Chapter 2

The Chemical Context of Life

You will 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

Fig. 1-4

oIn the previous chapter, we discussed the levels of

biological organization
The biosphere
Cells
10 m
Organs and
organ systems
Cell
Ecosystems
Organelles
Communities
1 m

Atoms

Tissues

50 m

Molecules

Populations
Organisms

oIn Chapter 2, our discussions will be focused at the lowest

level of biological organization the chemical components
that make up matter

Concept 2.1: Matter consists of

chemical elements in pure form and in
combinations called compounds
o Organisms are composed of matter
o Matter is anything that takes up space and has
mass

oCopyright 2008 Pearson Education, Inc., publishing as Benjamin

Cummings

Elements and Compounds

o Matter is made up of elements
o An element is a substance that cannot be
broken down to other substances by
chemical reactions
o A compound is a substance consisting of
two or more (2+) elements in a fixed ratio
o A compound has characteristics different
from those of its elements
o The elements are bound together to become
something new and novel

Fig. 2-3

ELEMENT

Sodium

Grey Metal

+ ELEMENT = COMPOUND

Chlorine

Green Gas

Sodium
chloride

White crystal

Compounds = Total Different

Material
Components (elements) of compound cannot
be separated, without a Chemical Reaction
NOT a compound

Oxygen

Hydrogen

Water
Compound

Essential Elements of Life

o About 25 of the 92 elements are essential to life
o Carbon, Hydrogen, Oxygen, and Nitrogen make up
96% of living matter
o Most of the remaining 4% consists of Calcium,
Phosphorus, Potassium, and Sulfur
o Trace elements are those required by an organism in
minute quantities

Table 2-1

Concept 2.2: An elements properties

depend on the structure of its atoms
o Each element consists of unique atoms
o 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

Subatomic Particles
o Atoms are composed of subatomic particles
o Relevant subatomic particles include:
oNeutrons (no electrical charge)
oProtons (positive charge)
oElectrons (negative charge)

Behavior of Charges
o Opposite charges (positive & negative)
attract each other
o Same charges (positive & positive,
negative & negative) repel (push away)
each other

o Neutrons and protons form the atomic

nucleus
o Electrons form a cloud around the nucleus
o Neutron mass and proton mass are almost
identical and are measured in daltons
(electrons are very, very small)

Nucleus
Protons (+ charge)
determine element
Neutrons (no charge)
determine isotope

Electrons ( charge)
form negative cloud
and determine
chemical behavior
Atom

(Atoms have a lot of empty space)

Atomic Number and Atomic Mass

o Atoms of the various elements differ in number
of subatomic particles
o An elements atomic number is the number
of protons in its nucleus
o Defines an Element

o An elements mass number is the sum of

protons + neutrons in the nucleus
o Atomic mass, the atoms total mass, can be
approximated by the mass number
Mass Number
Atomic Number

1. Protons = 4
Neutrons = 4
Electrons = 4
Atomic # = ?
Mass # = ?

# of protons?
# of neutrons?

2. Protons = 6
Neutrons = 5
Electrons = 6
Atomic # = ?
Mass # = ?

3. Protons = 8
Neutrons = 5
Electrons = 8
Atomic # = ?
Mass # = ?

# of protons?
# of neutrons?

1. Protons = 4
Neutrons = 4
Electrons = 4
Atomic # = 4
Mass # = 8

# of protons? 2
# of neutrons? 2

2. Protons = 6
Neutrons = 5
Electrons = 6

3. Protons = 8
Neutrons = 5
Electrons = 8

Atomic # = 6
Mass # = 11

Atomic # = 8
Mass # = 13

# of protons? 3
# of neutrons? 4

Isotopes
o All atoms of an element have the same number of
protons (atomic number), but may differ in number of
neutrons
o Isotopes are two atoms of an element that differ in
number of neutrons, thus different mass numbers
o Generally, behave similarly to each other
Atomic Number
Mass Number

o Radioactive isotopes decay

spontaneously, giving off particles and
energy
o Sometimes nucleus gets so big, it falls apart
by ejecting particles
o If protons emitted, atomic number can
change, and element can change Ex
radioactive carbon decays to form nitrogen
o These emissions can be detected and
measured
o Emission occurs at characteristic rate, so we
can figure out how long it has been and will
go on.

o Some applications of radioactive isotopes in

biological research are:
o Dating fossils
o Tracing atoms through metabolic processes
o Diagnosing medical disorders

The Energy Levels of Electrons

o Energy is the capacity to cause change
o Potential energy is the energy that matter has because of
its location or structure (the potential to do work!)
o The electrons of an atom differ in their amounts of potential
energy
o An electrons state of potential energy is called its energy
level, or electron shell
o Electron shells are different distances from the nucleus and
can hold different numbers of electrons

