AP Bio Ch. 1-3

Intro to Biology and Basic
Chemistry
Ch. 1,2,3

We are living in a golden age of biology
Biology is woven into the fabric of society as never
before
Knowledge of biological concepts is more important than
ever

 Biology is the scientific study of life
THE SCOPE OF BIOLOGY
Biology’s scope stretches across
the enormous diversity of life on
Earth

 Biologists explore life at levels ranging from the biosphere
to the molecules that make up cells
Figure 1.2.2
Cells Nucleus within cell
Cells in squirrel
DNA

The Unity of Life
Amoebas, molds, trees, and
people are all made from
similar cells
All organisms share a
common chemical
language for their
genetic material, DNA

 Diversity is the hallmark of life
Life in Its Diverse Forms
•The diversity of known life includes 1.7 million species
•Estimates of the total diversity range from 5 million to
over 30 million species

 Biodiversity can be both beautiful
and overwhelming
Grouping Species: The Basic Concept
Taxonomy is the
branch of biology that
names and classifies
species
It formalizes the
hierarchical ordering
of organisms
Figure 1.7

 The three domains of
life are
The Three Domains of Life
Bacteria
Archaea
Eukarya
Figure 1.8.1
Domain Bacteria Domain Archaea
Domain Eukarya
Kingdom Protista Kingdom Plantae
Kingdom Fungi Kingdom Animalia

 Bacteria and Archaea are both
prokaryotic domains
Figure 1.8.2
Domain Bacteria Domain Archaea

 Eukarya
includes at
least four
kingdoms
Protista
Plantae
Fungi
Animalia
Figure 1.8.3
Domain Eukarya
Kingdom Protista Kingdom Plantae
Kingdom Fungi Kingdom Animalia

Quick Think
 What are the 2 classifications of
prokaryotes?
 All eukaryotes belong to which group?
 Can you list the characteristics of the
prokaryotic domain Archaea?

 Underlying the
diversity of life is a
striking unity, especially
at the lower levels of
structure
Unity in the Diversity of Life
Example: the universal
genetic language of DNA
Evolution accounts for this
combination of unity and
diversity

 The universal architecture of eukaryotic cilia
Figure 1.9
(a) Paramecium (b) Cells from
fallopian
tube
(c) Cross section of cilium

Think-Pair-Share
What is studied
under the scope of
biology?
 Think/Write 30 seconds
 Pair 1 minute
 Share with class when
asked to

 The history of life
is a saga of a
restless Earth
billions of years
old
EVOLUTION:
BIOLOGY’S
UNIFYING THEME
Fossils document
this history
Figure 1.10

 Life evolves
Each species is one twig of a branching tree of life
extending back in time
Figure 1.11
Giant
panda
Spectacled
bear
Sloth
bear
Sun
bear
American
black bear
Asiatic
black bear
Polar
bear
Brown bear
Ancestral bear

 The evolutionary
view of life came into
focus in 1859 when
Charles Darwin
published The Origin
of Species
The Darwinian
View of Life
Figure 1.12

 Darwin’s book developed two main points
Descent with modification
Natural selection

 Darwin was struck by the diversity of
animals on the Galápagos Islands
Natural Selection
He thought of adaptation to
the environment and the
origin of new species as
closely related processes
As populations
separated by a
geographic barrier
adapted to local
environments, they
became separate
species

 Fourteen
species of
Galápagos
finches have
beak shapes
adapted to suit
their
environments
Medium
ground
finch
Cactus
ground
finch
Small
tree finch
Medium
tree finch
Woodpecker
finch
Large
ground
finch
Small
ground
finch
Large
cactus
ground
finch
Vegetarian
finch
Large
tree finch
Mangrove
finch
Green
warbler
finch
Gray
warbler
finch
Sharp-beaked
ground finch
Seed-eaters Cactus-flower
-eaters
Bud-eater Insect-eaters
Ground finches Tree finches Warbler finches
Common ancestor from
South American mainland Figure 1.13

 Darwin synthesized the concept of natural
selection from two observations that were
neither profound nor original
Darwin’s Inescapable
Conclusion
Others had the pieces of the puzzle, but Darwin could see
how they fit together
Darwin
&
Wallace

 Fact 1: Overproduction and struggle for existence
 Fact 2: Individual variation
The inescapable conclusion: Unequal reproductive success
It is this unequal reproductive success that Darwin called
natural selection
The product of natural selection is adaptation

