Chapter 2

Atoms and
Molecules

Lecture Presentations by
Nicole Tunbridge and
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Kathleen Fitzpatrick
A Chemical Connection to Biology

▪ Biology is the study of life

▪ Organisms and their environments are subject to
basic laws of physics and chemistry
▪ One example is the use of formic acid by ants to
protect themselves against predators and microbial
parasites

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Figure 2.1

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Concept 2.1: Matter consists of chemical
elements in pure form and in combinations
called compounds
▪ Organisms are composed of matter
▪ Matter is anything that takes up space and has mass

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Elements and Compounds

▪ Matter is made up of elements

▪ An element is a substance that cannot be broken
down to other substances by chemical reactions
▪ A compound is a substance consisting of two or
more elements in a fixed ratio
▪ A compound has characteristics different from those
of its elements

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Figure 2.2

Na Cl NaCl
Sodium Chlorine Sodium chloride

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The Elements of Life

▪ About 20–25% of the 92 natural elements are

required for life (essential elements)
▪ Carbon, hydrogen, oxygen, and nitrogen make up
96% of living matter
▪ Most of the remaining 4% consists of calcium,
phosphorus, potassium, and sulfur
▪ Trace elements are required by an organism in only
minute quantities

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Table 2.1

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Case Study: Evolution of Tolerance to Toxic
Elements
▪ Some elements can be toxic
▪ Some species can become adapted to environments
containing toxic elements
▪ For example, some plant communities are adapted to
serpentine+
▪ Chromium, Nıckel and Cobalt

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Figure 2.3

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Concept 2.2: An element’s properties depend
on the structure of its atoms
▪ Each element consists of unique atoms
▪ An atom is the smallest unit of matter that still
retains the properties of an element

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Subatomic Particles

▪ Atoms are composed of subatomic particles

▪ Relevant subatomic particles include
▪ Neutrons (no electrical charge)
▪ Protons (positive charge)
▪ Electrons (negative charge)

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▪ Neutrons and protons form the atomic nucleus
▪ Electrons form a “cloud” of negative charge around
the nucleus
▪ Neutron mass and proton mass are almost identical
and are measured in daltons

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Figure 2.4

Cloud of negative Electrons

charge (2 electrons)
Nucleus − −

+ +
+ +

(a) (b)

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Atomic Number and Atomic Mass

▪ Atoms of the various elements differ in number of

subatomic particles
▪ An element’s atomic number is the number of
protons in its nucleus
▪ An element’s mass number is the sum of protons
plus neutrons in the nucleus
▪ Atomic mass, the atom’s total mass, can be
approximated by the mass number

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Isotopes

▪ All atoms of an element have the same number of

protons but may differ in number of neutrons
▪ Isotopes are two atoms of an element that differ in
number of neutrons
▪ Radioactive isotopes decay spontaneously, giving
off particles and energy

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The Energy Levels of Electrons

▪ Energy is the capacity to cause change

▪ Potential energy is the energy that matter has
because of its location or structure
▪ The electrons of an atom differ in their amounts of
potential energy
▪ An electron’s state of potential energy is called its
energy level, or electron shell

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Figure 2.6
(a) A ball bouncing down a flight
of stairs can come to rest only
on each step, not between steps.

Third shell (highest energy

level in this model)

Second shell (higher Energy

energy level) absorbed

First shell (lowest energy

level)
Energy
lost
Atomic
nucleus
(b)
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Electron Distribution and Chemical Properties

▪ The chemical behavior of an atom is determined by

the distribution of electrons in electron shells
▪ The periodic table of the elements shows the
electron distribution for each element

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Figure 2.7

Hydrogen 2 Atomic number Helium

1H He 2He
Atomic mass 4.00 Element symbol
First
3
shell
Electron
distribution
diagram
Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon
3Li 4Be 5B 6C 7N 8O 9F 10Ne

Second
shell

Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon

11 Na 12Mg 13AI 14SI 15P 16S 17CI 18Ar

Third
shell

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▪ Valence electrons are those in the outermost shell,
or valence shell
▪ The chemical behavior of an atom is mostly
determined by the valence electrons
▪ Elements with a full valence shell are
chemically inert

