The

Chemical
Basis of Life

A chemistry
review
 Classification of Matter
Everything
Matter Energy
(anything that takes
Up space and has mass)

Pure Substance Mixture

(made of more than
(made of only 1 type of particle) One type of particle

Element Compound Homogenous Heterogeneous

(2 or more elements (SOLUTION: particles spread
(cannot be broken down
chemically combined) out in one phase)
by simple chemical means)

Organic Colloid Suspension

Inorganic (Particles never (Particles settle out.
(contains carbon) (does not have carbon) settle out. Example: sand and water)
Example: cytoplasm)
 Elements
• 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

Campbell Biology (2005)

Table 2.1
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Effect of Element
Deficiencies

(a) Nitrogen deficiency (b) Iodine deficiency

 Structure of Matter

An atom
– Is the smallest unit of matter that still retains the properties of
an element

Protons – positive charge

- p+
Neutrons – no charge
- n0
Electrons – negative charge
- e-
 Isotopes
-same atomic number but different
atomic mass due to different number
of neutrons
 Radioactive isotopes
Spontaneously and give off particles
(decay) and energy
• Radioisotopes can be used to help
understand chemical and biological
processes in organisms.
• They can also be used in radiometric
dating which is useful in determining the
age of fossils
• They also have numerous medical
applications
 Uses in biology

Cancerous
throat
tissue

Figure 2.6
1. Brachytherapy
• radiation therapy
• radioactive isotopes in the
form of small pellets
(called seeds) are inserted into
cancerous tumours to destroy
cancer cells
• reducing the exposure of healthy tissue to
radiation.
• treatment of prostate cancer and cancers of the
head and neck. (Possibly lung cancer)
Radioimmunotherapy (RIT)
2. Radioimmunotherapy,
• doctors inject antibodies
that have isotopes
attached.
• Radioactive antibodies flow
through the bloodstream
and bind proteins on the
cancerous cells.
• RIT is used the treatment of
blood cell cancers, such as
leukemia and lymphoma. It
is also being looked at for
treatment of prostate,
colorectal and pancreatic
cancers.
• A solution of phosphate, containing
radioactive phosphorus-32, is
injected into the root system of a
plant.
• Since phosphorus-32 behaves
identically to that of phosphorus-31,
the more common form of the
element, it is used by the plant in the
same way.
• A Geiger counter is used to detect
the movement of the radioactive
phosphorus-32 throughout the plant.
• This information helps scientists
understand the detailed mechanism
of how plants utilized phosphorus to
grow and reproduce.
 Half Life
-the time it take for half of the nuclei in a
radioactive sample to decay
 Electron shells and orbitals
Orbitals: volumes of space around the nucleus
where electrons are most likely found

Electron orbitals.
Each orbital holds
up to two electrons. x Y

Z
1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals
Electron-shell diagrams.
Each shell is shown with
its maximum number of
electrons, grouped in pairs.

(a) First shell (b) Second shell (c) Neon, with two filled shells
(maximum (maximum (10 electrons)
Figure 2.9 2 electrons) 8 electrons)
Campbell (2005)
Valence electrons are those electrons that are
available for bonding.
The number and arrangement of its valence electrons
determine behaviour of the atom.
 Chemical Bonds
• Atoms react to achieve stability
• Results in the release of energy
• As atoms combine to complete their
outer shell they form chemical bonds
• During bonding an energy exchange
occurs and atoms assume a more
stable configuration
 Ionic and Molecular Compounds
• Formation of sodium chloride:
 
Na  + Cl  Na+ [ Cl ]






 

• Formation of hydrogen chloride:

 
H + Cl

 H Cl





 

A metal and a nonmetal transfer electrons

to form an ionic compound. Two nonmetals
share electrons to form a molecular
(covalent) compound.
 Types of Chemical Bonds

Electronegativity
• is a measure of an
atom's ability to attract
a shared electron pair
when it is participating
in a covalent bond with
another atom

The Pauling scale of

electronegativity
 Electronegativity
• nonpolar bond: electrons are shared equally

H2,
Cl2:

• polar bond: electrons are shared unequally

because of the difference in electronegativity.