 Natural selection
is the mechanism
of evolution
Figure 1.14
Population with varied inherited
traits
Elimination of individuals with
certain traits
Reproduction of survivors
Increasing frequency of traits that enhance
survival and reproductive success
1
2
3
4

 Artificial selection is the selective breeding of domesticated
plants and animal by humans
Observing Artificial Selection
Figure 1.15

 There are many examples of natural
selection in action
Observing Natural Selection
The development of antibiotic-resistant bacteria is one
Figure 1.16

 Darwin’s publication of The Origin of Species fueled an
explosion in biological research
Evolution is one of
biology’s best
demonstrated, most
comprehensive, and
longest lasting theories
Evolution is the unifying
theme of biology

Think-Pair-Share
How would you
explain
evolution and
natural selection
to someone
(briefly)?

The Chemistry of
Life
 Take any
biological
system apart
and you
eventually end
up at the
chemical level
Ecosystem
African savanna
Community
All organisms in savanna
Population
Herd of zebrasOrganism Zebra
Organ system
Circulatory system
Organ
Heart
Cell
Heart muscle cell
Tissue
Heart muscle
tissue
Molecule
DNA
Atom
Oxygen atom

Building Blocks of Matter
 Matter is the amount of
material in an object; it is
measured using mass (not
weight!)

Matter is composed of chemical
elements
 There are 92 naturally occuring
elements
 25 are essential to life
 Four of these make up ~ 96% of the
weight of the human body
 Trace elements occur in smaller
amounts

Trace elements are also
essential for life
 Trace elements are
required for all
organisms in very
small amounts
 Iron is essential to all
organisms
 Iodine is essential to
vertebrates
An iodine deficiency causes goiter

Atoms: smallest
unit of matter
that retains its
characteristics
-ex. H, C, Na
 Nucleus = protons
and neutrons
 Electrons = in
clouds around the
nucleus, at
varying energy
levels

The type of atom is determined
by the number of protons in its
nucleus.
Atomic Number
•the number of protons in the nucleus
What is the atomic number of carbon?
Mass Number
• the sum of the protons and neutrons
What is the mass number of carbon?
Atomic Elements

 Isotopes are alternate mass forms of an element
Isotopes
They have the same number of protons and electrons
But they have a different number of neutrons
Change in # of neutrons changes the mass number

 Radioactive isotopes
The nucleus decays, giving off particles and energy
Radioactive isotopes have many uses in research and
medicine
Example: PET scans

 Electrons determine how an
atom behaves when it
encounters other atoms
 The properties of an atom are
determined by the configuration
of its outer electrons (aka
valence electrons)
Electron Arrangement and the
Chemical Properties of Atoms

Stable Electron Configuration
The most stable electron
configuration is 8 in the outer
shell (2 for H and He)
All elements will try to gain,
lose or share outer electrons in
order to reach this
configuration.

Electrons tend to exist at the lowest state
of potential energy - the lowest shell
 1st shell - holds
2 electrons max
 2nd shell -
holds up to 8
electrons
 3rd shell - holds
up to 8
electrons

Shell Relationships
Elements with the same number of
valence electrons tend to behave
similarly

 Atoms of the four elements most abundant in life
Figure 2.7
Electron
First
electron shell
(can hold
2 electrons)
Outermost
electron shell
(can hold
8 electrons)
Carbon (C)
Atomic number = 6
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8
Hydrogen (H)
Atomic number = 1

Energy Emission
Energy may hit an electron and raise it to a higher level
This is an unstable condition
The electron emits energy as it drops down
to original level

Think-Pair-Share
What is an atom,
what are the parts
of an atom, and
which of these
parts is most
important to
reactivity and
why?

Chemical Bonding and
Molecules
 Chemical reactions enable atoms to give up or
acquire electrons in order to complete their
outer shells
 These interactions usually result in atoms staying
close together
 The atoms are held together by chemical bonds

 When an atom loses
or gains electrons, it
becomes electrically
charged
Ionic Bonds
Charged atoms are
called ions
Cations - positive charge
Anions - negative charge
Sodium atom (Na) Chlorine atom (Cl)
Complete
outer shells
Sodium ion (Na+
) Chloride ion (Cl−
)
Sodium chloride (NaCl)

Ionic Bonds
 Ionic bonds are formed
between oppositely
charged ions
 Ionic compounds are
salts
 Salts do not consist of
individual molecules
• They are just an
aggregate of cations and
anions

 A covalent bond forms when two atoms share one or more
pairs of outer-shell electrons
Covalent Bonds

