CHAPTER 2

CHEMICAL BASIS OF LIFE

CONTENT
 Atoms
 Elements

 Chemical compounds

 Molecules, formulas

 Ionic compounds

 Chemical reactions

 Acid and bases

The hierarchy of biological organizations
WHY LEARNING THIS CHAPTER IS IMPORTANT?
 Living and non-living things have the same kind
of atoms joined together as molecules.
 However, those molecules may differ in their
proportion of elements and how the atoms of
those elements are arranged.
 Life’s unique organization starts with the
properties of atoms that make up certain
elements.
 Thus, some basic chemistry knowledge is crucial
for understanding organisms.
ATOMS
 Atoms are the building blocks of all substances.
 Each consists of smaller subatomic particles:
◦ Protons carry +ve charge
 Their quantity is called the atomic number (unique for
each element).
◦ Electrons carry –ve charge
 Their quantity is equal to that of the protons
◦ Neutrons have no charge
 Protons and electrons are responsible to attract
or repel other subatomic particles.
 Atoms differ from one another based on the
number of subatomic particles.
ATOMS
 Protons + neutrons = atomic mass

◦ Expressed by the atomic mass unit (amu), also

known as dalton

◦ Indicated by a superscript to the left of the

chemical symbol
 Eg: 12C, 14N -Check periodic table
ATOMS
CHARACTERISTICS OF PROTONS, NEUTRONS,
ELECTRONS
ELEMENTS
 Elements are pure substances; each consists
entirely of atoms with the same number of
protons (this is called atomic number).
 Exp: A chunk of carbon contains only carbon atoms,
all of which have 6 protons in their nucleus.
 The body is a collection of elements.
 Oxygen, hydrogen, carbon, and nitrogen are the
most abundant of life.
 Quantities of elements in the body vary.
ELEMENTS
FUNCTIONS OF ELEMENTS
THE PERIODIC TABLE
 Is an arrangement of elements based on their
atomic number.
 Those in the same column of the table have the
same number of electrons available for
interactions with other atoms, and behave in
similar ways.
 This permits chemists to predict the chemical
behavior of an element.
ISOTOPES
 Isotopes are variant forms of atoms.
 Atoms with the same number of protons but a
different number of neutrons.
 Means that isotopes have different …..????
 Example, carbon have six proton and can have
six, seven, or eight neutrons are called isotopes
(12C, 13C, 14C).
CARBON ISOTOPES
RADIOACTIVE ISOTOPES
 In most cases, elements like to have an equal number
of protons and neutrons, as this makes them the most
stable.
 Stable atoms have a binding energy that is strong
enough to hold the protons and neutrons together.
 However, an additional neutron or two may cause the
atom to become unstable.
 In an unstable atom, the nucleus changes by giving off
a neutron to get back to a balanced state.
 As the unstable nucleus changes, it gives off radiation
and is said to be radioactive.
 Radioactive isotopes are often called radioisotopes.
RADIOACTIVE ISOTOPES
 Radioactive isotopes with an unstable nucleus that
decays, emitting alpha, beta and gamma rays.
 Decay occurs independent of external factors
◦ Temperature, pressure, or chemical bonds with
other atoms.
RADIOACTIVE ISOTOPES
 This process occurs at a constant rate, and allows
researchers to use this predictability to estimate the
age of rocks and fossils by their radioisotope content.
 Some radioisotopes can be used as tracers to follow
the path of an atom in a series of reactions.
 Example: Radioisotopes used in PET (Positron
Emission Tomography) to follow a particular
chemical in the body and determine its patterns of
metabolism.
PET TECHNOLOGY IN RADIOPHARMACEUTICAL
ELECTRONS AND ENERGY LEVELS
 Electrons travel in different orbitals (shells).
 Orbitals occupying shells around the nucleus.
 Orbitals closest to the nucleus are lowest in energy
level.
 Orbitals further from the nucleus have higher energy
levels.
ELECTRONS AND ENERGY LEVELS
 Maximum number of electrons that can be
accommodated in a shell is given by 2n2 where n =
shell number.
 The shell closest to the nucleus has 1 orbital holding a
maximum of 2 electrons.
 The next shell can have 4 orbitals with 2 electrons
each for a total of 8 electrons.
WHY ATOMS INTERACT
 Orbitals are filled with electrons from the closest
to the furthest orbitals.
 If the outermost orbital (shell) has vacancies, it
will tend to interact with other atoms by giving
up, acquiring, or sharing electrons until the
vacancy is filled.
ATOMS AND IONS
FROM ATOMS TO MOLECULES
 Bonds occur when atoms tend to reach the state in
which they have no vacancies.
 A chemical bond is an attractive force that arises
between atoms when their electrons interact.
 A molecule forms when two or more atoms of the same
or different elements join in chemical bonds.
 A compound consists of two or more different elements.