Electron Shells
o Distance = Potential Energy
o That is, electrons in the 1st shell closest to the nucleus
have the lowest potential energy
o The further out the electrons are from the nucleus, the
greater the potential energy
o First Shell (Closest to Nucleus)-Up to 2 electrons
o Second Shell-Up to 8 Electrons
o Third Shell Up to 8 electrons
o Electrons fill up inner shells first
o If an electron gains extra energy and jumps to higher
shell, it will ~immediately lose that energy and fall back

Fig. 2-8

(a) A ball bouncing down a flight

of stairs provides an analogy
for energy levels of electrons

Third shell (highest energy

level)
Second shell (higher
energy level)

Energy
absorbed

First shell (lowest energy

level)

(b)

Energy
lost

Atomic
nucleus

Electron Distribution and Chemical

Properties
o The chemical behavior of an atom is
determined by the distribution of
electrons in electron shells
o The periodic table of the elements shows
the electron distribution for each element

Fig. 2-9

Hydrogen
1H
Atomic mass

First
shell

2
He
4.00

Atomic number

Helium
2He

Element symbol
Electrondistribution
diagram

Lithium
3Li

Beryllium
4Be

Boron
5B

Carbon
6C

Nitrogen
7N

Oxygen
8O

Fluorine
9F

Neon
10Ne

Silicon
14Si

Phosphorus
15P

Sulfur
16S

Chlorine
17Cl

Argon
18Ar

Second
shell

Sodium Magnesium Aluminum

12Mg
11Na
13Al
Third
shell

o Valence electrons are those in the

outermost shell, or valence shell
o The chemical behavior of an atom & how
on element interacts with other elements
is mostly determined by the valence
electrons
o Elements with a full valence shell are
chemically inert (chemically unreactive)

Electron Orbitals
An orbital is the three-dimensional space where
an electron is found 90% of the time
Because electrons from bonded atoms will repel
each other, orbitals contribute to the shapes of
complex molecules
Each electron shell consists of a specific number
of orbitals

Fig. 2-10-3

Neon, with two filled shells (10 electrons)

(a) Electron-distribution
diagram

(b) Separate electron

orbitals

First shell

Second shell

x
z

1s orbital

Fig. 2-10-4

2s orbital

Three 2p orbitals

Neon, with two filled shells (10 electrons)

(a) Electron-distribution
diagram

(b) Separate electron

orbitals

First shell

Second shell

x
z

1s orbital

2s orbital

Three 2p orbitals

(c) Superimposed electron

orbitals

1s, 2s, and 2p orbitals

The formation and function of

molecules depend on chemical
bonding between atoms
oValence shells want to be full
oAtoms with incomplete valence shells can
share or transfer valence electrons with certain
other atoms
oThese interactions usually result in atoms
staying close together, held by attractions
called chemical bonds
oBecome something new with new properties

10

Covalent Bonds
o A covalent bond is the sharing of a pair of
valence electrons by two atoms
o In a covalent bond, the shared electrons
count as part of each atoms valence shell

Hydrogen
atoms (2 H)

o2 Hydrogen atoms each has

1 electron
oThe valence shells can hold
2
oWhen they get close enough,
each electron is attracted to
the other nucleus (+ and -).
oThe 2 electrons become
shared between atoms,
orbiting both: a Covalent Bond
Hydrogen
molecule (H2)

o A molecule consists of two or more atoms

held together by covalent bonds
o A single covalent bond, or single bond, is
the sharing of 1 pair of valence electrons
o A double covalent bond, or double bond, is
the sharing of 2 pairs of valence electrons

Animation: Covalent Bonds

11

o The notation used to represent atoms and

bonding is called a structural formula
o For example, HH, O=O

o This can be abbreviated further with a

molecular formula
o For example, H2

o Lewis Dot Structure: Shows outermost,

shared electrons
Single
covalent bond

Double
covalent bond

Fig. 2-12a

Name and
Molecular
Formula

ElectronLewis Dot
distribution Structure and
Diagram
Structural
Formula

Spacefilling
Model

Lewis Dot
Electrondistribution Structure and
Structural
Diagram
Formula

Spacefilling
Model

(a) Hydrogen (H2)

Fig. 2-12c

Name and
Molecular
Formula

(c) Water (H2O)

12

o Covalent bonds can form between atoms of the same

element or atoms of different elements
o A compound is a combination of two or more different
elements
o Bonding capacity is called the atoms valence
o How many electrons it wants, thus how many covalent
bonds it can form (Note: single vs. double)
o H atomic number = 1, how many valence electrons?
how many bonds can it form?
o O atomic number = 8, valence electrons? bonds?
o N atomic number = 7, valence electrons? bonds?
o C atomic number = 6, valence electrons? bonds?