 Cells constantly rearrange molecules by breaking existing
chemical bonds and forming new ones
Chemical Reactions
Such changes in the chemical composition of matter are
called chemical reactions
Hydrogen gas Oxygen gas Water
Reactants Products

 Chemical reactions can be symbolized with
equations
On the left side of
the equation are
the reactants, the
starting materials
On the right side
of the equation are
the products, the
end materials

Balancing Equations
 Amount of matter on both sides of a chemical reaction
must stay the same
 Matter cannot be created or destroyed
 Numbers (coefficients) are added in front of chemical
formulas to BALANCE equations.
2NaOH + H2SO4 2H2O + Na2SO4

Molecules
 Formed from atoms that
“share” their electrons
(covalent bonding)
 Together they have a
neutral charge
 Often contain carbon and
are then known as
“organic” molecules
 Can have single, double
or triple bonding

Organic Molecules
 Must include Carbon atom(s)

Think-Pair-Share
Why do we
say that
matter
cannot be
created or
destroyed?

Your Objective
Be able to state at least 1 property
of water that helps support life
AND
Be able to explain how the
chemical nature of water gives
rise to that property

Water
and Life
 Life on Earth
began in
water and
evolved
there for 3
billion years.
 Modern life still remains tied
to water
 Cells are composed of 70%-
95% water

•Water is foundWater is found
as a liquid overas a liquid over
71% of the71% of the
earthearth
•The abundanceThe abundance
of water is aof water is a
major reasonmajor reason
Earth isEarth is
habitablehabitable

 Studied in isolation, the water molecule is
deceptively simple
 Its two hydrogen atoms are joined to one
oxygen atom by single covalent bonds
The structure of water
H
O
H

 But the electrons of the covalent bonds are not
shared equally between oxygen and hydrogen
This unequal sharing makes water a polar
molecule
Oxygen is more electronegative than
hydrogen, so it has a greater pull on the
electrons
(+) (+)
(−) (−)

 The polarity of
water results in
weak electrical
attractions
between
neighboring water
molecules
These
interactions
are called
hydrogen
bonds
(b)
(−)
Hydrogen bond
(+)
(+)
(−)
(−)
(+)
(+)
(−)

Quick Think
 Why is a molecule
of water said to
have polar covalent
bonds?
 What kind of bonds
hold individual
water molecules
together?

Water’s Life Supporting
Properties
 The polarity of water molecules and the
hydrogen bonding that results explain most
of water’s life-supporting properties
 Water’s cohesive nature
 Water’s ability to moderate temperature
 Floating ice
 Versatility of water as a solvent

 Water molecules
stick together as a
result of hydrogen
bonding
The Cohesion of Water
This is called
cohesion
Cohesion is
vital for water
transport in
plants
Microscopic tubes

Surface tension is the measure of how difficult
it is to stretch or break the surface of a liquid
Hydrogen
bonds give
water an
unusually high
surface tension
Cohesion
between water
molecules form
a skin-like
surface
Can support animals like “waterCan support animals like “water
striders” in pondsstriders” in ponds

Surface Tension
 Water drops are round because all the
molecules on the edge are pulled to the
middle.

Adhesion
 Water will also
adhere to other polar
substances
 This is called
adhesion
 It is due to the polar
nature of the water
molecule
Caused by adhesion the water runs
along the glass and does not fall
straight.

Capillary Action
 Glass has polar
molecules.
 Glass can hydrogen
bond.
 Attracts the water
molecules.
 Some of the pull is up.

Meniscus
 Water curves up
along the side.
 This makes the
meniscus.

Quick Think
 How are adhesion and
cohesion similar and
different?
 Give an example of how
these properties help
support life.

Water moderates temperature
 Because of hydrogen bonding, water has
a strong resistance to temperature
change

 Heat and temperature are related, but
different
 Heat is a measure of the amount of kinetic
energy in the atoms and molecules in
something
 Temperature measures the intensity of the
heat
 Whenever 2 objects meet, the cooler object
absorbs heat from the warmer object until
they are the same temperature

 Water has a high specific heat
 Specific heat = the amount of heat that mustSpecific heat = the amount of heat that must
be absorbed or lost to change thebe absorbed or lost to change the
temperature of 1g of the substance 1° Ctemperature of 1g of the substance 1° C

 Since water has a high specific heat, it
will not change temperature much when it
absorbs or loses heat
 This is because much of the absorbed
heat is used to break hydrogen bonds,
not increase the kinetic energy of the
molecules