 In a mixture, two or more elements interact, and their

proportions may vary.
CHEMICAL BONDS
 Chemical bonds are forces of attraction that hold
atoms of a compound together.
 Atoms with ―unfilled‖ orbitals in their outermost shell
(valence shell) tend to be reactive with other atoms.
 The number or the distribution of its electrons
changes when an atom gives up, gains, or shares
electrons.
CHEMICAL REACTIONS
 Can be described by chemical equations
 Reactants are written on the left
 Products are written on the right
 Reactions can proceed simultaneously in both
directions
 At dynamic equilibrium, forward and reverse rates of
reaction are equal.

 Example:

HCl + NaOH ⇄ NaCl + H20

Reactant Products
CHEMICAL FORMULA
 A chemical formula describes the chemical composition
of a substance
 Empirical formula (Simplest formula)
 Molecular formula
 Structural formula
CHEMICAL FORMULA
Empirical Molecular Structural
Substance
formula formula formula

Water H2O H2O H-O-H

Methane
CH4 CH4

Glucose
CH2O C6H12O6
MOLECULAR MASS
 Sum of the atomic masses of the component atoms of
a single molecule.
 One mole is the amount of an element or compound
whose mass in grams is equivalent to its atomic or
molecular mass.
 The mole allows for comparison of atoms and
molecules of very different mass.
WHAT HAPPENS WHEN ATOMS INTERACT
Ionic Bonding
 Particle with one or more units of electrical charge is
called ion.
 +vely charged ions: Cations
 -vely charged ions: Anions
 A measure of an atom’s ability to pull electrons away
from another atom is called electronegativity.
Electronegativity is dependent on: Atom’s size (?? How?)
and electron vacancies.
 A weakly electronegative atoms tends to lose one of its
electrons, thus becoming a +vely charged ion.
 In contrast, a strong electronegative atom tends to gain
an electron, thus becoming a –vely charged ion.
 Cations and anions are involved in biological processes,
such as muscle contraction.
Ionic Bonding
 Two atoms with a large difference in electronegativity
may stay together in a ionic bond, which is a strong
mutual attraction of two oppositely charged ions.
Covalent Bonding
 In a covalent bond, two atoms share a pair of
electrons.
 This bond usually form between atoms with similar
electronegativity and unpaired electrons.
 By sharing electrons, each atom’s vacancy becomes
partially filled.
 Covalent bonds are usually much stronger than ionic
bonds.
 In a nonpolar covalent bond, atoms share electrons
equally.
 In a polar covalent bond, atoms share the electron
unequally, resulting in a slight difference in charge
between the two poles of the bond; water is an
example.
Covalent Bonding
Covalent Bonding
Example of polar bonds
Example of non-polar bonds
Hydrogen Bonding
 This bonding always form between polar regions of
two molecules or regions of the same molecule.
 A hydrogen bond is an attraction between a hydrogen
atom and an electronegative atom, both of which are
taking part in separate polar covalent bonds.
 Hydrogen bonds are not chemical bonds as they do not
make molecules out of atoms.
 These bonds are weaker than ionic or covalent bonds,
easily forming and breaking (but strong enough to
help hold molecules in 3-D shapes).
 These bonds are critical to life-
◦ impart structure to liquid water
◦ stabilize nucleic acids and other large organic
molecules
Hydrogen Bonding
Hydrogen bonds
WATER’S LIFE-GIVING PROPERTIES
Water is so essential for life because of its unique
hydrogen bonding properties which includes:
1. Polarity of the water molecule
2. Water’s temperature-stabilizing effects
3. Water’s solvent properties
4. Water’s cohesion
1. Polarity of the Water Molecule:
 Water is a polar molecule as it has a slightly
negative charge end (oxygen) and a slightly positive
charge end (hydrogen) due to unequal sharing of
electrons.
 The polarity of each water molecule attracts other
water molecules, and hydrogen bonds form.
 Water also forms hydrogen bonds with other polar
molecules.
 Polar substances are hydrophilic (water loving)

 Non-polar substances are hydrophobic (water

dreading, like oils) and are repelled by water.
Slightly negative (-) charge on the
oxygen atom (electronegative)
_

O The positive and

negative charges
balance each
other; overall, the
H H
molecule carries
+ +
no charge

Slightly positive (+) charge

on the hydrogen atom
2. Water's Temperature-Stabilizing Effects:
 Molecules move faster as they absorb heat.

