1/6/14

CAMPBELL BIOLOGY IN FOCUS

Urry Cain Wasserman Minorsky Jackson Reece

Instructor: Susan S Golden, PhD

BILD 1 The Cell

BILD 1 is a one-quarter introduction to molecular and

cell biology
A thorough understanding of basic chemistry is
assumed.
It is the student's responsibility to address
deficiencies in prerequisites
Discussion sections do not meet the first week.
You will sign up for a section at:
http://sections.ucsd.edu/

Questions prepared by

Brad Stith, University of Colorado Denver

Janet Lanza, University of Arkansas at Little Rock
Louise Paquin, McDaniel College

TA discussion sections and office hours are for

questions and extra help to understand material.

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BILD 1 Materials Posted on TED

Syllabus
read it, put exam dates on your calendar

FAQ
Lecture slides
TA information (office hours, handouts)
Announcements
Q&A
Grades
Practice exams, exam keys, challenges

You will need

Campbell: Biology in Focus
Mastering Biology (online)
Masteringbiology.com

i>clicker (original or i>clicker2)

Register it on TED

To sign up for a section

Meet the TAs

To check TED frequently for

announcements

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How to Succeed in BILD 1

Keep up!
Come to class, read the textbook, use the MasteringBiology
resources, attend section, and study every week

Read all textbook sections related to lecture material

The textbook provides depth and examples that will help your
understanding

Understand the material, dont just memorize it

Apply your knowledge to different situations and contexts
Integrate information and concepts between topics and chapters

Know what you dont know

Your Grade will come from

850 points from exams
2 midterm exams (40 questions, mc)
A final (62 questions, mc)

150 points from assignments

Mastering Biology (watch due dates)

Up to 3% "extra credit from class participation

i>clicker

Grade scale in syllabus

Not curved

Test yourself to identify areas of weakness to focus your study

Please,
Turn off or silence your mobile
phones &
Mute your computers
If you are using a computer in class, please sit in the side
sections to leave the center section free of screens and
keyboards for others who find computers distracting.
In general, have respect for your classmates (and
instructor) and avoid distracting others.
For example, please do not start packing up to leave
before the lecture is over because it is distracting to others
(and to me).

CAMPBELL BIOLOGY IN FOCUS

Urry Cain Wasserman Minorsky Jackson Reece

2
The Chemical
Context of Life

Lecture Presentations by
Kathleen Fitzpatrick and Nicole Tunbridge
2014 Pearson Education, Inc.

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You are responsible for all of Chapter 2

Chem 6A is a prerequisite for BILD 1
And you should have 6B or be taking it now

There will be questions from this chapter on your

exams
Even if those slides are not covered in lecture

Chapter 2 homework in Mastering Biology

Emergent Properties
Emergent properties result from the arrangement
and interaction of parts within a system
Biological systems are much more than the sum of
their parts
Emergent properties characterize non-biological
entities as well

To make sure you understand this material

Knowledge of basic chemistry is essential for

understanding how biological molecules behave
the way they do, and why biological processes
exhibit their emergent properties
2011 Pearson Education, Inc.

2011 Pearson Education, Inc.

Emergent Properties
Emergent properties
Examples from chemistry
Examples from mechanical objects

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
This usually results in atoms staying close together,
held by attractions called chemical bonds
Reviewed in Mastering Biology assignment

Figure 2.2

Sodium

Chloride

Sodium Chloride
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Weak Chemical Bonds

In a nonpolar covalent bond, the atoms share the
electron equally

Most of the strongest bonds in organisms are

covalent bonds that form a cells molecules

In a polar covalent bond, one atom is more

electronegative, and the atoms do not share the
electron equally

Weak chemical bonds, such as ionic bonds and

hydrogen bonds, are also important

Unequal sharing of electrons causes a partial positive

or negative charge for each atom or molecule

Many large biological molecules are held in their

functional form by weak bonds
Molecular shape determines how biological
molecules recognize and respond to one another

Animation: Covalent Bonds

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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

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Figure 2.12

Water (H2O)