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Electron Orbitals

▪ 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

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Figure 2.8
First shell Second shell

x y
Neon, First
with two shell
filled shells z
(10 electrons) Second 1s orbital 2s orbital Three 2p orbitals
shell
(a) Electron distribution (b) Separate electron orbitals
diagram

1s, 2s, and

2p orbitals

(c) Superimposed electron orbitals

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Concept 2.3: The formation and function of
molecules depend on chemical bonding
between atoms
▪ Atoms with incomplete valence shells can share or
transfer valence electrons with certain other atoms
▪ These interactions usually result in atoms staying
close together, held by attractions called
chemical bonds

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Covalent Bonds

▪ A covalent bond is the sharing of a pair of valence

electrons by two atoms
▪ In a covalent bond, the shared electrons count as
part of each atom’s valence shell

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Figure 2.9_1
Hydrogen atoms (2 H)

+ +

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Figure 2.9_2
Hydrogen atoms (2 H)

+ +

+ +

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Figure 2.9_3
Hydrogen atoms (2 H)

+ +

+ +

+ +

Hydrogen
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molecule (H2)
▪ A molecule consists of two or more atoms held
together by covalent bonds
▪ A single covalent bond, or single bond, is the
sharing of one pair of valence electrons
▪ A double covalent bond, or double bond, is the
sharing of two pairs of valence electrons

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▪ The notation used to represent atoms and bonding is
called a structural formula
▪ For example, H—H
▪ This can be abbreviated further with a molecular
formula
▪ For example, H2

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Figure 2.10

Name and Electron Lewis Dot Space-

Molecular Distribution Structure and Filling
Formula Diagram Structural Model
Formula
(a) Hydrogen (H2)

H H

(b) Oxygen (O2)

O O

(c) Water (H2O)

O H

(d) Methane (CH4)

H

H C H

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Figure 2.10a

Name and Electron Lewis Dot Space-

Molecular Distribution Structure and Filling
Formula Diagram Structural Model
Formula
(a) Hydrogen (H2)

H H

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Figure 2.10b

Name and Electron Lewis Dot Space-

Molecular Distribution Structure and Filling
Formula Diagram Structural Model
Formula
(b) Oxygen (O2)

O O

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Figure 2.10c

Name and Electron Lewis Dot Space-

Molecular Distribution Structure and Filling
Formula Diagram Structural Model
Formula
(c) Water (H2O)

O H

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Figure 2.10d

Name and Electron Lewis Dot Space-

Molecular Distribution Structure and Filling
Formula Diagram Structural Model
Formula
(d) Methane (CH4)
H

H C H

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▪ Bonding capacity is called the atom’s valency
▪ Covalent bonds can form between atoms of the
same element or atoms of different elements
▪ A compound is a combination of two or more
different elements

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▪ Atoms in a molecule attract electrons to varying
degrees
▪ Electronegativity is an atom’s attraction for the
electrons in a covalent bond
▪ The more electronegative an atom is, the more
strongly it pulls shared electrons toward itself
▪ PAULİNG SCALE electronegativity
▪ H(2.2)<C(2.5)<N(3.04)<O(3.44)
▪ F(3.98)

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Bruice, Organic Chemistry | 7th Edition
▪ In a nonpolar covalent bond, the atoms share the
electron equally
▪ In a polar covalent bond, one atom is more
electronegative, and the atoms do not share
the electron equally
▪ Unequal sharing of electrons causes a partial
positive or negative charge for each atom
or molecule

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Figure 2.11

δ−
δ−
O

H H
δ+ δ+
H 2O

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Ionic Bonds

▪ Atoms sometimes strip electrons from their bonding

partners
▪ An example is the transfer of an electron from
sodium to chlorine
▪ After the transfer of an electron, both atoms have
charges
▪ A charged atom (or molecule) is called an ion

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Figure 2.12_1

Na Cl

Na Cl
Sodium atom Chlorine atom

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Figure 2.12_2

+ −

Na Cl Na Cl

Na Cl Na+ Cl−
Sodium atom Chlorine atom Sodium ion Chloride ion
(a cation) (an anion)
Sodium chloride (NaCl)