o Electronegativity is an atoms attraction for

the electrons in a covalent bond
o The more electronegative an atom, the more
strongly it pulls shared electrons toward
itself, so the electrons spend more time
around the more electronegative atom
o In a nonpolar covalent bond, the atoms
share the electron equally
H2

13

Fig. 2-12d

Name and
Molecular
Formula

Spacefilling
Model

ElectronLewis Dot
distribution Structure and
Diagram
Structural
Formula

(d) Methane
(CH4)

o In a polar covalent bond, one atom is

more electronegative, and the atoms do
not share the electron equally
o Unequal sharing of electrons causes a
partial positive or negative charge for
each atom or molecule

Water
O
+

H
H2 O

Protons & Electrons

o Protons (usually) = Electrons
o Can ~assume electron # from Atomic Number
o Know Atomic Number# ElectronsElectron
ConfiguationValence

o (+) + (-) = 0 (Neutral)

o Lose Proton OR Gain Electron = (-) charged Atom
o Gain Proton OR Lose Electron = (+) charged Atom

14

Ionic Bonds
o Very electronegative atoms sometimes steal
electrons from their bonding partners
o An example is the transfer of an electron from
sodium (Na) to chlorine (Cl)

o After the transfer of an electron, both atoms have

charges (Na+ & Cl-)
o A charged atom (or molecule) is called an ion

Fig. 2-14-2

Na

Cl

Na

Cl

Na
Sodium atom

Cl
Chlorine atom

Na+
Sodium ion
(a cation)

Cl
Chloride ion
(an anion)

Sodium chloride (NaCl)

o A cation is a positively charged ion (+)

o More protons than electrons

o An anion is a negatively charged ion (-)

o More electrons than protons

o An ionic bond is an attraction between an

anion and a cation
o This bond is strong, but fragile, and usually
comes apart in water
Animation: Ionic Bonds

15

o Compounds formed by ionic bonds are

called ionic compounds, or salts
o Salts, such as sodium chloride (table salt),
are often found in nature as crystals

Na+
Cl

Weak Chemical Bonds

o Most of the strongest bonds in organisms
are covalent bonds that form a cells
molecules
o Weak chemical bonds such as ionic bonds
and hydrogen bonds are also important
o Weak chemical bonds reinforce shapes of
large molecules & help molecules adhere
to each other

Hydrogen Bonds
Fig. 2-16

Water (H2O)

o A hydrogen bond forms when

a hydrogen atom covalently
bonded to one electronegative
atom is also attracted to
another electronegative atom

+
Hydrogen
bond

o In living cells, the

electronegative partners are
usually oxygen or nitrogen
atoms

Ammonia (NH3)

+
+

16

Van der Waals Interactions

o If electrons are distributed
asymmetrically in
molecules or atoms, they
can result in hot spots of
positive or negative
charge
o Van der Waals
interactions are
attractions between
molecules that are close
together as a result of
these charges

o Collectively, such interactions can be strong,

as between molecules of a geckos toe hairs
and a wall surface

Molecular Shape and Function

o A molecules shape is usually very important
to its function
o A molecules shape is determined by the
positions of its atoms valence orbitals
o In a covalent bond, the s and p
orbitals may merge and change,
creating complex
molecular shapes

17

Fig. 2-17

s orbital

Four hybrid orbitals

z
x

Three p
orbitals

Tetrahedron
(a) Hybridization of orbitals
Space-filling
Model

Ball-and-stick Hybrid-orbital Model

Model
(with ball-and-stick
model superimposed)
Unbonded
electron
pair
104.5

Water (H2O)

Methane (CH4)
(b) Molecular-shape models

o Biological molecules bind and interact with

each other with a specificity based on
molecular shape
o Molecules with similar shapes can have
similar biological effects

Figure 2.18

Carbon
Hydrogen
Natural endorphin

Nitrogen
Sulfur
Oxygen
Morphine

(a) Structures of endorphin and morphine

Natural
endorphin

Brain cell

Morphine

Endorphin
receptors

(b) Binding to endorphin receptors

18

Chemical reactions make and break

chemical bonds
o Chemical reactions are the making and
breaking of chemical bonds
o The starting molecules of a chemical
reaction are called reactants
o The final molecules of a chemical reaction
are called products

o Some chemical reactions go to completion: all

reactants are converted to products
o All chemical reactions are reversible: products
of the forward reaction become reactants for
the reverse reaction
o Chemical equilibrium is reached when the
forward and reverse reaction rates are equal

o Photosynthesis is an
important chemical reaction
o The solar energy powered
rearrangement of carbon
dioxide (from air or water) &
water
o Sunlight powers the
conversion of carbon dioxide
and water to glucose and
oxygen
o 6 CO2 + 6 H20 C6H12O6 +
6 O2

19

Fig. 2-UN9

Example of what type of bonds?

Fig. 2-UN10

Fig. 2-UN11

20