+
and OH- .
o The cells own metabolism produces acids and bases
o Many of the foods we eat are acidic. Absorbing these acids could affect the pH
balance of blood.
Q: How does the cell tolerate these acids and bases and still survive?
A: The answer is BUFFERS!
o Buffers: are substances that minimize changes in the concentration of H+ and
OH-.
 E.g. The blood pH is around 7.4
 A drop in pH (ACIDOSIS) or a rise in pH (ALKALOSIS) is
dangerous.
 A person would not survive more than few minutes
So, how do you survive?
o A buffer works by accepting H+ ions from the solution when they are in
excess and donating H+ ions to the solution when they have been depleted.
o In living organisms, buffers consist of conjugate acid-base pairs in
equilibrium.
o One of the most important buffers in human blood is carbonic acid
(H2CO3)
15
SBI 3U7
The Chemical Basis of Life
Breaking and Making Bonds (Condensation and Hydrolysis Reactions)
Condensation Reactions
 Are chemical reactions in which molecules of water are removed
 It permit the assembly of smaller molecules into larger molecules
 Are the basis for the assembly of building-block molecules into larger
macromolecules (anabolism)
 They require energy to proceed, thus it is costly to an organism to make
macromolecules
 Are endergonic reactions meaning that it will not occur spontaneously and require
energy to make it occur
 E.g.
CH3O-H + HO-CH3  CH3-O-CH3 + H2O
Hydrolysis Reactions
 Are chemical reactions in which molecules of water are added
 Are important in breaking apart the large molecules into smaller building-block
molecules during metabolism (catabolism)
 They always produce energy, therefore they are exergonic reactions
 Living organisms take advantage of this as a means of storing energy as chemical
energy
 Central to this processes is the use of ADP and ATP as
sinks and sources of chemical energy
ADP + P + 30 KJ  ATP
ATP ADP + P + 30 KJ
{ANSWER ON P. 23, Section 1.1 Questions #1-16}
16