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Animation: Ionic Bonds

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▪ A cation is a positively charged ion
▪ An anion is a negatively charged ion
▪ An ionic bond is an attraction between an anion and
a cation

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▪ Compounds formed by ionic bonds are called ionic
compounds, or salts
▪ Salts, such as sodium chloride (table salt), are often
found in nature as crystals

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Figure 2.13

Na+
Cl−

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Weak Chemical Interactions

▪ Most of the strongest bonds in organisms are

covalent bonds that form a cell’s molecules
▪ Many large biological molecules are held in their
functional form by weak bonds
▪ The reversibility of weak bonds can be an advantage

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Hydrogen Bonds

▪ A hydrogen bond forms when a hydrogen atom

covalently bonded to one electronegative atom is
also attracted to another electronegative atom
▪ In living cells, the electronegative partners are
usually oxygen or nitrogen atoms

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Figure 2.14
δ– δ+

Water (H2O) δ–

δ+
Hydrogen bond
δ–

Ammonia (NH3)

δ+ δ+

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δ+
Van der Waals Interactions

▪ If electrons are not evenly distributed, they may

accumulate by chance in one part of a molecule
▪ Van der Waals interactions are attractions between
molecules that are close together as a result of
these charges

[Link]

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▪ Collectively, such interactions can be strong, as
between molecules of a gecko’s toe hairs and a wall
surface

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Bio-inspired designs

[Link]
Molecular Shape and Function

▪ A molecule’s size and shape are key to its function

▪ A molecule’s shape is determined by the positions of
its atoms’ orbitals
▪ In a covalent bond, the s and p orbitals may
hybridize, creating specific molecular shapes

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Figure 2.15
z Four hybrid orbitals
s orbital Three p orbitals

y
Tetrahedron
(a) Hybridization of orbitals

Space-Filling Ball-and-Stick Hybrid-Orbital Model

Model Model (with ball-and-stick
model superimposed)

O Unbonded
O
H H
electron
H H
104.5º pairs
Water (H2O)

H H

C C
H H H H
H H
Methane (CH4)

(b) Molecular-shape models

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Figure 2.15a

z Four hybrid orbitals

s orbital Three p orbitals

y
Tetrahedron

(a) Hybridization of orbitals

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Figure 2.15b

Space-Filling Ball-and-Stick Hybrid-Orbital Model

Model Model (with ball-and-stick
model superimposed)

O Unbonded
electron O
H H pairs H
104.5º H

Water (H2O)

H H

C C
H H H H
H H
Methane (CH4)

(b) Molecular-shape models

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▪ Molecular shape determines how biological
molecules recognize and respond to one another
▪ Opiates, such as morphine, and naturally produced
endorphins have similar effects because their
shapes are similar and they bind the same receptors
in the brain

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Figure 2.16
Carbon Nitrogen
Hydrogen Sulfur
Natural
Oxygen
endorphin

Morphine

(a) Structures of endorphin and morphine

Natural
endorphin
Morphine

Endorphin
Brain cell receptors
(b) Binding to endorphin receptors
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Concept 2.4: Chemical reactions make and
break chemical bonds
▪ Chemical reactions are the making and breaking of
chemical bonds
▪ The starting molecules of a chemical reaction are
called reactants
▪ The final molecules of a chemical reaction are called
products

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Figure 2.UN03

2 H2 O2 2 H2O

Reactants Chemical Products

reaction

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▪ Photosynthesis is an important chemical reaction
▪ Sunlight powers the conversion of carbon dioxide
and water to glucose and oxygen
6 CO2 + 6 H2O → C6H12O6 + 6 O2

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Figure 2.17

Leaf Bubbles of O2

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▪ All chemical reactions are theoretically reversible:
Products of the forward reaction become reactants
for the reverse reaction
▪ The two opposite-headed arrows indicate that a
reaction is reversible
3 H2 + N ⇌ 2 NH3

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▪ Chemical equilibrium is reached when the forward
and reverse reactions occur at the same rate
▪ At equilibrium the relative concentrations of
reactants and products do not change

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