In living cells, the electronegative partners are

usually oxygen or nitrogen atoms

Hydrogen bond

Ammonia (NH3)
+

2014 Pearson Education, Inc.

2014 Pearson Education, Inc.

+
+

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Concept 2.5: Hydrogen bonding gives water

properties that help make life possible on Earth
All organisms are made mostly of water and live in
an environment dominated by water
Water molecules are polar, with the oxygen region
having a partial negative charge () and the
hydrogen region a slight positive charge (+)

Polar covalent bonds in water molecules

result in hydrogen bonding
The water molecule is a polar molecule: the
opposite ends have opposite charges
Polarity allows water molecules to form hydrogen
bonds with each other

Two water molecules are held together by a

hydrogen bond

The abundance of water is the main reason the

Earth is habitable

+
Animation: Water Structure

2014 Pearson Education, Inc.

H
H 2O

2011 Pearson Education, Inc.

Water is a Polar Molecule

The polarity of water molecules
Allows them to form up to 4 hydrogen bonds with
each other or other molecules

Four emergent properties of water contribute to

Earths suitability for life:
Cohesive behavior
Ability to moderate temperature

+
H
+

Hydrogen
bonds

Expansion upon freezing

Versatility as a solvent

Figure 2.16

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

2014 Pearson Education, Inc.

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(1) Cohesion
Water molecules exhibit cohesion
the bonding of molecules to each other
due to hydrogen bonding
Helps pull water up through the microscopic vessels of
plants (along with adhesion)

Surface tension is a measure of how hard it is to

break the surface of a liquid
Surface tension is related to cohesion

Adhesion, clinging of one 

substance to another, 
causes water to adhere 
to the wall of vessels

Figure 3.3
Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

(2) Moderation of Temperature by Water

Water absorbs heat from warmer air and releases
stored heat to cooler air
Water can absorb or release a large amount of heat
with only a slight change in its own temperature
For temperature to increase, more heat must be
absorbed to break hydrogen bonds

2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright
2011 Pearson
Education, Inc.

Heat and Temperature

Kinetic energy is the energy of motion
Heat is a measure of the total amount of kinetic
energy due to molecular motion
Temperature measures the intensity of heat due to
the average kinetic energy of molecules

Heat is released when hydrogen bonds reform

Allows water to moderate temperatures

2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright
2011 Pearson
Education, Inc.

2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright
2011 Pearson
Education, Inc.

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(4) The Solvent of Life

(3) Floating of Ice on Liquid Water
Ice floats in liquid water because hydrogen bonds in
ice are more ordered, making ice less dense

Water is a versatile solvent due to its polarity

It can form aqueous solutions of a large variety of
charged and polar solutes (dissolved molecules)

Water reaches its greatest density at 4C

Salts

If ice sank, all bodies of water would eventually freeze

solid, making life impossible on Earth

Amino acids
Sugars
Etc.

2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright
2011 Pearson
Education, Inc.

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Hydrophilic and Hydrophobic Substances

Water is a versatile solvent due to its polarity, which
allows it to form hydrogen bonds easily
When an ionic compound is dissolved in water, each
ion is surrounded by a sphere of water molecules
called a hydration shell
Even large nonionic polar molecules such as proteins
can dissolve in water if they have ionic and polar
regions

A hydrophilic substance
Has an affinity for water
charged molecules, ions
polar molecules, which contain O-H or N-H polar
covalent bonds

A hydrophobic substance
Does not have an affinity for water
Noncharged and nonpolar molecules such as fats
and oils
which do not form aqueous solutions

2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright
2011 Pearson
Education, Inc.

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

1/6/14

Solute Concentration in Aqueous Solutions

Effects of Changes in pH

Life requires chemical reactions

Water molecules can react

Chemical reactions are affected by the concentrations

of reactants and products
the relative numbers of molecules in solution

Since most biochemical reactions occur in water

It is important to define the concentration of solutes in
an aqueous solution

to form hydronium and hydroxide ions

a hydrogen ion (H+) is transferred from one water molecule to
another
By convention, H+ is used to represent the hydronium ion
these ions are reactive

The concentration of these ions affects:

biological chemistry

the weak bonds of proteins and cell structures resulting in

changes in their shape

Review your knowledge of

+
H

Molecular weight
Moles

H
Figure on p. 34 of water
dissociating

H
Hydronium
ion (H3O+)

