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CAMPBELL
BIOLOGY
Outline
TENTH
EDITION
Reece • Urry • Cain • Wasserman • Minorsky • Jackson
I. Why study Chemistry
II. Atoms
2
The Chemical
Context of Life
Chemistry is the basis for studying much of biology

Estuaries and wetlands can detoxify water:

Runoff from agricultural land may have high levels of
some elements such as selenium.

Plants can take up selenium and convert it to gas,
removing it from the water.

We can use these plants to remove selenium =
bioremediation
Isotopes
C.
Electrons/orbitals
D.
Bonding
A.
Covalent bonds
B.
Polarity
C.
Ionic bonds
D.
Hydrogen bonding
E.
Van der Waals Interactions
F.
Shape/Structure
G.
Chemical Rxns
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Why study Chemistry?

Periodic Table
B.
III. Bonds
Dr Burns
Napa Valley College
© 2014 Pearson Education, Inc.
A.
Why study Chemistry?

Biology follows the rules of physics and
chemistry.

Understanding chemistry is key to
understanding how biological systems work

What will cross a membrane?

How is energy transferred through biological
systems?

What is a protein?
© 2014 Pearson Education, Inc.
© 2014 Pearson Education, Inc.
Definitions and the Basics
The Elements of Life

Matter – any substance that has mass and takes
up space

Elements are substances that can not be broken
down into simpler substances by ordinary
chemical reactions.


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 those required by an
organism in minute quantities
The smallest unit of an element is the atom. If it
is divided it will loose its unique properties
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© 2014 Pearson Education, Inc.
1
Table 2.1
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
 Atoms are composed of subatomic particles
 Neutrons and protons form the atomic nucleus
 Subatomic particles include
 Electrons form a cloud around the nucleus
 Neutrons (no electrical charge)
 Protons (positive charge)
 Electrons (negative charge)
 In each neutral atom the # of electrons = the # of
protons
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© 2014 Pearson Education, Inc.
Figure 2.5
Electrons are found in the nucleus.
Cloud of negative
charge (2 electrons)
Electrons
1. True
Nucleus
2. False
50%
Fa
lse
e
(b)
Tr
u
(a)
50%
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2
Atomic Number
 An element’s atomic number is the number of
protons in its nucleus
Atomic Mass
 An element’s mass number is the sum of
protons plus neutrons in the nucleus, this is the
number at the bottom of the periodic table entry.
 Atomic mass, the atom’s actual total mass, can
be approximated by the mass number
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© 2014 Pearson Education, Inc.
Atomic Mass
Isotopes

Mass of a proton ≈1 dalton

Mass of a neutron ≈ 1 dalton

Mass of an electron ≈ 1/1800 dalton

Isotopes are atoms of the same element that
have different numbers of neutrons

Every atom of an element has the same number
of protons. So all carbon atoms have six
protons
© 2014 Pearson Education, Inc.
© 2014 Pearson Education, Inc.
Radioactive Isotopes
Periodic Table

Radioactive isotopes are unstable, and become
more stable by emitting energy and particles

In contrast, most isotopes are stable

Radioactive isotopes are used to date fossils
and in medicine

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The periodic table is a chart of the elements
arranged by atomic number
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3
Figure 2.7a
Answer the following questions for beryllium
2
Atomic number
He
Atomic mass
4.003

The atomic number = the # of protons in an atom

Uncharged atoms have equal numbers of protons and
electrons.
The mass = #protons + #neutrons

How many protons does beryllium (Be) have?
1. One
20%
20%
20%
20%
How many electrons does beryllium (Be) have?
20%
1. One
2. Two
2. Two
3. Three
3. Three
4. Four
4. Four
5. Five
5. Five
1
2
3
4
1
5
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20%
20%
20%
2
3
20%
20%
4
5
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How many neutrons does beryllium (Be) have?
1. One
20%
20%
20%
20%
20%
What is the charge of an atom containing 12 protons, 11
neutrons, and 12 electrons?
1. -1
33%
2. Two
2. 0
3. Three
3. +1
33%
33%
4. Four
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ur
ve
Fi
Fo
o
re
e
Th
Tw
O
ne
5. Five
1
2
3
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4
Isotopes are atoms of the same element that differ in
their number of …
1. electrons
25%
25%
25%
25%
What is the mass number of an ion with 15 electrons, 16
neutrons, and a +1 charge?
20%
1. 31
20%
20%
2
3
20%
20%
2. neutrons
2. 32
3. protons
3. 46
4. none of the above
4. 47
5. 16
1
2
3
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4
1
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
5
Figure 2.6
(a) A ball bouncing down a flight
of stairs provides an analogy
for energy levels of electrons.
Third shell (highest energy
level in this model)
Second shell (higher
energy level)
First shell (lowest energy
level)
(b)
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2014
Pearson
Education,
Inc.
2011
Pearson
Education,
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© 2014 Pearson Education, Inc.
Energy
absorbed
Energy
lost
Atomic
nucleus
Inc.