HCl:
 Bond Polarity
A polar bond can be pictured using
partial charges:
+ 
H Cl  = 0.9
2.1 3.0
Electronegativity
Difference Bond Type
0 - 0.5 Nonpolar
0.5 – 1.7 Polar
1.7  Ionic
 Intramolecular vs
Intermolecular forces
Intramolecular Intermolecular
• Bonds that hold (also known as van der
Waals forces)
atoms of a molecule
• Forces of attraction
together
between molecules
• Example: Ionic, • Example: dipole-dipole
covalent bonds forces, London forces,
Hydrogen bonds
 London Forces
• Weak forces of attraction between all atoms
and molecules
• Help hold nonpolar molecules to one another
 Dipole-dipole forces
• Hold polar molecules
together
• Stronger than
London forces
 Hydrogen bonds
• Strongest of the
three
intermolecular
bonds
• Occurs between a
hydrogen of one
molecule and a very
electronegative
atom of another
neighboring
molecule (N, O, F)
 Properties of Water

1. Water is a Versatile Solvent

• More substances dissolve in water than
any other liquid
• Reason: Water is a polar molecule;
water molecules provide partial positive
and negative charges to which other
polar molecules can attach
 2. Cohesiveness of Liquid Water
• Water molecules stick
together due to hydrogen
bonds
• Allows for high surface
tension
– Causes water to bead into
spheres
• Capillary action
– Water can move up against
gravity in plants (xylem)
 3. High Specific Heat
Specific Heat – amount of heat
absorbed or lost for 1 g of that
substance to change its temperature
by 1° C
Water has a high specific heat
capacity; it resists change due to
hydrogen bonding
It helps organisms maintain a constant
body temperature.
4. High Heat of Vaporization
Heat of Vaporization –
quantity of heat a liquid
must absorb for 1 g of it
to be converted from
liquid to gas
Water: 540 cal/g (high)
Evaporative Cooling: enables
animals to dissipate heat
by evaporating water
 5. Freezing and Expansion of
water
Water is less dense as a solid than a liquid
due to hydrogen bonding (ice floats!)

Allows fish and other aquatic organisms

to survive in winter
 Hydrogen Ion
Concentrations
• aqueous environments of biological systems
have [H+] ( Hydrogen ion concentration)
that remain remarkably constant.
• Maintenance of appropriate [H+] is vitally
important for the life of any organism
because biochemical reactions are highly
sensitive to fluctuations in the
concentration of this ion.
 Acids and Bases
An acid is any substance that increases the hydrogen ion
concentration of a solution (more H+ ions)

A base is any substance that reduces the hydrogen ion

concentration of a solution (more OH- ions)
• pH is defined as
the negative
logarithm of the
hydrogen ion
concentration
• pH=7 is neutral
• pH  7 means
high H+
• pH > 7 means
high OH-
Relationship between pH and Hydrogen Ion
Concentration
 Characteristics
Acids Bases
• neutralize bases • neutralize acids
• turn the indicator, blue • turn the indicator,
litmus, red red litmus, blue
• decompose carbonates, • absorb CO2, forming
producing CO2 and H2O carbonates
acid + carbonate- CO2 and H2O + ‘salt’ base + CO2 - carbonate
• dissolve active metals to • feel slippery
produce hydrogen gas • taste bitter
• taste sour • can donate a
• can donate a hydrogen ion hydroxide ion
 Hydronium Ion
In aqueous solution, an acid dissolves to produce a
hydronium ion, H3O+, also could be written in short
form as a proton, H+
H2O
HA  H O
2
 H3O+ + A-  H+ + A-
 Neutralization Reaction

Acid + Base --- Salt + water

HA + BOH ---- AB + H2O
Ex.

HCl + NaOH  NaCl + H2O

•It is critical that the
pH of blood
remains constant
•seemingly small
changes of ±0.2-
0.4 of a pH unit
result in serious
medical conditions
which, if not
corrected, can lead
to death.
 Buffers
•Are substances that minimize changes in the
concentrations of hydrogen and hydroxide ions in a
solution
•Consist of an acid-base pair that reversibly
combines with hydrogen ions

Example:
CH3COOH    < -------- >    CH3COO-    +   H+

The acetic acid molecule (CH3COOH) acts as a store of base

and acid ions.
The acetate ion (CH3COO-) acts like a base which accepts H+
and neutralizes them.
The hydrogen ion (H+) acts like an acid which accepts OH- and
neutralizes them.
BUFFER DATA
 Questions to Consider
1.  Explain why it is so important to maintain a specific
and constant pH in the human body.
2.  How does the concentration of H ions vary in acids
and bases?
3.   If pH changes from a pH of 8 to a pH of 10, how
does the H+ concentration change?
4. What is the formula for the hydronium ion? How,
exactly, is it formed?
5.  Define and describe a neutralization reaction.
6. Describe the importance of buffers in our bodies.
Why can we NOT function without them?
 Homework
• Review the chemistry found in biology in
the first part of the textbook . A link is
available on the class website.
• Better yet, read ahead!