 So water can absorb
and store large
amounts of heat
while only changing
a few degrees in
temperature

Large bodies of water help to
moderate temperature
 Earth’s giant water supply
causes temperatures to stay
within limits that permit life
 Evaporative cooling
removes heat from the
Earth and from organisms

How water moderates
temperature
Water also has:Water also has:
High heat of fusionHigh heat of fusion
• The temp at which liquid turns solidThe temp at which liquid turns solid
High heat of vaporizationHigh heat of vaporization
• The temp at which liquid turns to gasThe temp at which liquid turns to gas

 When water molecules get cold, they move
apart, forming ice
The Biological Significance of Ice
Floating
A chunk of ice has fewer molecules than an equal volume
of liquid water
IceLiquid
water

 The density of ice is lower than liquid water
 This is why ice floats
Figure 2.15
Hydrogen bond
Liquid water
Hydrogen bonds
constantly break and re-form
Ice
Stable hydrogen bonds

Dipole Structure
 Ice floats in water because all ice
molecules are held in hexagons
 Center is open
space, making
ice 8% less
dense than
water.

 Since ice floats, ponds, lakes, and even the
oceans do not freeze solid
Marine life could not survive if bodies of water froze solid

 Floating ice insulates water below,
preventing freezing: critical for ocean
animals

Maximum density: 3.98o
C
 Below this temp, form hexagonal polymers and
decrease density
 Above this, molecules are energetic, water behaves
like other liquids - expanding when warm and
contracting when cool

 A solution is a liquid consisting of two or
more substances evenly mixed
Water as the Solvent of Life
The dissolving agent is called the solvent
The dissolved substance is called the solute
Ion in solution
Salt crystal

 When water is the
solvent, the result is
called an aqueous
solution
 Water is a good
solvent because it is
polar
 Ionic (salts) and polar
(sugars) compounds
dissolve readily in
water

Solvent Properties
 Water dissolves salts by surrounding the atoms in the
salt molecule and neutralizing the ionic bond holding the
molecule together

Quick Think
What are some unique
properties of water that
allow it to support life and
how is this related to its
polar nature?

 Acid
Acids, Bases,
and pH
A chemical compound that donates H+
ions to solutions
Base
A compound that accepts H+
ions and removes them from
solution or a compound that dissociates in water to form
hydroxide ions

Basic
solution
Neutral
solution
Acidic
solution
Oven cleaner
Household bleach
Household ammonia
Milk of magnesia
Seawater
Human blood
Pure water
Urine
Tomato juice
Grapefruit juice
Lemon juice;
gastric juice
pH scale
To
describe
the acidity
of a
solution,
we use the
pH scale

pH scale (log scale)
Each number on the scale is 10x difference
from the number next to it
• pH 1 is 10x more acidic than pH 2, 100x more
acidic than pH 3, 1000x more acidic that pH 4,
and so on

pH - Percent Hydronium
A measure of the percent of hydronium ions
in the solution
The greater the percent hydronium ions, the
more acidic the solution is
HH22COCO33 -------------> H-------------> H++
++ HCOHCO33 --
CARBONIC ACIDCARBONIC ACID HYDRONIUM BICARBONATEHYDRONIUM BICARBONATE
IONION IONION

 Buffers are substances that resist pH change
They accept H+
ions when they are in excess
They donate H+
ions when they are depleted
Buffering is not
foolproof
Example: acid
precipitation
normal rain water
(pH of 5-6)
pH of acid rain is
between 3-4

Buffers
 Dissolved CO2 in water acts as a buffer, a
substance that prevents large shifts in
pH.
Buffers help keep pool
and spa water clean

Buffer Systems
CO2 + H2O ←→ H2CO3 ←→ H+
+ HCO3
-
←→ H+
+ CO3
-2
H2CO3 is carbonic acid,
H+
is the hydronium ion
HCO3
-
is the bicarbonate ion
CO3
-2
is the carbonate ion

Buffer Systems
CO2 + H2O ←→ H2CO3 ←→ H+
+ HCO3
-
←→H+
+ CO3
-2
 Adding CO2 shifts the reaction to the right and
produces more H+
ions making the water more
acid.

Buffer Systems
CO2 + H2O ←→ H2CO3 ←→ H+
+ HCO3
-
←→ H+
+ CO3
-2
 Removing CO2 shifts the reaction to the left,
combining H+
ions with carbonate and
bicarbonate ions reducing the acidity.

AP Bio Ch. 1-3

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AP Bio Ch. 1-3