This is not a correct illustration of their
location, it is used to illustrate energy states
5
Shell Model of Electrons

Electrons can be visualized as residing in shells
around the nucleus (but they don’t reside here).

The first shell can have up to two electrons

The second shell and third shells can have up to
eight electrons

The outer most shell is the valence shell with
the highest energy

The chemical behavior of an atom depends
mostly on the number of valence electrons
Electron Orbitals

An orbital is the three-dimensional space
where an electron is found 90% of the time
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© 2014 Pearson Education, Inc.
Chemical Bonds
Electrons and Bonding

Chemical bonds are unions between electron
structure from different atoms

Molecules are when two or more atoms join
together. They can be the same element (H2)
or different elements (H2O)

When different elements join together, the
molecule is referred to as a compound
molecule
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
If the valence shell is full, then the atom is nonreactive, inert, and does not form chemical
bonds.

Incompletely filled outer orbital, then the atom
is reactive and will form chemical bonds.

How many bonds, and what type of bond it can
form depends on how many unfilled spots in
outer shell
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Covalent Bonding
Covalent Bonds
 A covalent bond is the sharing of a pair of
valence electrons by two atoms
 A single covalent bond, or single bond, is the
sharing of one pair of valence electrons


Each atom has an attractive force for the other
atoms unshared electrons, but not enough to
take it completely away
 A double covalent bond, or double bond, is the
sharing of two pairs of valence electrons
There can be single, double or triple covalent
bonds
 A triple covalent bond, or triple bond, is the
sharing of three pairs of valence electrons
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© 2014 Pearson Education, Inc.
6
Figure 2.12a
Animation: Covalent Bonds
Name and
Molecular
Formula
Electron
Distribution
Diagram
Lewis Dot
Structure and
Structural
Formula
SpaceFilling
Model
Electron
Distribution
Diagram
Lewis Dot
Structure and
Structural
Formula
SpaceFilling
Model
(a) Hydrogen (H2)
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Figure 2.12b
Name and
Molecular
Formula
Figure 2.12c
Electron
Distribution
Diagram
Lewis Dot
Structure and
Structural
Formula
Name and
Molecular
Formula
SpaceFilling
Model
(b) Oxygen (O2)
(c) Water (H2O)
Figure 2.12d
How many covalent bonds can an atom form?
Name and
Molecular
Formula
(d) Methane (CH4)
Electron
Distribution
Diagram
Lewis Dot
Structure and
Structural
Formula
SpaceFilling
Model

Each atom wants their outer shell filled.

Hydrogen only has one electron in its shell –
wants two, so it can form one bond.

Carbon has four electrons in outer shell, wants
eight, so it can form four bonds.
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7
How many bonds can hydrogen form?
How many bonds can carbon form?
1. One
1. One
25%
25%
25%
25%
25%
2. Two
2. Two
3. Three
3. Three
4. Four
4. Four
1
2
3
1
4
25%
25%
2
3
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© 2014 Pearson Education, Inc.
How many bonds can helium form?
How many bonds can nitrogen form?
1. None
25%
25%
25%
1. One
25%
2. One
2. Two
3. Two
3. Three
4. Three
4. Four
1
2
3
25%
1
4
© 2014 Pearson Education, Inc.
© 2014 Pearson Education, Inc.
How many bonds can oxygen form?
Electronegativity
25%
25%
2
3
25%
4
25%

Some atoms have a greater pull on shared
electron than other atoms
2. Two

The measure of this pull is electronegativity
3. Three

When a molecule is made up of atoms with
different electronegativities it is a polar molecule

The greater the pull the more electronegative
(remember that electrons are negative)
1. One
25%
25%
25%
25%
4. Four
1
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2
3
4
4
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Figure 2.13
Types of Covalent Bonds

–
Covalent bonds can be polar or nonpolar

Nonpolar bonds the atoms have same pull on
O
the shared electrons (H2)
+

H
H
H2O
Polar bonds – the atoms don’t equally share the
+
electrons (H2O)
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Tab 2.2
Polarity

Water
Polar Covalent Bonding occurs with strong
electrophiles (electronegative): atoms with nuclei
that have a strong pull on electrons. Common
examples in biological molecules include:

Oxygen

Nitrogen

Sulfur (less than oxygen or nitrogen)
Alcohol
H
H
H
H
O
C
H
H
H
H
S
N
O
H
CH3
CH3
Aldehyde
Ketone
O
O
H2
C
H3C
H2
C
C
C
H2
CH3
H3C
C
C
H2
H
H
C
HC
CH
Hydrocarbons
H2
C
H3C
H2
C
C
H2
HC
H
H2
C
C
H2
CH3
C
H2
H
H
C
CH
C
H
H
9
Polar Functional Groups
Carboxyl