 Temperature is a way of measuring the energy of

molecular motion.
 Hydrogen bonding restricts the movements of
individual water molecules by absorbing some of the
energy.
 Water can absorb more heat before it gets hotter due
to the extensive hydrogen bonding presence in water
molecules.
 Water functions as a heat reservoir (stabilizing the
surrounding air temperature).
2. Water's Temperature-Stabilizing Effects:
 At higher water temperatures, the input of heat
energy increases molecular motion thus:
 Hydrogen bonds are broken faster than they form,
and water molecules escape into the air, thus cooling
the surface (evaporation).
 At temperatures below freezing point, water
molecules do not move enough to break hydrogen
bond:
 Water molecules are locked up in the bonding
patterns of ice.
Hydrogen bonds form as fast as they
break

Hydrogen bonds break and form rapidly

Hydrogen bonds in rigid lattice  Water

molecule farther apart and less dense
3. Water's solvent properties:
 Solvent is a substance that dissolves other substances.

 Water is an excellent solvent.

 The solvent properties of water are greatest with

respect to polar molecules with which they interact by
pulling on ions or molecules, dispersing them.
 ―Spheres of hydration‖ are formed around the solute
(dissolved) molecules.
Salt

Water

Sphere of
hydration
around ions.
Water molecules
that surround
an ionic solid
pull its atom
apart, thereby
dissolving them
4. Water's cohesion:
 Cohesion means molecules resist separating from one
another.
 Hydrogen bonding of water molecules exert a
continuous pull on individual water molecules, thus
resist separating and imparts surface tension.
 Cohesion contributes to pulling water through plant
tissues.
ACIDS AND BASES
The pH Scale
 pH is a measure of the H+ concentration in a solution;
the greater the H+ the concentration the lower the pH
scale.
 The scale extends from 0 (acidic) to 7 (neutral) to 14
(basic).
 A unit change in pH reflects a 10-fold change in H+
concentration.
pH values of the
common solutions
ACIDS AND BASES
 How to calculate pH, hydroxide ions and hydrogen
ions concentration?
 The equations are:
 pH = - log [H+]
 pOH = - log [OH-]

 Example 1:
 If an acid has an H+ concentration of 0.0001 M, find the
pH.
First convert the number to exponential notation, find the
log, then solve the pH equation.
 H+ = 0.0001M = 10-4; log of 10-4 = -4;
 pH = - log [ H+] = - log (10-4) = - (-4) = +4 = pH

 The purpose of the negative sign in the log

definition is to give a positive pH value.

ACIDS AND BASES
 Example 2:
 If the base has an OH- concentration of 0.001M, find
the pH.
 First find the pOH, (similar to finding the pH,) then subtract
the pOH from 14.
OH- = 0.001M = 10-3;
 pOH = -log [OH-] = -log (10-3) = +3 = pOH
 pH = 14 - pOH; pH = 14 - 3 = 11 = pH
How Do Acids and Bases Differ?
 Acid: A substance that releases hydrogen ions (H +) in
solution—for example, HCl.
 Bases: Substances that release ions such as (OH –) and
accept hydrogen ions when dissolved in water.
Salts and Water
 A salt is any compound that dissolves easily in water
and releases ions other than H+ and OH–.
 Salts are formed when an acid reacts with a base;
example: HCl + NaOH  NaCl + H2O.
 Salts dissociate into useful ions (examples: Na+ and
Ca++) in body fluids.
Buffers against shifts in pH:
 Buffers are chemicals, often weak acids or bases and
its salt, that help keep the pH of a solution stable.
 Buffer molecules act by combining with, or releasing,
H+ to prevent changes in pH.
 Bicarbonate (HCO3) is one of the body’s major buffers.