Molarity
Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

H
Hydroxide
ion (OH)

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Dissociation of Water

Acids and Bases

A simpler view of this process

An acid

is that a water molecule dissociates into a hydrogen

ion and a hydroxide ion:

Is any substance that increases the hydrogen ion

concentration of a solution

H2O <=> H+ + OH-

For example, when hydrochloric acid is added to

water, hydrogen ions dissociate from chloride ions:

Like almost all reactions, this is reversible

At equilibrium, the concentrations of H+ and OH- in
pure water are both very low, 10-7M (at 25C)

HCl -> H+ + Cl-

Only one water molecule in 554 million is dissociated

Though statistically rare, the dissociation of water

molecules has a great effect on organisms
Changes in concentrations of H+ and OH can
drastically affect the chemistry of a cell
Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

1/6/14

Acids and Bases

The pH Scale

A base
Is any substance that decreases the hydrogen ion
concentration of a solution
Some bases reduce [H+] directly by accepting hydrogen ions

For example, ammonia, NH3 + H+ <=> NH4+

Other bases reduce [H+] indirectly by producing OH- that then

combines with an H+ to form water

In any aqueous solution at 25C, the product of H+

and OH is constant and can be written as

NaOH -> Na+ + OH-

and then

OH- + H+ -> H2O

which removes hydrogen ions

[H+][OH] = 1014
The pH of a solution is defined by the negative
logarithm of H+ concentration, written as
pH = log [H+]
For a neutral aqueous solution, [H+] is 107, so
log [H+] = (7) = 7

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2014 Pearson Education, Inc.

Figure 3.10

For convenience, the H+ concentrations can be

expressed via the logarithmic pH scale.
pH = - log [H+]
for example, pH 7 =

The pH scale
[OH-]

Values for
can be easily
calculated
because

[H+]

10-7 M

Each pH unit represents a tenfold difference in H+

concentrations

H+

H+
- H+
H+ OH
+
OH- H H+
H+ H+

Acidic
solution

Increasingly Acidic
[H+] > [OH-]

The H+ and OH- concentrations of aqueous solutions

can vary by a factor of 100 trillion or more.

pH Scale
0

[H+] [OH-] = 10-14

Example: at pH
8,
[H+] = 10-8 and
[OH-] = 10-6

Battery acid

Gastric juice, lemon juice

Vinegar, wine,
cola

Tomato juice
Beer
Black coffee

5
6

OH-

OH-

H+ H+ OH
OH- OH +
H
H+
H+

Neutral
solution

OH-

OH-

OH-

H+ OHOH- OH
H+ OH

Basic
solution

Neutral
[H+] = [OH-]

7
8

Increasingly Basic
[H+] < [OH-]

The pH Scale

Saliva
Pure water
Human blood, tears
Seawater
Inside of small intestine

9
10
Milk of magnesia

11
Household ammonia

12
13
14

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Rainwater
Urine

Household
bleach
Oven cleaner

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Buffers
Most biological fluids have pH values in the range of 6
to 8
cells and organisms need to control their internal pH

Buffers
Are substances that minimize changes in the
concentrations of hydrogen and hydroxide ions in a
solution

We don't have time for the details of the chemistry, but buffers

can accept H+ ions from solution if an acid is added

and donate H+ to solution if a base is added

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The burning of fossil fuels is a major source of sulfur

oxides and nitrogen oxides
These compounds react with water in the air to form
strong acids that fall in rain or snow
Acid precipitation is rain, fog, or snow with a pH
lower than 5.2
Acid precipitation damages life in lakes and streams
and changes soil chemistry on land

2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright
2011 Pearson
Education, Inc.

Acidification: A Threat to Our Oceans

Burning fossil fuels threaten water quality
CO2 is the main product of fossil fuel combustion
About 25% of human-generated CO2 is absorbed by
the oceans
CO2 dissolved in seawater forms carbonic acid
As seawater acidifies, H+ ions combine with carbonate
ions to produce bicarbonate
Carbonate is required for calcification (production of
calcium carbonate) by many marine organisms,
including reef-building corals
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