Oxygen containing:

Carboxyl = - COOH

Hydroxyl (alcohol) = - OH

Phosphates = -PO4

Carbonyl

Ketone = - CO

Aldehyde = - CHO

Nitrogen containing: Amino (-NH2)

Thiols - Sulfur containing compounds (-SH)
Alcohol
CH3CH2CH2OH
Ketone
Aldehyde
Ether
Hydrocarbons
CH3-O-CH2CH3
CH3CH2CH3
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Which molecule is the most polar?
Nonpolar compounds
1. CH3-SH

Hydrocarbons – lots of carbons and hydrogens
bonded together
2. CH3-NH2
3. CH3-O-CH3
4. CH3-OH
5. CH3-COOH
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Terminology
Ionic Bonds

Ion = atom that has gained or lost electrons, It
no longer has a balance between protons and
electrons, it is positive or negative charge

Ionic bond is an association between ions of
opposite charge: cations (positive) and anions
(negative)
 Hydrophilic (water-loving) – polar molecules that
are attracted to water
 Hydrophobic (water-fearing) – nonpolar
molecules that are pushed aside by water
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10
Ionic Bonds
Ionic Bonds
+
-
Na
Cl
Na
Cl
Na
Cl
Na
Sodium atom
Cl
Chlorine atom
Na
Sodium atom
Cl
Chlorine atom
Na+
Sodium ion
(a cation)
ClChloride ion
(an anion)
Sodium chloride (NaCl)
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© 2014 Pearson Education, Inc.
Page 21
Animation: Ionic Bonds
Animation: Ionic Bonds
Right-click slide / select “Play”
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11
In the reaction between sodium and chloride, which is
being oxidized?
1. Sodium
50%
50%
2. Chloride
Weak Chemical Bonds
 Most of the strongest bonds in organisms are
covalent bonds that form a cell’s molecules
 Weak chemical bonds are also indispensable
 Many large biological molecules are held in their
functional form by weak bonds
 The reversibility of weak bonds can be an
advantage
1
2
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© 2014 Pearson Education, Inc.
Hydrogen Bonds
Hydrogen Bonding

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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2014
Pearson
Education,
Inc.
2011
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Education,
Fig. 2.11a
Inc.

Weak attraction between a slightly positive
hydrogen atom and an electronegative atom such
as oxygen, nitrogen, or less commonly sulfur.

Individually weak, but many together can be
strong.

Determines shapes of many biological molecules
including proteins and DNA
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Figure 2.14
-
+
Water (H2O)
+
-
Hydrogen bond
Ammonia (NH3)
+
+
+
12
Fig. 2.11b
Which of the following statements is correct about the
atoms in ammonia (NH3)?
1. The N will have a
slight positive charge
25%
25%
25%
2.
3.
25%
2. The N will have a
strong positive charge
3. The H will have a
slight positive charge
4. The H will have a
slight negative charge
1.
4.
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Van der Waals Interactions

If electrons are distributed asymmetrically in
molecules or atoms, they can result in “hot
spots” of positive or negative charge
What type of chemical bond results from an unequal
sharing of electrons between two atoms?
1. Polar covalent
25%
25%
25%
2.
3.
25%
2. Nonpolar covalent
3. Ionic

Van der Waals interactions are attractions
between molecules that are close together as a
result of these charges
4. Van der Waals
1.
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Molecular Shape and Function

A molecule’s shape is usually very important to
its function

A molecule’s shape is determined by the
positions of its atoms’ valence orbitals
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2014
Pearson
Education,
Inc.
2011
Pearson
Education,
4.
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Inc.
Molecular Shape and Function

Biological molecules recognize and interact
with each other with a specificity based on
molecular shape

Molecules with similar shapes can have
similar biological effects
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2014
Pearson
Education,
Inc.
2011
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Education,
Inc.
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Figure 2.UN07
Which of the following molecules is drawn correctly?
Important Concepts

Reading for next lecture: Chapter 3

Know the vocabulary in the lecture/chapter

What are the particles of an atom, their location,
charge, and mass?

Be able to read a periodic table and determine
how many protons, neutrons, and electrons are
in a neutral atom for each element.

What are isotopes and radioactive isotopes,
what are their similarities and differences?
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Important Concepts

Be able to determine how many bonds each
element can form. Understand the shell model
and valence shells, valence electrons and how
they are related to chemical bonds

What are the four major types of bonds
discussed in lecture and be able to describe
them

Identify polar and nonpolar molecules

Be able to draw two molecules hydrogen
bonding with each other
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14