Matter consists of chemical elements in pure form and in

combination called compounds,

An element’s properties depend on the structure of its atoms,
The formation and fuction of molecules depend on chemical
bonding between atoms.
Overview:
A Chemical Connection to Biology
• Biology is a multidisciplinary science
• Living organisms are subject to basic laws of
physics and chemistry
• One example is the use of formic acid by ants
to maintain “devil’s gardens,” stands of Duroia
trees

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

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

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

1.1 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

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2-3

Figure 2.3 The emergent properties of a

compound

Sodium Chlorine Sodium

chloride
1.2 Essential Elements of Life

• About 25 of the 92 elements are essential to

life
• Carbon (C), hydrogen (H), oxygen (O2), and
nitrogen (N) make up 96% of living matter
• Most of the remaining 4% consists of calcium
(Ca), phosphorus (P), potassium (K), and
sulfur (S)
• Trace elements are those required by an
organism in minute quantities
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Table 2-1
Fig. 2-4

Figure 2.4 The effects of essential-element deficiencies

Nitrogen-rich soil Nitrogen-poor soil

(a) Nitrogen deficiency (b) Iodine deficiency

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

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

2.1 Subatomic Particles

• Atoms are composed of subatomic particles

• Relevant subatomic particles include:

– Neutrons (no electrical charge)
– Protons (positive charge)
– Electrons (negative charge)
• Neutrons and protons form the atomic nucleus
• Electrons form a cloud around the nucleus
• Neutron mass and proton mass are almost
identical and are measured in daltons
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-5

Figure 2.5 Simplified models of a helium (He)

Cloud of negative atom
charge (2 electrons) Electrons

Nucleus

(a) (b)
2.2 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

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

2.3 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
• Some applications of radioactive isotopes in
biological research are:
– Dating fossils
– Tracing atoms through metabolic processes
– Diagnosing medical disorders
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
 Fig. 2-7

Figure 2.7 A PET (positron emission

tomography) scanner, a medical use for
radioactive isotopes

Radioactively
labeled
glucose

Cancerous
throat
tissue
2.4 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

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2-8
(a) A ball bouncing down a flight
of stairs provides an analogy
for energy levels of electrons

Figure 2.8 Energy levels of an atom’s

electrons
Third shell (highest energy
level)

Second shell (higher Energy

energy level) absorbed

First shell (lowest energy

level)
Energy
lost
Atomic
nucleus
(b)
2.5 Electron Distribution and Chemical Properties
• The chemical behavior of an atom is determined by
the distribution of electrons in the atom’s electron
shells
• The periodic table of the elements shows the
electron distribution for each element
• 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
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 2.9 Electron distribution diagrams for the first
18 elements in the periodic table
2.6 Electron Orbitals

• The electron shells of an atom are considered

as concentric circles of electrons around the
nucleus, similar to planets orbiting the sun

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

 Fig. 2-10-4
Neon, with two filled shells (10 electrons)
(a) Electron-distribution
diagram

First shell Second shell

(b) Separate electron
orbitals

x y
Figure 2.8 Electron
orbitals z
1s orbital 2s orbital Three 2p orbitals

(c) Superimposed electron

orbitals

1s, 2s, and 2p orbitals

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

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

3.1 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

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2-11
Hydrogen
atoms (2 H)

Hydrogen
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
• 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
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-12
Name and Electron- Lewis Dot Space-
Molecular distribution Structure and filling
Formula Diagram Structural Model
Formula

(a) Hydrogen (H2)

(b) Oxygen (O2)

(c) Water (H2O)

(d) Methane (CH4)

Figure 2.12 Covalent bonding in four

• 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
• Bonding capacity is called the atom’s valence

• Electronegativity is an atom’s attraction for the

electrons in a covalent bond
• The more electronegative an atom, the more
strongly it pulls shared electrons toward itself

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

• 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

Because oxygen is more

electronegative than
hydrogen, shared electrons
are pulled more toward
oxygen

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

3.2 Ionic Bonds

• Atoms sometimes strip electrons from their

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

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2-14-2

Each resulting ion has a

The lone valence electron of a sodium completed valence shell. An
atom is transferred to join the 7 valence ionic bond can form between
electrons of a chlorine atom the oppositely charged ions

Na Cl Na Cl

Na Cl Na+ Cl–
Sodium atom Chlorine atom Sodium ion Chloride ion
(a cation) (an anion)

Sodium chloride (NaCl)

• 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
• Compounds formed by ionic bonds are called
ionic compounds, or salts
• Salts, such as sodium chloride (NaCl) (table
salt), are often found in nature as crystals
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-15

Na+
Cl–
3.3 Weak Chemical Bonds

• Most of the strongest bonds in organisms are

covalent bonds that form a cell’s molecules
• Weak chemical bonds, such as ionic bonds and
hydrogen bonds, are also important
• Weak chemical bonds reinforce shapes of large
molecules and help molecules adhere to each
other

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

3.3.1 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

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2-16
 +

Water (H2O)

Hydrogen bond
results from the
attraction
+ between the
partial positive
 charge on the
hydrogen atom
of the water and
Ammonia (NH3) the partial
negative charge
on the nitrogen
atom of
+ + ammonia

+
3.3.2 Van der Waals Interactions

Temporary dipoles are formed due to the

unbalanced distribution of electrons in the molecule

The induced dipole interaction network is formed by

the transient dipole
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• Van der waals is the weak interaction
between electrically neutral molecules that
stay very close to each other.

• The interaction perfomed by the attraction

between electron-rich regions of one
molecule and electron-poor regions of
another.
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

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

• 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
• Some chemical reactions go to completion: all
reactants are converted to products
• All chemical reactions are reversible: products of
the forward reaction become reactants for the
reverse reaction
• Chemical equilibrium is reached when the forward
and reverse reaction rates are equal
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-19
Fig. 2-UN3

REVIEW

Nucleus

Protons (+ charge)
determine element Electrons (–
charge) form
Neutrons (no negative cloud
charge) and determine
determine isotope Atom chemical behavior
Fig. 2-UN5

Single Double
covalent bond covalent bond
Fig. 2-UN6

Ionic bond

Electron
transfer
forms ions

Na Cl Na+ Cl–
Sodium atom Chlorine atom Sodium ion Chloride ion
(a cation) (an anion)
Fig. 2-UN9
Fig. 2-UN10
Fig. 2-UN11
You should now be able to:

1. Identify the four major elements

2. Distinguish between the following pairs of
terms: neutron and proton, atomic number
and mass number, atomic weight and
mass number
3. Distinguish between and discuss the
biological importance of the following:
nonpolar covalent bonds, polar covalent
bonds, ionic bonds, hydrogen bonds, and
van der Waals interactions

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings