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 beforeKnowledge of biological concepts is more important than ever

Biology is the scientific study of lifeTHE 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 cellsAll organisms share a common chemical language for their genetic material, DNA

Diversity is the hallmark of lifeLife 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

ProtistaPlantaeFungiAnimalia

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

Giantpanda

Spectacledbear

Slothbear

Sunbear

Americanblack bear

Asiaticblack bear

Polarbear

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 modificationNatural 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

Fourteenspecies of Galápagos finches have beak shapes adapted to suit their environments

Mediumgroundfinch

Cactusgroundfinch

Smalltree finch

Mediumtree finch

Woodpeckerfinch

Largegroundfinch

Smallgroundfinch

Large cactusground finch

Vegetarianfinch

Largetree finch

Mangrovefinch

Greenwarbler

finch

Graywarbler

finch

Sharp-beakedground finch

Seed-eaters Cactus-flower-eaters

Bud-eater Insect-eaters

Ground finches Tree finches Warbler finches

Common ancestor fromSouth 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 successIt is this unequal reproductive success that Darwin called natural selectionThe 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 theoriesEvolution is the unifying theme of biology

Think-Pair-Share

How would you explain evolution and natural selection to someone (briefly)?

Atoms & Molecules

The Chemistry of Life

Take any biological system apart and you eventually end up at the chemical level

Ecosystem African savanna

CommunityAll organisms in savanna

PopulationHerd of zebrasOrganism Zebra

Organ systemCirculatory system

OrganHeart

CellHeart muscle cell

TissueHeart muscletissue

MoleculeDNA

AtomOxygen 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 neutronsChange in # of neutrons changes the mass number

Radioactive isotopes

The nucleus decays, giving off particles and energyRadioactive 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

Firstelectron shell(can hold2 electrons)

Outermostelectron shell(can hold8 electrons)

Carbon (C)Atomic number = 6

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

Hydrogen (H)Atomic number = 1

Energy EmissionEnergy 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)

Completeouter shells

Sodium ion (Na) Chloride ion (Cl)

Sodium chloride (NaCl)

Opposites attract

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 materialsOn 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

Inorganic Molecules

Organic Molecules

Must include Carbon atom(s)

Organic Molecules

Think-Pair-Share

Why do we say that matter cannot be created or destroyed?

Chemical Properties of Water

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 found Water is found

as a liquid over as a liquid over

71% of the 71% of the

earthearth•The abundance The abundance

of water is a of water is a

major reason major reason

Earth is Earth 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 moleculeOxygen 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()

()()

()

()

()

()

Polar Structure

Electronegativity of H20

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 cohesionCohesion 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 “water Can 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

Water moderates temperature

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 moderates temperature

Water has a high specific heat Specific heat = the amount of heat that must Specific heat = the amount of heat that must

be absorbed or lost to change the be absorbed or lost to change the temperature of 1g of the substance 1°Ctemperature of 1g of the substance 1°C

Water moderates temperature 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

Water moderates temperature

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 bondsconstantly break and re-form

Ice

Stable hydrogen bonds

Change of State

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: 3.98oC

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 solventThe dissolved substance is called the solute

Ion in solutionSalt 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?

Acids, Bases &

Buffers

Acid

Acids, Bases, and pH

A chemical compound that donates H+ ions to solutionsBase

A compound that accepts H+ ions and removes them from solution or a compound that dissociates in water to form hydroxide ions

Basicsolution

Neutralsolution

Acidicsolution

Oven cleaner

Household bleach

Household ammonia

Milk of magnesia

Seawater

Human bloodPure 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 BICARBONATE HYDRONIUM BICARBONATE

ION ION IONION

Measuring Acidity

Buffers are substances that resist pH change

They accept H+ ions when they are in excessThey 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.

Ocean Buffers